From d9a3fcc42d5f3671dcb2ac6597ea663b9b259433 Mon Sep 17 00:00:00 2001 From: mntlra Date: Tue, 18 Apr 2023 13:30:25 +0200 Subject: [PATCH] [v2] Added Celiac Disease use case Added Celiac Disease use case --- compute_stats.py | 4 +- dataset/original/celiac/README.md | 3 + evaluate_sket.py | 41 +- run_med_sket.py | 23 +- run_sket.py | 16 +- sket/nerd/nerd.py | 1229 +- sket/nerd/rules/rules.txt | 34 +- sket/ont_proc/ontology/examode.owl | 19153 ++++++------------ sket/ont_proc/ontology_processing.py | 145 +- sket/ont_proc/rules/hierarchy_relations.txt | 3 +- sket/rdf_proc/rdf_processing.py | 1047 +- sket/rep_proc/report_processing.py | 181 +- sket/rep_proc/rules/report_fields.txt | 2 +- sket/sket.py | 61 +- sket/utils/utils.py | 206 +- 15 files changed, 8730 insertions(+), 13418 deletions(-) create mode 100644 dataset/original/celiac/README.md diff --git a/compute_stats.py b/compute_stats.py index 73a5573..c6bbd0b 100644 --- a/compute_stats.py +++ b/compute_stats.py @@ -4,8 +4,8 @@ import numpy as np parser = argparse.ArgumentParser() -parser.add_argument('--outputs', default='./outputs/concepts/refined/colon/*.json', type=str, help='SKET results file.') -parser.add_argument('--use_case', default='colon', choices=['colon', 'cervix', 'lung'], help='Considered use-case.') +parser.add_argument('--outputs', default='./outputs/concepts/refined/aoec/colon/*.json', type=str, help='SKET results file.') +parser.add_argument('--use_case', default='colon', choices=['colon', 'cervix', 'lung', 'celiac'], help='Considered use-case.') args = parser.parse_args() diff --git a/dataset/original/celiac/README.md b/dataset/original/celiac/README.md new file mode 100644 index 0000000..dd2d962 --- /dev/null +++ b/dataset/original/celiac/README.md @@ -0,0 +1,3 @@ +# Celiac datasets + +Put here datasets containing Celiac Disease pathology reports. diff --git a/evaluate_sket.py b/evaluate_sket.py index 95b7a07..affad27 100644 --- a/evaluate_sket.py +++ b/evaluate_sket.py @@ -8,9 +8,9 @@ parser = argparse.ArgumentParser() -parser.add_argument('--gt', default='./ground_truth/lung/aoec/lung_labels_allDS.json', type=str, help='Ground truth file.') -parser.add_argument('--outputs', default='./outputs/labels/aoec/lung/*.json', type=str, help='SKET results file.') -parser.add_argument('--use_case', default='lung', choices=['colon', 'cervix', 'lung'], help='Considered use-case.') +parser.add_argument('--gt', default='./ground_truth/celiac/aoec/celiac_labels_allDS.json', type=str, help='Ground truth file.') +parser.add_argument('--outputs', default='./outputs/labels/aoec/celiac/*.json', type=str, help='SKET results file.') +parser.add_argument('--use_case', default='celiac', choices=['colon', 'cervix', 'lung', 'celiac'], help='Considered use-case.') parser.add_argument('--hospital', default='aoec', choices=['aoec', 'radboud'], help='Considered hospital.') parser.add_argument('--debug', default=False, action='store_true', help='Whether to use evaluation for debugging purposes.') args = parser.parse_args() @@ -41,6 +41,11 @@ 'Cancer - non-small cell cancer, squamous cell carcinoma': 'cancer_nscc_squamous', 'Cancer - small cell cancer': 'cancer_scc', 'Cancer - non-small cell cancer, large cell carcinoma': 'cancer_nscc_large' + }, + 'celiac': { + 'Normal': 'normal', + 'Celiac disease': 'celiac_disease', + 'Non-specific duodenitis': 'duodenitis', } } @@ -56,22 +61,25 @@ def main(): gt = {} # prepare ground-truth for evaluation - if args.use_case == 'colon' and args.hospital == 'aoec': - gt = ground_truth + if args.hospital == 'aoec' or args.use_case == 'celiac': + ground_truth = ground_truth['groundtruths'] else: ground_truth = ground_truth['ground_truth'] - for data in ground_truth: + for data in ground_truth: + if args.hospital == 'aoec' or args.use_case == 'celiac': + rid = data['id_report'] + else: rid = data['report_id_not_hashed'] - if len(rid.split('_')) == 3 and args.hospital == 'aoec': # contains codeint info not present within new processed reports - rid = rid.split('_') - rid = rid[0] + '_' + rid[2] + if len(rid.split('_')) == 3 and args.hospital == 'aoec': # contains codeint info not present within new processed reports + rid = rid.split('_') + rid = rid[0] + '_' + rid[2] - gt[rid] = {label2class[args.use_case][label]: 0 for label in label2class[args.use_case].keys()} - for datum in data['labels']: - label = label2class[args.use_case][datum['label']] - if label in gt[rid]: - gt[rid][label] = 1 + gt[rid] = {label2class[args.use_case][label]: 0 for label in label2class[args.use_case].keys()} + for datum in data['labels']: + label = label2class[args.use_case][datum['label']] + if label in gt[rid]: + gt[rid][label] = 1 # gt name gt_name = args.gt.split('/')[-1].split('.')[0] @@ -93,7 +101,7 @@ def main(): for rid, rdata in rs.items(): if args.use_case == 'colon' and args.hospital == 'aoec' and '2ndDS' in args.gt: rid = rid.split('_')[0] - if args.hospital == 'radboud' and args.use_case == 'colon': + if args.hospital == 'radboud': sket[rid] = rdata['labels'] else: sket[rid] = rdata @@ -101,6 +109,8 @@ def main(): # fix class order to avoid inconsistencies rids = list(sket.keys()) classes = list(sket[rids[0]].keys()) + if args.use_case == 'celiac': + classes.remove('inconclusive') # obtain ground-truth and SKET scores gt_scores = [] @@ -118,6 +128,7 @@ def main(): if args.debug: first = True for c in classes: + #if c != 'inconclusive': gt_rscores.append(gt[rid][c]) sket_rscores.append(sket[rid][c]) if args.debug: # perform debugging diff --git a/run_med_sket.py b/run_med_sket.py index f824160..8ace590 100644 --- a/run_med_sket.py +++ b/run_med_sket.py @@ -6,20 +6,21 @@ warnings.filterwarnings("ignore", message=r"\[W008\]", category=UserWarning) parser = argparse.ArgumentParser() -parser.add_argument('--src_lang', default='it', type=str, help='Considered source language.') -parser.add_argument('--use_case', default='colon', choices=['colon', 'cervix', 'lung'], help='Considered use-case.') +parser.add_argument('--src_lang', default='en', type=str, help='Considered source language.') +parser.add_argument('--use_case', default='celiac', choices=['colon', 'cervix', 'lung', 'celiac'], help='Considered use-case.') parser.add_argument('--spacy_model', default='en_core_sci_sm', type=str, help='Considered NLP spacy model.') -parser.add_argument('--w2v_model', default=False, action='store_true', help='Considered word2vec model.') +parser.add_argument('--w2v_model', default=True, action='store_true', help='Considered word2vec model.') parser.add_argument('--fasttext_model', default=None, type=str, help='File path for FastText model.') parser.add_argument('--bert_model', default=None, type=str, help='Considered BERT model.') -parser.add_argument('--string_model', default=False, action='store_true', help='Considered string matching model.') +parser.add_argument('--string_model', default=True, action='store_true', help='Considered string matching model.') parser.add_argument('--gpu', default=None, type=int, help='Considered GPU device. If not specified (default to None), use CPU instead.') -parser.add_argument('--thr', default=0.9, type=float, help='Similarity threshold.') -parser.add_argument('--store', default=False, action='store_true', help='Whether to store concepts, labels, and graphs.') +parser.add_argument('--thr', default=1.8, type=float, help='Similarity threshold.') +parser.add_argument('--store', default=True, action='store_true', help='Whether to store concepts, labels, and graphs.') parser.add_argument('--rdf_format', default='all', choices=['n3', 'trig', 'turtle', 'all'], help='Whether to specify the rdf format for graph serialization. If "all" is specified, serialize w/ the three different formats') parser.add_argument('--raw', default=False, action='store_true', help='Whether to consider full pipeline or not.') parser.add_argument('--debug', default=False, action='store_true', help='Whether to use flags for debugging.') -parser.add_argument('--dataset', default='', type=str, help='Dataset file path.') +parser.add_argument('--preprocess', default=True, action='store_true', help='Whether to preprocess input data or not.') +parser.add_argument('--dataset', default=None, type=str, help='Dataset file path.') args = parser.parse_args() @@ -31,14 +32,14 @@ def main(): dataset = args.dataset else: # use sample "stream" dataset dataset = { - 'text': 'adenocarcinoma con displasia lieve, focalmente severa. Risultati ottenuti con biopsia al colon.', - 'gender': 'M', + "text": "polyp 40 cm: tubular adenoma with moderate dysplasia.", + 'gender': 'F', 'age': 56, - 'id': 'test' + 'id': 'test_colon' } # use SKET pipeline to extract concepts, labels, and graphs from dataset - sket.med_pipeline(dataset, args.src_lang, args.use_case, args.thr, args.store, args.rdf_format, args.raw, args.debug) + sket.med_pipeline(dataset, args.preprocess, args.src_lang, args.use_case, args.thr, args.store, args.rdf_format, args.raw, args.debug) if args.raw: print('processed data up to concepts.') diff --git a/run_sket.py b/run_sket.py index b53b929..5443495 100644 --- a/run_sket.py +++ b/run_sket.py @@ -6,19 +6,19 @@ warnings.filterwarnings("ignore", message=r"\[W008\]", category=UserWarning) parser = argparse.ArgumentParser() -parser.add_argument('--dataset', default='./dataset/original/colon/radboud/ExaMode_3rdDS_Radboudumc_Colon_2ndBatch.xlsx', type=str, help='Dataset file.') -parser.add_argument('--sheet', default='Sheet1', type=str, help='Considered dataset sheet.') +parser.add_argument('--dataset', default='./dataset/original/celiac/aoec/ExaMode_0thDS_AOEC_Celiac.xlsx', type=str, help='Dataset file.') +parser.add_argument('--sheet', default='Sheet 1', type=str, help='Considered dataset sheet.') parser.add_argument('--header', default=0, type=str, help='Header row within dataset.') -parser.add_argument('--ver', default=1, type=str, help='Considered versioning for operations.') -parser.add_argument('--use_case', default='colon', choices=['colon', 'cervix', 'lung'], help='Considered use-case.') -parser.add_argument('--hospital', default='radboud', choices=['aoec', 'radboud'], help='Considered hospital.') +parser.add_argument('--ver', default=2, type=str, help='Considered versioning for operations.') +parser.add_argument('--use_case', default='celiac', choices=['colon', 'cervix', 'lung', 'celiac'], help='Considered use-case.') +parser.add_argument('--hospital', default='aoec', choices=['aoec', 'radboud'], help='Considered hospital.') parser.add_argument('--spacy_model', default='en_core_sci_sm', type=str, help='Considered NLP spacy model.') -parser.add_argument('--w2v_model', default=False, action='store_true', help='Considered word2vec model.') +parser.add_argument('--w2v_model', default=True, action='store_true', help='Considered word2vec model.') parser.add_argument('--fasttext_model', default=None, type=str, help='File path for FastText model.') parser.add_argument('--bert_model', default=None, type=str, help='Considered BERT model.') -parser.add_argument('--string_model', default=False, action='store_true', help='Considered string matching model.') +parser.add_argument('--string_model', default=True, action='store_true', help='Considered string matching model.') parser.add_argument('--gpu', default=None, type=int, help='Considered GPU device. If not specified (default to None), use CPU instead.') -parser.add_argument('--thr', default=2.0, type=float, help='Similarity threshold.') +parser.add_argument('--thr', default=1.8, type=float, help='Similarity threshold.') parser.add_argument('--raw', default=False, action='store_true', help='Whether to return concepts within semantic areas (deployment) or mentions+concepts (debugging)') parser.add_argument('--debug', default=False, action='store_true', help='Whether to use flags for debugging.') args = parser.parse_args() diff --git a/sket/nerd/nerd.py b/sket/nerd/nerd.py index e0b556a..1436f16 100644 --- a/sket/nerd/nerd.py +++ b/sket/nerd/nerd.py @@ -4,7 +4,9 @@ import fasttext import itertools import re +import copy +from copy import deepcopy from tqdm import tqdm from textdistance import ratcliff_obershelp from spacy.tokens import Span @@ -94,7 +96,8 @@ def __init__(self, biospacy="en_core_sci_lg", biow2v=True, str_match=False, biof self.ad_hoc_linking = { 'colon': self.ad_hoc_colon_linking, 'cervix': self.ad_hoc_cervix_linking, - 'lung': self.ad_hoc_lung_linking + 'lung': self.ad_hoc_lung_linking, + 'celiac': self.ad_hoc_celiac_linking } # set parameter to None before choosing use case self.use_case_ad_hoc_linking = None @@ -102,7 +105,8 @@ def __init__(self, biospacy="en_core_sci_lg", biow2v=True, str_match=False, biof self.ad_hoc_post_processing = { 'colon': self.ad_hoc_colon_post_processing, 'cervix': self.ad_hoc_cervix_post_processing, - 'lung': self.ad_hoc_lung_post_processing + 'lung': self.ad_hoc_lung_post_processing, + 'celiac': self.ad_hoc_celiac_post_processing } # set parameter to None before choosing use case self.use_case_ad_hoc_post_processing = None @@ -111,6 +115,11 @@ def __init__(self, biospacy="en_core_sci_lg", biow2v=True, str_match=False, biof # set parameter to store dysplasia mappings restricted to a specific use-case self.use_case_dysplasia = dict() + # list of valued-data properties + self.valued_props = ['modified marsh classification of histologic findings in celiac disease', 'villi degree of atrophy', + 'duodenum villi length', 'villi to crypt of lieberkuhn ratio', 'intraepithelial lymphocyte count', + 'number of mitosis per crypt', 'duodenitis severity'] + # COMMON FUNCTIONS def restrict2use_case(self, use_case): # @smarchesin TODO: remove all the triggers within PhraseMacher by looping over use cases - then consider only the use case ones @@ -512,7 +521,7 @@ def associate_mention2candidate(self, mention, labels, sim_thr=0.7): else: # return (mention, None) pair return [[mention.text, None]] - def link_mentions_to_concepts(self, mentions, labels, use_case_ontology, sim_thr=0.7, raw=False, debug=False): + def link_mentions_to_concepts(self, use_case, mentions, labels, use_case_ontology, sim_thr=0.7, raw=False, debug=False): """ Link identified entity mentions to ontology concepts @@ -526,14 +535,17 @@ def link_mentions_to_concepts(self, mentions, labels, use_case_ontology, sim_thr Returns: a dict of identified ontology concepts {semantic_area: [iri, mention, label], ...} """ - # link mentions to concepts mentions_and_concepts = [self.use_case_ad_hoc_linking(mention, labels, sim_thr, debug) for mention in mentions] mentions_and_concepts = list(itertools.chain.from_iterable(mentions_and_concepts)) # post process mentions and concepts based on the considered use case mentions_and_concepts = self.use_case_ad_hoc_post_processing(mentions_and_concepts) # extract linked data from ontology - linked_data = [(mention_and_concept[0], use_case_ontology.loc[use_case_ontology['label'].str.lower() == mention_and_concept[1]][['iri', 'label', 'semantic_area_label']].values[0].tolist()) for mention_and_concept in mentions_and_concepts if mention_and_concept[1] is not None] + if use_case == 'celiac': + # Store value for valued-data properties + linked_data = [(mention_and_concept[0], use_case_ontology.loc[use_case_ontology['label'].str.lower() == mention_and_concept[1]][['iri', 'label', 'semantic_area_label']].values[0].tolist(), mention_and_concept[2] if mention_and_concept[1] in self.valued_props else None) for mention_and_concept in mentions_and_concepts if mention_and_concept[1] is not None] + else: + linked_data = [(mention_and_concept[0], use_case_ontology.loc[use_case_ontology['label'].str.lower() == mention_and_concept[1]][['iri', 'label', 'semantic_area_label']].values[0].tolist()) for mention_and_concept in mentions_and_concepts if mention_and_concept[1] is not None] # filter out linked data 'semantic_area_label' == None linked_data = [linked_datum for linked_datum in linked_data if linked_datum[1][2] is not None] if raw: # return mentions+concepts @@ -542,7 +554,14 @@ def link_mentions_to_concepts(self, mentions, labels, use_case_ontology, sim_thr # return linked concepts divided into semantic areas linked_concepts = {area: [] for area in set(use_case_ontology['semantic_area_label'].tolist()) if area is not None} for linked_datum in linked_data: - linked_concepts[str(linked_datum[1][2])].append([linked_datum[1][0], linked_datum[1][1]]) + if use_case == 'celiac': + # Store value for valued-data properties + if linked_datum[2] is not None: + linked_concepts[str(linked_datum[1][2])].append([linked_datum[1][0], linked_datum[1][1], linked_datum[2]]) + else: + linked_concepts[str(linked_datum[1][2])].append([linked_datum[1][0], linked_datum[1][1]]) + else: + linked_concepts[str(linked_datum[1][2])].append([linked_datum[1][0], linked_datum[1][1]]) return linked_concepts # COLON SPECIFIC LINKING FUNCTIONS @@ -724,8 +743,7 @@ def link_colon_biopsy(self, mention, labels, sim_thr=0.7): # @smarchesin TODO: # COLON SPECIFIC POST PROCESSING OPERATIONS - @staticmethod - def ad_hoc_colon_post_processing(mentions_and_concepts): # @TODO: use it if post processing operations are required for colon + def ad_hoc_colon_post_processing(self, mentions_and_concepts): # @TODO: use it if post processing operations are required for colon """ Perform set of post processing operations @@ -735,7 +753,57 @@ def ad_hoc_colon_post_processing(mentions_and_concepts): # @TODO: use it if pos Returns: mentions and concepts after post processing operations """ - return mentions_and_concepts + new_mentions_and_concepts = self.remove_colon_unrelated_concepts(mentions_and_concepts) + return new_mentions_and_concepts + + @staticmethod + def remove_colon_unrelated_concepts(mentions_and_concepts): + """ + Remove mentions containing terms unrelated to dysplasia, adenocarcinoma and hyperplastic polyp. + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after unrelated concepts removal + """ + + new_mentions_and_concepts = [] + for m_and_c in mentions_and_concepts: + if m_and_c[1] is not None: + if 'dysplasia' in m_and_c[1]: # concept refers to 'dysplasia' + if 'dysplasia' in m_and_c[0]: # mention refers to 'dysplasia' + # mention related to dysplasia -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to dysplasia -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'metastatic' in m_and_c[1]: + if 'metastatic' in m_and_c[0]: # mention refers to 'metastatic' + # mention related to metastatic -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to metastatic -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'carcinoma' in m_and_c[1]: # concept refers to 'carcinoma' + if 'carcinoma' in m_and_c[0]: # mention refers to 'carcinoma' + # mention related to carcinoma -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to carcinoma -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'hyperplastic' in m_and_c[1]: # concept refers to 'hyperplastic' + if 'hyperplastic' in m_and_c[0]: # mention refers to 'hyperplastic' + # mention related to hyperplastic -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to hyperplastic -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + else: + new_mentions_and_concepts.append(m_and_c) + else: + new_mentions_and_concepts.append(m_and_c) + + return new_mentions_and_concepts # CERVIX SPECIFIC LINKING FUNCTIONS @@ -957,8 +1025,34 @@ def ad_hoc_cervix_post_processing(self, mentions_and_concepts): Returns: mentions and concepts after post processing operations """ + new_mentions_and_concepts = self.remove_unrelated_adeno_concepts(mentions_and_concepts) + return self.associate_cervix_in_situ_invasive_concepts(new_mentions_and_concepts) + + @staticmethod + def remove_unrelated_adeno_concepts(mentions_and_concepts): + """ + Remove mentions containing terms unrelated to cervical adenocarcinoma. + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after unrelated adenocarcinoma removal + """ + + new_mentions_and_concepts = [] + adeno = ['cervical adenocarcinoma in situ', 'cervical adenocarcinoma'] - return self.associate_cervix_in_situ_invasive_concepts(mentions_and_concepts) + for m_and_c in mentions_and_concepts: + if m_and_c[1] in adeno: # concept refers to 'adenocarcinoma' + if 'adeno' in m_and_c[0]: # mention refers to 'adenocarcinoma' + # mention related to adenocarcinoma -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to adenocarcinoma -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + else: + new_mentions_and_concepts.append(m_and_c) + return new_mentions_and_concepts @staticmethod def associate_cervix_in_situ_invasive_concepts(mentions_and_concepts): @@ -1267,6 +1361,1061 @@ def remove_lung_neoplasm_unrelated_concepts(mentions_and_concepts): # return post processed mentions and concepts return new_mentions_and_concepts + # CELIAC SPECIFIC LINKING FUNCTIONS + + def ad_hoc_celiac_linking(self, mention, labels, sim_thr=0.7, debug=False): + """ + Perform set of celiac ad hoc linking functions + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + labels (list(spacy.token.span.Span)): list of concept labels from reference ontology + sim_thr (float): keep candidates with sim score greater than or equal to sim_thr + debug (bool): whether to keep flags for debugging + + Returns: matched ontology concept label(s) + """ + findings = ['granulocyte', 'eosinophil', 'neutrophil', 'leukocyte', 'lymphocyte', 'enterocyte'] + mucosa_abnormalities = ['edema', 'mucosa', 'hyperemic', 'hyperaemia'] + celiac_synonyms = ['celiac disease', 'malabsorb disease', 'gluten hypersensitivity', 'marsh'] + negative_trigs = ['normal', 'no abnormalities', 'without abnormalities'] + if 'cd3' in mention.text: # mention contains 'cd3' + return self.link_cd3_test(mention) + elif 'her2' in mention.text: # mention contains 'her2' + return self.link_her2_test(mention) + elif any(key in mention.text for key in celiac_synonyms): # mention contains 'celiac disease' + return self.link_celiac_disease(mention) + elif 'duodenitis' in mention.text: # mention contains 'duodenitis' + return self.link_duodenitis(mention) + elif 'gland' in mention.text or 'hyperplasia' in mention.text: # mention contains 'glands' or 'hyperplasia' + return self.link_duodenal_gland(mention) + elif any(key in mention.text for key in mucosa_abnormalities): # mentions contains a mucosa abnormality + return self.link_mucosa_abnormality(mention) + elif 'heterotopia' in mention.text or 'heterotopic' in mention.text: # mention contains 'heterotopia' + return self.link_heterotopia(mention) + elif 'phlogosis' in mention.text or 'inflammatory' in mention.text: # mention contains 'phlogosis' + return self.link_inflammation(mention) + elif 'congestion' in mention.text: # mention contains 'congestion' + return self.link_congestion(mention) + elif 'ulceration' in mention.text: # mention contains 'ulceration' + return self.link_ulcer(mention) + elif 'erosion' in mention.text: # mention contains 'erosion' + return self.link_erosion(mention) + elif 'atrophy' in mention.text: # mention contains 'atrophy' + return self.link_atrophy(mention) + elif 'flat' in mention.text: # mention contains 'flat' + return self.link_flattened_villi(mention) + elif 'ratio' in mention.text: # mention contains 'ratio' + return self.link_crypt_ratio(mention) + elif 'mitosis' in mention.text: # mention contains 'mitosis' + return self.link_mitosis_number(mention) + elif any(k in mention.text for k in ['height', 'length']): # mention contains information about villi status + return self.link_villi_height(mention) + elif any(k in mention.text for k in findings) or \ + any(k in mention.text for k in findings+['lymphoplasmocitary', 'lymphocital', 'granulocitary']): + # mention contains celiac findings + return self.link_celiac_finding(mention, findings) + elif 'biopsy' in mention.text: # mention contains 'biopsy' + return self.link_biopsy(mention) + elif 'villo-ghiandular' in mention.text: # mention contains 'villo-ghiandular' + return self.link_villi_mucosa(mention) + elif 'lamina' in mention.text: # mention contains 'lamina' + return self.link_duodenal_lamina(mention) + elif 'epithelium' in mention.text: # mention contains 'epithelium' + return self.link_duodenal_epithelium(mention) + elif 'jejunum' in mention.text: # mention contains 'jejunum' + return self.link_jejunum(mention) + elif 'small intestine' in mention.text: # mention contains 'small intestine' + return self.link_small_intestine(mention) + elif 'duodenal' in mention.text: # mention contains 'duodenal' + return self.link_duodenal_location(mention) + if any(key in mention.text for key in negative_trigs): # mention contains negative result triggers + return self.link_negative_outcome(mention) + else: # none of the ad hoc functions was required -- perform similarity-based linking + return self.associate_mention2candidate(mention, labels, sim_thr) + # return [[mention.text, None]] + + @staticmethod + def link_cd3_test(mention): + """ + Link cd3 to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: cluster of differentation 3 concept. + """ + return [[mention.text, 'cluster of differentation 3']] + + @staticmethod + def link_her2_test(mention): + """ + Link her2 to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: her2 (cb11) concept. + """ + return [[mention.text, 'her2 (cb11)']] + + @staticmethod + def link_duodenal_gland(mention): + """ + Link gland mention to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: associated gland concept. + """ + gland_mention = mention.text + if 'hyperplasia' in gland_mention: # mention contains 'hyperplasia' + return [[mention.text, 'brunner\'s gland hyperplasia']] + elif 'atrophy' in gland_mention: # mention contains 'atrophy' + return [[mention.text, 'glandular atrophy'], [mention.text, 'duodenal gland']] + else: + return [[mention.text, 'duodenal gland']] + + + @staticmethod + def link_duodenal_lamina(mention): + """ + Link lamina to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenal lamina propria concept. + """ + return [[mention.text, 'duodenal lamina propria']] + + @staticmethod + def link_duodenal_epithelium(mention): + """ + Link epithelium to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenal epithelium concept. + """ + return [[mention.text, 'duodenal epithelium']] + + @staticmethod + def link_inflammation(mention): + """ + Link phlogosis to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: inflammation concept based on the degree of inflammation. + """ + inflammation_mention = mention.text + if inflammation_mention == 'phlogosis' or inflammation_mention == 'inflammatory': + return [[mention.text, 'inflammation']] + elif 'acute' in mention.text or 'active' in mention.text or 'activity' in mention.text: + return [[mention.text, 'chronic active inflammation']] + elif 'chronic' in mention.text: + return [[mention.text, 'chronic inflammation']] + else: + return [[mention.text, 'inflammation']] + + @staticmethod + def link_celiac_disease(mention): + """ + Link celiac disease to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: positive to celiac disease concept. + """ + triggers = ['0', '1', '2', '3', '4'] + negative_trigs = ['no indications', 'no evidence', 'no more signs'] + type_mention = None + if 'type' in mention.text or 'marsh' in mention.text: + # Check for type inside the mention + if any(t in mention.text for t in triggers): + type_text = [tok.text for tok in mention if any(t in tok.text for t in triggers)][0] + type_mention = [mention.text, 'modified marsh classification of histologic findings in celiac disease', type_text] + # Check next token + elif mention.end < len(mention.doc) and any(t in mention.doc[mention.end].text for t in triggers): + type_text = mention.doc[mention.end].text + type_mention = [mention.text, 'modified marsh classification of histologic findings in celiac disease', type_text] + if any(neg in mention.text for neg in negative_trigs): + # Negative Result + return [[mention.text, 'negative result']] + elif type_mention is not None: + return [[mention.text, 'positive to celiac disease'], type_mention] + else: + return [[mention.text, 'positive to celiac disease']] + + @staticmethod + def link_mucosa_abnormality(mention): + """ + Link mucosa to the correct concepts. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenal mucosa concept. + """ + celiac_mention = mention.text + if celiac_mention == 'mucosa': + return [[mention.text, 'duodenal mucosa']] + elif 'antral' in celiac_mention or 'pyloric' in celiac_mention: + return [[mention.text, 'mucosa of pyloric antrum']] + else: + abnormality_mentions = [] + if 'mucosa' in celiac_mention: + if 'hyperemi' in celiac_mention: + abnormality_mentions.append([mention.text, 'hyperemia']) + if 'edema' in celiac_mention: + abnormality_mentions.append([mention.text, 'edema']) + return [[mention.text, 'duodenal mucosa']] + abnormality_mentions + if 'hyperemi' in celiac_mention: + abnormality_mentions.append([mention.text, 'hyperemia']) + if 'edema' in celiac_mention: + abnormality_mentions.append([mention.text, 'edema']) + if len(abnormality_mentions) > 0: + return abnormality_mentions + else: + return [[mention.text, None]] + + @staticmethod + def link_celiac_finding(mention, findings): + """ + Link celiac finding to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + findings: (list(str)) list of possible celiac findings + + Returns: finding concept. + """ + finding_mention = mention.text + if 'lymphocyte' in finding_mention or 'lymphocital' in finding_mention: + if 'iel' in finding_mention: + i_end = [tok.i for tok in mention.doc[mention.end:] if mention.doc[tok.i].text == ')'] + value = mention.doc[mention.end:i_end[0]] + return [[mention.text, 'lymphocyte'], [mention.text, 'intraepithelial lymphocyte count'], [mention.text, value.text]] + else: + return [[mention.text, 'lymphocyte']] + elif 'lymphoplasmocitary' in finding_mention: + return[[mention.text, 'lymphocyte']] + elif 'granulocitary' in finding_mention: + return [[mention.text, 'granulocyte']] + elif any(k in finding_mention for k in findings): + find_mentions = [k for k in findings if k in finding_mention] + mentions2concepts = [] + for finding in find_mentions: + mentions2concepts.append([mention.text, finding]) + return mentions2concepts + elif finding_mention in findings: + return [[mention.text, [find for find in findings if finding_mention == find][0]]] + else: + return [[mention.text, None]] + + @staticmethod + def link_duodenitis(mention): + """ + Link duodenitis to the correct concepts and extract additional information if present. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenitis concept, duodenitis severity and additional concepts. + """ + triggers = ['chronic', 'active', 'acute', 'moderate', 'mild', 'erosive', 'mild-activity', 'activity', 'ulcerative'] + annotation = None + start_i = mention.start if mention.start == 0 else mention.start-1 + if 'ulcerative' in mention.doc[start_i:mention.end+4].text: + annotation = [[mention.text, 'ulcer']] + if 'erosive' in mention.doc[start_i:mention.end+4].text: + annotation = [[mention.text, 'erosion']] + if any(trig in mention.doc[start_i:mention.end+4].text for trig in triggers): + start_i = mention.start + end_i = mention.end + finished = False + # Check for any other trigger right before the mention + while start_i > 0 and not finished: + start_i = start_i - 1 + tmp = mention.doc[start_i] + if tmp.text in triggers + ['with', 'to', ',', 'slightly']: + if start_i == 0 or mention.doc[start_i-1].text not in triggers + ['with', 'to', ',', 'slightly']: + finished = True + else: + start_i = start_i + 1 + finished = True + if mention.doc[start_i].text in ['with', 'to', ',', 'slightly']: + start_i = start_i + 1 + # Check for any other trigger after the mention + if any(trig in mention.doc[mention.end:].text for trig in triggers): + # We keep span until the next token is no longer a trigger or conjunction + end_i = [tok.i for tok in mention.doc[mention.end:] if tok.text in triggers + ['with', 'to', ','] + and mention.doc[tok.i+1].text not in triggers][0]+1 + if annotation is not None: + return [[mention.text, 'duodenitis'], [mention.text, 'duodenitis severity', mention.doc[start_i:end_i].text]] + annotation + else: + return [[mention.text, 'duodenitis'], [mention.text, 'duodenitis severity', mention.doc[start_i:end_i].text]] + else: + return [[mention.text, 'duodenitis']] + + @staticmethod + def link_ulcer(mention): + """ + Link ulcer concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: ulcer concept. + """ + return [[mention.text, 'ulcer']] + + @staticmethod + def link_villi_mucosa(mention): + """ + Link correct duodenal location to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenal location concept. + """ + location_mention = mention.text + if location_mention == 'villo-ghiandular mucosa': + return [[mention.text, 'duodenal mucosa']] + else: + return [[mention.text, 'intestinal villus of duodenum'], [mention.text, 'duodenal gland']] + + @staticmethod + def link_negative_outcome(mention): + """ + Link negative outcome concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: negative outcome concept. + """ + normal_mention = mention.text + if normal_mention in ['within the limit of normal', 'within the limits of normal', 'normal morphology', + 'normal appearance', 'no abnormality', 'no abnormalities']: + return [[mention.text, 'negative result']] + else: + # Check next entity + next_ent = mention.doc.ents[mention.ent_id+1] + if 'architecture' in next_ent.text: + return [[mention.text, 'negative result']] + else: # mention is not a negative outcome + return [[mention.text, None]] + + @staticmethod + def link_erosion(mention): + """ + Link erosion concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: erosion concept. + """ + return [[mention.text, 'erosion']] + + @staticmethod + def link_congestion(mention): + """ + Link congestion concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: congestion concept. + """ + return [[mention.text, 'tissue congestion']] + + @staticmethod + def link_heterotopia(mention): + """ + Link heterotopia concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: heterotopia concept. + """ + return [[mention.text, 'gastric heterotopia of the small intestine']] + + @staticmethod + def link_atrophy(mention): + """ + Link correct atrophy concept and extract additional information if present. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: atrophy concept and villi degree of atrophy information. + """ + triggers = ['moderate', 'severe', 'total', 'mild', 'moderate-severe', 'focal'] + if 'glandular' in mention.text: + return [[mention.text, 'glandular atrophy'], [mention.text, 'duodenal gland']] + elif 'crypt' in mention.text: + return [[mention.text, 'glandular atrophy'], [mention.text, 'crypt of lieberkuhn of duodenum']] + elif 'villi' in mention.text: + # Check for specified degree of atrophy + if any(trig in mention.text for trig in triggers): + value = [trig for trig in triggers if trig in mention.text][0] + return [[mention.text, 'villi degree of atrophy', value]] + elif any(trig in mention.doc[mention.start-1].text for trig in triggers): + value = [trig for trig in triggers if trig in mention.doc[mention.start-1].text][0] + if value == 'moderate': + # Check if degree of atrophy if 'mild to moderate' + if mention.doc[mention.start-3:mention.start].text == 'mild to moderate': + return [[mention.text, 'villi degree of atrophy', 'mild to moderate']] + return [[mention.text, 'villi degree of atrophy', value]] + else: + return [[mention.text, 'villi degree of atrophy', 'not specified']] + else: + return [[mention.text, None]] + + @staticmethod + def link_biopsy(mention): + """ + Link correct biopsy concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: biopsy concept. + """ + biopsy_mention = mention.text + biopsy_output = [] + if 'duodenum' in biopsy_mention or 'duodenal' in biopsy_mention: # mention contains 'duodenum' + biopsy_output.append([mention.text, 'biopsy of duodenum']) + biopsy_output.append([mention.text, 'duodenum']) + if any(tok in biopsy_mention for tok in ['pyloric', 'antrum', 'antrum/body']): # mention contains 'antrum pylori' + biopsy_output.append([mention.text, 'biopsy of the pyloric antrum']) + biopsy_output.append([mention.text, 'antrum pylori']) + if 'stomach' in biopsy_mention or 'corpus' in biopsy_mention: # mention contains 'stomach' + if 'antrum' not in biopsy_output: + biopsy_output.append([mention.text, 'biopsy of the greater curvature']) + biopsy_output.append([mention.text, 'greater curvature of stomach']) + if 'endoscopic' in biopsy_mention: + biopsy_output.append([mention.text, 'endoscopic biopsy']) + if 'small intestine' in biopsy_mention: + biopsy_output.append([mention.text, 'biopsy of small intestine']) + biopsy_output.append([mention.text, 'small intestine']) + if 'jejunum' in biopsy_mention: + biopsy_output.append([mention.text, 'biopsy of jejunum']) + biopsy_output.append([mention.text, 'jejunum']) + if len(biopsy_output) == 0: # default biopsy is 'duodenum biopsy' + return [[mention.text, 'biopsy of duodenum'], [mention.text, 'duodenum']] + else: + return biopsy_output + + @staticmethod + def link_flattened_villi(mention): + """ + Link correct flattened villi concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: flattened villi concept. + """ + flat_mention = mention.text + if 'villi' in flat_mention or 'villuses' in flat_mention: + return [[mention.text, 'has flattened villi'], [mention.text, 'intestinal villus of duodenum']] + else: + return [[mention.text, None]] + + @staticmethod + def link_crypt_ratio(mention): + """ + Link correct villi to crypt ratio concept and value. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: villi to crypt ratio concept and value. + """ + if mention.doc[mention.start-1].text == '(': + # extract value in between brackets (if bracket is not closed, skip value) + i_end = [tok.i for tok in mention.doc[mention.start:] if mention.doc[tok.i].text == ')'] + if len(i_end) > 0: + value = mention.doc[mention.start:i_end[0]] + return [[mention.text, 'villi to crypt of lieberkuhn ratio', value.text]] + return [[mention.text, None]] + + @staticmethod + def link_villi_height(mention): + """ + Link correct villi to crypt ratio concept and value. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: villi to crypt ratio concept and value. + """ + triggers = ['decreased', 'normal', 'maintained', 'reduced', 'reduction', 'irregular', 'regular'] + if 'vill' in mention.text: + if any(trig in mention.text for trig in triggers): + return [[mention.text, 'duodenum villi length', mention.text]] + elif any(trig in mention.doc[mention.start-3:mention.end+2].text for trig in triggers): + tok_i = [tok.i for tok in mention.doc[mention.start-3:mention.end+3] if mention.doc[tok.i].text in triggers] + if tok_i[0] < mention.start: + # trigger before mention + return [[mention.text, 'duodenum villi length', mention.doc[tok_i[0]:mention.end].text]] + else: + # trigger after mention + return [[mention.text, 'duodenum villi length', mention.doc[mention.start:tok_i[0]+1].text]] + else: + return [[mention.text, None]] + else: + return [[mention.text, None]] + + @staticmethod + def link_mitosis_number(mention): + """ + Link correct villi to crypt ratio concept and value. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: villi to crypt ratio concept and value. + """ + triggers = ['normal', 'increase', 'norm', 'rare'] + if any(trig in mention.doc[mention.start-3:mention.end].text for trig in triggers): + value = [trig for trig in triggers if trig in mention.doc[mention.start-3:mention.end].text][0] + if value == 'norm': + value = 'normal' + return [[mention.text, 'number of mitosis per crypt', value]] + else: + return [[mention.text, None]] + + @staticmethod + def link_duodenal_location(mention): + """ + Link correct duodenal location to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: duodenal location concept. + """ + location_mention = mention.text + if 'mucosa' in location_mention: + return [[mention.text, 'duodenal mucosa']] + elif 'ampulla' in location_mention or 'bulb' in location_mention: + return [[mention.text, 'duodenal ampulla']] + elif 'lamina' in location_mention: + return [[mention.text, 'duodenal lamina propria']] + elif 'gland' in location_mention: + return [[mention.text, 'duodenal gland']] + else: + return [[mention.text, 'duodenum']] + + @staticmethod + def link_jejunum(mention): + """ + Link jejunum to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: jejunum concept. + """ + return [[mention.text, 'jejunum']] + + @staticmethod + def link_small_intestine(mention): + """ + Link small intestine to the correct concept. + + Params: + mention (spacy.tokens.span.Span): entity mention extracted from text + + Returns: small intestine concept. + """ + return [[mention.text, 'small intestine']] + + # CELIAC SPECIFIC POST PROCESSING OPERATIONS + + def ad_hoc_celiac_post_processing(self, mentions_and_concepts): + """ + Perform set of post processing operations + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after post processing operations + """ + new_mentions_and_concepts = self.remove_not_celiac_reports(mentions_and_concepts) + new_mentions_and_concepts = self.remove_celiac_unrelated_concepts(new_mentions_and_concepts) + new_mentions_and_concepts = self.remove_unrelated_props(new_mentions_and_concepts, self.valued_props) + # Consistency Checks + new_mentions_and_concepts = self.remove_unreliable_outcomes(new_mentions_and_concepts) + return new_mentions_and_concepts + + @staticmethod + def remove_not_celiac_reports(mentions_and_concepts): + """ + Remove mentions containing terms unrelated to celiac use-case + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after removal or reports unrelated to celiac use case. + """ + unrelated_triggers = ['neoplas', 'tumor', 'adenocarcinoma', 'polyp', 'adenoma', 'perforation', 'cervical', + 'colon', 'lung', 'hpv'] + unrelated = False + for m_and_c in mentions_and_concepts: + if unrelated or any(trig in m_and_c[0] for trig in unrelated_triggers): # mention contains unrelated triggers + # mentions not related to celiac use-case -- remove all + unrelated = True + + if unrelated: + # mentions not related to celiac use-case -- removed all + new_mentions_and_concepts = [] + for m_and_c in mentions_and_concepts: + new_mentions_and_concepts.append([m_and_c[0], None]) + return new_mentions_and_concepts + else: + # mentions related to celiac use-case -- keep all + return mentions_and_concepts + + @staticmethod + def remove_celiac_unrelated_concepts(mentions_and_concepts): + """ + Remove mentions containing terms unrelated to cell-based carcinoma + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after unrelated cell-based carcinoma removal + """ + + new_mentions_and_concepts = [] + for m_and_c in mentions_and_concepts: + if m_and_c[1] is not None: + if 'metaplasia' in m_and_c[1]: # concept refers to 'metaplasia' + if 'metaplasia' in m_and_c[0]: # mention refers to 'metaplasia' + # mention related to metaplasia -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to metaplasia -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'inflammation' in m_and_c[1]: # concept refers to 'inflammation' + if 'inflammat' in m_and_c[0] or 'phlogosis' in m_and_c[0]: # mention refers to 'inflammation' + # mention related to inflammation -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to inflammation -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'jejunum' in m_and_c[1]: # concept refers to 'jejunum' + if 'jejunum' in m_and_c[0]: # mention refers to 'jejunum' + # mention related to jejunum -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to jejunum -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'small intestine' in m_and_c[1]: # concept refers to 'small intestine' + if 'small intestine' in m_and_c[0]: # mention refers to 'small intestine' + # mention related to small intestine -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to small intestine -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'crohn disease' == m_and_c[1]: # concept refers to 'crohn disease' + if 'crohn' in m_and_c[0]: # mention refers to 'crohn disease' + # mention related to chron disease -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to chron disease -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'intestinal fibrosis' in m_and_c[1]: # concept refers to 'intestinal fibrosis' + if 'fibrosis' in m_and_c[0]: # mention refers to 'fibrosis' + # mention related to fibrosis -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to fibrosis -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'malabsorption' in m_and_c[1]: # concept refers to 'malabsorption' + if 'malabsorption' in m_and_c[0]: # mention refers to 'malabsorption' + # mention related to malabsorption -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to malabsorption -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'duodenitis' == m_and_c[1]: # concept refers to 'duodenitis' + if 'duodenitis' in m_and_c[0]: # mention refers to 'duodenitis' + # mention related to duodenitis -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to duodenitis -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'lamina' in m_and_c[1]: # concept refers to 'lamina' + if 'lamina' in m_and_c[0]: # mention refers to 'lamina' + # mention related to lamina -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to lamina -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'epithelium' in m_and_c[1]: # concept refers to 'epithelium' + if 'epithelium' in m_and_c[0]: # mention refers to 'epithelium' + # mention related to epithelium -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to epithelium -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'mucosa' in m_and_c[1]: # concept refers to 'mucosa' + if 'mucosa' in m_and_c[0]: # mention refers to 'mucosa' + # mention related to mucosa -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to mucosa -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'congestion' in m_and_c[1]: # concept refers to 'congestion' + if 'congestion' in m_and_c[0]: # mention refers to 'congestion' + # mention related to congestion -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to congestion -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'heterotopia' in m_and_c[1]: # concept refers to 'heterotopia' + if 'heterotopia' in m_and_c[0] or 'heterotopic' in m_and_c[0]: # mention refers to 'heterotopia' + # mention related to heterotopia -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to heterotopia -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'has flattened villi' in m_and_c[1]: # concept refers to 'flattened villi' + if 'flat' in m_and_c[0]: # mention refers to 'flattened villi' + # mention related to flattened villi -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to flattened villi -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'absence of villi' in m_and_c[1]: # concept refers to 'villi absence' + if 'villi' in m_and_c[0] and any(k in m_and_c[0] for k in ['free', 'without', 'absent']): # mention refers to 'villi absence' + # mention related to villi absence -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to flattened villi -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'inconclusive outcome' == m_and_c[1]: # concept refers to 'inconclusive outcome' (we only set them later) + # mention not related to inconclusive outcome -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + elif 'negative result' == m_and_c[1]: # concept refers to 'negative outcome' + if m_and_c[0] in ['within the limit of normal', 'within the limits of normal', + 'normal morphology', 'normal appearance', 'no abnormalities']: + # mention related to negative outcomee -- keep it + new_mentions_and_concepts.append(m_and_c) + elif 'normal' in m_and_c[0]: + # mention related to negative outcome -- keep it + new_mentions_and_concepts.append(m_and_c) + else: + # mention not related to negative outcome -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + else: + new_mentions_and_concepts.append(m_and_c) + else: + new_mentions_and_concepts.append(m_and_c) + # return post processed mentions and concepts + return new_mentions_and_concepts + + @staticmethod + def remove_unreliable_outcomes(mentions_and_concepts): + """ + Remove mentions containing unreliable outcomes. + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after unreliable outcomes removal + """ + new_mentions_and_concepts = [] + negative, celiac, duodenitis = 0, 0, 0 + for m_and_c in mentions_and_concepts: + if 'negative result' == m_and_c[1]: # mention refers to 'negative result' + negative = 1 + negative_mention = m_and_c[0] + elif 'positive to celiac disease' == m_and_c[1]: # mention refers to 'positive to celiac disease' + celiac = 1 + celiac_mention = m_and_c[0] + elif 'duodenitis' == m_and_c[1]: # mention refers to 'duodenitis' + duodenitis = 1 + duodenitis_mention = m_and_c[0] + else: + new_mentions_and_concepts.append(m_and_c) + + if negative == 1 and all([celiac == 0, duodenitis == 0]): # only negative result + # mention related to negative result -- keep it + new_mentions_and_concepts.append([negative_mention, 'negative result']) + elif negative == 1 and any([celiac == 1, duodenitis == 1]): + # unreliable outcome -- set to inconclusive + new_mentions_and_concepts.append(['post processed inconclusive outcome', 'inconclusive outcome']) + elif negative == 0 and all([celiac == 1, duodenitis == 1]): + # unreliable outcome -- set to inconclusive + new_mentions_and_concepts.append(['post processed inconclusive outcome', 'inconclusive outcome']) + elif celiac == 1: + # mention related to celiac result -- keep it + new_mentions_and_concepts.append([celiac_mention, 'positive to celiac disease']) + elif duodenitis == 1: + # mention related to duodenitis result -- keep it + new_mentions_and_concepts.append([duodenitis_mention, 'duodenitis']) + + """ + elif len(mentions_and_concepts) > 0 and all([celiac == 0, duodenitis == 0]): + # negative result -- add mention + new_mentions_and_concepts.append(['post processed negative result', 'negative result']) + """ + + # return post processed mentions and concepts + return new_mentions_and_concepts + + @staticmethod + def remove_unrelated_props(mentions_and_concepts, valued_props): + """ + Remove mentions containing terms unrelated to valued-data properties. + + Params: + mentions_and_concepts (list(list(str))): list of mentions and concepts extracted from report + + Returns: mentions and concepts after unrelated valued-data properties removal + """ + new_mentions_and_concepts = [] + for m_and_c in mentions_and_concepts: + if any(m_and_c[1] == props for props in valued_props): # mention refers to a data property + if len(m_and_c) == 3: # mention contains a value for the data property + # mention related to a data property -- keep it + new_mentions_and_concepts.append(m_and_c) + else: # mention not related to a data property -- remove it + new_mentions_and_concepts.append([m_and_c[0], None]) + else: # mention does not refer to a data property + new_mentions_and_concepts.append(m_and_c) + # return post processed mentions and concepts + return new_mentions_and_concepts + + def check_inconclusive_outcomes(self, diagnoses): + """ + Remove concepts containing unreliable outcomes. + + Params: + diagnoses (list(list(str))): list of concepts extracted from report + + Returns: concepts after unreliable outcomes removal + """ + celiac, duodenitis, normal = 0, 0, 0 + # make diagnosis section a set + diagnosis = set([concept[1].lower() for concept in diagnoses]) + # update pre-defined labels w/ 1 in case of label presence + for d in diagnosis: + if 'positive to celiac disease' == d: + celiac = 1 + elif 'duodenitis' == d: + duodenitis = 1 + elif 'negative result' == d: + normal = 1 + # update when no label has been set to 1 + if sum([celiac, duodenitis, normal]) > 1: + new_diagnoses = [] + for d in diagnoses: + if d[1].lower() not in ['positive to celiac disease', 'duodenitis', 'negative result']: + new_diagnoses.append(d) + new_diagnoses.append(['https://w3id.org/examode/ontology/InconclusiveOutcome', 'Inconclusive Outcome']) + return new_diagnoses + else: + return diagnoses + + def celiac_additional_concepts(self, concepts, tissue, procedure, shorts): + """ + Add additional concepts and check outcome consistency by looking at other report fields. + + Params: + concepts (dict): dict of identified ontology concepts {semantic_area: [iri, mention, label], ...} + tissue (str): examined tissue + procedure (str): procedure performed + shorts (list(str)): diagnosis summary + + Return: updated dict of identified ontology concepts {semantic_area: [iri, mention, label], ...} + """ + new_concepts = dict() + # Copy test, procedure and anatomical locations concepts already extracted + new_concepts['Test'] = copy.deepcopy(concepts['Test']) + new_concepts['Anatomical Location'] = copy.deepcopy(concepts['Anatomical Location']) + new_concepts['Procedure'] = copy.deepcopy(concepts['Procedure']) + new_concepts['Diagnosis'] = [] + + # Check for additional information about anatomical location in 'tissue' field + if tissue != '': + new_concepts['Anatomical Location'] = self.link_additional_locations(new_concepts['Anatomical Location'], tissue) + + # Check for additional information about procedure in 'procedure' field + if procedure != '': + new_concepts = self.link_additional_procedures(new_concepts, procedure) + + # Check for additional information about diagnosis in 'short' field + if len(shorts) > 0: + # Check diagnosis concepts already extracted + negative, celiac, duodenitis = 0, 0, 0 + celiac_property, duodenitis_property = [], [] + for diagnosis in concepts['Diagnosis']: + if 'negative result' == diagnosis[1]: # concept refers to 'negative result' + negative = 1 + diagnosis_concept = diagnosis + elif 'positive to celiac disease' == diagnosis[1]: # concept refers to 'positive to celiac disease' + celiac = 1 + diagnosis_concept = diagnosis + celiac_property = [diagnosis for diagnosis in concepts['Diagnosis'] if diagnosis[1] == + 'modified Marsh classification of histologic findings in celiac disease'] + elif 'duodenitis' == diagnosis[1]: # concept refers to 'duodenitis' + duodenitis = 1 + diagnosis_concept = diagnosis + duodenitis_property = [diagnosis for diagnosis in concepts['Diagnosis'] if diagnosis[1] == + 'duodenitis severity'] + elif diagnosis[1] not in ['modified Marsh classification of histologic findings in celiac disease', 'duodenitis severity']: + # concept does not refer to outcome, append it + new_concepts['Diagnosis'].append(diagnosis) + if any(short in ['celiac disease', 'no abnormalities'] for short in shorts): + if any('celiac' in short for short in shorts): + new_concepts['Diagnosis'].append(['https://w3id.org/examode/ontology/PositiveToCeliacDisease', + 'Positive to Celiac Disease']) + if celiac == 1 and len(celiac_property) > 0: + new_concepts['Diagnosis'].append(celiac_property[0]) + if any('no abnormalities' in short for short in shorts): + # Negative result + new_concepts['Diagnosis'].append(['https://w3id.org/examode/ontology/NegativeResult', + 'Negative Result']) + elif any('dubious' in short for short in shorts) and all(short not in ['celiac disease', 'no abnormalities'] for short in shorts): + if sum([negative, celiac, duodenitis]) == 0: + # Set to inconclusive outcome + new_concepts['Diagnosis'].append(['https://w3id.org/examode/ontology/InconclusiveOutcome', + 'Inconclusive Outcome']) + else: + # Keep diagnosis outcome as it is + new_concepts['Diagnosis'].append(diagnosis_concept) + # Add data properties, if present + if celiac == 1 and len(celiac_property) > 0: + new_concepts['Diagnosis'].append(celiac_property[0]) + if duodenitis == 1 and len(duodenitis_property) > 0: + new_concepts['Diagnosis'].append(duodenitis_property[0]) + elif sum([negative, celiac, duodenitis]) == 1: + # Keep diagnosis outcome as it is + new_concepts['Diagnosis'].append(diagnosis_concept) + # Add data properties, if present + if celiac == 1 and len(celiac_property) > 0: + new_concepts['Diagnosis'].append(celiac_property[0]) + if duodenitis == 1 and len(duodenitis_property) > 0: + new_concepts['Diagnosis'].append(duodenitis_property[0]) + if len(shorts) > 0: + new_concepts['Diagnosis'] = self.link_additional_diagnoses(new_concepts['Diagnosis'], shorts) + # Remove duplicates + for sem_area in new_concepts.keys(): + new_concepts[sem_area] = [list(tpl) for tpl in list(dict.fromkeys(tuple(cpt) for cpt in new_concepts[sem_area]))] + return new_concepts + + @staticmethod + def link_additional_locations(anatomical_locations, tissue): + """ + Link additional anatomical location concepts based on 'tissue' field value. + + Params: + anatomical_locations (list(str)): anatomical locations concepts already extracted + tissue (str): examined tissue + + Return: updated list of identified anatomical locations concepts + """ + if tissue == 'duodenum': + anatomical_locations.append( + ['http://purl.obolibrary.org/obo/UBERON_0002114', 'Duodenum']) + if tissue == 'duodenal bulb': + anatomical_locations.append( + ['http://purl.obolibrary.org/obo/UBERON_0013644', 'Duodenal Ampulla']) + if tissue == 'stomach': + anatomical_locations.append( + ['http://purl.obolibrary.org/obo/UBERON_0001164', 'Greater Curvature of Stomach']) + return anatomical_locations + + @staticmethod + def link_additional_procedures(concepts, procedure): + """ + Link additional procedures or anatomical locations based on 'procedure' field value. + + Params: + concepts (dict): dict of identified ontology concepts {semantic_area: [iri, mention, label], ...} + procedure (str): procedure performed + + Return: updated dict of identified ontology concepts {semantic_area: [iri, mention, label], ...} + """ + if procedure in ['biopsy', 'duodenum']: + concepts['Procedure'].append(['http://purl.obolibrary.org/obo/NCIT_C51683', 'Biopsy of Duodenum']) + concepts['Anatomical Location'].append( + ['http://purl.obolibrary.org/obo/UBERON_0002114', 'Duodenum']) + if procedure == 'duodenal bulb': + concepts['Anatomical Location'].append( + ['http://purl.obolibrary.org/obo/UBERON_0013644', 'Duodenal Ampulla']) + concepts['Procedure'].append( + ['http://purl.obolibrary.org/obo/NCIT_C51683', 'Biopsy of Duodenum']) + if procedure == 'small intestine': + concepts['Procedure'].append( + ['http://purl.obolibrary.org/obo/NCIT_C51600', 'Biopsy of Small Intestine']) + concepts['Anatomical Location'].append( + ['http://purl.obolibrary.org/obo/UBERON_0002108', 'Small Intestine']) + if procedure == 'jejunum': + concepts['Procedure'].append(['http://purl.obolibrary.org/obo/NCIT_C51902', 'Biopsy of Jejunum']) + concepts['Anatomical Location'].append( + ['http://purl.obolibrary.org/obo/UBERON_0002115', 'Jejunum']) + if procedure == 'stomach': + concepts['Procedure'].append( + ['https://w3id.org/examode/ontology/GeaterCurvatureBiopsy', 'Biopsy of the Greater Curvature']) + concepts['Anatomical Location'].append( + ['http://purl.obolibrary.org/obo/UBERON_0001164', 'Greater Curvature of Stomach']) + return concepts + + @staticmethod + def link_additional_diagnoses(diagnoses, shorts): + """ + link additional diagnosis concepts based on 'short' fields value. + + Params: + diagnoses (list(str)): list of diagnosis concepts already extracted + shorts (list(str)): diagnosis summary + + Return: updated list of identified diagnosis concepts + """ + for short in shorts: + if short == 'atrophy': + diagnoses.append(['https://w3id.org/examode/ontology/glandularAtrophy', 'Glandular Atrophy']) + if 'inflammation' in short: # 'inflammation' in short + if short == 'inflammation' and len( + [diagnosis for diagnosis in diagnoses if 'inflammation' in diagnosis[1].lower()]) == 0: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C3137', 'Inflammation']) + elif 'active' in short or 'acute' in short: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C82901', 'Chronic Active Inflammation']) + elif 'chronic' in short and 'chronic active inflammation' not in [diagnosis[1].lower() for diagnosis in diagnoses]: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C174450', 'Chronic Inflammation']) + if 'lymphocyte' in short: # 'lymphocyte' in short + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C12535', 'Lymphocyte']) + if 'metaplasia' in short: # 'metaplasia' in short + if 'gastric' in short: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C8361', 'Gastric Metaplasia']) + else: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C8360', 'Intestinal Metaplasia']) + if short == 'villi atrophy': + diagnoses.append(['https://w3id.org/examode/ontology/villiAtrophy', 'villi degree of atrophy', 'not specified']) + if 'esoniphil' in short: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C12532', 'Eosinophil']) + if 'edema' in short: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C3002', 'Edema']) + if 'erosion' in short: + diagnoses.append(['http://purl.obolibrary.org/obo/NCIT_C50443', 'Erosion']) + return diagnoses + # ONTOLOGY-RELATED FUNCTIONS def process_ontology_concepts(self, labels): @@ -1349,25 +2498,27 @@ def aoec_entity_linking(self, reports, onto_proc, use_case_ontology, labels, use concepts = dict() # loop over AOEC reports and perform linking for rid, rdata in tqdm(reports.items()): - concepts[rid] = dict() - # sanitize diagnosis diagnosis = utils.en_sanitize_record(rdata['diagnosis_nlp'], use_case) # extract entity mentions from diagnosis diagnosis = self.extract_entity_mentions(diagnosis) - - # sanitize materials - materials = utils.en_sanitize_record(rdata['materials'], use_case) - if use_case == 'colon': # consider 'polyp' as a stopwords in materials @smarchesin TODO: what about the other use cases? - materials = re.sub('polyp[s]?(\s|$)+', ' ', materials) - # extract entity mentions from materials - materials = self.extract_entity_mentions(materials) - - # combine diagnosis and materials mentions - mentions = diagnosis + materials + if 'materials' in rdata: + # sanitize materials + materials = utils.en_sanitize_record(rdata['materials'], use_case) + if use_case == 'colon': # consider 'polyp' as a stopwords in materials @smarchesin TODO: what about the other use cases? + materials = re.sub('polyp[s]?(\s|$)+', ' ', materials) + # extract entity mentions from materials + materials = self.extract_entity_mentions(materials) + + # combine diagnosis and materials mentions + mentions = diagnosis + materials + else: + # no materials available + mentions = diagnosis # link and store 'nlp' concepts - nlp_concepts = self.link_mentions_to_concepts(mentions, labels, use_case_ontology, sim_thr, raw, debug) + nlp_concepts = self.link_mentions_to_concepts(use_case, mentions, labels, use_case_ontology, sim_thr, raw, debug) if raw: # keep 'nlp' concepts for debugging purposes + concepts[rid] = dict() concepts[rid] = nlp_concepts else: # merge 'nlp' and 'struct' concepts # link and store 'struct' concepts @@ -1375,7 +2526,17 @@ def aoec_entity_linking(self, reports, onto_proc, use_case_ontology, labels, use utils.sanitize_codes(rdata['diagnosis_struct']) + utils.sanitize_codes(rdata['procedure']) + utils.sanitize_codes(rdata['topography']), use_case_ontology) - concepts[rid] = onto_proc.merge_nlp_and_struct(nlp_concepts, struct_concepts) + if use_case == 'celiac' and len(nlp_concepts) > 0: + concepts[rid] = dict() + concepts[rid] = onto_proc.merge_nlp_and_struct(nlp_concepts, struct_concepts) + # Remove duplicates, if any + for sem_area in concepts[rid].keys(): + concepts[rid][sem_area] = [list(tpl) for tpl in list(dict.fromkeys(tuple(cpt) for cpt in concepts[rid][sem_area]))] + concepts[rid]['Diagnosis'] = self.check_inconclusive_outcomes(concepts[rid]['Diagnosis']) + else: + concepts[rid] = dict() + concepts[rid] = onto_proc.merge_nlp_and_struct(nlp_concepts, struct_concepts) + # return concepts return concepts @@ -1404,12 +2565,17 @@ def radboud_entity_linking(self, reports, use_case_ontology, labels, use_case, s # extract entity mentions from conclusions mentions = self.extract_entity_mentions(utils.en_sanitize_record(rdata['diagnosis'], use_case)) # link and store concepts from conclusions - nlp_concepts = self.link_mentions_to_concepts(mentions, labels, use_case_ontology, sim_thr, raw, debug) + nlp_concepts = self.link_mentions_to_concepts(use_case, mentions, labels, use_case_ontology, sim_thr, raw, debug) + if use_case == 'celiac' and len(nlp_concepts) > 0: + nlp_concepts = self.celiac_additional_concepts(nlp_concepts, utils.en_sanitize_record(rdata['tissue'], use_case), + utils.en_sanitize_record(rdata['procedure'], use_case), + [utils.en_sanitize_record(short, use_case) for short in rdata['short']]) # assign conclusion concepts to concepts dict - concepts[rid]['concepts'] = nlp_concepts + concepts[rid] = nlp_concepts # assign slide ids to concepts dict if present if 'slide_ids' in rdata: concepts[rid]['slide_ids'] = rdata['slide_ids'] + # return linked concepts divided per diagnosis return concepts @@ -1434,11 +2600,16 @@ def entity_linking(self, reports, use_case_ontology, labels, use_case, sim_thr=0 concepts = dict() # loop over translated and processed reports and perform linking for rid, rdata in tqdm(reports.items()): - concepts[rid] = dict() # extract entity mentions from text mentions = self.extract_entity_mentions(utils.en_sanitize_record(rdata['text'], use_case)) # link and store concepts from text - concepts[rid] = self.link_mentions_to_concepts(mentions, labels, use_case_ontology, sim_thr, raw, debug) - + nlp_concepts = self.link_mentions_to_concepts(use_case, mentions, labels, use_case_ontology, sim_thr, raw, debug) + if raw or use_case != 'celiac': + concepts[rid] = dict() + concepts[rid] = nlp_concepts + elif len(nlp_concepts) > 0: + # reports unrelated to celiac disease return an empty list of concepts, discard them + concepts[rid] = dict() + concepts[rid] = nlp_concepts # return concepts divided per diagnosis return concepts diff --git a/sket/nerd/rules/rules.txt b/sket/nerd/rules/rules.txt index 2414b93..21908d5 100644 --- a/sket/nerd/rules/rules.txt +++ b/sket/nerd/rules/rules.txt @@ -20,4 +20,36 @@ leep cervical BOTH EXACT cervix epithelium exocervical,endocervical BOTH EXACT cervix squamous intraepithelial lesion low-grade,low grade,low,high-grade,high grade,high BOTH LOOSE cervix neuroendocrine large-cell,large cell,large,non-small cell,non small cell,small-cell,small cell,small PRE EXACT lung -cell non-small,non small,small,large,clear PRE EXACT lung \ No newline at end of file +cell non-small,non small,small,large,clear PRE EXACT lung +duodenal bulb biopsy,biopsy POST EXACT celiac +biopsy 2nd duodenum,ii duodenal,according to duodenum,according to duodenal, duodenum ii BOTH EXACT celiac +duodenal mucosa POST LOOSE celiac +intraepithelial lymphocytes,lymphocytic quota (iel,lymphocytic quota (iel:,lymphocyte infiltrate (iel,lymphocyte infiltrate (iel POST EXACT celiac +hyperplasia of the brunner glands,brunner gland,of glandular crypts,of the glands of brunner BOTH EXACT celiac +celiac disease type POST LOOSE celiac +gluten hypersensitivity type POST LOOSE celiac +phlogosis chronic,chronic active,chronic acute,active,acute,with marked activity,with activity BOTH EXACT celiac +inflammatory chronic,acute BOTH EXACT celiac +chronic gastritis,phlogosis,inflammation POST LOOSE celiac +active gastritis,phlogosis,inflammation POST LOOSE celiac +acute gastritis,phlogosis,inflammation POST LOOSE celiac +chronic duodenitis POST EXACT celiac +brunner glands,glands of BOTH EXACT celiac +normal morphology,within the limits of,within the limit of,devoid of,appearance BOTH EXACT celiac +antral type mucous membranes of PRE EXACT celiac +atrophy glandular,of the crypts,crypt,villi,of the villi,villial BOTH EXACT celiac +atrophic villi,crypt PRE LOOSE celiac +flattened villuses,villi BOTH LOOSE celiac +flattening of the villi,of the villus POST LOOSE celiac +lymphocyte (iel(iel:,infiltrate (iel,infiltrate (iel: POST EXACT celiac +infiltration lymphocytic,(iel,(iel: BOTH EXACT celiac +villi free of PRE EXACT celiac +villi atrophy BOTH EXACT celiac +villi height,length BOTH LOOSE celiac +height of the villi POST EXACT celiac +height villi,villus PRE LOOSE celiac +mitosis number of,proportion of,proportion of cryptic,number of cryptic,share of,share of cryptic PRE EXACT celiac +duodenitis chronic,moderate,mild,active,erosive,mild-activity,acute,ulcerative,chronic active ulcerative,moderate chronic,chronic mild,chronic active,chronic moderate,mild chronic,chronic active and erosive,chronic severe,chronic erosive,chronic active erosive,erosive chronic,acute erosiva BOTH EXACT celiac +intraepithelial lymphocyte POST EXACT celiac +celiac no indications of,no more signs of,no evidence of PRE EXACT celiac +abnormalities without,no PRE EXACT celiac \ No newline at end of file diff --git a/sket/ont_proc/ontology/examode.owl b/sket/ont_proc/ontology/examode.owl index ca38569..f85d9ee 100644 --- a/sket/ont_proc/ontology/examode.owl +++ b/sket/ont_proc/ontology/examode.owl @@ -1,9818 +1,208 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The ExaMode Ontology - - - - The ExaMode Ontology, version 0.2, based from assumptions inferred from the data in the file DokemDam/material/EXAMODE_datasets/EXAMODE_1stDS_AOEC. It was inferred from the NL text in these files an from information taken around the internet, then validated by the experts of the Cannizzaro Hospital in Catania. This ontology models four types of clinical cases: cervix cancer, lung cancer, colon cancer, celiac disease. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://dbpedia.org/page/Radboud_University_Nijmegen - Radboud University Nijmegen (abbreviated as RU, Dutch: Radboud Universiteit Nijmegen, formerly Katholieke Universiteit Nijmegen) is a public university with a strong focus on research located in Nijmegen, the Netherlands. It was established on 17 October 1923 and is situated in the oldest city of the Netherlands. The RU has seven faculties and enrolls over 19,900 students. It was internationally ranked 156th by the QS World University Rankings. - - - - http://dbpedia.org/page/Radboud_University_Nijmegen - Radboud Universiteit Nijmegen - - - - http://dbpedia.org/page/Radboud_University_Nijmegen - Radboud Universiteit Nijmegen - - - - http://dbpedia.org/page/Radboud_University_Nijmegen - Radboud University Nijmegen - - - - http://dbpedia.org/page/Radboud_University_Nijmegen - General - - - - umls:C0521191 - PRE-CANCEROUS DYSPLASIA, SUSP.FOR MALIGNANCY - - - - umls:C0521191 - Precancerous conditions of the cervix are changes to cervical cells that make them more likely to develop into cancer. These conditions are not yet cancer. But if they aren’t treated, there is a chance that these abnormal changes may become cervical cancer. If left untreated, it may take 10 years or more for precancerous conditions of the cervix to turn into cervical cancer, but in rare cases this can happen in less time. - -Precancerous conditions of the cervix happen in an area called the transformation zone. This is where columnar cells (a type of glandular cell) are constantly being changed into squamous cells. The transformation of columnar cells into squamous cells is a normal process, but it makes the cells more sensitive to the effect of the human papillomavirus (HPV). - - - - umls:C0521191 - Displasia pre-cancerosa - - - - umls:C0521191 - Pre-Cancerous Dysplasia - - - - umls:C0521191 - Pre-kanker dysplasie - - - - umls:C0521191 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - umls:C0521191 - M74009 - - - - umls:C0521191 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - umls:C0521191 - umls:C0521191 - - - - http://purl.obolibrary.org/obo/BTO_0002073 - FMA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,UWDA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,NCI: Epithelium composed of a single layer of cells attached to a basement membrane. - - - - http://purl.obolibrary.org/obo/BTO_0002073 - Squamous epithelium composed of a single layer of cells. - - - - http://purl.obolibrary.org/obo/BTO_0002073 - bestrating epitheel - - - - http://purl.obolibrary.org/obo/BTO_0002073 - epitelio della pavimentazione - - - - http://purl.obolibrary.org/obo/BTO_0002073 - pavement epithelium - - - - http://purl.obolibrary.org/obo/BTO_0002073 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/BTO_0002073 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/BTO_0002073 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/BTO_0002073 - umls:C0682574 - - - - http://purl.obolibrary.org/obo/CL_0000094 - polymorphonuclear leukocyte; granular leucocyte; granular leukocyte - - - - http://purl.obolibrary.org/obo/CL_0000094 - A leukocyte with abundant granules in the cytoplasm. - - - - http://purl.obolibrary.org/obo/CL_0000094 - granulociti - - - - http://purl.obolibrary.org/obo/CL_0000094 - granulocyte - - - - http://purl.obolibrary.org/obo/CL_0000094 - granulocyte - - - - http://purl.obolibrary.org/obo/CL_0000094 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/CL_0000094 - “infiltrato” + “granulociti”/“granulocitario" - - - - http://purl.obolibrary.org/obo/CL_0000094 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/CL_0000542 - A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - - - - http://purl.obolibrary.org/obo/CL_0000542 - Linfocita - - - - http://purl.obolibrary.org/obo/CL_0000542 - lymfocyt - - - - http://purl.obolibrary.org/obo/CL_0000542 - lymphocyte - - - - http://purl.obolibrary.org/obo/CL_0000542 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/CL_0000542 - “infiltrato” + “linfociti”/“linfocitario" - - - - http://purl.obolibrary.org/obo/CL_0000542 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/FMA_7397 - Right upper lobar bronchus; Right upper lobe bronchus - - - - http://purl.obolibrary.org/obo/FMA_7397 - Part of the right bronchus. - - - - http://purl.obolibrary.org/obo/FMA_7397 - Bronco lobare superiore destro - - - - http://purl.obolibrary.org/obo/FMA_7397 - Rechter superieure lobaire bronchus - - - - http://purl.obolibrary.org/obo/FMA_7397 - Right superior lobar bronchus - - - - http://purl.obolibrary.org/obo/FMA_7397 - http://purl.obolibrary.org/obo/NCIT_C32998 - - - - http://purl.obolibrary.org/obo/FMA_7397 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/FMA_7397 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/FMA_7397 - umls:C0225610 - - - - http://purl.obolibrary.org/obo/FMA_7404 - Bronchus of right lower lobe; Right lower lobe bronchus; Right lower lobar bronchus. - - - - http://purl.obolibrary.org/obo/FMA_7404 - A region of the bronchus in the lung. - - - - http://purl.obolibrary.org/obo/FMA_7404 - Bronco lobare inferiore destro - - - - http://purl.obolibrary.org/obo/FMA_7404 - Rechter inferieure lobaire bronchus - - - - http://purl.obolibrary.org/obo/FMA_7404 - Right inferior lobar bronchus - - - - http://purl.obolibrary.org/obo/FMA_7404 - http://purl.obolibrary.org/obo/NCIT_C32998 - - - - http://purl.obolibrary.org/obo/FMA_7404 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/FMA_7404 - umls:C0225621 - - - - http://purl.obolibrary.org/obo/FMA_7423 - Left upper lobar bronchus; Bronchus of left upper lobe; Left upper lobe bronchus - - - - http://purl.obolibrary.org/obo/FMA_7423 - Part of the left bronchus. - - - - http://purl.obolibrary.org/obo/FMA_7423 - Bronco lobare superiore sinistro - - - - http://purl.obolibrary.org/obo/FMA_7423 - Left superior lobar bronchus - - - - http://purl.obolibrary.org/obo/FMA_7423 - Linker superieure lobaire bronchus - - - - http://purl.obolibrary.org/obo/FMA_7423 - http://purl.obolibrary.org/obo/NCIT_C32998 - - - - http://purl.obolibrary.org/obo/FMA_7423 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/FMA_7423 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/FMA_7423 - umls:C0225632 - - - - http://purl.obolibrary.org/obo/FMA_7432 - Bronchus of left lower lobe; Left lower lobe bronchus; Left lower lobar bronchus - - - - http://purl.obolibrary.org/obo/FMA_7432 - A region of the bronchus in the lungs. - - - - http://purl.obolibrary.org/obo/FMA_7432 - Bronco lobare inferiore sinistro - - - - http://purl.obolibrary.org/obo/FMA_7432 - Left inferior lobar bronchus - - - - http://purl.obolibrary.org/obo/FMA_7432 - Links inferieure lobaire bronchus - - - - http://purl.obolibrary.org/obo/FMA_7432 - http://purl.obolibrary.org/obo/NCIT_C32998 - - - - http://purl.obolibrary.org/obo/FMA_7432 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/FMA_7432 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/FMA_7432 - umls:C0225641 - - - - http://purl.obolibrary.org/obo/GO_0070265 - necrosis - - - - http://purl.obolibrary.org/obo/GO_0070265 - cellular necrosis; necrotic cell death - - - - http://purl.obolibrary.org/obo/GO_0070265 - metastasize; Metastasis, NOS; metastasis; Tumor Cell Migration; Metastasize; Metastasis - - - - http://purl.obolibrary.org/obo/GO_0070265 - Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals. - - - - http://purl.obolibrary.org/obo/GO_0070265 - necrose - - - - http://purl.obolibrary.org/obo/GO_0070265 - necrosi - - - - http://purl.obolibrary.org/obo/GO_0070265 - necrosis - - - - http://purl.obolibrary.org/obo/GO_0070265 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/GO_0070265 - A type of cell death that is morphologically characterized by an increasingly translucent cytoplasm, swelling of organelles, minor ultrastructural modifications of the nucleus (specifically, dilatation of the nuclear membrane and condensation of chromatin into small, irregular, circumscribed patches) and increased cell volume (oncosis), culminating in the disruption of the plasma membrane and subsequent loss of intracellular contents. Necrotic cells do not fragment into discrete corpses as their apoptotic counterparts do. Moreover, their nuclei remain intact and can aggregate and accumulate in necrotic tissues. - - - - http://purl.obolibrary.org/obo/GO_0070265 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/GO_0070265 - umls:C0027540 - - - - http://purl.obolibrary.org/obo/IDOMAL_0000603 - A person under health care. The person may be waiting for this care or may be receiving it or may have already received it. - - - - http://purl.obolibrary.org/obo/IDOMAL_0000603 - Patient - - - - http://purl.obolibrary.org/obo/IDOMAL_0000603 - Paziente - - - - http://purl.obolibrary.org/obo/IDOMAL_0000603 - geduldig - - - - http://purl.obolibrary.org/obo/IDOMAL_0000603 - General - - - - http://purl.obolibrary.org/obo/MONDO_0000001 - disease; disease or disorder; disease or disorder, non-neoplastic; other disease; diseases; condition; disorder; disorders; medical condition; diseases and disorders - - - - http://purl.obolibrary.org/obo/MONDO_0000001 - A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - - - http://purl.obolibrary.org/obo/MONDO_0000001 - Disease or Disorder - - - - http://purl.obolibrary.org/obo/MONDO_0000001 - Malattia o disturbo - - - - http://purl.obolibrary.org/obo/MONDO_0000001 - Ziekte of aandoening - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - polyp of the cervix uteri; adenomatous polyp of the uterine cervix; uterine cervix polyp; cervical polyp; adenomatous polyp of cervix; uterine cervix adenomatous polyp; adenomatous polyp of uterine cervix; cervix uteri polyp; polyp of cervix; polyp of the uterine cervix; cervix adenomatous polyp; cervix polyp; polyp of cervix uteri; polyp of uterine cervix; cervix uteri adenomatous polyp; polyp of the cervix; adenomatous polyp of the cervix - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - A polyp that arises from the surface of the cervix. - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - cervical polyp - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - cervicale poliep - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - polipo cervicale - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - M768003 - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0000751 - umls:C0007855 - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - atrophy of vulva; atrophic vulva - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - atrophic vulvitis - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - Vaginal atrophy (atrophic vaginitis) is thinning, drying and inflammation of the vaginal walls that may occur when your body has less estrogen. Vaginal atrophy occurs most often after menopause. - -For many women, vaginal atrophy not only makes intercourse painful but also leads to distressing urinary symptoms. Because the condition causes both vaginal and urinary symptoms, doctors use the term "genitourinary syndrome of menopause (GSM)" to describe vaginal atrophy and its accompanying symptoms. - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - Atrofische vulva - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - Atrophic vulva - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - Vulva atrofica - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - M580000 - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0001932 - umls:C0156393 - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - colonic carcinoma; carcinoma of colon; colon carcinoma; colon cancer; carcinoma of the colon - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - A carcinoma that arises from epithelial cells of the colon [database_cross_reference: MONDO:DesignPattern] - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - carcinoma del colon - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - colon carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - coloncarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - General - - - - http://purl.obolibrary.org/obo/MONDO_0002032 - umls:C0699790 - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - inflammation of lymph node; acute adenitis; chronic lymphadenitis; lymphadenitis; Inflammation of lymph node; acute lymphadenitis; adenitis; lymph node inflammation; chronic adenitis; lymph nodeitis - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - lymph gland infection - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - Linfoadenite - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - Lymfadenitis - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - Lymphadenitis - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - M400000 - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0002052 - umls:C0024205 - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - colonic adenocarcinoma; adenocarcinoma of the colon; colon adenocarcinoma; adenocarcinoma of colon; adenocarcinoma - colon - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - COAD - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - A carcinoma that arises from glandular epithelial cells of the colon. - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - Adenocarcinoma del colon - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - Colon Adenocarcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - Colon adenocarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0002271 - umls:C0338106 - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - cervical neoplasm; tumor of the cervix uteri; uterine cervical neoplasm - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - malignant tumor of uterine cervix; uterine cervix cancer; malignant neoplasm of cervix; malignant neoplasm of uterine cervix; malignant tumor of the uterine cervix; malignant tumor of cervix uteri; malignant cervical neoplasm; cervix cancer; malignant neoplasm of cervix uteri; neoplasm of uterine cervix; malignant neoplasm of the uterine cervix; malignant cervix uteri neoplasm; malignant uterine cervix neoplasm; malignant tumor of cervix; malignant cervix neoplasm; malignant tumor of the cervix uteri; malignant neoplasm of the cervix uteri; malignant cervix uteri tumor; malignant cervix tumor; malignant uterine cervix tumor; cancer of uterine cervix; cervix uteri cancer; malignant cervical tumor; malignant tumor of the cervix; malignant neoplasm of the cervix - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - A primary or metastatic malignant neoplasm involving the cervix. - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - baarmoederhalskanker - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - cancro cervicale - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - cervical cancer - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - General - - - - http://purl.obolibrary.org/obo/MONDO_0002974 - umls:C0007847 - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - lung large cell carcinoma; large cell lung carcinoma; large cell lung cancer; large cell undifferentiated lung carcinoma; large cell carcinoma of the lung; large cell carcinoma of lung; anaplastic lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - LCLC - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - A poorly differentiated non-small cell lung carcinoma composed of large polygonal cells without evidence of glandular or squamous differentiation. There is a male predilection. - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - carcinoma polmonare a grandi cellule - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - grootcellig longcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - lung large cell carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - M801090 - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0003050 - umls:C0345958 - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - duodenitis; duodenum inflammation; inflammation of duodenum - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - hemorrhagic duodenitis - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - A form of inflammation - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - Acute or chronic inflammation of the duodenum. Causes include bacterial and viral infections and gastroesophageal reflux disease. Symptoms include vomiting and abdominal pain. - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - Duodenite - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - Duodenitis - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - Duodenitis - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - flogosi - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - M400000 - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0004627 - umls:C0013298 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - squamous carcinoma in situ; cervical intraepithelial neoplasia grade III with severe dysplasia; stage 0 uterine cervix carcinoma; severe dysplasia of the cervix uteri; stage 0 squamous cell carcinoma; CIN III - carcinoma in situ of cervix; squamous cell carcinoma in-situ; epidermoid cell carcinoma in situ; CIN III - severe dyskaryosis; grade III SIN; carcinoma in situ of uterine cervix; carcinoma, squamous cell, in situ, malignant; grade 3 SIN; uterine cervix in situ carcinoma; squamous intraepithelial neoplasia, grade III; carcinoma in situ of cervix; CIN III; intraepithelial squamous cell carcinoma; grade 3 squamous intraepithelial neoplasia; squamous cell carcinoma in situ; epidermoid carcinoma in situ; grade III squamous intraepithelial neoplasia; severe dysplasia of cervix; cervix Ca in situ - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - squamous carcinoma in situ - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - A malignant epithelial neoplasm confined to the squamous epithelium, without invasion of the underlying tissues. - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - Cervicale squameuze intra-epitheliale neoplasie graad 3 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - Neoplasia cervicale squamosa intraepiteliale di grado 3 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - squamous carcinoma in situ - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - M740080 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - umls:C0334245 - - - - http://purl.obolibrary.org/obo/MONDO_0004693 - originally the SNOMED code was M74008* - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - adenocarcinoma a cellule chiare - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - clear cell adenocarcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - heldercellig adenocarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - MSH: An adenocarcinoma characterized by the presence of varying combinations of clear and hobnail-shaped tumor cells. There are three predominant patterns described as tubulocystic, solid, and papillary. These tumors, usually located in the female reproductive organs, have been seen more frequently in young women since 1970 as a result of the association with intrauterine exposure to diethylstilbestrol. (From Holland et al., Cancer Medicine, 3d ed),NCI: A rare type of tumor, usually of the female genital tract, in which the insides of the cells look clear when viewed under a microscope.,NCI: A malignant neoplasm comprising glandular epithelial clear cells.,NCI: A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005004 - umls:C0206681 - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - lung adenocarcinoma; bronchogenic lung adenocarcinoma; nonsmall cell adenocarcinoma; non-small cell lung adenocarcinoma; adenocarcinoma of the lung; adenocarcinoma of lung - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - A carcinoma that arises from the lung and is characterized by the presence of malignant glandular epithelial cells. There is a male predilection with a male to female ratio of 2:1. Usually lung adenocarcinoma is asymptomatic and is identified through screening studies or as an incidental radiologic finding. If clinical symptoms are present they include shortness of breath, cough, hemoptysis, chest pain, and fever. Tobacco smoke is a known risk factor. - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - lung adenocarcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - M814030 - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005061 - umls:C0152013 - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - coeliac disease; non tropical sprue; idiopathic steatorrhea; gluten-induced enteropathy; celiac sprue - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - celiac disease - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - celiachia - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - coeliakie - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - General - - - - http://purl.obolibrary.org/obo/MONDO_0005130 - umls:C0007570 - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - cervix cancer; cervical cancer, NOS; cervical cancer; cancer of cervix; uterine cervix cancer - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - cancer of the uterine cervix; carcinoma of the cervix; carcinoma of cervix; carcinoma of the cervix uteri; carcinoma cervix uteri; cancer of uterine cervix; cervical carcinoma; carcinoma of uterine cervix; cervix carcinoma; uterine cervix carcinoma; carcinoma of cervix uteri; cancer of the cervix; cervix uteri carcinoma; carcinoma of the uterine cervix; cancer of cervix - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are: squamous carcinoma, adenocarcinoma, adenosquamous carcinoma, adenoid cystic carcinoma and undifferentiated carcinoma. - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - carcinoma cervicale - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - cervicaal carcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - cervical carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005131 - umls:C0302592 - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - cancer of lung; cancer of the lung; lung cancer; lung cancer, NOS - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - lung carcinoma; carcinoma of lung; carcinoma of the lung - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - A carcinoma that arises from epithelial cells of the lung - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - carcinoma polmonare - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - longcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - M801030 - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005138 - umls:C0684249 - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - adenocarcinoma of the uterine cervix; uterine cervix adenocarcinoma; adenocarcinoma of cervix; adenocarcinoma of cervix uteri; adenocarcinoma - cervix; cervix adenocarcinoma; adenocarcinoma of the cervix; adenocarcinoma of the cervix uteri; adenocarcinoma cervix uteri; adenocarcinoma of uterine cervix; cervix uteri adenocarcinoma; cervical adenocarcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - cervical adenocarcinoma, NOS; cervical adenocarcinoma, not otherwise specified - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type. - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - adenocarcinoma cervicale - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - cervicaal adenocarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - cervical adenocarcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0005153 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - A cervix disease may present or not the human papilloma virus. - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - Humaan papillomavirus-infectie - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - Human Papilloma Virus Infection - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - Infezione da papillomavirus umano - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - presence of code D0445** in field 'Diagnosi' - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - Human papilloma Virus infection; Human papillomavirus disease or disorder; Human Papillomavirus infection; Human papillomavirus infectious disease; Human papillomavirus caused disease or disorder - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - D044500 - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - umls:C0343641 - - - - http://purl.obolibrary.org/obo/MONDO_0005161 - original SNOMED D0445 - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - NSCLC - non-small cell lung cancer; non-small cell lung carcinoma; non-small cell carcinoma of lung; non-small cell carcinoma of the lung; non-small cell cancer of lung; non-small cell lung cancer; non-small cell cancer of the lung; NSCLC - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - non-small cell lung cancer, NOS; non small cell lung cancer NOS - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - A group of at least three distinct histological types of lung cancer, including non-small cell squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. Non-small cell lung carcinomas have a poor response to conventional chemotherapy. - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - carcinoma polmonare non a piccole cellule - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - niet-kleincellig longcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - non-small cell lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - M807030 - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005233 - umls:C0007131 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - Lymphadenitis; colitis; colon inflammation; inflammation of colon - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - Inflammation of the colon. - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - Colite - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - Colitis - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - Colitis - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - M400000 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - M400700 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - umls:C0009319 - - - - http://purl.obolibrary.org/obo/MONDO_0005292 - previously it had snomed codes M40000 and M40070 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - cervical intraepithelial neoplasia grade 2/3; high grade dysplasia; moderate or severe dysplasia - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - A neoplastic process in the cervix characterized by morphologic features of both moderate and severe intraepithelial neoplasia. - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - cervical intraepithelial neoplasia grade 2/3 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - cervicale intra-epitheliale neoplasie graad 2/3 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - neoplasia intraepiteliale cervicale di grado 2/3 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0006137 - umls:C2986622 - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - squamous cervical cancer; cervical squamous cell cancer; squamous cell carcinoma of cervix uteri; squamous cell carcinoma of cervix; squamous cell carcinoma of the uterine cervix; cervix uteri squamous cell carcinoma; uterine cervix squamous cell carcinoma; cervical squamous cell carcinoma; cervix squamous cell carcinoma; squamous cell carcinoma of the cervix uteri; squamous cell carcinoma of the cervix; squamous cell carcinoma of uterine cervix -has_related_synonym: cervical squamous cell carcinoma, NOS; CESC; cervical squamous cell carcinoma, not otherwise specified - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - A squamous cell carcinoma arising from the cervical epithelium. It usually evolves from a precancerous cervical lesion. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors for cervical squamous cell carcinoma. The following histologic patterns have been described: conventional squamous cell carcinoma, papillary squamous cell carcinoma, transitional cell carcinoma, lymphoepithelioma-like carcinoma, verrucous carcinoma, condylomatous carcinoma and spindle cell carcinoma. Survival is most closely related to the stage of disease at the time of diagnosis. - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - Carcinoma a cellule squamose cervicali - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - Cervicaal plaveiselcelcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - Cervical Squamous Cell Carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - M807030 - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - umls:C0279671 - - - - http://purl.obolibrary.org/obo/MONDO_0006143 - previous SNOME M80703* - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - inflammatory polyp of colon; inflammatory polyp of the colon; colonic inflammatory polyp. - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - A non-neoplastic polypoid lesion in the colon. It may arise in a background of inflammatory bowel disease or colitis. It is characterized by the presence of a distorted epithelium, inflammation, and fibrosis. - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - Colon Inflammatory Polyp - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - Colon ontstekingspoliep - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - Polipo infiammatorio del colon - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0006152 - umls:C0267392 - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - colonic adenomatous polyp; adenomatous polyp of colon; colon adenomatous polyp; adenomatous polyp of the colon; Adenomatous polyp - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - A polypoid adenoma that arises from and protrudes into the lumen of the colon. Epithelial dysplasia is always present. According to the architectural pattern it is classified as tubular, tubulovillous, or villous. - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - Adenoma - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - Adenoma - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - Adenoom - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - M814000 - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0006498 - umls:C0007131 - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - oat cell carcinoma of the lung; small cell neuroendocrine carcinoma of the lung; small cell neuroendocrine carcinoma of lung; small cell lung carcinoma; small cell carcinoma of lung; oat cell carcinoma of lung; lung oat cell carcinoma; oat cell lung carcinoma; lung small cell carcinoma; small cell lung cancer; small cell carcinoma of the lung; lung small cell neuroendocrine carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - small cell cancer of the lung; SCLC1 - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - Small cell lung cancer (SCLC) is a highly aggressive malignant neoplasm, accounting for 10-15% of lung cancer cases, characterized byrapid growth, and early metastasis. SCLC usually manifests as a large hilar mass with bulky mediastinal lymphadenopathy presenting clinically with chest pain, persistent cough, dyspnea, wheezing, hoarseness, hemoptysis, loss of appetite, weight loss, and neurological and endocrine paraneoplastic syndromes. SCLC is primarily reported in elderly people with a history of long-term tobacco exposure. - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - carcinoma polmonare a piccole cellule - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - kleincellig longcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - small cell lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - M804130 - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0008433 - umls:C0149925 - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - https://www.examode.dei.unipd.it/ontology/General - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - malignant neoplasm of the lung; lung cancer; malignant lung neoplasm; cancer of lung; malignant tumor of the lung; malignant tumor of lung; malignant neoplasm of lung; malignant lung tumor. - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - lung neoplasm; Nonsmall cell lung cancer; alveolar cell carcinoma; lung cancer, protection against. - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - A malignant neoplasm involving the lung. - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - cancro ai polmoni - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - longkanker - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - lung cancer - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - General - - - - http://purl.obolibrary.org/obo/MONDO_0008903 - umls:C0007847 - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - besnier-Boeck-Schaumann syndrome; sarcoid; Darier-Roussy sarcoid; Boeck's sarcoid; Besnier-Boeck-Schaumann disease; Boeck's sarcoidosis; lymphogranulomatosis; sarcoidosis; Boeck sarcoid - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - benign lymphogranulomatosis of Schaumann; lupus pernio of Besnier; miliary lupoid of boeck - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - Sarcoidosis is a multisystemic disorder of unknown cause characterized by the formation of immune granulomas in involved organs. - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - sarcoidosi - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - sarcoidosis - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - sarcoïdose - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - D028280 - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0019338 - umls:C0036202 - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - villous adenoma of colon - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - A villous adenoma that involves the colon. - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - Adenoma del colon villoso - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - Colon Villous Adenoma - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - Colon Villous Adenoma - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - M826110 - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - umls:C0149862 - - - - http://purl.obolibrary.org/obo/MONDO_0021271 - previous SNOMED code M82611 - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - colon polyp; polyp of the colon; colonic polyp - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - A polyp that involves the colon. - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - Poliep van de dikke darm - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - Polipo del colon - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - Polyp of Colon - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0021400 - umls:C0009376 - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - cervical intraepithelial neoplasia - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - Intraepithelial Neoplasia of the Uterine Cervix; Intraepithelial Neoplasms, Cervical; Neoplasm, Cervical Intraepithelial; Intraepithelial Neoplasm, Cervical; Cervix Intraepithelial Neoplasia; Cervical Intraepithelial Neoplasms; Intraepithelial Neoplasia of the Cervix Uteri; Neoplasms, Cervical Intraepithelial; Intraepithelial Neoplasia of Uterine Cervix; Neoplasia, Cervical Intraepithelial; Cervical Intraepithelial Neoplasm; Intraepithelial Neoplasia, Cervical; Cervical intraepithelial neoplasia; NEOPL CERVICAL INTRAEPITHELIAL; Uterine Cervix Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix Uteri; Intraepithelial Neoplasia of the Cervix; Cervix Uteri Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix; Cervical Dysplasia; Cervical Intraepithelial Neoplasia - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - Cervical intraepithelial neoplasia (CIN), also known as cervical dysplasia, is the abnormal growth of cells on the surface of the cervix that could potentially lead to cervical cancer. More specifically, CIN refers to the potentially precancerous transformation of cells of the cervix. - -CIN most commonly occurs at the squamocolumnar junction of the cervix, a transitional area between the squamous epithelium of the vagina and the columnar epithelium of the endocervix. It can also occur in vaginal walls and vulvar epithelium. CIN is graded on a 1-3 scale, with 3 being the most abnormal (see classification section below). - -Human papilloma virus (HPV) infection is necessary for the development of CIN, but not all with this infection develop cervical cancer.[3] Many women with HPV infection never develop CIN or cervical cancer. Typically, HPV resolves on its own. However, those with an HPV infection that lasts more than one or two years have a higher risk of developing a higher grade of CIN. - -Like other intraepithelial neoplasias, CIN is not cancer and is usually curable.[3] Most cases of CIN either remain stable or are eliminated by the person's immune system without need for intervention. However, a small percentage of cases progress to cervical cancer, typically cervical squamous cell carcinoma (SCC), if left untreated. - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - cervical intraepithelial neoplasia - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - cervicale intra-epitheliale neoplasie - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - neoplasia intraepiteliale cervicale - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0022394 - umls:C0206708 - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - Metastatic Tumor; metastasis; Neoplasm, metastatic; Metastatic Disease; Tumor, metastatic; Metastatic; Metastatic Neoplasm; Metastasis - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - metastatic disease; metastatic neoplasm; metastatic tumor - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - metastatic neoplasm - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - neoplasia metastatica - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - uitgezaaide neoplasma - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - M800060 - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - M814060 - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0024883 - umls:C2939420 - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - severe dysplasia of the cervix uteri aJCC v6; uterine cervix intraepithelial neoplasia grade 3 aJCC v6; intraepithelial neoplasia of the cervix grade 3 aJCC v6; carcinoma in situ of the uterine cervix aJCC v6; intraepithelial neoplasia of the cervix uteri grade 3 aJCC v6; severe dysplasia of cervix aJCC v6; severe dysplasia of cervix; intraepithelial neoplasia of uterine cervix grade 3 aJCC v6; cervical intraepithelial neoplasia grade 3 aJCC v6; uterine cervix carcinoma in situ aJCC v6; carcinoma in situ of the cervix aJCC v6; FIGO stage 0 carcinoma of uterine cervix; severe dysplasia of cervix uteri aJCC v6; cervix uteri intraepithelial neoplasia grade 3 aJCC v6; grade 3 cervical intraepithelial neoplasia aJCC v6; stage 0 uterine cervix carcinoma; carcinoma in situ of uterine cervix aJCC v6; CIN III - severe dyskaryosis; cervix uteri Severe dysplasia aJCC v6; FIGO stage 0 cervical carcinoma; cervix uteri carcinoma in situ aJCC v6; stage 0 cervical cancer aJCC v6; FIGO stage 0 carcinoma of the cervix uteri; cervical carcinoma in situ aJCC v6; uterine cervix Severe dysplasia aJCC v6; carcinoma in situ of the cervix uteri aJCC v6; severe cervical dysplasia aJCC v6; FIGO stage 0 carcinoma of cervix uteri; carcinoma in situ of cervix aJCC v6; carcinoma in situ of uterine cervix; carcinoma in situ of cervix uteri aJCC v6; cervix intraepithelial neoplasia grade 3 aJCC v6; FIGO stage 0 carcinoma of the uterine cervix; CIN III; cervical intraepithelial neoplasia grade III with severe dysplasia; cervical Severe dysplasia aJCC v6; CIN III - carcinoma in situ of cervix; FIGO stage 0 uterine cervix carcinoma; CIN 3 aJCC v6; severe dysplasia of the uterine cervix aJCC v6; carcinoma of cervix stage 0; intraepithelial neoplasia of cervix uteri grade 3 aJCC v6; squamous intraepithelial neoplasia, grade III; stage 0 cervical cancer; cervix Severe dysplasia aJCC v6; FIGO stage 0 carcinoma of the cervix; carcinoma in situ of cervix; CIN grade 3 aJCC v6; cervical cancer stage 0 aJCC v6; intraepithelial neoplasia of cervix grade 3 aJCC v6; intraepithelial neoplasia of the uterine cervix grade 3 aJCC v6; FIGO stage 0 carcinoma of cervix; cervix carcinoma in situ aJCC v6; severe dysplasia of the cervix aJCC v6; severe dysplasia of uterine cervix aJCC v6; cervix Ca in situ; FIGO stage 0 cervix carcinoma; severe dysplasia of the cervix uteri; FIGO stage 0 cervix uteri carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - cervix uteri carcinoma in situ - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - uterine cervix carcinoma in situ - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - Slightly abnormal cells are found on the surface of the cervix. Cervical squamous intraepithelial neoplasia 1 is usually caused by infection with certain types of human papillomavirus (HPV) and is found when a cervical biopsy is done. Cervical squamous intraepithelial neoplasia 1 is not cancer and usually goes away on its own without treatment, but sometimes it can become cancer and spread into nearby tissue. Cervical squamous intraepithelial neoplasia 1 is sometimes called low-grade or mild dysplasia. Also called CIN 1. - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - neoplasia intraepiteliale squamosa - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - squameuze intra-epitheliale neoplasie - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - squamous intraepithelial neoplasia - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0042487 - umls:C0851140 - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - non-small cell squamous lung cancer; non-small cell squamous lung carcinoma; squamous non-small cell lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - A squamous cell carcinoma that arises from the lung. It is characterized by the presence of large malignant cells. It includes the clear cell and papillary variants of squamous cell carcinoma. - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - carcinoma polmonare squamoso non a piccole cellule - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - niet-kleincellig plaveiselcelcarcinoom - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - non-small cell squamous lung carcinoma - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - M807030 - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/MONDO_0056806 - umls:C4324656 - - - - http://purl.obolibrary.org/obo/MP_0011748 - intestinal synechia; intestinal adhesions - - - - http://purl.obolibrary.org/obo/MP_0011748 - Formation of fibrous tissue in any part of the intestine as a result of repair or a reactive process. - - - - http://purl.obolibrary.org/obo/MP_0011748 - fibrosi intestinale - - - - http://purl.obolibrary.org/obo/MP_0011748 - intestinal fibrosis - - - - http://purl.obolibrary.org/obo/MP_0011748 - intestinale fibrose - - - - http://purl.obolibrary.org/obo/MP_0011748 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/MP_0011748 - fibrosi - - - - http://purl.obolibrary.org/obo/MP_0011748 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - Mainstem bronchus; Main Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - The left and right main bronchi considered as a group. - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - Belangrijkste bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - Bronco principale - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - Main Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - http://purl.obolibrary.org/obo/UBERON_0002185 - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C12284 - umls:C0024496 - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - MSH: The mucous membrane lining of the uterine cavity that is hormonally responsive during the MENSTRUAL CYCLE and PREGNANCY. The endometrium undergoes cyclic changes that characterize MENSTRUATION. After successful FERTILIZATION, it serves to sustain the developing embryo.,CSP: tissue lining the uterus, it is sloughed off during the woman's menstrual period, and afterward grows back and slowly gets thicker and thicker until the next period.,NCI: The layer of tissue that lines the uterus.,NCI: The endometrium, or tunica mucosa, is the mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle.,NCI: The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thicknes - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - The layer of tissue that lines the uterus.; The mucous membrane comprising the inner layer of the uterine wall. - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle. - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - Endometrio - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - Endometrium - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - baarmoederslijmvlies - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - http://purl.obolibrary.org/obo/NCIT_C13166 - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C12313 - umls:C0014180 - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Amino Acid, Peptide, or Protein - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Tumor protein 63 isoform 2 is the product of an alternative promoter and start codon located in exon 3 of the human TP63 gene. It also has an N-terminally truncated transactivation domain. Expression of isoform 2 may be tissue specific and aberrant expression may be associated with head and neck squamous cell carcinoma. (Atlas of Genetics and Cytogenetics in Oncology and Haematology) - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Delta Np63 Alpha; Tumor Protein 63 Isoform 2; Delta-N p63-Alpha; p51; DeltaN-Alpha; P51delNalpha; DeltaNp63 Alpha - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Tumor protein 63 isoform 2 (586 aa, ; 66 kDa) is encoded by the human TP63 gene. This protein plays a role in the mediation of both transcription and skin development. - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Tumor Protein 63 Isoform 2 - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - P63 - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - Test - - - - http://purl.obolibrary.org/obo/NCIT_C128298 - umls:C4284135 - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - Mucosal; MUCOSA; Mucous Membrane; mucous membrane; Mucosa; mucosa - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - MSH: An EPITHELIUM with MUCUS-secreting cells, such as GOBLET CELLS. It forms the lining of many body cavities, such as the DIGESTIVE TRACT, the RESPIRATORY TRACT, and the reproductive tract. Mucosa, rich in blood and lymph vessels, comprises an inner epithelium, a middle layer (lamina propria) of loose CONNECTIVE TISSUE, and an outer layer (muscularis mucosae) of SMOOTH MUSCLE CELLS that separates the mucosa from submucosa.,CSP: mucus-secreting membrane lining all body cavities or passages that communicate with the exterior.,NCI: The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid).,NCI: Mucous membrane. (NCI),NCI: Mucous membrane. - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - Mucosa - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - mucosa - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - slijmvlies - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C13166 - umls:C0026724 - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - Pathologic Function - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - A rare hyperplastic lesion of Brunner's gland in the duodenum. Although it is usually asymptomatic and discovered incidentally during upper gastrointestinal endoscopy, it may cause hemorrhage. - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - Brunner's Gland Hyperplasia - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - Hyperplasie van de klier van Brunner - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - Iperplasia della ghiandola di Brunner - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - “Brunner” + “iperplasia” + “ghiandole” - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - Usually hyperplasia of Brunner’s glands. NB: the mere Presence of Brunner’s glands is not automatically an hyperplasia. Rather, hyperplasia Is something the glands may have or not. If they have it, it may be a problem - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C135565 - umls:C0341253 - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - Location; Anatomic Site - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - We use this as a semantical class for a location of the body. Similar to Topology, but since we are already using that as a class, we did not want to use the same class for this role. - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - Anatomical Location - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - Anatomische locatie - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - Posizione anatomica - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - Named locations of or within the body. - - - - http://purl.obolibrary.org/obo/NCIT_C13717 - umls:C1515974 - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - Bx; BIOPSY; biopsy; Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - The removal of cells or tissues for examination by a pathologist. The pathologist may study the tissue under a microscope or perform other tests on the cells or tissue. There are many different types of biopsy procedures. The most common types include: (1) incisional biopsy, in which only a sample of tissue is removed; (2) excisional biopsy, in which an entire lump or suspicious area is removed; and (3) needle biopsy, in which a sample of tissue or fluid is removed with a needle.; The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - Biopsia - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - Biopsie - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15189 - umls:C0005558 - - - - http://purl.obolibrary.org/obo/NCIT_C15220 - The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation. - - - - http://purl.obolibrary.org/obo/NCIT_C15220 - Diagnose - - - - http://purl.obolibrary.org/obo/NCIT_C15220 - Diagnosi - - - - http://purl.obolibrary.org/obo/NCIT_C15220 - Diagnosis - - - - http://purl.obolibrary.org/obo/NCIT_C15220 - General - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - Surgery to remove the uterus and, sometimes, the cervix. When the uterus and the cervix are removed, it is called a total hysterectomy. When only the uterus is removed, it is called a partial hysterectomy. - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - A surgical procedure to remove the uterine body (partial hysterectomy) or the uterine body and cervix (total hysterectomy). - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - Hysterectomie - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - Hysterectomy - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - Isterectomia - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15256 - umls:C0020699 - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Health Care Activity - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - A procedure to remove or repair a part of the body or to find out whether disease is present. An operation. - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Operation; surgery; Surgery; Surgical Interventions; Surgical Procedures; Surgically; Surgical Procedure; Type of Surgery; Surgical - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Chirurgische procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Operazione chirurgica - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Surgical Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Type of Intervention that is a surgical procedure. - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15329 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Endoscopy and Biopsy; Endoscopic Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. In the case of an endoscopic biopsy, an endoscope is used to obtain the sample. - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Biopsia endoscopica - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Endoscopic Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Endoscopische biopsie - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - P410000 - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - umls:C0184980 - - - - http://purl.obolibrary.org/obo/NCIT_C15389 - previous SNOMED P41 - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - cone biopsy; LEEP - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Bx; BIOPSY; biopsy; Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Surgical removal of a cone-shaped portion of tissue from the uterine cervix. - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Conization - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Conization - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Conizzazione - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15402 - umls:C0195324 - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - A procedure in which the mucous membrane of the cervical canal is scraped using a spoon-shaped instrument called a curette. - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - A procedure in which the mucous membrane of the cervical canal is scraped using a curette. - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - Curettage endocervicale - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - Endocervical curettage - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - Endocervicale curettage - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C15403 - umls:C0195344 - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - Finding - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - A subjective characterization of the phenomenon of dysplasia, based on microscopic examination of the architectural and/or cytological changes in a tissue sample, that is determined to be high. - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - Displasia di alto grado - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - High Grade Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - Hoogwaardige dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C156083 - umls:C156083 - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - Therapeutic or Preventive Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - A procedure to connect healthy sections of tubular structures in the body after the diseased portion has been surgically removed.; A natural or surgically-induced connection between tubular structures in the body. - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - A natural or surgically-induced connection between tubular structures in the body. - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - Anastomose - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - Anastomosi - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - Anastomosis - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - M182000 - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - umls:C0677554 - - - - http://purl.obolibrary.org/obo/NCIT_C15609 - previous snomed was M18200 - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - Removal Technique; Resection; Surgical Resection - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - A surgical procedure in which tissue is removed. - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - Resectie - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - Resection - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - Resezione - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - P110000 - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - umls:C0015252 - - - - http://purl.obolibrary.org/obo/NCIT_C158758 - previous SNOMED was P11000 - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Laboratory Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Antigen aggregation with antibody, in the right ratios, to cause precipitation. - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - IMMUNOPRECIPITATION; IP; Immunoprecipitation; I.P. REACTION - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Antigen aggregation with antibody, in the right ratios, to cause precipitation. [def-source: NCI] - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Immunoprecipitatie - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Immunoprecipitation - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Immunoprecipitazione - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - P382000 - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - Test - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - umls:C0021069 - - - - http://purl.obolibrary.org/obo/NCIT_C16724 - previous SNOMED was P38200 - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - Subject self-identification re: masculine/feminine. [IOM] See also sex. - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - Gender - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - gender - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - We defined our gender as one of two: male or female. - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - Genere - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - gender - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - geslacht - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - køn - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes. - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - General - - - - http://purl.obolibrary.org/obo/NCIT_C17357 - umls:C0079399 - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - The spread of cancer from one part of the body to another. A tumor formed by cells that have spread is called a "metastatic tumor" or a "metastasis." The metastatic tumor contains cells that are like those in the original (primary) tumor. - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - Metastasis - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - metastase - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - metastasi - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C19151 - umls:C0027627 - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - Finding - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - A specific result or effect that can be measured. Examples of outcomes include decreased pain, reduced tumor size, and improvement of disease.; 1. events or experiences that clinicians or investigators examining the impact of an intervention or exposure measure because they believe such events or experiences may be influenced by the intervention or exposure. 2. (SDTM) The result of carrying out a mathematical or statistical procedure. NOTE: 1. such events and experiences are called clinical outcomes independently of whether they are part of the original question/protocol of the investigation. [1. Guyatt, G., Schunemann H., Dept. epidemiology & statistics, McMaster University-personal communication] See also variable; outcome can be a result of analysis; outcome is more general than endpoint in that it does not necessarily relate to a planned objective of the study.outcome. The measureable characteristic (clinical outcome assessment, biomarker) that is influenced or affected by an individual's baseline state or an intervention as in a clinical trial or other exposure. - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - OUT; result; Result; Outcome; outcome - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - A class representing a general outcome, whatever it may be (positive, negative, uncertain, not enough information etc). - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - Outcome - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - Resultaat - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - Risultato - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - The result of an action. - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C20200 - umls:C1274040 - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - The drug, device, therapy, or process under investigation in a clinical study that is believed to have an effect on outcomes of interest in a study (e.g., health-related quality of life, efficacy, safety, pharmacoeconomics). See also: test articles; devices; drug product; medicinal product; combination product.; In medicine, a treatment or action taken to prevent or treat disease, or improve health in other ways. - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - interventionDescription; intervention; Intervention; Procedure; Intervention Strategies; Interventional; Intervention or Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - This general class represents the intervention performed on the patient to obtain the samples that are then studied to find the disease. In particular, this class represents the attribute 'MATERIALI' in the AOEC Database, and the attribute METHOD in the TCGA database. - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - Intervention eller procedure - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - Intervention or Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - Intervento o Procedura - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - Tussenkomst of procedure - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - General - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C25218 - umls:C0184661 - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Polypectomy - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Complete or partial removal of a polypoid lesion from the mucosal surface. - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Polipectomia - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Polypectomie - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Polypectomy - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Presence of jeyword "polipectomia" in "Materiali" - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - Complete or partial removal of a polypoid lesion from the mucosal surface. - - - - http://purl.obolibrary.org/obo/NCIT_C25349 - umls:C0149684 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Disease or Syndrome - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Cervicitis - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - An acute or chronic inflammatory process that affects the cervix. Causes include sexually transmitted diseases and bacterial infections. Clinical manifestations include abnormal vaginal bleeding and vaginal discharge. [def-source: NCI] - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Cervicite - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Cervicitis - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Cervicitis - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - M400000 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - M430000 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - umls:C0007860 - - - - http://purl.obolibrary.org/obo/NCIT_C26716 - Previously, this class presented SNOMED coded M40000 and M30000* - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - Chronic inflammation of the cervix. - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - Cervicite cronica - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - Chronic Cervicitis - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - Chronische cervicitis - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C27057 - umls:C0269062 - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - A raised growth on the surface of the genitals caused by human papillomavirus (HPV) infection. The HPV in genital warts is very contagious and can be spread by skin-to-skin contact, usually during oral, anal, or genital sex with an infected partner.; A wart of the perianal region or genitalia that is caused by sexual transmission of the human papillomavirus. - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - genital wart; condyloma; Genital Warts; Condyloma Acuminatum; Condyloma Acuminata; Genital Wart; Condyloma; Venereal Wart - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - A sexually transmitted papillary growth caused by the human papillomavirus. It usually arises in the skin and mucous membranes of the perianal region and external genitalia. - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - Condiloma - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - Condyloma - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - Condyloma - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - M767000 - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - umls:C0302180 - - - - http://purl.obolibrary.org/obo/NCIT_C2960 - previous SNOMED was M76700 - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Conversion of a mature, normal cell or groups of mature cells to other forms of mature cells.; A change of cells to a form that does not normally occur in the tissue in which it is found. - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Metaplasia; METAPLASIA; Metaplastic Change; metaplasia - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy. - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Metaplasia - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Metaplasia - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - Metaplasie - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - MSH: A condition in which there is a change of one adult cell type to another similar adult cell type.,CSP: transformation of a normal to a similar but abnormal mature cell type.,NCI: A change of cells to a form that does not normally occur in the tissue in which it is found.,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,NCI: Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy. - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - M730000 - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C3236 - umls:C0025568 - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - A morphologic finding indicating the transformation of glandular or transitional epithelial cells to, usually, mature squamous epithelial cells. Representative examples include squamous metaplasia of bronchial epithelium, cervix, urinary bladder, and prostate gland. - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - Metaplasia squamosa - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - Plaveiselcelmetaplasie - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - Squamous Metaplasia - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - M732200 - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C3237 - umls:C0025570 - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - cassock - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - The connective tissue coat of a mucous membrane including the epithelium and basement membrane. - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - Lamina Propria - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - Lamina Propria - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - Lamina propria - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - http://purl.obolibrary.org/obo/NCIT_C13166 - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - NCI: A type of connective tissue found under the thin layer of tissues covering a mucous membrane.,NCI: The connective tissue coat of a mucous membrane including the epithelium and basement membrane. - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C32918 - umls:C1179187 - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - MAIN BRONCHUS, LEFT; Left Main Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - One of the two main bronchi. It is narrower but longer than the right main bronchus and connects to the left lung. - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - Bronco principale sinistro - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - Left Main Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - Linker hoofdbronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - http://purl.obolibrary.org/obo/NCIT_C12284 - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C32968 - umls:C0225630 - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - Lobar Bronchus; Secondary Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - A part the bronchial tree, arising from the primary bronchi, with each one serving as the airway to a specific lobe of the lung. - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - Bronco lobare - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - Lobar Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - Lobar Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - http://purl.obolibrary.org/obo/UBERON_0002185 - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C32998 - umls:C0225653 - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - Right Main Bronchus; MAIN BRONCHUS, RIGHT - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - One of the two main bronchi. It is wider but shorter than the left main bronchus and connects to the right lung. - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - Bronco principale destro - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - Rechter hoofdbronchus - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - Right Main Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - http://purl.obolibrary.org/obo/NCIT_C12284 - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C33486 - umls:C0225608 - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Simple Epithelium - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Unilaminar epithelium - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Epithelium composed of a single layer of cells attached to a basement membrane. - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Eenlagig epitheel - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Epitelio semplice - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - Simple Epithelium - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C33554 - umls:C0682574 - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - A circumscribed loss of integrity of the skin or mucous membrane.; Destruction of an epithelial surface extending into or beyond the basement membrane. - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - Ulcerative Inflammation; Ulcer; Ulceration; Ulcers; Ulcerated; ulcer; ULCER; Ulcerative - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - Ulcer - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - Ulcera - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - Zweer - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - M400300 - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - umls:C0041582 - - - - http://purl.obolibrary.org/obo/NCIT_C3426 - previous SNOMED was M40030 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - Diffuse hypertrophy of the stratum spinosum layer of the epidermis. - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - Acanthosis - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - Acanthosis - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - Acantosi - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - G000900 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - M727100 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - umls:C4230612 - - - - http://purl.obolibrary.org/obo/NCIT_C35265 - previous SNOMED G0009 - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - Thickening of the outermost layer of stratified squamous epithelium.; A condition marked by thickening of the outer layer of the skin, which is made of keratin (a tough, protective protein). It can result from normal use (corns, calluses), chronic inflammation (eczema), or genetic disorders (X-linked ichthyosis, ichthyosis vulgaris). - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - Hypertrophy of the outermost layer of the epidermis. It may be caused by physical or chemical irritants, irradiation, infection, or neoplastic processes. - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - Hyperkeratose - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - Hyperkeratosis - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - Ipercheratosi - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - umls:C0334061 - - - - http://purl.obolibrary.org/obo/NCIT_C35541 - M740100 - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - Koilocyte; Koilocytotic Squamous Cell - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - Cellula squamosa cilocitotica - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - Koilocytotic Squamous Cell - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - Koilocytotische plaveiselcel - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C36808 - umls:C1517678 - - - - http://purl.obolibrary.org/obo/NCIT_C38034 - The description of an anatomical region or of a body part. - - - - http://purl.obolibrary.org/obo/NCIT_C38034 - Topografia - - - - http://purl.obolibrary.org/obo/NCIT_C38034 - Topografie - - - - http://purl.obolibrary.org/obo/NCIT_C38034 - Topography - - - - http://purl.obolibrary.org/obo/NCIT_C38034 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - Traditional Serrated Adenoma; Serrated Adenoma; TSA; Serrated Adenoma Type II; Serrated adenoma; Traditional serrated adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - An adenoma that arises from the large intestine and the appendix. It is characterized by prominent serration of the glands. - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - Adenoma seghettato - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - Serrated Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - Serrated Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C38458 - umls:C1266025 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - Mild Squamous Dysplasia of the Cervix; Low Grade Cervical Squamous Intraepithelial Neoplasia; Low-Grade Cervical SIL; Low-Grade Cervical Squamous Intraepithelial Lesion; Low Grade Cervical Squamous Intraepithelial Lesion; Low-Grade CIN; Cervical Squamous Intraepithelial Neoplasia 1; Low Grade Cervical Squamous Intraepithelial Neoplasia; LSIL; low grade dysplasia; mild dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - A precancerous neoplastic process that affects the cervical squamous epithelium without evidence of invasion. It is usually associated with human papillomavirus infection. It is characterized by the presence of mild atypia in the superficial epithelial layer that may be associated with koilocytosis. Maturation is present in the upper two thirds of the epithelium. Mitotic figures are not numerous and are present in the basal third of the epithelium. - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - Cervicale squameuze intra-epitheliale neoplasie graad 1 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - Low Grade Cervical Squamous Intraepithelial Neoplasia - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - Neoplasia cervicale squamosa intraepiteliale di grado 1 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - M740060 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - umls:C1518005 - - - - http://purl.obolibrary.org/obo/NCIT_C40196 - old SNOMED M74006* - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - A condition in which moderately abnormal cells grow on the thin layer of tissue that covers the cervix. These abnormal cells are not malignant (cancer) but may become cancer. - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - CIN 2; Cervical Squamous Intraepithelial Neoplasia 2; Moderate Squamous Dysplasia of the Cervix; cervical squamous intraepithelial neoplasia 2 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - Cervical squamous intraepithelial neoplasia characterized by the presence of maturation in the upper half of the squamous epithelium and conspicuous nuclear atypia which is present in all epithelial layers. Mitotic figures are present in the basal two thirds of the epithelium. - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - Cervical Squamous Intraepithelial Neoplasia 2 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - Cervicale squameuze intra-epitheliale neoplasie graad 2 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - Neoplasia cervicale squamosa intraepiteliale di grado 2 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - M740070 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - umls:C0349459 - - - - http://purl.obolibrary.org/obo/NCIT_C40198 - original SNOMED M74007* - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - Dyscrasia; Dysplasia; Dysplastic; dyscrasia; dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer. - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - Displasia - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - Dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - M740000 - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - umls:C0334044 - - - - http://purl.obolibrary.org/obo/NCIT_C4086 - original SNOMED M74000 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - Metastatic Adenocarcinoma - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - An adenocarcinoma which has spread from its original site of growth to another anatomic site. - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - Adenocarcinoma metastatico - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - Gemetastaseerd adenocarcinoom - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - Metastatic Adenocarcinoma - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - M80106 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - M814060 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - umls:C0334277 - - - - http://purl.obolibrary.org/obo/NCIT_C4124 - old SNOMED M81406 - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - A benign, slow-growing tumor arising from the soft tissues usually in the mid-thoracic region of the elderly. It is characterized by the presence of paucicellular collagenous tissue, adipocytes and a predominance of large coarse elastic fibers arranged in globules. - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - Elastofibroma - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - Elastofibroma - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - Elastofibroma - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4245 - umls:C0334460 - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - Neoplastic Process - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - Uterine Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of the Uterine Cervix; Cervix Uteri Adenocarcinoma in situ; Adenocarcinoma in situ of Uterine Cervix; Cervical Adenocarcinoma In Situ AJCC v7; Adenocarcinoma in situ of the Cervix; Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of Cervix Uteri; Adenocarcinoma in situ of Cervix; Adenocarcinoma in situ of the Cervix Uteri; Cervical Adenocarcinoma In Situ - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - Adenocarcinoma in situ (AIS) represents a pre-cancerous condition that can progress to cervical adenocarcinoma. Cervical adenocarcinoma in situ occurs in the glandular tissue of the cervix and is the condition which leads to invasive adenocarcinoma. - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - adenocarcinoma cervicale in situ - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - cervicaal adenocarcinoom in situ - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - cervical adenocarcinoma in situ - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - tage 0 includes: (Tis, N0, M0). Tis: Carcinoma in situ. N0: No regional lymph node metastasis. M0: No distant metastasis. FIGO no longer includes stage 0. - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4520 - umls:C0346203 - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - Qualitative Concept - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - Male Gender, Self Report; Male; Male Gender; Male Gender, Self Reported - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - genere maschile - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - male gender - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - mannelijk geslacht - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - An individual who reports belonging to the cultural gender role distinction of male - - - - http://purl.obolibrary.org/obo/NCIT_C46109 - umls:C1706180 - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - Female Gender, Self Reported; Female Gender, Self Report; Female; Female Gender - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. [def-source: NCI] - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - female gender - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - genere femminile - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - vrouwelijk geslacht - - - - http://purl.obolibrary.org/obo/NCIT_C46110 - An individual who reports belonging to the cultural gender role distinction of female. - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - Activity - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - A general class representing a test. - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - test - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - test - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - A procedure for critical evaluation; a means of determining the presence, quality, or truth of something - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - Test - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - https://www.examode.dei.unipd.it/ontology/Text - - - - http://purl.obolibrary.org/obo/NCIT_C47891 - umls:C0392366 - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - Finding - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - Dysplasia of the Colon; Colonic Dysplasia; Dysplasia of Colon; Colon Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - A morphologic finding indicating the presence of dysplastic glandular epithelial cells in the colonic mucosa. There is no evidence of invasion. - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - Colon Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - Colon dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - Displasia del colon - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4847 - umls:C1302363 - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - Low Grade Dysplasia of the Colon; Low-Grade Dysplasia of Colon; Low-Grade Dysplasia of the Colon; Mild Dysplasia of Colon; Low-Grade Colon Dysplasia; Mild Colon Dysplasia; Low-Grade Colonic Dysplasia; Mild Colonic Dysplasia; Mild Dysplasia of the Colon; Low Grade Colon Dysplasia; Low Grade Colonic Dysplasia; Low Grade Dysplasia of Colon - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - A morphologic finding indicating the presence of mild dysplastic cellular changes and mild architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - Displasia del colon lieve - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - Mild Colon Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - Milde colondysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4848 - umls:C0586367 - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - Finding - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - Moderate Dysplasia of the Colon; Moderate Colonic Dysplasia; Moderate Colon Dysplasia; Moderate Dysplasia of Colon - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - A morphologic finding indicating the presence of moderate dysplastic cellular changes and moderate architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - Displasia moderata del colon - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - Matige colondysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - Moderate Colon Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4849 - umls:C0586368 - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - Disease or Syndrome - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - Hyperplastic Colonic Polyp; Colon HP; Metaplastic Polyp of the Colon; Metaplastic Polyp of Colon; Metaplastic Colonic Polyp; Hyperplastic Polyp of the Colon; Metaplastic Colon Polyp; Hyperplastic Polyp of Colon; Colon Metaplastic Polyp; Colon MP; Colon Hyperplastic Polyp; Colonic Hyperplastic Polyp - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - A serrated polypoid lesion that arises in the colon. It is usually found in the distant colon and it rarely produces symptoms. This group includes goblet cell rich, mucin poor, and microvesicular hyperplastic polyps. - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - Colon Hyperplastic Polyp - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - Colon Hyperplastic Polyp - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - Polipo iperplastico del colon - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - M720400 - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - umls:C0742608 - - - - http://purl.obolibrary.org/obo/NCIT_C4930 - old SNOMED M72040 - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - Slide; Slide Device Component; Slide Device; Microscope Slide - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - A flat rectangular piece of glass on which specimens can be mounted for microscopic study. - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - Slide Device - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - schuif - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - vetrino - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - General - - - - http://purl.obolibrary.org/obo/NCIT_C50178 - C1705201 - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Biopsy (cervical); Other method, specify: ECC - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Removal of tissue from the cervix for microscopic examination. - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Biopsia cervicale - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Cervical biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Cervicale biopsie - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51628 - umls:C0195314 - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Colonoscopic Biopsy; Colonoscopy and Biopsy; Biopsy of Colon - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Removal of tissue from the colon for microscopic examination, using an endoscope. - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Biopsia del colon - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Biopsie van de dikke darm - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Biopsy of Colon - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - P114000 - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - P400000 - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - umls:C0192867 - - - - http://purl.obolibrary.org/obo/NCIT_C51678 - previous SNOMED was P11400, P40 - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Endoscopic Biopsy of Duodenum; Duodenal Biopsy; Biopsy of Duodenum - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Removal of tissue from the duodenum for microscopic examination, using an endoscope. - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Biopsia del duodeno - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Biopsie van de twaalfvingerige darm - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Biopsy of Duodenum - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Biopsia duodeno - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51683 - umls:C0399805 - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Colonoscopic Polypectomy; Colonic Polypectomy - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Complete or partial removal of a polypoid lesion from the mucosal surface of the large intestine. - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Colonoscopic polypectomy - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Colonoscopische polypectomie - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Polipectomia colonscopia - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51688 - umls:C0589347 - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Therapeutic or Preventive Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Surgical removal of all of the uterus, via an abdominal approach. - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Isterectomia addominale totale - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Total Abdominal Hysterectomy - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Totale abdominale hysterectomie - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Other method, specify: total Abdominal Hysterectomy - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51695 - umls:C0404079 - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Removal of tissue from the lung, for microscopic examination. - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - The removal of a small piece of lung tissue to be checked by a pathologist for cancer or other diseases. The tissue may be removed using a bronchoscope (a thin, lighted, tube-like instrument that is inserted through the trachea and into the lung). It may also be removed using a fine needle inserted through the chest wall, by surgery guided by a video camera inserted through the chest wall, or by an open biopsy. In an open biopsy, a doctor makes an incision between the ribs, removes a sample of lung tissue, and closes the wound with stitches. - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Biopsia polmonare - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Longbiopsie - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Lung Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51748 - umls:C0189485 - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - A technique that uses electric current passed through a thin wire loop to remove abnormal tissue. - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - Uses a thin, low-voltage electrified wire loop to cut out a thin layer of abnormal tissue; generally used to remove abnormal cells on the surface of the cervix. - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - Escissione elettrochirurgica ad anello - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - Loop Electrosurgical Excision - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - Loop elektrochirurgische excisie - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - "Leep cervicale" in AOEC - - - - http://purl.obolibrary.org/obo/NCIT_C51760 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Diagnostic Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Bronchial Biopsy; Biopsy of Bronchus - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Removal of tissue from the bronchus for microscopic examination. - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Biopsia bronchiale - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Bronchial Biopsy - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Bronchiale biopsie - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Removal of tissue from the bronchus for microscopic examination. - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C51782 - umls:C0740463 - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - Occupational Activity - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - A diagnostic test in which an antibody is used to link a cellular antigen specifically to a stain that can be seen with a microscope. - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - Immunohistochemical Test - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - Immunohistochemische test - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - Test immunoistochimico - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - presence of word “CD3”/“test immunoistochimico” -/“colorazione immunoistochimica” - - - - http://purl.obolibrary.org/obo/NCIT_C51944 - Test - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - Gene or Genome - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - Tubulovillous Adenoma of Colon; Colon Tubulovillous Adenoma; Tubulovillous Adenoma of the Colon; Colonic Tubulovillous Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - A neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by tubular and villous architectural patterns. The neoplastic glandular cells have dysplastic features - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - Adenoma tubulovilloso del colon - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - Colon Tubulovillous Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - Colon Tubulovillous Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - M826300 - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C5496 - umls:C1112748 - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - Dyskeratosis is abnormal keratinization occurring prematurely within individual cells or groups of cells below the stratum granulosum.[1] - -Dyskeratosis congenita is congenital disease characterized by reticular skin pigmentation, nail degeneration, and leukoplakia on the mucous membranes associated with short telomeres. - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - Discheratosi - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - Dyskeratose - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - Dyskeratosis - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - M740100 - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C62570 - umls:C0334061 - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - Colon Tubular Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - A usually polypoid neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by a tubular architectural pattern. The neoplastic glandular cells have dysplastic features. - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - Adenoma tubulare del colon - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - Colon Tubular Adenoma - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - Colon tubulair adenoom - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - M821100 - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C7041 - umls:C1112503 - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - Malignant Lung Tumor; Malignant Lung Neoplasm; Malignant Tumor of the Lung; Malignant Neoplasm of Lung; Malignant Neoplasm of the Lung; Malignant Tumor of Lung - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - A primary or metastatic malignant neoplasm involving the lung. - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - Kwaadaardige longneoplasma - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - Malignant Lung Neoplasm - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - Neoplasia polmonare maligna - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - M800034 - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - M800130 - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C7377 - umls:C0242379 - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - Laboratory Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - Cytokeratin 5/6 Expression; CK 5/6 Immunohistochemical Expression; CK 5/6 Expression; CK5/6; Cytokeratin 5/6 Immunohistochemical Expression - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - An immunohistochemical diagnostic test utilizing an antibody to detect both cytokeratin 5 and 6 in tissues. - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - Cytokeratin 5/6 - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - CK5/6 - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - Test - - - - http://purl.obolibrary.org/obo/NCIT_C80497 - umls:C2825225 - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - An inflammatory process characterized by the localized collection of polymorphonuclear neutrophils. - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - Focal Acute Inflammation - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - Focale acute ontsteking - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - Infiammazione acuta focale - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - M410000 - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - umls:C1265832 - - - - http://purl.obolibrary.org/obo/NCIT_C82967 - old SNOMED M41000 - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - CIN 1; DYSPLASIA, MILD; MILD DYSPLASIA, CIN 1 - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - A morphologic finding indicating the presence of mild cellular atypia associated with mild architectural changes in a tissue sample. - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - Displasia lieve - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - Mild Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - Milde dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - M740060 - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - umls:C0334046 - - - - http://purl.obolibrary.org/obo/NCIT_C8362 - original SNOMED M74006 - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - Moderate Dysplasia; CIN 2; DYSPLASIA, MODERATE; MODERATE DYSPLASIA, CIN 2 - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - A morphologic finding indicating the presence of moderate cellular atypia associated with moderate architectural changes in a tissue sample. - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - Displasia moderata - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - Matige dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - Moderate Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - M740070 - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - umls:C0334047 - - - - http://purl.obolibrary.org/obo/NCIT_C8363 - original SNOMED M74007 - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - Finding - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - Severe Dysplasia; CIN 3; DYSPLASIA, SEVERE; SEVERE DYSPLASIA, CIN 3 - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - A morphologic finding indicating the presence of severe cellular atypia associated with severe architectural changes in a tissue sample. - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - Displasia grave - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - Ernstige dysplasie - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - Severe Dysplasia - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - svær dysplasi - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/NCIT_C8364 - umls:C0334048 - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Hemicolectomy - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Surgical removal of approximately half of the colon. - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Emicolectomia - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Hemicolectomie - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Hemicolectomy - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - P111500 - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - umls:C0546535 - - - - http://purl.obolibrary.org/obo/NCIT_C86074 - old SNOMED P11150 - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - Radical hysterectomy refers to the excision of the uterus en bloc with the parametrium (ie, round, broad, cardinal, and uterosacral ligaments) and the upper one-third to one-half of the vagina. The surgeon usually also performs a bilateral pelvic lymph node dissection. The procedure requires a thorough knowledge of pelvic anatomy, meticulous attention to sharp dissection, and careful technique to allow dissection of the ureters and mobilization of both bladder and rectum from the vagina. Particular care must be taken with the vasculature of the pelvic side walls and the venous plexuses at the lateral corners of the bladder to avoid excessive blood loss. Removal of the ovaries and fallopian tubes is not part of a radical hysterectomy; they may be preserved if clinically appropriate. - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - Isterectomia radicale - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - Radical Hysterectomy - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - Radicale hysterectomie - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - Procedure - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - https://www.examode.dei.unipd.it/ontology/Intervention - - - - http://purl.obolibrary.org/obo/NCIT_C94470 - umls:C2987682 - - - - http://purl.obolibrary.org/obo/NCIT_P106 - Semantic_Type - - - - http://purl.obolibrary.org/obo/NCIT_P106 - Semantic_Type - - - - http://purl.obolibrary.org/obo/NCIT_P106 - In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. NB: this property is different from hasSemanticArea since this property serves as an annotation to give, when possible, a label indicating the semantic type. This label is taken from Ontobee. hasSemanticArea is used instead to give a tag to every entity, identifying what type of entity that is. - - - - http://purl.obolibrary.org/obo/NCIT_P106 - Used to specify the semantic type of something. - - - - http://purl.obolibrary.org/obo/NCIT_P106 - ha tipo semantico - - - - http://purl.obolibrary.org/obo/NCIT_P106 - has semantic type - - - - http://purl.obolibrary.org/obo/NCIT_P106 - heeft een semantisch type - - - - http://purl.obolibrary.org/obo/NCIT_P106 - A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. - - - - http://purl.obolibrary.org/obo/NCIT_P106 - Semantic Type - - - - http://purl.obolibrary.org/obo/NCIT_P108 - Preferred Term; Preferred_Name; Preferred Name - - - - http://purl.obolibrary.org/obo/NCIT_P108 - When something has a preferred name, you should specify it. - - - - http://purl.obolibrary.org/obo/NCIT_P108 - Preferred Name - - - - http://purl.obolibrary.org/obo/NCIT_P108 - A property representing the word or phrase that NCI uses by preference to refer to the concept. - - - - http://purl.obolibrary.org/obo/NCIT_P325 - To give an alternative definition (coming from another authoritative source) to the annotated entity. - - - - http://purl.obolibrary.org/obo/NCIT_P325 - Alternatieve definitie - - - - http://purl.obolibrary.org/obo/NCIT_P325 - Alternativ definition - - - - http://purl.obolibrary.org/obo/NCIT_P325 - Alternative Definition - - - - http://purl.obolibrary.org/obo/NCIT_P325 - Definizione alternativa - - - - http://purl.obolibrary.org/obo/OAE_0001850 - An inflammation AE that shows localized nodular inflammation found in tissues. - - - - http://purl.obolibrary.org/obo/OAE_0001850 - Granuloma - - - - http://purl.obolibrary.org/obo/OAE_0001850 - Granuloma - - - - http://purl.obolibrary.org/obo/OAE_0001850 - Granuloom - - - - http://purl.obolibrary.org/obo/OAE_0001850 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/OAE_0001850 - M440000 - - - - http://purl.obolibrary.org/obo/OAE_0001850 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/OAE_0001850 - umls:C0018188 - - - - http://purl.obolibrary.org/obo/OAE_0001850 - old SNOMED M44000 - - - - http://purl.obolibrary.org/obo/OBA_0004525 - intra-epitheliale lymfocythoeveelheid - - - - http://purl.obolibrary.org/obo/OBA_0004525 - intraepithelial lymphocyte amount - - - - http://purl.obolibrary.org/obo/OBA_0004525 - quantità di linfociti intraepiteliali - - - - http://purl.obolibrary.org/obo/OBA_0004525 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/OBA_0004525 - LIE, ILE, “linfociti intraepiteliali pari a”, “linfociti”, ”entorociti" - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - Buildup of fluid in the body's tissue. - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - Edema - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - Edema - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - Oedeem - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/OMIT_0005738 - Edema - - - - http://purl.obolibrary.org/obo/OMIT_0018522 - Cervical Intraepithelial Neoplasia - - - - http://purl.obolibrary.org/obo/OMIT_0018522 - Cervicale intra-epitheliale neoplasie - - - - http://purl.obolibrary.org/obo/OMIT_0018522 - Neoplasia intraepiteliale cervicale - - - - http://purl.obolibrary.org/obo/OMIT_0018522 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/OMIT_0018522 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - hyperaemia; hyperemic - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - Hyperemia is a hemic system symptom consisting of an excess of blood in a body part as from an increased flow of blood due to vasodilation. - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - hyperemia - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - hyperemie - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - iperemia - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - iperemia - - - - http://purl.obolibrary.org/obo/SYMP_0000299 - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - cervix mucus - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation [WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - baarmoederhalsslijm - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - cervical mucus - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - muco cervicale - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0000316 - umls:C1619816 - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - doudenal mucosa; mucosa of duodenum; mucous membrane of duodenum; duodenal mucous membrane - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - duodenum mucosa - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - A mucosa that is part of a duodenum. - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - duodenal mucosa - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - mucosa duodenale - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - slijmvlies van de twaalfvingerige darm - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - mucosa duodenale - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0000320 - umls:C0227284 - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - abdominopelvis; abdominopelvic region - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - belly; celiac region; adult abdomen - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - Abdomen - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - Addome - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - Buik - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - TY4100 - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - umls:C0000726 - - - - http://purl.obolibrary.org/obo/UBERON_0000916 - original SNOMED TY4100 - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - Borstvlies - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - Pleura - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - Pleura - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - MSH: The thin serous membrane enveloping the lungs (LUNG) and lining the THORACIC CAVITY. Pleura consist of two layers, the inner visceral pleura lying next to the pulmonary parenchyma and the outer parietal pleura. Between the two layers is the PLEURAL CAVITY which contains a thin film of liquid.,NCI: A thin layer of tissue that covers the lungs and lines the interior wall of the chest cavity. It protects and cushions the lungs. This tissue secretes a small amount of fluid that acts as a lubricant, allowing the lungs to move smoothly in the chest cavity while breathing.,NCI: The tissue that lines the wall of the thoracic cavity and the surface of the lungs. (NCI),NCI: The tissue that lines the wall of the thoracic cavity and the surface of the lungs. - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0000977 - umls:C0032225 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - terminal portion of intestine - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - terminal portion of large intestine; rectal sac; intestinum rectum - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - Rectum, Not Otherwise Specified. - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - Rectum, NOS - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - Rectum, niet anders gespecificeerd. - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - Retto, non altrimenti specificato. - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - http://purl.obolibrary.org/obo/UBERON_0012652 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - Presence of keyword "Rectum NOS" in "Materiali" field in AOEC Database. - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - The terminal portion of the intestinal tube, terminating with the anus. - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - T680000 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - umls:C0034896 - - - - http://purl.obolibrary.org/obo/UBERON_0001052 - original SNOMED T68000 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - caecum; cecum; intestinum crassum caecum - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - intestinum crassum cecum; intestinum caecum; blindgut; blind intestine - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - Caecum - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - Cieco - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - blinde darm - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - Keyword Caecum in "Materiali" field - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - T671000 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - umls:C0007531 - - - - http://purl.obolibrary.org/obo/UBERON_0001153 - original SNOMED T67100 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - large bowel - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - hindgut - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - Colon, Not Otherwise Specified - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - Colon, NOS - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - Colon, non altrimenti specificato - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - Dikke darm, niet anders gespecificeerd - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - http://purl.obolibrary.org/obo/UBERON_0012652 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - Last portion of the large intestine before it becomes the rectum. - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - T670000 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - umls:C0009368 - - - - http://purl.obolibrary.org/obo/UBERON_0001155 - original SNOMED T67000 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - colon ascendens - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - spiral colon - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - Section of colon which is distal to the cecum and proximal to the transversecolon. - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - Ascending Colon - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - Colon ascendente - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - Oplopende dubbele punt - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - T672000 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - umls:C0227375 - - - - http://purl.obolibrary.org/obo/UBERON_0001156 - original SNOMED T67200 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - colon transversum - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon. - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - Colon trasverso - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - Dwars dubbele punt - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - Transverse Colon - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - Keyword "trasverso" in "Materiali" field. - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - T674000 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - umls:C0227386 - - - - http://purl.obolibrary.org/obo/UBERON_0001157 - original SNOMED T67400 - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - colon descendens - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - Aflopende dubbele punt - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - Colon discendente - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - Descending colon - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - T676000 - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001158 - umls:C0227389 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - colon sigmoideum; pelvic colon; sigmoid colon; sigmoid flexure - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - Colon sigmoideo - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - Sigmoid colon - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - Sigmoid colon - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - T677000 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - umls:C0227391 - - - - http://purl.obolibrary.org/obo/UBERON_0001159 - original SNOMED T67700 - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - has_exact_synonym: stomach greater curvature - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature. - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - Curvatura maggiore dello stomaco - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - Greater curvature of stomach - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - Grotere kromming van de maag - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - Corpo - - - - http://purl.obolibrary.org/obo/UBERON_0001164 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - antrum - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - antrum of stomach; stomach pyloric antrum - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - antrum pyloricum; antrum of Willis; stomach antrum; antrum pylori; gastric antrum - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells. - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - antro pilorico - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - pyloric antrum - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - pylorus antrum - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - Antro - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001165 - umls:C0034193 - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. [database_cross_reference: http://en.wikipedia.org/wiki/Brunner's_glands] - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - duodenal gland - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - duodenale klier - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - ghiandola duodenale - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - editor note: currently defined as equivalent to any submucosal gland in the duodenum. -database_cross_reference: EMAPA:36522; GAID:314; NCIT:C13010; FMA:15060; http://www.snomedbrowser.com/Codes/Details/41298001; http://en.wikipedia.org/wiki/Brunner's_glands; MESH:A03.492.411.620.270.322; UMLS:C0006323; MA:0001551; http://linkedlifedata.com/resource/umls/id/C0006323; BTO:0002376 -has_exact_synonym: submucosal gland of duodenum; Brunner's gland; gland of Brunner -has_obo_namespace: uberon -has_related_synonym: glandula duodenales Brunneri; glandula duodenales -http://www.geneontology.org/formats/oboInOwl#id: UBERON:0001212 -in_subset: http://purl.obolibrary.org/obo/uberon/core#organ_slim; http://purl.obolibrary.org/obo/uberon/core#pheno_slim; http://purl.obolibrary.org/obo/uberon/core#uberon_slim -taxon_notes: Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds - - - - http://purl.obolibrary.org/obo/UBERON_0001212 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - proliferative endometrium - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - baarmoederslijmvlies - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - endometrio - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - endometrium - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - http://purl.obolibrary.org/obo/NCIT_C13166 - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - M793100 - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0001295 - umls:C0334186 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air. - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - pulmo - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - Respiration organ that develops as an oupocketing of the esophagus. - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - Long - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - Lung - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - Polmone - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - T280000 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - umls:C0024109 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - original SNOMED T28000 - - - - http://purl.obolibrary.org/obo/UBERON_0002048 - respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - upper intestine; proximal intestine - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - Duodeno - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - Duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - Twaalfvingerige darm - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - T643000 - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - umls:C001330 - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - original SNOMED T-64300 - - - - http://purl.obolibrary.org/obo/UBERON_0002114 - In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.; In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - intestinum ileum; lower intestine; posterior intestine; distal intestine - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - The portion of the small intestine that extends from the jejunum to the colon - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - Ileo - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - Ileum - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - Ileum - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - T679210 - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - umls:C1709868 - - - - http://purl.obolibrary.org/obo/UBERON_0002116 - The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum. - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - bronchi; bronchial trunk - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - bronchial tissue - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - The upper conducting airways of the lung; these airways arise from the terminus of the trachea - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - Bronchus - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - Bronchus - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - Bronco - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - T260000 - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - umls:C0006255 - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - original SNOMED T26000 - - - - http://purl.obolibrary.org/obo/UBERON_0002185 - In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - mucous membrane of rectum; rectum mucous membrane; mucosa of organ of rectum; rectal mucosa; rectum mucosa; rectal mucous membrane; rectum mucosa of organ; organ mucosa of rectum; rectum organ mucosa - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - A mucosa that is part of a rectum - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - Membrana mucosa rettale - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - Rectaal slijmvlies - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - Rectal mucous membrane - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - T680100 - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0003346 - umls:C0227395 - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - mediastinal part of chest - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - The central part of the thoracic cavity enclosed by the left and right pleurae. - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - Mediastino - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - Mediastinum - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - Mediastinum - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - TY2300 - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - umls:C0025066 - - - - http://purl.obolibrary.org/obo/UBERON_0003728 - original SNOMED TY2300, I decided to left it untouched since it is quite peculiar - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium. - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - cervical epithelium; epithelium of cervix; cervix epithelial tissue; cervical canal epithelial tissue; cervical canal epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - An epithelium that is part of a uterine cervix - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - cervix epitheel - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - cervix epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - epitelio della cervice - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0004801 - umls:C1711358 - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - cervical squamous epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - cervix plaveiselepitheel - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - cervix squamous epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - epitelio squamoso della cervice - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0006922 - umls:C1707351 - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - lymph node of thorax - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - deep thoracic lymph node - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - Linfonodo toracico - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - Thoracale lymfeknoop - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - Thoracic lymph node - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - T083000 - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0007644 - umls:C0229745 - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - An intestinal villus in the duodenum. - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - intestinal villus of duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - intestinale villus van de twaalfvingerige darm - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - villi intestinali del duodeno - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0008342 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - epithelium of duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - An epithelium that is part of a duodenum. - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - duodenaal epitheel - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - duodenal epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - epitelio duodenale - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0008346 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - distal colon - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - The distal portion of the colon; it develops embryonically from the hindgut and functions in the storage and elimination of waste. - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - Colon sinistro - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - Left colon - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - Linker dubbele punt - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - T679950 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - umls:C0227388 - - - - http://purl.obolibrary.org/obo/UBERON_0008971 - previous SNOMED T67995 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - proximal colon - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - The proximal portion of the colon, extending from the ileocecal valve usually to a point proximal to the left colic flexure; it develops embryonically from the terminal portion of the midgut and functions in absorption. - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - Colon destro - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - Rechter dubbele punt - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - Right colon - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - T679650 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - umls:C1305188 - - - - http://purl.obolibrary.org/obo/UBERON_0008972 - original SNOMED T67965 - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - cervix columnar epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - A glandular epithelium that is part of a uterine cervix. - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - cervix glandulair epitheel - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - cervix glandular epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - epitelio ghiandolare della cervice - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0012250 - umls:C2987682 - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - ectocervical epithelium; exocervical epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - A epithelium that is part of a ectocervix. - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - epitelio esocervicale - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - exocervicaal epitheel - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - exocervical epithelium - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0012251 - umls:C1283920 - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - squamocolumnar junction - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - squamocolumnar junction of uterine cervix; squamo-columnar junction of uterine cervix - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - cervical squamo-columnar junction - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - cervicale squamocolumnaire overgang - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - giunzione squamocolonnare cervicale - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - http://purl.obolibrary.org/obo/UBERON_0004801 - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0012253 - umls:C3273256 - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - The subdivision of the digestive tract that consists of the colon and the rectum - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - colorectum - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - colorectum - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - coloretto - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0012652 - umls:C1711309 - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - duodenal crypt; duodenal crypt of Lieberkuhn - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - An intestinal crypt that is located in the duodenum. - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - cripta di Lieberkuhn del duodeno - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - crypt of Lieberkuhn of duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - crypte van Lieberkuhn van de twaalfvingerige darm - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - database_cross_reference: EMAPA:37838; FMA:269063 -has_exact_synonym: duodenal crypt; duodenal crypt of Lieberkuhn -has_obo_namespace: uberon -http://www.geneontology.org/formats/oboInOwl#id: UBERON:0013482 -in_subset: http://purl.obolibrary.org/obo/uberon/core#pheno_slim - - - - http://purl.obolibrary.org/obo/UBERON_0013482 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - duodenal cap; bulbus (duodenum); ampulla duodeni; duodenal cap viewed radiologically; bulbus duodeni; ampulla (duodenum); ampulla of duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - The very first part of the duodenum which is slightly dilated. - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - ampolla duodenale - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - duodenal ampulla - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - duodenale ampulla - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0013644 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - lamina propria of duodenum; duodenal lamina propria; lamina propria mucosae of duodenum - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - A lamina propria that is part of a duodenum. - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - duodenum lamina propria - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - duodenum lamina propria - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - lamina propria del duodeno - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - http://purl.obolibrary.org/obo/UBERON_0002114 - - - - http://purl.obolibrary.org/obo/UBERON_0015834 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - Pulmonary lymph nodes are a common and underrecognized cause of a peripheral SPN. These lymph nodes are usually found at the bifurcation of the bronchi, before the fourth branch, where they are referred to as peribronchial lymph nodes. Lymph nodes are occasionally present within the lung parenchyma, where they are designated intrapulmonary lymph nodes (IPLNs) or perifissural nodules (PFNs). - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - linfonodo polmonare - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - pulmonale lymfeknoop - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - pulmonary lymph node - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - T080000 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - T083110 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - T083120 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - T083200 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - T083210 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0035764 - previous SNOMED was T08311, T08312, T08320, T08321, T08000 - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - rectosigmoid region - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - An anatomical junction that is between the sigmoid colon and rectum. - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - Giunzione rettosigmoidea - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - Rectosigmoid junctie - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - Rectosigmoid junction - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - http://purl.obolibrary.org/obo/UBERON_0001155 - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - T679210 - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - http://purl.obolibrary.org/obo/UBERON_0036214 - umls:C1709868 - - - - http://purl.obolibrary.org/obo/UBPROP_0000001 - A definition coming from a source external to the ones commonly used in Examode, or from a non-authoritative one. - - - - http://purl.obolibrary.org/obo/UBPROP_0000001 - Definizione esterna - - - - http://purl.obolibrary.org/obo/UBPROP_0000001 - Ekstern definition - - - - http://purl.obolibrary.org/obo/UBPROP_0000001 - Externe definitie - - - - http://purl.obolibrary.org/obo/UBPROP_0000001 - external definition - - - - http://purl.obolibrary.org/obo/UBPROP_0000010 - Notes about the structure of some entity, e.g. a location or an intervention. - - - - http://purl.obolibrary.org/obo/UBPROP_0000010 - Note strutturali - - - - http://purl.obolibrary.org/obo/UBPROP_0000010 - Structurele opmerkingen - - - - http://purl.obolibrary.org/obo/UBPROP_0000010 - Strukturelle noter - - - - http://purl.obolibrary.org/obo/UBPROP_0000010 - structure notes - - - - http://purl.obolibrary.org/obo/VT_0010209 - duodenum villi lengte - - - - http://purl.obolibrary.org/obo/VT_0010209 - duodenum villi length - - - - http://purl.obolibrary.org/obo/VT_0010209 - lunghezza dei villi del duodeno - - - - http://purl.obolibrary.org/obo/VT_0010209 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - http://purl.obolibrary.org/obo/VT_0010209 - "villi" + characterization - - - - fabio:ClinicalCaseReport - This is the main class of the ontology. The Clinical Case is one record in the database, and in this version of the ontology may be of one of four diseases: celiac disease, lung cancer, cervix cancer, colon cancer. This class is sub-instantiated to the other different sub-classes - - - - fabio:ClinicalCaseReport - https://www.examode.dei.unipd.it/ontology/ - - - - fabio:ClinicalCaseReport - Caso clinico - - - - fabio:ClinicalCaseReport - Clinical Case Report - - - - fabio:ClinicalCaseReport - Klinisch casusrapport - - - - fabio:ClinicalCaseReport - Klinisk sagsrapport - - - - fabio:ClinicalCaseReport - General - - - - dc:identifier - An unambiguous reference to the resource within a given context. + xmlns:skos="http://www.w3.org/2004/02/skos/core#" + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:ontology="https://w3id.org/examode/ontology/"> + + + + + + ExaMode focuses on histopathological diagnosis of tissues with the aim of detecting diseases. We take into account the future cancer incidence and mortality burden worldwide which is predicted to be increasing (by 63% from 2018 until 2040); hence, we decided to focus our attention mainly on four use-cases: Colon cancer, Cervix cancer, Lung cancer, Celiac disease + +In this ontology we model the main aspects concerning these diseases and the patients' histopathological reports concerning them. +The focus of the ontology is on the pathological report and not on the diseases and their modeling. The reports can have a positive, negative or inconclusive outcome. The ExaMode ontology defines a formal classification schema to encode the medical reports in histopathology and to define the formal relationships between diseases, their anatomical locations and the procedures to withdrawn and analyse the human tissues. + +We model the anatomical location of the disease, the main information about the disease itself and the procedure adopted to withdraw and analyse the tissues. + Copyright 2020-2022 University of Padua, Italy + +Licensed under the + +Creative Commons Attribution-ShareAlike 4.0 International License + https://creativecommons.org/licenses/by-sa/4.0/ + +You may obtain a copy of the License at + https://creativecommons.org/licenses/by-sa/4.0/legalcode + +This work has been supported by the EXAMODE project + https://www.examode.eu/ + + funded by the European Union’s Horizon 2020 research and innovation programme + under the grant agreement No 825292 + The EXAMODE ontology + EXAMODE stands for Extreme-scale Analytics via Multimodal Ontology Discovery & Enhancement + This ontology is encoded in OWL 2 DL + + + + + + + + + + + + + Semantic_Type + In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. NB: this property is different from hasSemanticArea since this property serves as an annotation to give, when possible, a label indicating the semantic type. This label is taken from Ontobee. hasSemanticArea is used instead to give a tag to every entity, identifying what type of entity that is. + Used to specify the semantic type of something. + ha tipo semantico + has semantic type + heeft een semantisch type + A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network. + + + + + + + + + + To give an alternative definition (coming from another authoritative source) to the annotated entity. + alternatieve definitie + alternative definition + definzione alternativa + + + + + + + + + + + A definition coming from a source external to the ones commonly used in Examode, or from a non-authoritative one. + definizione esterna + external definition + externe definitie + + + + + + + + + Notes about the structure of some entity, e.g. a location or an intervention. + note strutturali + structure notes + structurele opmerkingen + + + + + -Property connecting a case to its id. It follows dublin core specification http://www.ukoln.ac.uk/metadata/dcmi-ieee/identifiers/, that says: Recommended practice is to identify the resource by means of a string conforming to an identification system. Examples include International Standard Book Number (ISBN), Digital Object Identifier (DOI), and Uniform Resource Name (URN). Persistent identifiers should be provided as HTTP URIs. -In this ontology it is supposed that this property connects a clinical case to a string representing an URL. - - - - dc:identifier - identificatore - - - - dc:identifier - identifier - - - - dc:identifier - identifier - - - - dc:title - The title of something. - - - - oboinowl:hasBroadSynonym - A property to connect an entity to broad synobyms. - - - - oboinowl:hasBroadSynonym - ha sinonimi generici - - - - oboinowl:hasBroadSynonym - har generiske synonymer - - - - oboinowl:hasBroadSynonym - has broad synonym - - - - oboinowl:hasExactSynonym - An alias in which the alias exhibits true synonymy. - - - - oboinowl:hasExactSynonym - ha sinonimi esatti - - - - oboinowl:hasExactSynonym - har nøjagtige synonymer - - - - oboinowl:hasExactSynonym - hasExactSynonym - - - - oboinowl:hasRelatedSynonym - To connect an entity to sinonims that are only related to it, and not completely equivalent to it. - - - - oboinowl:hasRelatedSynonym - ha sinonimi correlati - - - - oboinowl:hasRelatedSynonym - har relaterede synonymer - - - - oboinowl:hasRelatedSynonym - has related synonym - - - - oboinowl:hasSynonym - To connect an entity to strings representing synonims to the xsd:string given as label. They should be accompanies by the annotation specifying the corresponding language. - - - - oboinowl:hasSynonym - ha sinonimo - - - - oboinowl:hasSynonym - har synonym - - - - oboinowl:hasSynonym - has synonym - - - - oboinowl:hasSynonym - heeft synoniem - - - - rdf:Bag - The rdf:Bag class is the class of RDF 'Bag' containers. It is a subclass of rdfs:Container. Whilst formally it is no different from an rdf:Seq or an rdf:Alt, the rdf:Bag class is used conventionally to indicate to a human reader that the container is intended to be unordered. - - - - rdf:Bag - Bag - - - - xsd:anyURI - internal ID (different from the dublin core specification for ID, http://www.ukoln.ac.uk/metadata/dcmi-ieee/identifiers/), used for internal use. This ID can be considered as the one to identify the single records. - - - - xsd:anyURI - ID interno - - - - xsd:anyURI - Interne ID - - - - xsd:anyURI - internal ID - - - - xsd:anyURI - internt id - - - - owl:cardinality - The cardinality constraint owl:cardinality is a built-in OWL property that links a restriction class to a data value belonging to the range of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:cardinality constraint describes a class of all individuals that have exactly N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property to connect an entity to broad synobyms. + ha sinonimi generici + has broad synonym + heeft een breed synoniem + + + + + + + + + + + An alias in which the alias exhibits true synonymy. + ha sinonimi esatti + has exact synonym + heeft een exact synoniem + + + + + + + + + + + To connect an entity to sinonims that are only related to it, and not completely equivalent to it. + ha sinonimi correlati + has related synonym + heeft verwant synoniem + + + + + + + + + + + To connect an entity to strings representing synonims to the xsd:string given as label. They should be accompanies by the annotation specifying the corresponding language. + ha sinonimo + has synonym + heeft synoniem + + + + + + + + + + The cardinality constraint owl:cardinality is a built-in OWL property that links a restriction class to a data value belonging to the range of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:cardinality constraint describes a class of all individuals that have exactly N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. This construct is in fact redundant as it can always be replaced by a pair of matching owl:minCardinality and owl:maxCardinality constraints with the same value. It is included as a convenient shorthand for the user. @@ -9821,24 +211,34 @@ The following example describes a class of individuals that have exactly two par <owl:Restriction> <owl:onProperty rdf:resource="#hasParent" /> <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:cardinality> -</owl:Restriction> - - - - owl:maxCardinality - The cardinality constraint owl:maxCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:maxCardinality constraint describes a class of all individuals that have at most N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. +</owl:Restriction> + + + + + + + + + + The cardinality constraint owl:maxCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:maxCardinality constraint describes a class of all individuals that have at most N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. The following example describes a class of individuals that have at most two parents: <owl:Restriction> <owl:onProperty rdf:resource="#hasParent" /> <owl:maxCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:maxCardinality> -</owl:Restriction> - - - - owl:minCardinality - The cardinality constraint owl:minCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:minCardinality constraint describes a class of all individuals that have at least N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. +</owl:Restriction> + + + + + + + + + + The cardinality constraint owl:minCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:minCardinality constraint describes a class of all individuals that have at least N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. The following example describes a class of individuals that have at least two parents: @@ -9847,3157 +247,5982 @@ The following example describes a class of individuals that have at least two pa <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minCardinality> </owl:Restriction> -Note that an owl:minCardinality of one or more means that all instances of the class must have a value for the property. - - - - owl:partOf - Tells that an object is part of another object. - - - - owl:partOf - partOf - - - - owl:sameAs - The property that determines that two given individuals are equal. - - - - owl:sameAs - owl: - - - - owl:sameAs - same as - - - - skos:broader - Property used to build a hierarchy among the elements of an annotation. When one thing that can be an annotation to an outcome is inside a hierarchy, it is connected to its parent through this property. - - - - skos:broader - has broader - - - - skos:related - The property skos:related is used to assert an associative link between two SKOS concepts. - -skos:related enables the representation of associative (non-hierarchical) links, such as the relationship between one type of event and a category of entities which typically participate in it. Another use for skos:related is between two categories where neither is more general or more specific. Note that skos:related enables the representation of associative (non-hierarchical) links, which can also be used to represent part-whole links that are not meant as hierarchical relationships. - -Note that, although skos:related is a symmetric property, this condition does not place any restrictions on sub-properties of skos:related (i.e., sub-properties of skos:related could be symmetric, not symmetric or antisymmetric, and still be consistent with the SKOS data model). - - - - skos:related - has Related - - - - foaf:maker - An agent that made this thing. - - - - foaf:maker - In this ontology the property maker is used to connect a clinical case report to the organization that produced it. For future possibilities, we put domain and range to owl:Thing. - - - - foaf:maker - maker - - - - foaf:maker - maker - - - - foaf:maker - producent - - - - foaf:maker - produttore - - - - foaf:maker - The maker property relates something to a Agent that made it. As such it is an inverse of the made property. +Note that an owl:minCardinality of one or more means that all instances of the class must have a value for the property. + + + + + + + + + + + + + + + + + + + + + + This property is used to annotated classes with a comment representing the rule that we inferred during the process of definition of this ontology. This rule may be implemented to extract entities from a clinical case record. + +NB: we do not guarantee that these rules are always valid, or that they are the only valid. It may be the case that they are inaccurate since we were only able to infer them from the cases that were provided to us. Treat these annotations only as a documentation of our process and for a first implementation of the entities extractor. + annotated rule + annotatieregel + regola per l'annotazione + + + + + + + + + + In this ontologies different entities were developed to deal with specific entities. This property is used to link one entity to the corresponding disease it was defined for. It is just some more information to keep track of the nature of entities and to what disease they originally belong. + associated disease + geassocieerde ziekte + malattia associata + + + + + + + + + + Property to take notes (for reminding us/ help us define rule/ maybe do some reasoning in the future) about which keywords to look for in the Diagnosis + associated keyword in diagnosis + bijbehorende trefwoorden in de diagnose + parole chiave associate nella diagnosi + + + + + + + + + + Connects one class (a location or a intervention) to the keyword in the field Materiali that, if found, indicates the presence of that class. + associated keyword in materiali + bijbehorende trefwoorden in het veld materialen + parole chiave associate nel field materiali + + + + + + + + + + Property representing the definition in the ontobee website. In later versions of the ontology we prefer rdfs:comment since it is more universally used. + definitie + definition + definizione + + + + + + + + + + A property to connect one entity to the annotations found for that entitiy in the corresponding page in Ontobee (http://www.ontobee.org/). + ha annotazione da Ontobee + has Ontobee annotation + heeft een record van Ontobee + + + + + + + + + + Use this property to annotate one entity with its corresponding SNOMED code. + ha codice SNOMED + has SNOMED code + heeft SNOMED-code + + + + + + + + + + Connects one ontology class or Individual to the semantic area to which it belongs. For example, a Poly is a diagnosis, therefore the Polyp belongs to the semantic area of Diagnosis. + has semantic area + presenta area semantica + presenteert semantisch gebied + + + + + + + + + + Use this property to annotate a resource with some notes that may be useful to those who will work on building the ontology. + internal notes + interne notities + note interne + + + + + + + + + + A field found sometimes for entities taken from Ontobee's ontologies. You can treat it as an ulterior/alternative definition. + note tassonomiche + structurele opmerkinegen + taxon notes + + + + + + + + + + + + + + + + + + + + + + + + + skos vocabulary + related + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An agent that made this thing. + An agent that made this thing. + In this ontology the property maker is used to connect a clinical case report to the organization that produced it. For future possibilities, we put domain and range to owl:Thing. + + maker + maker + producent + produttore + stable + The maker property relates something to a Agent that made it. As such it is an inverse of the made property. The name (or other rdfs:label) of the maker of something can be described as the dc:creator of that thing. -For example, if the thing named by the URI http://danbri.org/ has a maker that is a Person whose name is 'Dan Brickley', we can conclude that http://danbri.org/ has a dc:creator of 'Dan Brickley'. - - - - foaf:organization - https://www.examode.dei.unipd.it/ontology/General - - - - foaf:organization - An organization that, in the context of the ExaMode program, provides clinical case records. It is usually an Hospital (e.g. AOEC or Radbound). - - - - foaf:organization - https://www.examode.dei.unipd.it/ontology/ - - - - foaf:organization - Organisatie - - - - foaf:organization - Organization - - - - foaf:organization - Organizzazione - - - - foaf:organization - General - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - Adult onset - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - Gruppo d'età adulta - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - voksen alder gruppe - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - volwassen aanvang - - - - https://hpo.jax.org/app/browse/term/HP:0003581 - General - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - A type of adult onset with onset of symptoms after the age of 60 years. - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - Gruppo d'età tarda - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - Laat begin - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - Late onset - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - Sen aldersgruppe - - - - https://hpo.jax.org/app/browse/term/HP:0003584 - General - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - A type of adult onset with onset of symptoms at the age of 40 to 60 years. - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - Aldersgruppe i middelalderen - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - Begin op middelbare leeftijd - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - Gruppo d'età della mezza età - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - Middle age onset - - - - https://hpo.jax.org/app/browse/term/HP:0003596 - General - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - The age group in which disease manifestations appear. - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - This class represents a generic age group. - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - Gruppo d'età - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - Onset - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - aldersgruppe - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - leeftijdsgroep - - - - https://hpo.jax.org/app/browse/term/HP:0003674 - General - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - Onset of disease at the age of between 16 and 40 years. - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - Begin bij jonge volwassenen - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - Gruppo d'età giovane adulto - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - Ung voksen aldersgruppe - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - Young adult onset - - - - https://hpo.jax.org/app/browse/term/HP:0011462 - General - - - - Annotation - A general class to represent all the kionds of annnotations that may be needed in an ExaMode report. - - - - Annotation - Annotatie - - - - Annotation - Annotation - - - - Annotation - Annotazione - - - - AntrumPyloriBiopsy - Biopsy executed in the pyloric antrum, a form of endoscopic biopsy. - - - - AntrumPyloriBiopsy - Biopsia dell'antro pilorico - - - - AntrumPyloriBiopsy - Biopsie van het pylorusantrum - - - - AntrumPyloriBiopsy - Biopsy of the pyloric antrum - - - - AntrumPyloriBiopsy - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - AntrumPyloriBiopsy - “Biopsia” + “STOMACO” + “Antro” - - - - AntrumPyloriBiopsy - Procedure - - - - AntrumPyloriBiopsy - https://www.examode.dei.unipd.it/ontology/Intervention - - - - AssociatedDisease - In this ontologies different entities were developed to deal with specific entities. This property is used to link one entity to the corresponding disease it was defined for. It is just some more information to keep track of the nature of entities and to what disease they originally belong. - - - - AssociatedDisease - Malattia associata - - - - AssociatedDisease - associated disease - - - - AssociatedDisease - geassocieerde ziekte - - - - AssociatedDisease - tilknyttet sygdom - - - - BooleanCheckElement - A set of checks controlled on an Immunohistochemical test that can only have a boolean result (positive - negative). - - - - BooleanCheckElement - Booleaans controle-element - - - - BooleanCheckElement - Boolean Check Element - - - - BooleanCheckElement - Elemento di controllo booleano - - - - BooleanCheckElement - Test - - - - C0908867 - One of the tests that can be made for the lung cancer. - - - - C0908867 - cytokeratin 34bE12 - - - - C0908867 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - C0908867 - CK34BE12 - - - - C0908867 - Test - - - - C0908867 - umls:C0908867 - - - - C0909069 - One of the tests that can be performed to check lung cancer. - - - - C0909069 - endonuclease P40 - - - - C0909069 - https://uts.nlm.nih.gov//metathesaurus.html?cui=C0909069 - - - - C0909069 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - C0909069 - P40 - - - - C0909069 - Test - - - - C0909069 - umls:C0909069 - - - - CD3 - Cluster of Differentiation 3 - - - - CD3 - Cluster of Differentiation 3 - - - - CD3 - n immunology, the CD3 (cluster of differentiation 3) T cell co-receptor helps to activate both the cytotoxic T cell (CD8+ naive T cells) and also T helper cells (CD4+ naive T cells). It consists of a protein complex and is composed of four distinct chains. In mammals, the complex contains a CD3γ chain, a CD3δ chain, and two CD3ε chains. These chains associate with the T-cell receptor (TCR) and the ζ-chain (zeta-chain) to generate an activation signal in T lymphocytes. The TCR, ζ-chain, and CD3 molecules together constitute the TCR complex. - - - - CD3 - CD3 - - - - CD3 - cluster van differentiatie 3 - - - - CD3 - gruppo di differenziazione 3 - - - - CD3 - klynge af differentiering 3 - - - - CD3 - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - CD3 - presence of word "CD3" - - - - CD3 - Test - - - - Cannizzaro_Hospital - Entity representing the Cannizzaro Hospital as producer of medical report - - - - Cannizzaro_Hospital - Cannizzaro Hospital - - - - Cannizzaro_Hospital - Ospedale Cannizzaro - - - - Cannizzaro_Hospital - Ziekenhuis Cannizzaro - - - - Cannizzaro_Hospital - cannizzaro hospital - - - - Cannizzaro_Hospital - General - - - - CeliacAbnormality - Class for abnormalities that can be found in a patient looking for the celiac disease. Some of these include the Edema, Hyperemia, Intestinal fibrosis, Brunner's Gland Hyperplasia. - - - - CeliacAbnormality - Annotazione riguardo anormalità relativa a celiachia - - - - CeliacAbnormality - Celiac Abnormality - - - - CeliacAbnormality - Coeliakie abnormaliteit - - - - CeliacAbnormality - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - CeliacClinicalCaseReport - General - - - - CeliacClinicalCaseReport - Class representing all the celiac disease clinical cases. - - - - CeliacClinicalCaseReport - Caso clinico di malattia celiaca - - - - CeliacClinicalCaseReport - Celiac Clinical Case Report - - - - CeliacClinicalCaseReport - Klinisch geval van coeliakie - - - - CeliacClinicalCaseReport - klinisch geval van coeliakie - - - - CeliacClinicalCaseReport - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - CeliacDiseaseAnnotation - A subclass containing Annotations only for the celiac disease. - - - - CeliacDiseaseAnnotation - Annotazione riguardo Celiachia - - - - CeliacDiseaseAnnotation - Celiac Disease Annotation - - - - CeliacDiseaseAnnotation - Coeliakie Annotatie - - - - CeliacDiseaseAnnotation - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - CeliacDiseaseAnnotationBag - This object is defined as a sort of bag. Every instance may have certain triples that talk about the status of the patient. The engine will need to mint a new url (a blank node is good) to create this object. These bag objects are used in particular to contain information about the coeliac disease, the IEL, the villli to crypt ratio and the villi status. - - - - CeliacDiseaseAnnotationBag - Annotatiezak voor coeliakie - - - - CeliacDiseaseAnnotationBag - Annotationspose til cøliaki - - - - CeliacDiseaseAnnotationBag - Bag di annotazione per celiachia - - - - CeliacDiseaseAnnotationBag - Celiac Disease Annotation Bag - - - - CeliacDiseaseAnnotationBag - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - CeliacDiseaseAnnotationBag - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - CervixAnnotation - A class that is intended to be a set for information that may or may not be found in a cervix case. Instances of this class are 'things' that may be found (or not) in a patient with cervix cancer. For example, the Human Papilloma Virus. The HPV is an instance of this class and every time we annotate a case with HPV we use that instance, of type this class, without every time creating a HPV instance. - - - - CervixAnnotation - Annotatie van de baarmoederhals - - - - CervixAnnotation - Annotazione riguardo Cervice - - - - CervixAnnotation - Cervix Annotation - - - - CervixAnnotation - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - CervixClinicalCaseReport - General - - - - CervixClinicalCaseReport - Class representing the clinical cases about cervix cancer. - - - - CervixClinicalCaseReport - Caso Clinico di Cancro alla Cervice - - - - CervixClinicalCaseReport - Cervix Clinical Case Report - - - - CervixClinicalCaseReport - Klinisch geval van baarmoederhalskanker - - - - CervixClinicalCaseReport - casusrapport van darmkanker - - - - CervixClinicalCaseReport - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - CheckElement - This is a set of elements containing all the possible checks that a patient may do for a generic disease. - - - - CheckElement - Check Element - - - - CheckElement - Controleer Element - - - - CheckElement - Controllo - - - - CheckElement - Test - - - - ColonAnnotation - A class that is a container for elements that may or may not be found in a colon case. Originally thought to contain the presence of Dysplasia. - - - - ColonAnnotation - Annotazione riguardo Colon - - - - ColonAnnotation - Colon Annotation - - - - ColonAnnotation - dubbele punt annotatie - - - - ColonAnnotation - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - ColonClinicalCaseReport - General - - - - ColonClinicalCaseReport - Class representing all colon cancer cases. - - - - ColonClinicalCaseReport - Caso Clinico di Cancro al Colon - - - - ColonClinicalCaseReport - Colon Clinical Case Report - - - - ColonClinicalCaseReport - Klinisch geval van darmkanker - - - - ColonClinicalCaseReport - casusrapport van darmkanker - - - - ColonClinicalCaseReport - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - DiseaseAnnotation - A container class for elements that may or may not be present in diseases. One disease may present some elements that are not exaclty directly correlated to the presence/absence of the disease. or elements that are just there, and it is useful to note their presence/absence. This is the class of all elements that can be considered a sort of addendum, information extracted from the clinical case record but not directly related to the presence outcome. The inspiration for this class first came when we had to deal with the Annotations to the Case of the Celiac Disease. You can also think of this class as a superclass for other containers. - - - - DiseaseAnnotation - Annotazione di malattia - - - - DiseaseAnnotation - Disease Annotation - - - - DiseaseAnnotation - Notatie van een ziekte - - - - FloatCheckElement - A set of checks that can be performed on a Immunohistochemical Test that present a float as output value. - - - - FloatCheckElement - Elemento di controllo del galleggiante - - - - FloatCheckElement - Float Check Element - - - - FloatCheckElement - Float Check-element - - - - FloatCheckElement - Test - - - - General - In this ontology there are different semantic areas. These are: diagnosis, procedure, test, anatomical location, and general. -General is the area of entities that are common to all clinical cases. Organization, clinical case reports, diseases, are classes with entities that do not belong to the other 4 semantic areas, therefore we classified them in general. These are the classes that, in our documentation, are contained in the green box. - - - - General - Algemene entiteit - - - - General - Entità Generica - - - - General - General Entity - - - - General - generieke entiteit - - - - GreaterCurvatureBiopsy - Biopsy produced in the greater curvature area, a region in the stomach. - - - - GreaterCurvatureBiopsy - Biopsia della grande curvatura - - - - GreaterCurvatureBiopsy - Biopsie van de grotere kromming - - - - GreaterCurvatureBiopsy - Biopsy of the Greater Curvature - - - - GreaterCurvatureBiopsy - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - GreaterCurvatureBiopsy - Biopsia + Stomaco + Corpo - - - - GreaterCurvatureBiopsy - Procedure - - - - GreaterCurvatureBiopsy - https://www.examode.dei.unipd.it/ontology/Intervention - - - - InconclusiveOutcome - Inconclusive Outcome. Not enough tissue or not enough evidence was present to decide for a negative or positive outcome. - - - - InconclusiveOutcome - Inconclusive Outcome - - - - InconclusiveOutcome - Onduidelijk resultaat - - - - InconclusiveOutcome - Risultato inconcludente - - - - InconclusiveOutcome - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - InsufficientMaterial - Inconclusive outcome where not enough material was present for the diagnosis. - - - - InsufficientMaterial - Insufficient Material - - - - InsufficientMaterial - Materiale Insufficiente - - - - InsufficientMaterial - Onvoldoende Materiaal - - - - InsufficientMaterial - M010100 - - - - InsufficientMaterial - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - InsufficientMaterial - umls:C0332630 - - - - InterventionHasLocation - every intervention/procedure is performed in a location. We use the topology entities to codify the information about this location. We use this property supposing to reference one subclass of Topography. We need to check that it is possible to use as range the whole class topography or if we need to go to a superclass. - - - - InterventionHasLocation - interventie heeft topografie - - - - InterventionHasLocation - intervention has topography - - - - InterventionHasLocation - leasing af interventionen - - - - InterventionHasLocation - locazione intervento - - - - LungAnnotation - This class, as the others, is used to instantiate annotations over clinical cases. - - - - LungAnnotation - Annotazione riguardo Polmone - - - - LungAnnotation - Longannotatie - - - - LungAnnotation - Lung Annotation - - - - LungAnnotation - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - LungClinicalCaseReport - Class representing all lung cancer cases. - - - - LungClinicalCaseReport - Caso clinico di cancro ai polmoni - - - - LungClinicalCaseReport - Klinisch geval van longkanker - - - - LungClinicalCaseReport - Lung Clinical Case Report - - - - LungClinicalCaseReport - klinisch geval van longkanker - - - - LungClinicalCaseReport - General - - - - NegativeResult - The presence of a negative result, i.e. normal tissue - - - - NegativeResult - Negatief resultaat - - - - NegativeResult - Negative Result - - - - NegativeResult - Risultato negativo - - - - NegativeResult - M001000 - - - - NegativeResult - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - NegativeResult - original SNOMED M00100 - - - - NoMalignancy - No Evidence of Malignancy - - - - NoMalignancy - No present of malignancy for one of the diseases included in the ExaMode ontology. - - - - NoMalignancy - Geen maligniteit - - - - NoMalignancy - Nessuna malignità - - - - NoMalignancy - No Malignancy - - - - NoMalignancy - M094500 - - - - NoMalignancy - original SNOMED M09450 - - - - PositiveOutcome - Positive Outcome, i.e., something has been found in the patient. This is the higher class for the positive outcome. - - - - PositiveOutcome - Positieve uitkomst - - - - PositiveOutcome - Positive Outcome - - - - PositiveOutcome - Risultato positivo - - - - PositiveOutcome - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - PositiveToCeliacDisease - Represents the fact that the patient is actually positive to celiac disease. We use a different entity, instead of the entity "celiac disease", because that one is a Individual in this ontology, and it is not good to have entities that are both Individuals and General Classes in the same ontology. - - - - PositiveToCeliacDisease - Positive to Celiac Disease - - - - PositiveToCeliacDisease - Positivo alla celiachia - - - - PositiveToCeliacDisease - positief voor coeliakie - - - - PositiveToCeliacDisease - positief voor coeliakie - - - - PositiveToCeliacDisease - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - PositiveToCeliacDisease - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - Procedure - Semantic class to describe the semantic area of the interventions. We defined our own class (and not used the ncit one) because we wanted to keep the two separated to not entangle too much queries and also because here we are using it with a slightly different semantic meaning. - - - - Procedure - Procedura - - - - Procedure - Procedure - - - - Procedure - procedure - - - - Procedure - Intervention - - - - SemantcArea - A general container for entities that represent semantical areas. Examples of semantical areas include "general" (common to all diseases), "Anatomic Site", "Procedure", "Diagnosis". - - - - SemantcArea - Area Semantica - - - - SemantcArea - Semantic Area - - - - SemantcArea - semantisch gebied - - - - SemantcArea - semantisk område - - - - SevereColonDysplasia - Severe Colon Dysplasia; Severe dysplasia of colon - - - - SevereColonDysplasia - Dysplasia is a term that describes how much your polyp looks like cancer under the microscope. Polyps that are more abnormal and look more like cancer are said to have high-grade (severe) dysplasia. - - - - SevereColonDysplasia - Ernstige colondysplasie - - - - SevereColonDysplasia - Grave Displasia del Colon - - - - SevereColonDysplasia - Severe Colon Dysplasia - - - - SevereColonDysplasia - alvorlig kolon dysplasi - - - - SevereColonDysplasia - http://purl.obolibrary.org/obo/MONDO_0002032 - - - - SevereColonDysplasia - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - SevereColonDysplasia - umls:C0586369 - - - - SpecimenUnsatisfactory - Campione insoddisfacente per la diagnosi - - - - SpecimenUnsatisfactory - Specimen Unsatisfactory for Diagnosis - - - - SpecimenUnsatisfactory - Specimen onbevredigend voor diagnose - - - - SpecimenUnsatisfactory - M090000 - - - - SpecimenUnsatisfactory - http://purl.obolibrary.org/obo/NCIT_C15220 - - - - SpecimenUnsatisfactory - umls:C0702119 - - - - Test - Test is a semantic area encompassing all those entities representing one test. One example are the immunistochemical tests like the immunoprecipitation. These tests may have different outcome, like being true or false, or a non-negative integer. - - - - Test - Test - - - - Test - prøve - - - - Test - test - - - - Test - test - - - - Test - Test (Semantic Area) - - - - annotatedRule - This property is used to annotated classes with a comment representing the rule that we inferred during the process of definition of this ontology. This rule may be impkemented to extract entities from a clinical case record. NB: we do not guarantee that these rules are always valid, or that they are the only valid. It may be the case that they are inaccurate since we were only able to infer them from the cases that were provided to us. Treat these annotations only as a documentation of our process and for a first implementation of the entities extractor. - - - - annotatedRule - annotated rule - - - - annotatedRule - annotatieregel - - - - annotatedRule - regel for annotering - - - - annotatedRule - regola per l'annotazione - - - - associatedKeywordInDiagnosis - property to take notes (for reminding us/ help us define rule/ maybe do some reasoning in the future) about which keywords to look for in the Diagnosis - - - - associatedKeywordInDiagnosis - associated keyword in diagnosis - - - - associatedKeywordInDiagnosis - bijbehorende trefwoorden in de diagnose - - - - associatedKeywordInDiagnosis - nøgleord, der er knyttet til diagnosen - - - - associatedKeywordInDiagnosis - parole chiave associate nella diagnosi - - - - associatedKeywordInMateriali - Connects one class (a location or a intervention) to the keyword in the field Materiali that, if found, indicates the presence of that class. - - - - associatedKeywordInMateriali - associated keyword in Materials - - - - associatedKeywordInMateriali - bijbehorende trefwoorden in het veld Materialen - - - - associatedKeywordInMateriali - parole chiave associate nel field Materiali - - - - associatedKeywordInMateriali - tilknyttede nøgleord i feltet Materialer - - - - checkOutcome - Connects one annotation to its boolean value. - - - - checkOutcome - outcome - - - - checkOutcome - presenta outcome - - - - checkOutcome - presenteert resultaten - - - - checkOutcome - udfald - - - - definition - Property representiong the definition in the ontobee website. In later versions of the ontology we prefer rdfs:comment since it is more universally used. - - - - definition - Definitie - - - - definition - Definition - - - - definition - Definition - - - - definition - Definizione - - - - detectedHumanPapillomaVirus - If this property is present, it signals the presence of a human papilloma virus in the outcome. - - - - detectedHumanPapillomaVirus - detected human papilloma virus - - - - detectedHumanPapillomaVirus - gedetecteerd humaan papillomavirus - - - - detectedHumanPapillomaVirus - identificato HPV - - - - detectedHumanPapillomaVirus - påvist human papillomavirus - - - - detectedHumanPapillomaVirus - 1 - - - - detectedHumanPapillomaVirus - 0 - - - - hasAge - Connects the Report to the age of the patient. - - - - hasAge - età - - - - hasAge - har alder - - - - hasAge - has age - - - - hasAge - heeft leeftijd - - - - hasAgeOnset - Links one record to its age group, or 'onset'. - - - - hasAgeOnset - ha gruppo d'età - - - - hasAgeOnset - har aldersgruppe - - - - hasAgeOnset - has age onset - - - - hasAgeOnset - heeft leeftijdsgroep - - - - hasBlockNumber - The block number identifies the part of the image connected to the diagnosis (for Radbound). For AOC this property is not necessary. We use it to contain the "internal id". - - - - hasBlockNumber - ha numero di blocco - - - - hasBlockNumber - has block number - - - - hasBlockNumber - heeft bloknummer - - - - hasBlockNumber - heeft bloknummer - - - - hasCeliacAnnotation - Connects a celiac clinical case to an annotation bag created to contain information about thecase. - - - - hasCeliacAnnotation - has celiac annotation - - - - hasCeliacAnnotation - heeft coeliakie-annotatie - - - - hasCeliacAnnotation - presenta annotazione riguardo malattia celiaca - - - - hasClinicalCaseReport - Coonects one patient to its clinical case report. - - - - hasClinicalCaseReport - ha Caso Clinico - - - - hasClinicalCaseReport - has Clinical Case Report - - - - hasClinicalCaseReport - heeft een klinische casus - - - - hasDiagnosisText - Connects an instance of clinical case to its diagnosis, i.e. the text written by the doctor. - - - - hasDiagnosisText - har diagnosefelt - - - - hasDiagnosisText - has textual diagnosis - - - - hasDiagnosisText - presenta campo diagnosi - - - - hasDiagnosisText - presenteert diagnoseveld - - - - hasDysplasia - This property connects an instance of outcome for a case of Colon cancer to a presence of Dysplasia (if it is present). Cardinality between 0 and 1. - - - - hasDysplasia - has dysplasia - - - - hasDysplasia - heeft dysplasie - - - - hasDysplasia - presenta displasia - - - - hasDysplasia - præsenterer dysplasi - - - - hasDysplasia - 1 - - - - hasDysplasia - 0 - - - - hasGender - To connect a record with the gender of the corresponding person. - - - - hasGender - har køn - - - - hasGender - has gender - - - - hasGender - heeft geslacht - - - - hasGender - presenta genere - - - - hasIEL - Connects an annotation about a celiac disease to the corresponding intraepithelial lympochyte amount. - - - - hasIEL - has IEL - - - - hasIEL - presenta IEL - - - - hasIEL - presenteert IEL - - - - hasIEL - præsenterer IEL - - - - hasIEL - 1 - - - - hasImage - Connects a clinical case report to the name of its corresponding image. - - - - hasImage - has image - - - - hasImage - heeft een afbeelding - - - - hasImage - huidige afbeelding - - - - hasImage - presenta immagine - - - - hasInternalIdentifier - Connects a clinical case with the its ID used inside the ExaMode project. This property was thought to connect a case to its id given by the hospitals. In this ontology we use the dc:identifier property to connect one case with an URL identifying it. - - - - hasInternalIdentifier - Has Internal Identifier - - - - hasInternalIdentifier - heeft interne ID - - - - hasInternalIdentifier - presenta identificatore interno - - - - hasIntervention - A report is associated to an intervention (or procedure) that was performed to the patient to obtain the tissue used to study the presence (or absence) of the disease. - - - - hasIntervention - Has Intervention - - - - hasIntervention - Heeft interventie - - - - hasIntervention - intervento associato - - - - hasIntervention - tilknyttet intervention - - - - hasLocation - A clinical case record has a location where it is positioned. This property connects an instance of clinical case report (of whatever type) to a location, a member of the class topology. NB: since we are connecting a report to a location, we asked ourselves if a Topography location can be considered member of itself. For now, we are saying yes, that a subclass of topography is itself a topography, and can be directly referenced by this property. - - - - hasLocation - har placering - - - - hasLocation - has location - - - - hasLocation - heeft locatie - - - - hasLocation - presenta posizione - - - - hasOntobeeAnnotation - A property to connect one entity to the annotations found for that entitiy in the corresponding page in Ontobee (http://www.ontobee.org/). - - - - hasOntobeeAnnotation - ha annotazione da Ontobee - - - - hasOntobeeAnnotation - har rekord fra ontobee - - - - hasOntobeeAnnotation - has ontobee annotation - - - - hasOntobeeAnnotation - heeft een record van Ontobee - - - - hasOutcome - Every report has an outcome, whatever it may be (positive, negative, inconclusive etc.) - - - - hasOutcome - har resultatet - - - - hasOutcome - has outcome - - - - hasOutcome - heeft uitkomst - - - - hasOutcome - presenta risultato - - - - hasSNOMEDCode - Use this property to annotate one entity with its corresponding SNOMED code. - - - - hasSNOMEDCode - ha codice SNOMED - - - - hasSNOMEDCode - har SNOMED-kode - - - - hasSNOMEDCode - has SNOMED code - - - - hasSNOMEDCode - heeft SNOMED-code - - - - hasSemanticArea - Connects one ontology class or Individual to the semantic area to which it belongs. For example, a Poly is a diagnosis, therefore the Polyp belongs to the semantic area of Diagnosis. - - - - hasSemanticArea - har semantisk område - - - - hasSemanticArea - has Semantic Area - - - - hasSemanticArea - presenta area semantica - - - - hasSemanticArea - presenteert semantisch gebied - - - - hasSlide - Connects a clinical case report to one slide. This Slide class was generated due to the way Radbound deals with its data. Each patient is associated to one block. Each block is a diagnosis, and it can be associated to one or more slides that helped the medic to reach that diagnosis. - - - - hasSlide - has slide - - - - hasSlide - heeft glijbaan - - - - hasSlide - presenta vetrino - - - - hasSlideDiagnosis - Each slide can be associated to its own diagnosis. - - - - hasSlideDiagnosis - has slide diagnosis - - - - hasSlideDiagnosis - heeft dia-geassocieerde diagnose - - - - hasSlideDiagnosis - presenta diagnosi associata al vetrino - - - - hasSlideId - Each slide is associated to its own id - - - - hasSlideId - has slide id - - - - hasSlideId - presenta id vetrino - - - - hasSlideId - presenteert dia-id - - - - hasSynonymLabel - Use this property when you want to add a synonim label, based on information contained in Ontobee. You should not use this property when you want to add synonims that are going to be used in some algorithm or methodlogy. You should use hasSynonim for that. - - - - hasSynonymLabel - ha label sinonimo - - - - hasSynonymLabel - har synonym etiket - - - - hasSynonymLabel - has synonym label - - - - hasSynonymLabel - heeft een synoniem label - - - - hasTest - connects an instance of intervention to some trait found in the patient of the class Check Lung. - - - - hasTest - har test - - - - hasTest - has test - - - - hasTest - presenta test - - - - hasTest - presenteert een test - - - - hasUMLS - This property connects an element to its UMLS code - - - - hasUMLS - ha codice UMLS - - - - hasUMLS - har UMLS-kode - - - - hasUMLS - has UMLS code - - - - hasUMLS - heeft UMLS-code - - - - hasValue - Connects a test annotation to its float value - - - - hasValue - har værdi - - - - hasValue - has value - - - - hasValue - presenta valore - - - - hasValue - presenta valore - - - - hasValue - 1 - - - - hasVillusCryptRatio - Connects one annotation about a celiac disease case to its villi to Crypt of Lieberkuhn ratio value. - - - - hasVillusCryptRatio - has villi to crypt ratio - - - - hasVillusCryptRatio - heeft een verhouding tussen villi en crypt - - - - hasVillusCryptRatio - presenta rapporto villi/cripte - - - - hasVillusCryptRatio - viser villi / krypts-forhold - - - - internalNotes - Use this property to annotate a resource with some not that may be usefult to those who will work on building the ontology. - - - - isAboutDisease - This property is used to connect an instance of a clinical case to an instance of Disease. We want to note here, since we found ourselves thinking about this, that one disease, e.g. colon cancer, is itself a subclass of Disease, but also an instance of Disease (there may be many different types of colon cancer, but also colon cancer is a disease by itself). Thus, this property has as a range the disease and you should expect, every time you have a report, to have this property pointing to one of the four instances of disease. In the future this decision may change. - - - - isAboutDisease - Connessa alla malattia - - - - isAboutDisease - gaat over ziekte - - - - isAboutDisease - handler om sygdom - - - - isAboutDisease - is about disease - - - - isAboutDisease - 1 - - - - isSpecificationOf - We may have certain hyerarchies that are not exactly in a relation of type subClassOf or partOf. These are usually determined by specification of more general concepts. We use this property to express such hyerarchies. One example (the only one for now in ExaMode) is the one of the Dysplasia. - - - - isSpecificationOf - er specifik for - - - - isSpecificationOf - is specificatie van - - - - isSpecificationOf - is specification of - - - - isSpecificationOf - è specifica di - - - - koylociteDetected - Signals the presence of Koilocytotic Squamous Cell. It needs to have as object the Koilocytotic Squamous Cell named entity - - - - koylociteDetected - Koylocite Detected - - - - koylociteDetected - Koylocite gedetecteerd - - - - koylociteDetected - Rilevati Coilociti - - - - koylociteDetected - 1 - - - - koylociteDetected - 0 - - - - presenceOf - This property is used to connect an outcome instance to a generic annotation which signals the presence of some more information correlating the clinical case and which may not be directly pertinent to the disease but however still linked to it. - - - - presenceOf - aanwezigheid van - - - - presenceOf - individuata presenza di - - - - presenceOf - presence of - - - - presenceOf - tilstedeværelse af - - - - presenceOfCeliacAbnormality - Connets a celiac clinical case to an annotation containing information about celiac abnormalities regarding that case. - - - - presenceOfCeliacAbnormality - aanwezigheid van coeliakie-anomalie - - - - presenceOfCeliacAbnormality - presence of celiac abnormality - - - - presenceOfCeliacAbnormality - presenza di anomalia celiaca - - - - presenceOfCeliacAbnormality - tilstedeværelse af cøliaki anomali - - - - presenceOfCeliacElement - This property connects a celiac disease clinical case to annotations that may or may not be found in the patient. - - - - presenceOfCeliacElement - aanwezigheid van coeliakie-element - - - - presenceOfCeliacElement - presence of celiac element - - - - presenceOfCeliacElement - presenza di elemento celiaco - - - - presenceOfCeliacElement - tilstedeværelse af cøliaki element - - - - presenceOfCeliacElement - 1 - - - - presenceOfCeliacElement - 0 - - - - taxonNotes - A field found sometimes for entities taken from Ontobee's ontologies. You can treat it as an ulterior/alternative definition. - - - - taxonNotes - Note tassonimiche - - - - taxonNotes - Structurele opmerkingen - - - - taxonNotes - taksonomiske noter - - - - taxonNotes - taxon notes - - - - testUsed - the test being used in this report - - - - testUsed - test brugt - - - - testUsed - test gebruikt - - - - testUsed - test used - - - - testUsed - test utilizzato - - - - uterusNOS - he hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. - - - - uterusNOS - Uterus - - - - uterusNOS - The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. - - - - uterusNOS - baarmoeder, niet anders gespecificeerd - - - - uterusNOS - utero, non altrimenti specificato - - - - uterusNOS - uterus, NOS - - - - uterusNOS - http://purl.obolibrary.org/obo/MONDO_0002974 - - - - uterusNOS - http://purl.obolibrary.org/obo/NCIT_C13717 - - - - uterusNOS - Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. - - - - villiStatus - connects one bag of annotations for the celiac disease to the length of the villi. - - - - villiStatus - Staat van intestinale villi - - - - villiStatus - Stato dei villi intestinali - - - - villiStatus - villi status - - - - villusCryptRatio - Lieberkuhn villi / krypts-forhold - - - - villusCryptRatio - Rapporto villi / cripte di Lieberkhun - - - - villusCryptRatio - Villi to crypt of Lieberkuhn Ratio - - - - villusCryptRatio - Villi tot crypte van Lieberkuhn Ratio - - - - villusCryptRatio - http://purl.obolibrary.org/obo/MONDO_0005130 - - - - villusCryptRatio - check the presence of keywords “Rapporto villo cripta” - - - - doid:Disease - https://www.examode.dei.unipd.it/ontology/General - - - - doid:Disease - General class representing one disease. - - - - doid:Disease - Disease - - - - doid:Disease - Malattia - - - - doid:Disease - sygdom - - - - doid:Disease - ziekte - - - - doid:Disease - General - - - - UNIPROT:O96009 - May be involved in processing of pneumocyte surfactant precursors. - - - - UNIPROT:O96009 - Napsin A - - - - UNIPROT:O96009 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:O96009 - Napsina - - - - UNIPROT:O96009 - Test - - - - UNIPROT:O96009 - umls:C1538038 - - - - UNIPROT:P07988 - Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter. - - - - UNIPROT:P07988 - Proteina associata ai tensioattivi polmonari B - - - - UNIPROT:P07988 - Pulmonale surfactant-geassocieerd proteïne B. - - - - UNIPROT:P07988 - Pulmonary surfactant-associated protein B - - - - UNIPROT:P07988 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P07988 - Test - - - - UNIPROT:P07988 - umls:C0072599 - - - - UNIPROT:P08247 - Synaptophysin - - - - UNIPROT:P08247 - Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity. - - - - UNIPROT:P08247 - Synaptofysin - - - - UNIPROT:P08247 - Synaptophysin - - - - UNIPROT:P08247 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08247 - Sinaptofisina - - - - UNIPROT:P08247 - Syph Human - - - - UNIPROT:P08247 - Test - - - - UNIPROT:P08247 - umls:C0085255 - - - - UNIPROT:P08473 - Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573). - - - - UNIPROT:P08473 - Neprilysin - - - - UNIPROT:P08473 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08473 - CD10 - - - - UNIPROT:P08473 - Neprilysin - - - - UNIPROT:P08473 - Test - - - - UNIPROT:P08473 - umls:C0025250 - - - - UNIPROT:P08575 - Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity). -(Microbial infection) Acts as a receptor for human cytomegalovirus protein UL11 and mediates binding of UL11 to T-cells, leading to reduced induction of tyrosine phosphorylation of multiple signaling proteins upon T-cell receptor stimulation and impaired T-cell proliferation. - - - - UNIPROT:P08575 - Fosfatasi tirosina-proteina tipo recettore C - - - - UNIPROT:P08575 - Receptor-type tyrosine-eiwitfosfatase C. - - - - UNIPROT:P08575 - Receptor-type tyrosine-protein phosphatase C - - - - UNIPROT:P08575 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08575 - CD45 - - - - UNIPROT:P08575 - Test - - - - UNIPROT:P08575 - umls:C0054961 - - - - UNIPROT:P08670 - Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. -Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. - - - - UNIPROT:P08670 - Vimentin - - - - UNIPROT:P08670 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08670 - Test - - - - UNIPROT:P08670 - umls:C0042666 - - - - UNIPROT:P08727 - Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle. - - - - UNIPROT:P08727 - Keratin, type I cytoskeletal 19 - - - - UNIPROT:P08727 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08727 - CK19 - - - - UNIPROT:P08727 - Test - - - - UNIPROT:P08727 - umls:C4082253 - - - - UNIPROT:P08729 - Blocks interferon-dependent interphase and stimulates DNA synthesis in cells. Involved in the translational regulation of the human papillomavirus type 16 E7 mRNA (HPV16 E7). - - - - UNIPROT:P08729 - Keratin, type II cytoskeletal 7 - - - - UNIPROT:P08729 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P08729 - CK7 - - - - UNIPROT:P08729 - Test - - - - UNIPROT:P08729 - umls:C3272783 - - - - UNIPROT:P10645 - Pancreastatin: -Strongly inhibits glucose induced insulin release from the pancreas. +For example, if the thing named by the URI http://danbri.org/ has a maker that is a Person whose name is 'Dan Brickley', we can conclude that http://danbri.org/ has a dc:creator of 'Dan Brickley'. + + + -Catestatin: -Inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist (PubMed:15326220). Displays antibacterial activity against Gram-positive bacteria S.aureus and M.luteus, and Gram-negative bacteria E.coli and P.aeruginosa (PubMed:15723172 and PubMed:24723458). Can induce mast cell migration, degranulation and production of cytokines and chemokines (PubMed:21214543). Acts as a potent scavenger of free radicals in vitro (PubMed:24723458). May play a role in the regulation of cardiac function and blood pressure (PubMed:18541522). -Serpinin: -Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. + -Miscellaneous -Binds calcium with a low-affinity. - - - - UNIPROT:P10645 - Chromogranin-A - - - - UNIPROT:P10645 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P10645 - Chromogranina - - - - UNIPROT:P10645 - Test - - - - UNIPROT:P10645 - umls:C0055633 - - - - UNIPROT:P26371 - In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. - - - - UNIPROT:P26371 - Keratin-associated protein 5-9 - - - - UNIPROT:P26371 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P26371 - CK5 - - - - UNIPROT:P26371 - Test - - - - UNIPROT:P26371 - umls:C1956465 - - - - UNIPROT:P35900 - Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine. - - - - UNIPROT:P35900 - Keratin, type I cytoskeletal 20 - - - - UNIPROT:P35900 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P35900 - CK20 - - - - UNIPROT:P35900 - Test - - - - UNIPROT:P35900 - umls:C1433368 - - - - UNIPROT:P46013 - Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). - - - - UNIPROT:P46013 - Marcatore di proliferazione della proteina Ki-67 - - - - UNIPROT:P46013 - Proliferatie marker proteïne Ki-67 - - - - UNIPROT:P46013 - Proliferation marker protein Ki-67 - - - - UNIPROT:P46013 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:P46013 - Ki-67 - - - - UNIPROT:P46013 - Test - - - - UNIPROT:P46013 - umls:C4742498 - - - - UNIPROT:Q14574 - Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms. - - - - UNIPROT:Q14574 - Desmocollin-3 - - - - UNIPROT:Q14574 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:Q14574 - Test - - - - UNIPROT:Q14574 - umls:C1448860 - - - - UNIPROT:Q15361 - Transcription termination factor 1 - - - - UNIPROT:Q15361 - Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity. - - - - UNIPROT:Q15361 - TTF1 Human - - - - UNIPROT:Q15361 - http://purl.obolibrary.org/obo/MONDO_0008903 - - - - UNIPROT:Q15361 - Transcription termination factor 1 - - - - UNIPROT:Q15361 - Test - - - - UNIPROT:Q15361 - umls:C1610981 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - xsd:string - - - - xsd:string - - - - xsd:string - - - - xsd:string - - - - xsd:nonNegativeInteger - - - - xsd:nonNegativeInteger - - - - xsd:nonNegativeInteger - - - - owl:Thing - - - - doid:Disease - - - - xsd:string - - - - xsd:string - - - - xsd:string - - - - ColonAnnotation - - - - xsd:string - - - - xsd:string - - - - https://www.examode.dei.unipd.it/ontology/AreaAnnotation - - - - xsd:string - - - - xsd:string - - - - owl:Thing - - - - xsd:string - - - - xsd:string - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - - In theory, only a Positive Outcome can have Dysplasia. - - - PositiveOutcome - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - owl:Thing - - - - - - - - - - - - - - - - - - + + + + If this property is present, it signals the presence of a human papilloma virus (HPV) in the outcome. It needs to have as object the HPV infection named entity. + detected HPV + gedetecteerd HPV + identificato HPV + + + + + + + + + + + + Signals the presence of Koilocytotic Squamous Cell. It needs to have as object the Koilocytotic Squamous Cell named entity. + detected koilocyte + gedetecteerd koylocite + rilevati coilociti + + + + + + + + + + + + + Links one record to its age group, or "onset". + ha gruppo d'età + has age onset + heeft leeftijdsgroep + + + + + + + + + + + + Connects one patient to its clinical case report. + ha caso clinico + has clinical case report + heeft een klinische casus + + + + + + + + + + + Connects an instance of Polyp of Colon to a named individual of type Dysplasia. Cardinality between 0 and 1. + has dysplasia + heeft dysplasie + presenta displasia + + + + + + + + + + + + + To connect a record with the gender of the corresponding person. + has gender + heeft geslacht + presenta genere + + + + + + + + + + + A report is associated to an intervention (or procedure) that was performed to the patient to obtain the tissue used to study the presence (or absence) of the disease. + has intervention + heeft tussenkomst + intervento associato + + + + + + + + + + + Connects an intervention (or procedure) to its type. + has intervention type + soort tussenkomst + tipo di intervento + + + + + + + + + + + Connects an instance of celiac outcome to an instance of laboratory finding or any of its subclasses. + has laboratory finding + heeft laboratorium bevindingen + presenta risultati di laboratorio + + + + + + + + + + + + + + + + + + A clinical case record has a location where it is positioned. This property connects an instance of clinical case report (of whatever type) or an Intervention to a location, a member of the class anatomical entity. + has location + heeft locatie + è localizzato in + + + + + + + + + + + + Every report has an outcome, whatever it may be (positive, negative, inconclusive etc.) + has outcome + heeft uitkomst + presenta risultato + + + + + + + + + + + Connects a clinical case report to one slide. This Slide class was generated due to the way Radbound deals with its data. Each patient is associated to one block. Each block is a diagnosis, and it can be associated to one or more slides that helped the medic to reach that diagnosis. + has slide + heeft glijbaan + presenta vetrino + + + + + + + + + + + The test performed. + has test + heeft toets + presenta test + + + + + + + + + + + Connects an inconclusive outcome to its type. + inconclusive result type + onduidelijk resultaattype + tipo di risultato inconclusivo + + + + + + + + + + + + This property is used to connect an instance of a clinical case to an instance of Disease. Thus, this property has as a range the disease and you should expect, every time you have a report, to have this property pointing to one of the four instances of disease. + connesso alla malattia + handler om sygdom + is about disease + + + + + + + + + + + + + + + + + Connects a positive outcome to its type. + positief resultaattype + positive result type + tipo di risultato positivo + + + + + + + + + + + + + + + + + + + + + + + + + This property is used to connect an outcome instance to a generic annotation which signals the presence of some more information correlating the clinical case. Such information may not be directly pertinent to the disease however it can be still linked to it. + aanwezigheid van + individuata presenza di + presence of + + + + + + + + + + + Connects one celiac outcome to the intestinal abnormality detected in the specimen. + aanwezigheid van darm afwijkingen + individuata anomalia intestinale + presence of intestinal abnormality + + + + + + + + + + + + + + + + + An unambiguous reference to the resource within a given context. + +Property connecting a case to its id. It follows dublin core specification http://www.ukoln.ac.uk/metadata/dcmi-ieee/identifiers/, that says: Recommended practice is to identify the resource by means of a string conforming to an identification system. Examples include International Standard Book Number (ISBN), Digital Object Identifier (DOI), and Uniform Resource Name (URN). Persistent identifiers should be provided as HTTP URIs. + +In this ontology it is supposed that this property connects a clinical case to a string representing an URL. + identificatore + identifier + identifier + + + + + + + + + + + + + + + + 0 + + + + 1 + + + + 2 + + + + 3a + + + + 3b + + + + 3c + + + + + + + + + + + + + + + + The severity of celiac disease according to Marsh classification. + classificazione di Marsh della malattia celiaca + gewijzigde Marsh-classificatie van histologische bevindingen bij coeliakie + modified Marsh classification of histologic findings in celiac disease + + + + + + + + + + + + + The severity of the duodenitis. + duodenitis severity + ernst van duodenitis + gravità della duodenite + + + + + + + + + + + + Connects the Report to the age of the patient. + età + has age + heeft leeftijd + + + + + + + + + + + + The block number identifies the part of the image connected to the diagnosis (for Radbound). For AOEC this property is not necessary. We use it to contain the "internal id". + ha numero di blocco + has block number + heeft bloknummer + + + + + + + + + + + Connects an instance of clinical case to its diagnosis, i.e. the text written by the doctor. + has textual diagnosis + presenta campo diagnosi + presenteert diagnoseveld + + + + + + + + + + + + Whether the specimen presents falttened villi. + has flattened villi + heeft afgeplatte villi + presenta villi appiattiti + + + villi appiattiti, appiattimento dei villi + + + + + + + + + + + + The determination of the number of the intraepithelial lymphocytes in a sample. [Definition Source: NCI] + + intra-epitheliale lymfocythoeveelheid + intraepithelial lymphocyte count + quantità di linfociti intraeppiteliali + + LIE, ILE, “linfociti intraepiteliali pari a”, “linfociti”, ”entorociti" + + + + + + + + + + + + Connects a clinical case report to the name of its corresponding image (the name of the image, e.g. the name of the file). + has image + huidige afbeelding + presenta immagine + + + + + + + + + + + Connects a clinical case with the its ID used inside the ExaMode project. This property was thought to connect a case to its id given by the hospitals. In this ontology we use the dc:identifier property to connect one case with an URL identifying it. + has Internal Identifier + heeft interne ID + presenta identificatore interno + + + + + + + + + + + Each slide can be associated to its own diagnosis. + has slide diagnosis + heeft dia-geassocieerde diagnose + presenta diagnosi associata al vetrino + + + + + + + + + + + Each slide is associated to its own id + has slide id + presenta id vetrino + presenteert dia-id + + + + + + + + + + + + Connects a immunohistochemical test to its float value + has value + presenta valore + presenta valore + + + + + + + + + + + Ratio of villous height to crypt or Lieberkuhn depth + rapporto villi / cripte di Lieberkhun + villi to crypt of Lieberkuhn ratio + villi tot crypte van Lieberkuhn ratio + + check the presence of keywords “Rapporto villo cripta” + + + + + + + + + + + aantal mitoses per crypte + number of mitosis per crypt + numero di mitosi per cripta + + numero di mitosi per cripta + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Connects one immunohistochemical test to its boolean value. + has outcome + presenta outcome + presenteert resultaten + + + + + + + + + + + + Connects one immunohistochemical test to its string result. + has test result + heeft een testresultaat + presenta risultato + + + + + + + + + + + + Whether the tissue is without villi. + absence of villi + afwezigheid van villi + assenza di villi + + priva di villi + + + + + + + + + + + + + + + focal + + + + mild + + + + mild to moderate + + + + moderate + + + + moderate-severe + + + + not specified + + + + severe + + + + total + + + + + + + + + + + + + + + + + + + + + The degree of atrophy of villi. + grado di atrofia dei villi + villi atrofie graad + villi degree of atrophy + + atrofia dei villi + + + + + + + + + + + The distance from point to point along the longest axis of the finger-like projections of the mucosal layer of the duodenum. + + duodenum villi lengte + duodenum villi length + lunghezza dei villi del duodeno + + "villi" + characterization + + + + + + + + + + + + + + + + + + + + An abstract idea or notion; a unit of thought. + + + + + + + + + + + + + + + An organization that, in the context of the ExaMode program, provides clinical case records. It is usually an Hospital (e.g. AOEC or Radbound). + + Organisatie + Organization + Organizzazione + + + + + + + + + + Instelling + Institution + Instituzione + + + + + + + + + + + colonic adenomatous polyp; adenomatous polyp of colon; colon adenomatous polyp; adenomatous polyp of the colon; Adenomatous polyp + A polypoid adenoma that arises from and protrudes into the lumen of the colon. Epithelial dysplasia is always present. According to the architectural pattern it is classified as tubular, tubulovillous, or villous. [Definition Source: NCI] + + Adenoma + Adenoma + Adenoom + + M814000 + + + + + + + + + http://linkedlifedata.com/resource/umls/id/C1515976 + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. [ Definition Source: FMA : 62955 http://orcid.org/0000-0001-9114-8737 ] + + + Anatomical Entity + Anatomische Entiteit + Entità Anatomica + + + + + + + + + A general class to represent all the kionds of annnotations that may be needed in an ExaMode report. + Annotatie + Annotation + Annotazione + + + + + + + + + + A set of checks controlled on an Immunohistochemical test that can only have a boolean result (positive - negative). + Booleaans Controle-Element + Boolean Check Element + Elemento di Controllo Booleano + + + + + + + + + + + Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573). [Definition Source: UniProt] + + Neprilysin + + CD10 + Neprilysin + + + + + + + + + + + Consisting of cell surface type I membrane Delta, Epsilon, Gamma, Zeta, and Eta protein subunits with ITAM domains and noncovalently associated with the disulfide bound heterodimeric alpha/beta and gamma/delta TCR, the CD3 complex couples receptor antigen recognition to signal transduction pathways during T-cell activation. During TCR engagement with MHC-associated antigen on host cell surfaces and synapse formation, CD3 activity leads to Tyr-phosphorylated CD3 subunits, Tyr phosphorylation of LAT colocalized in lipid rafts, and MAPK activation. CD3 signal transduction appears to involve LCK, ZAP70, Nck, SLA, SLA2, and DOCK2. CD3 subunits may also associate with the cytoskeleton. CD3 also mediates TCR signal transduction during the developmental transition through positive selection of immature thymocytes to mature CD4+ or CD8+ T cells. (NCI) [Definition Source: NCI] + + Cluster of Differentation 3 + + Presence of the word "CD3" + + + + + + + + + + + Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity). +(Microbial infection) Acts as a receptor for human cytomegalovirus protein UL11 and mediates binding of UL11 to T-cells, leading to reduced induction of tyrosine phosphorylation of multiple signaling proteins upon T-cell receptor stimulation and impaired T-cell proliferation. [Definition Source: Uniprot] + + Fosfatasi tirosina-proteina tipo recettore C + Receptor-type tyrosine-eiwitfosfatase C. + Receptor-type tyrosine-protein phosphatase C + + CD45 + + + + + + + + + + + Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle. [Definition Source: UniProt] + + Keratin, type I cytoskeletal 19 + + CK19 + + + + + + + + + + + Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine. [Definition Source: UniProt] + + Keratin, type I cytoskeletal 20 + + CK20 + + + + + + + + + + + One of the tests that can be made for the lung cancer. + Cytokeratin 34bE12 + + CK34BE12 + + + + + + + + + + Laboratory Procedure + + Cytokeratin 5/6 Expression; CK 5/6 Immunohistochemical Expression; CK 5/6 Expression; CK5/6; Cytokeratin 5/6 Immunohistochemical Expression + An immunohistochemical diagnostic test utilizing an antibody to detect both cytokeratin 5 and 6 in tissues. [Definition Source: NCIT] + + Cytokeratin 5/6 + + CK5/6 + + + + + + + + + + + In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. [Definition Source: UniProt] + + Keratin-associated protein 5-9 + + CK5 + + + + + + + + + + + Blocks interferon-dependent interphase and stimulates DNA synthesis in cells. Involved in the translational regulation of the human papillomavirus type 16 E7 mRNA (HPV16 E7). [Definition Source: UniProt] + + Keratin, type II cytoskeletal 7 + + CK7 + + + + + + + + + + + Pancreastatin: +Strongly inhibits glucose induced insulin release from the pancreas. + +Catestatin: +Inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist (PubMed:15326220). Displays antibacterial activity against Gram-positive bacteria S.aureus and M.luteus, and Gram-negative bacteria E.coli and P.aeruginosa (PubMed:15723172 and PubMed:24723458). Can induce mast cell migration, degranulation and production of cytokines and chemokines (PubMed:21214543). Acts as a potent scavenger of free radicals in vitro (PubMed:24723458). May play a role in the regulation of cardiac function and blood pressure (PubMed:18541522). + +Serpinin: +Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. + +Miscellaneous +Binds calcium with a low-affinity. +[Definition Source: UniProt] + + Chromogranin-A + + Chromogranina + + + + + + + + + + + + + Class describing biological entities related to celiac disease. + Celiac Anatomical Entity + Coeliakie Anatomische Entiteit + Entità Anatomica relativa alla Celiachia + + + + + + + + + + + + + + + + + + + + + + + + + Class representing all the celiac disease clinical cases. + Caso Clinico di Malattia Celiaca + Celiac Clinical Case Report + Klinisch Geval van Coeliakie + + + + + + + + + + + + + + + Finding in celiac outcomes. + Celiac Disease Finding + Coeliakie Vinden + Scoperta riguardo la Malattia Celiaca + + + + + + + + + + + + + + + + + + + + Class describing interventions or procedures related to celiac disease. + Celiac Disease Intervention or Procedure + Coeliakie Tussenkomst of Procedure + Intervento o Procedura relativa allla Malattia Celiaca + + + + + + + + + + Class describing the type of intervention or procedure related to celiac disease. + Celiac Disease Intervention or Procedure Type + Tipo di Intervento o Procedura relativa allla Malattia Celiaca + Type Coeliakie Tussenkomst of Procedure + + + + + + + + + + + + + + + + + + + + + + + + + Class representing all outcomes of celiac clinical case report. + Celiac Outcome + Resultaat van Coeliakie + Risultato di Malattia Celiaca + + + + + + + + + + + + + Class describing for which type of celiac disease the clinical case tested positive. + Celiac Positive Outcome Type + Tipo di Risultato Positivo alla Malattia Celiaca + Type Coeliakie Positief Resultaat + + + + + + + + + + + + + + + + + + + + Positive Outcome, i.e., something related to celiac disease has been found in the patient. + Celiac Positive Outcome + Positieve Uitkomst van Coeliakie + Risultato Positivo di Malattia Celiaca + + + + + + + + + + + + + + Class describing surgical procedures related to celiac disease. + Celiac Disease Surgical Procedure + Coeliakie Chirurgische Ingreep + Intervento Chirurgico relativo allla Malattia Celiaca + + + + + + + + + + Class describing surgical procedure type related to celiac disease. + Celiac Disease Surgery Type + Tipo di Intervento Chirurgico relativo alla Malattia Celiaca + Type Coeliakie Chirurgische Ingreep + + + + + + + + + + + + Class describing biological entities related to cervix cancer. + Baarmoederhals Anatomische Entiteit + Cervix Anatomical Entity + Entità Anatomica relativa al Tumore alla Cervice + + + + + + + + + + + + + + + + + + Class representing the clinical cases about cervix cancer. + Caso Clinico di Cancro alla Cervice + Cervix Clinical Case Report + Klinisch Geval van Baarmoederhalskanker + + + + + + + + + + + + + + + + + + Class describing interventions or procedures related to cervix cancer. + Baarmoederhalskanker Tussenkomst of Procedure + Cervix Cancer Intervention or Procedure + Intervento o Procedura relativa al Cancro alla Cervice + + + + + + + + + + Class describing the type of intervention or procedure related to cervix cancer. + Cervix Intervention or Procedure Type + Tipo di Intervento o Procedura relativa al Cancro alla Cervice + Type Baarmoederhalskanker Tussenkomst of Procedure + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + + + + 0 + + + + + + + 1 + + + + + + + 1 + + + + + + + Class representing all outcomes of cervix clinical case reports. + Cervix Outcome + Resultaat van Baarmoederhalskanker + Risultato di Cancro alla Cervice + + + + + + + + + + + + Class describing for which type of cervix cancer the clinical case tested positive. + Cervix Positive Outcome Type + Tipo di Risultato Positivo al Cancro alla Cervice + Type Baarmoederhalskanker Positief Resultaat + + + + + + + + + + + + + + + + + + + Positive Outcome, i.e., something related to cervix cancer has been found in the patient. + Cervix Positive Outcome + Positieve Uitkomst van Baarmoederhalskanker + Risulato Positivo di Cancro alla Cervice + + + + + + + + + + + + + Class describing surgical procedures related to cervix cancer. + Baarmoederhalskanker Chirurgische Ingreep + Cervix Cancer Surgical Procedure + Intervento Chirurgico relativo al Cancro alla Cervice + + + + + + + + + + + Class describing surgical procedure type related to cervix cancer. + Cervix Surgery Type + Tipo di Intervento Chirurgico relativo al Tumore alla Cervice + Type Baarmoederhalskanker Chirurgische Ingreep + + + + + + + + + + This is a set of elements containing all the possible checks that a patient may do for a generic disease. + Check Element + Controleer Element + Controllo + + + + + + + + + + + A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. [Definition Source: NCI] + + Adenocarcinoma a Cellule Chiare + Clear Cell Adenocarcinoma + Heldercellig Adenocarcinoom + + MSH: An adenocarcinoma characterized by the presence of varying combinations of clear and hobnail-shaped tumor cells. There are three predominant patterns described as tubulocystic, solid, and papillary. These tumors, usually located in the female reproductive organs, have been seen more frequently in young women since 1970 as a result of the association with intrauterine exposure to diethylstilbestrol. (From Holland et al., Cancer Medicine, 3d ed),NCI: A rare type of tumor, usually of the female genital tract, in which the insides of the cells look clear when viewed under a microscope.,NCI: A malignant neoplasm comprising glandular epithelial clear cells.,NCI: A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. + M831030 + + + + + + + + + + + + 1 + + + + This is the main class of the ontology. The Clinical Case is one record in the database, and in this version of the ontology may be of one of four diseases: celiac disease, lung cancer, cervix cancer, colon cancer. This class is sub-instantiated to the other different sub-classes + Caso clinico + Clinical Case Report + Klinisch Casusrapport + + + + + + + + + + + Class describing biological entities related to colon cancer. + Colon Anatomical Entity + Dikke Darm Anatomische Entiteit + Entità Anatomica relativa al Tumore al Colon + + + + + + + + + + + + + + + + + Class representing all colon cancer cases. + Caso Clinico di Cancro al Colon + Colon Clinical Case Report + Klinisch Geval van Darmkanker + + + + + + + + + + Disease or Syndrome + + Hyperplastic Colonic Polyp; Colon HP; Metaplastic Polyp of the Colon; Metaplastic Polyp of Colon; Metaplastic Colonic Polyp; Hyperplastic Polyp of the Colon; Metaplastic Colon Polyp; Hyperplastic Polyp of Colon; Colon Metaplastic Polyp; Colon MP; Colon Hyperplastic Polyp; Colonic Hyperplastic Polyp + A serrated polypoid lesion that arises in the colon. It is usually found in the distant colon and it rarely produces symptoms. This group includes goblet cell rich, mucin poor, and microvesicular hyperplastic polyps. [Definition Source: NCI] + + Colon Hyperplastic Polyp + Colon Hyperplastic Polyp + Polipo Iperplastico del Colon + + M720400 + + old SNOMED M72040 + + + + + + + + + + inflammatory polyp of colon; inflammatory polyp of the colon; colonic inflammatory polyp. + A non-neoplastic polypoid lesion in the colon. It may arise in a background of inflammatory bowel disease or colitis. It is characterized by the presence of a distorted epithelium, inflammation, and fibrosis. [Definition Source: NCI] + + Colon Inflammatory Polyp + Colon Ontstekingspoliep + Polipo Infiammatorio del Colon + + + + + + + + + + + + + + + + + + Class describing interventions or procedures related to colon cancer. + Colon Cancer Intervention or Procedure + Darmkanker Tussenkomst of Procedure + Intervento o Procedura relativa al Cancro al Colon + + + + + + + + + + Class describing the type of intervention or procedure related to colon cancer. + Colon Intervention or Procedure Type + Tipo di Intervento o Procedura relativa al Cancro al Colon + Type Darmkanker Tussenkomst of Procedure + + + + + + + + + + + + + + + + + + + + + + + Class representing all outcomes of colon clinical case reports. + Colon Outcome + Resultaat van Darmkanker + Risultato di Cancro al Colon + + + + + + + + + + + Class describing for which type of colon cancer the clinical case tested positive. + Colon Positive Outcome Type + Tipo di Risultato Positivo al Cancro al Colon + Type Darmkanker Positief Resultaat + + + + + + + + + + + + 0 + + + + + + + 1 + + + + + + colon polyp; polyp of the colon; colonic polyp + A polyp that involves the colon. [Definition Source: MONDO] + + Poliep van de Dikke Darm + Polipo del Colon + Polyp of Colon + + + + + + + + + + + + + + + + + + + Positive Outcome, i.e., something related to colon cancer has been found in the patient. + Colon Positive Outcome + Positieve Uitkomst van Darmkanker + Risulato Positivo di Cancro al Colon + + + + + + + + + + + + Class describing surgical procedures related to colon cancer. + Colon Cancer Surgical Procedure + Darmkanker Chirurgische Ingreep + Intervento Chirurgico relativo al Cancro al Colon + + + + + + + + + + + Class describing surgical procedure type related to colon cancer. + Colon Surgery Type + Tipo di Intervento Chirurgico relativo al Tumore al Colon + Type Darmkanker Chirurgische Ingreep + + + + + + + + + + + Colon Tubular Adenoma + A usually polypoid neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by a tubular architectural pattern. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI] + + Adenoma Tubulare del Colon + Colon Tubulair Adenoom + Colon Tubular Adenoma + + M821100 + + + + + + + + + + Gene or Genome + + Tubulovillous Adenoma of Colon; Colon Tubulovillous Adenoma; Tubulovillous Adenoma of the Colon; Colonic Tubulovillous Adenoma + A neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by tubular and villous architectural patterns. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI] + + Adenoma Tubulovilloso del Colon + Colon Tubulovillous Adenoma + Colon Tubulovillous Adenoom + + M826300 + + + + + + + + + + + villous adenoma of colon + A villous adenoma that involves the colon. [Definition Source: NCI] + + Adenoma del Colon Villoso + Colon Villous Adenoma + Colon Villous Adenoom + + M826110 + + previous SNOMED code M82611 + + + + + + + + + + Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms. [Definition Source: UniProt] + + Desmocollin-3 + + + + + + + + + + + A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [Definition Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/] + + Disease or Disorder + Malattia o Disturbo + Ziekte of Aandoening + + + + + + + + + + + + + + + duodenitis; duodenum inflammation; inflammation of duodenum + hemorragic duodenitis + A form of inflammation + Acute or chronic inflammation of the duodenum. Causes include bacterial and viral infections and gastroesophageal reflux disease. Symptoms include vomiting and abdominal pain. [Definition Source: NCI] + + Duodenite + Duodenitis + Duodenitis + + + M400000 + + + + + + + + + + + + + + + Dyscrasia; Dysplasia; Dysplastic; dyscrasia; dysplasia + A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer. + A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer. [Definition Source: NCI] + + Displasia + Dysplasia + Dysplasie + + M740000 + + original SNOMED M74000 + + + + + + + + + A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. [Definition Source: NCI] + + Finding + Scoperta + Vinden + + + + + + + + + + A set of checks that can be performed on a Immunohistochemical Test that present a float as output value. + Elemento di Controllo del Galleggiante + Float Check Element + Voltter Controle-Element + + + + + + + + + + Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.) [Definition Source: NCI] + + Gender + Genere Biologico + Geslacht + + + + + + + + + + Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization. [Definition Source: UniProt] + + HER2 (CB11) + + HER2 + + + + + + + + + + + + + + A cervix disease may present or not the human papilloma virus. + An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. + + Humaan Papillomavirus-Infectie + Human Papilloma Virus Infection + Infezione da Papillomavirus Umano + presence of code D0445** in field 'Diagnosi' + + Human papilloma Virus infection; Human papillomavirus disease or disorder; Human Papillomavirus infection; Human papillomavirus infectious disease; Human papillomavirus caused disease or disorder + D044500 + + original SNOMED D0445 + + + + + + + + + Occupational Activity + + A diagnostic test in which an antibody is used to link a cellular antigen specifically to a stain that can be seen with a microscope. [Definition Source: NCI] + + Immunohistochemical Test + Immunohistochemische Test + Test Immunoistochimico + + presence of word “CD3”/“test immunoistochimico” +/“colorazione immunoistochimica” + + + + + + + + + + + Antigen aggregation with antibody, in the right ratios, to cause precipitation. [Definition Source: NCI] + + Immunoprecipitatie + Immunoprecipitation + Immunoprecipitazione + + P382000 + + + + + + + + + + + + + + + + + + + Inconclusive Outcome. Not enough tissue or not enough evidence was present to decide for a negative or positive outcome. + Inconclusive Outcome + Onduidelijk Resultaat + Risultato Inconcludente + + + + + + + + + Class describing why the clinical case resulted inconclusive. + Inconclusive Outcome Type + Onduidelijk Resultaattype + Tipo di Risultato Inconcludente + + + + + + + + + The drug, device, therapy, or process under investigation in a clinical study that is believed to have an effect on outcomes of interest in a study (e.g., health-related quality of life, efficacy, safety, pharmacoeconomics). See also: test articles; devices; drug product; medicinal product; combination product.; In medicine, a treatment or action taken to prevent or treat disease, or improve health in other ways. + + interventionDescription; intervention; Intervention; Procedure; Intervention Strategies; Interventional; Intervention or Procedure + This general class represents the intervention performed on the patient to obtain the samples that are then studied to find the disease. In particular, this class represents the attribute 'MATERIALI' in the AOEC Database, and the attribute METHOD in the TCGA database. + + Intervention or Procedure + Intervento o Procedura + Tussenkomst of Procedure + An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. + + + + + + + + + + Class describing the type of intervention or procedure performed. + Intervention or Procedure Type + Tipo di intervento o procedura + Type Tussenkomst of Procedure + + + + + + + + + + + + Abnormality in celiac outcomes. + Anomalia relativa all'Intestino + Intestinal Abnormality + Intestinale Afwijking + + + + + + + + + + + Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). [Definition Source: UniProt] + + Marcatore di proliferazione della proteina Ki-67 + Proliferatie marker proteïne Ki-67 + Proliferation marker protein Ki-67 + + Ki-67 + + + + + + + + + + + + Koilocyte; Koilocytotic Squamous Cell + Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031] + + Cellula Squamosa Cilocitotica + Koilocytotic Squamous Cell + Koilocytotische Plaveiselcel + + + + + + + + + + + + lung large cell carcinoma; large cell lung carcinoma; large cell lung cancer; large cell undifferentiated lung carcinoma; large cell carcinoma of the lung; large cell carcinoma of lung; anaplastic lung carcinoma + LCLC + A poorly differentiated non-small cell lung carcinoma composed of large polygonal cells without evidence of glandular or squamous differentiation. There is a male predilection. [Definition Source: NCI] + + Carcinoma Polmonare a Grandi Cellule + Grootcellig Longcarcinoom + Lung Large Cell Carcinoma + + M801090 + + + + + + + + + This class is used to contain information about the celiac disease, the IEL, the villli to crypt ratio and the villi status. + Laboratorium Bevinding + Laboratory Finding + Risultati di Laboratorio + + + + + + + + + + + lung adenocarcinoma; bronchogenic lung adenocarcinoma; nonsmall cell adenocarcinoma; non-small cell lung adenocarcinoma; adenocarcinoma of the lung; adenocarcinoma of lung + A carcinoma that arises from the lung and is characterized by the presence of malignant glandular epithelial cells. There is a male predilection with a male to female ratio of 2:1. Usually lung adenocarcinoma is asymptomatic and is identified through screening studies or as an incidental radiologic finding. If clinical symptoms are present they include shortness of breath, cough, hemoptysis, chest pain, and fever. Tobacco smoke is a known risk factor. [Definition Source: NCI] + + Adenocarcinoma Polmonare + Long Adenocarcinoom + Lung Adenocarcinoma + + M814030 + + + + + + + + + + Class describing biological entities related to lung cancer. + Entità Anatomica relativa al Tumore ai Polmoni + Long Anatomische Entiteit + Lung Anatomical Entity + + + + + + + + + + + + + + + + + cancer of lung; cancer of the lung; lung cancer; lung cancer, NOS + lung carcinoma; carcinoma of lung; carcinoma of the lung + A carcinoma that arises from epithelial cells of the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165] + + Carcinoma Polmonare + Longcarcinoom + Lung Carcinoma + + M801030 + + + + + + + + + + Finding in outcomes that tested positive for Lung Carcinoma or any of its subclasses. + Longcarcinoom Vinden + Lung Carcinoma Finding + Scoperta nel Carcinoma Polmonare + + + + + + + + + + + + + + + + + Class representing all lung cancer cases. + Caso Clinico di Cancro ai Polmoni + Klinisch Geval van Longkanker + Lung Clinical Case Report + + + + + + + + + + + + + + + + Class describing interventions or procedures related to lung cancer. + Intervento o Procedura relativa al Cancro ai Polmoni + Longkanker tussenkomst of procedure + Lung Cancer Intervention or Procedure + + + + + + + + + + Class describing the type of intervention or procedure related to lung cancer. + Lung Intervention or Procedure Type + Tipo di Intervento o Procedura relativa al Cancro ai Polmoni + Type Longkanker Tussenkomst of Procedure + + + + + + + + + + + + + + + + + + + + + + Class representing all outcomes of lung clinical case reports. + Lung Outcome + Resultaat van Longkanker + Risultato di Cancro ai Polmoni + + + + + + + + + + Class describing for which type of lung cancer the clinical case tested positive. + Lung Positive Outcome Type + Tipo di Risultato Positivo al Cancro ai Polmoni + Type Longkanker Positief Resultaat + + + + + + + + + + + + + + + + + Positive Outcome, i.e., something related to lung cancer has been found in the patient. + Lung Positive Outcome + Positieve Uitkomst van Longkanker + Risulato Positivo di Cancro ai Polmoni + + + + + + + + + + + Class describing surgical procedures related to lung cancer. + Intervento Chirurgico relativo al Cancro ai Polmoni + Longkanker Chirurgische Ingreep + Lung Cancer Surgical Procedure + + + + + + + + + + + Class describing surgical procedure type related to lung cancer. + Lung Surgery Type + Tipo di Intervento Chirurgico relativo al Tumore ai Polmoni + Type Longkanker Chirurgische Ingreep + + + + + + + + + + + Malignant Lung Tumor; Malignant Lung Neoplasm; Malignant Tumor of the Lung; Malignant Neoplasm of Lung; Malignant Neoplasm of the Lung; Malignant Tumor of Lung + A primary or metastatic malignant neoplasm involving the lung. [Definition Source: NCI] + + Kwaadaardige Longneoplasma + Malignant Lung Neoplasm + Neoplasia Polmonare Maligna + + M800034 + M800130 + + + + + + + + + + + Metastatic Tumor; metastasis; Neoplasm, metastatic; Metastatic Disease; Tumor, metastatic; Metastatic; Metastatic Neoplasm; Metastasis + metastatic disease; metastatic neoplasm; metastatic tumor + A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. [Definition Source: NCI] + + Metastatic Neoplasm + Neoplasia Metastatica + Uitgezaaide Neoplasma + + M800060 + M814060 + + + + + + + + + + + May be involved in processing of pneumocyte surfactant precursors. [Definition Source: UniProt] + + Napsin A + + Napsina + + + + + + + + + + + NSCLC - non-small cell lung cancer; non-small cell lung carcinoma; non-small cell carcinoma of lung; non-small cell carcinoma of the lung; non-small cell cancer of lung; non-small cell lung cancer; non-small cell cancer of the lung; NSCLC + non-small cell lung cancer, NOS; non small cell lung cancer NOS + A group of at least three distinct histological types of lung cancer, including non-small cell squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. Non-small cell lung carcinomas have a poor response to conventional chemotherapy. [Definition Source: NCI] + + Carcinoma Polmonare Non a Piccole Cellule + Niet-Kleincellig Longcarcinoom + Non-Small Cell Lung Carcinoma + + + M807030 + + + + + + + + + + + + + + + + + + + The presence of a negative result, i.e. normal tissue + Negatief Resultaat + Negative Result + Risultato Negativo + M010100 + + + + + + + + + + + + + + + + + + + No present of malignancy for one of the diseases included in the ExaMode ontology. + Geen Maligniteit + Nessuna Malignità + No Malignancy + M094500 + + + + + + + + + + The age group in which disease manifestations appear. [Definition Source: HPO] + This class represents a generic age group. + + Gruppo d'età + Leeftijdsgroep + Onset + + + + + + + + + + This class contains information about other laboratory finding related to celiac disease, e.g. IEL or number of mitosis per crypt. + Altri Risultati di Laboratorio + Andere Laboratorium Bevindingen + Other Laboratory Finding + + + + + + + + + + Finding + A specific result or effect that can be measured. Examples of outcomes include decreased pain, reduced tumor size, and improvement of disease.; 1. events or experiences that clinicians or investigators examining the impact of an intervention or exposure measure because they believe such events or experiences may be influenced by the intervention or exposure. 2. (SDTM) The result of carrying out a mathematical or statistical procedure. NOTE: 1. such events and experiences are called clinical outcomes independently of whether they are part of the original question/protocol of the investigation. [1. Guyatt, G., Schunemann H., Dept. epidemiology & statistics, McMaster University-personal communication] See also variable; outcome can be a result of analysis; outcome is more general than endpoint in that it does not necessarily relate to a planned objective of the study.outcome. The measureable characteristic (clinical outcome assessment, biomarker) that is influenced or affected by an individual's baseline state or an intervention as in a clinical trial or other exposure. + + OUT; result; Result; Outcome; outcome + A class representing a general outcome, whatever it may be (positive, negative, uncertain, not enough information etc). + + Outcome + Resultaat + Risultato + The result of an action. + + + + + + + + + + + One of the tests that can be performed to check lung cancer. + Endonuclease P40 + + + P40 + + + + + + + + + + Amino Acid, Peptide, or Protein + Tumor protein 63 isoform 2 is the product of an alternative promoter and start codon located in exon 3 of the human TP63 gene. It also has an N-terminally truncated transactivation domain. Expression of isoform 2 may be tissue specific and aberrant expression may be associated with head and neck squamous cell carcinoma. (Atlas of Genetics and Cytogenetics in Oncology and Haematology) + + Delta Np63 Alpha; Tumor Protein 63 Isoform 2; Delta-N p63-Alpha; p51; DeltaN-Alpha; P51delNalpha; DeltaNp63 Alpha + Tumor protein 63 isoform 2 (586 aa, ; 66 kDa) is encoded by the human TP63 gene. This protein plays a role in the mediation of both transcription and skin development. [Definition Source: NCI] + + Tumor Protein 63 Isoform 2 + + P63 + + + + + + + + + + + Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter. [Definition Source: UniProt] + + Proteina associata ai tensioattivi polmonari B + Pulmonale surfactant-geassocieerd proteïne B. + Pulmonary surfactant-associated protein B + + + + + + + + + + + A person under health care. The person may be waiting for this care or may be receiving it or may have already received it. [Definition source: RxList] + http://purl.obolibrary.org/obo/NCIT_C16960 + Geduldig + Patient + Paziente + + + + + + + + + + Positive Outcome, i.e., something has been found in the patient. This is the higher class for the positive outcome. + Positieve Uitkomst + Positive Outcome + Risultato Positivo + + + + + + + + + Class describing for what the clinical case tested positive. + Positieve Uitkomst Type + Positive Outcome Type + Tipo di Risultato Positivo + + + + + + + + + + + Represents the fact that the patient is actually positive to celiac disease. We use a different entity, instead of the entity "celiac disease", because that one is an individual in the ontology, and it is not good practice to have entities that are both individuals and General Classes in the same ontology. + Positief voor Coealiakie + Positive to Celiac Disease + Positivo alla Celiachia + + + D547100 + + + + + + + + + + + oat cell carcinoma of the lung; small cell neuroendocrine carcinoma of the lung; small cell neuroendocrine carcinoma of lung; small cell lung carcinoma; small cell carcinoma of lung; oat cell carcinoma of lung; lung oat cell carcinoma; oat cell lung carcinoma; lung small cell carcinoma; small cell lung cancer; small cell carcinoma of the lung; lung small cell neuroendocrine carcinoma + small cell cancer of the lung; SCLC1 + Small cell lung cancer (SCLC) is a highly aggressive malignant neoplasm, accounting for 10-15% of lung cancer cases, characterized byrapid growth, and early metastasis. SCLC usually manifests as a large hilar mass with bulky mediastinal lymphadenopathy presenting clinically with chest pain, persistent cough, dyspnea, wheezing, hoarseness, hemoptysis, loss of appetite, weight loss, and neurological and endocrine paraneoplastic syndromes. SCLC is primarily reported in elderly people with a history of long-term tobacco exposure. [Definition Source Orphanet 70573] + + Carcinoma Polmonare a Piccole Cellule + Kleincellig Longcarcinoom + Small Cell Lung Carcinoma + + M804130 + + + + + + + + + + Synaptophysin + + Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity. [Definition Source: UniProt] + + Synaptofysin + Synaptophysin + + Sinaptofisina + Syph Human + + + + + + + + + + A general container for entities that represent semantical areas. Examples of semantical areas include "General" (common to all diseases), "Anatomic Site", "Procedure", "Diagnosis". + Area Semantica + Semantic Area + Semantisch Gebied + + + + + + + + + + + Traditional Serrated Adenoma; Serrated Adenoma; TSA; Serrated Adenoma Type II; Serrated adenoma; Traditional serrated adenoma + An adenoma that arises from the large intestine and the appendix. It is characterized by prominent serration of the glands. [Definition Source: NCI] + + Adenoma Seghettato + Gekarteld Adenoom + Serrated Adenoma + + + + + + + + + + + Slide; Slide Device Component; Slide Device; Microscope Slide + A flat rectangular piece of glass on which specimens can be mounted for microscopic study. [Definition Source:NCI] + + Schuif + Slide Device + Vetrino + + + + + + + + + + + non-small cell squamous lung cancer; non-small cell squamous lung carcinoma; squamous non-small cell lung carcinoma + A squamous cell carcinoma that arises from the lung. It is characterized by the presence of large malignant cells. It includes the clear cell and papillary variants of squamous cell carcinoma. [Definition Source: NCI] + + Carcinoma Polmonare Squamoso Non a Piccole Cellule + Niet-Kleincellig Plaveiselcelcarcinoom + Non-Small Cell Squamous Lung Carcinoma + + M807030 + + + + + + + + + + A set of checks controlled on an Immunohistochemical test that can only have a string result. + Elemento di Controllo Testuale + String Check Element + Tekenreeks Controle-Element + + + + + + + + + + Class describing the type of surgical procedure performed. + Surgical Procedure Type + Tipo di Intervento Chirurgico + Type Chirurgische Ingreep + + + + + + + + + + + A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. [Definition Source: NCI] + + Chirurgische Ingreep + Intervento Chirurgico + Surgical procedure + + + + + + + + + + + Transcription termination factor 1 + Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity. [Definition Source: UniProt] + + TTF1 Human + + Transcription termination factor 1 + + + + + + + + + Activity + + A general class representing a test. + + Test + Test + Test + A procedure for critical evaluation; a means of determining the presence, quality, or truth of something + + + + + + + + + + + Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. +Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. [Definition Source: UniProt] + + Vimentin + + + + + + + + + + + This class contains information about villi status + Risultati di Laboratorio relativi ai Vilii + Villi Laboratorium Bevinding + Villi Laboratory Finding + + + + + + + + + + + + + + + + + Radboud University Nijmegen (abbreviated as RU, Dutch: Radboud Universiteit Nijmegen, formerly Katholieke Universiteit Nijmegen) is a public university with a strong focus on research located in Nijmegen, the Netherlands. It was established on 17 October 1923 and is situated in the oldest city of the Netherlands. The RU has seven faculties and enrolls over 19,900 students. It was internationally ranked 156th by the QS World University Rankings. + Radboud Universiteit Nijmegen + Radboud Universiteit Nijmegen + Radboud University Nijmegen + + + + + + + + + + Melissa Anne Haendel + + + + + + + + + + + + FMA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,UWDA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,NCI: Epithelium composed of a single layer of cells attached to a basement membrane. + + Squamous epithelium composed of a single layer of cells. [Defintion Source: Dorlands_Medical_Dictionary:MerckSource] + Bestrating Epitheel + Epitelio della Pavimentazione + Pavement Epithelium + + + + + + + + + + + + + + Mucosa found in the gastric antrum. [Definition Source: Humpath.com - Human pathology] + Mucosa dell'Antro Pilorico + Mucosa of Pyloric Antrum + Mucosa van Pylorus Antrum + + + + + + + + + + + + + + Right upper lobar bronchus; Right upper lobe bronchus + Part of the right bronchus. + Bronco Lobare Superiore Destro + Rechter Superieure Lobaire Bronchus + Right Superior Lobar Bronchus + + + + + + + + + + + + + + Bronchus of right lower lobe; Right lower lobe bronchus; Right lower lobar bronchus. + A region of the bronchus in the lung. + Bronco Lobare Inferiore Destro + Rechter Inferieure Lobaire Bronchus + Right Inferior Lobar Bronchus + + + + + + + + + + + + + + Left upper lobar bronchus; Bronchus of left upper lobe; Left upper lobe bronchus + Part of the left bronchus. + Bronco Lobare Superiore Sinistro + Left Superior Lobar Bronchus + Linker Superieure Lobaire Bronchus + + + + + + + + + + + + + + Bronchus of left lower lobe; Left lower lobe bronchus; Left lower lobar bronchus + A region of the bronchus in the lungs. + Bronco Lobare Inferiore Sinistro + Left Inferior Lobar Bronchus + Links Inferieure Lobaire Bronchus + + + + + + + + + + + + + necrosis + cellular necrosis; necrotic cell death + metastasize; Metastasis, NOS; metastasis; Tumor Cell Migration; Metastasize; Metastasis + Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals. + Necrose + Necrosi + Necrosis + + + A type of cell death that is morphologically characterized by an increasingly translucent cytoplasm, swelling of organelles, minor ultrastructural modifications of the nucleus (specifically, dilatation of the nuclear membrane and condensation of chromatin into small, irregular, circumscribed patches) and increased cell volume (oncosis), culminating in the disruption of the plasma membrane and subsequent loss of intracellular contents. Necrotic cells do not fragment into discrete corpses as their apoptotic counterparts do. Moreover, their nuclei remain intact and can aggregate and accumulate in necrotic tissues. [Defintion Source: PMID:18846107, PMID:20823910] + + + + + + + + + + + + polyp of the cervix uteri; adenomatous polyp of the uterine cervix; uterine cervix polyp; cervical polyp; adenomatous polyp of cervix; uterine cervix adenomatous polyp; adenomatous polyp of uterine cervix; cervix uteri polyp; polyp of cervix; polyp of the uterine cervix; cervix adenomatous polyp; cervix polyp; polyp of cervix uteri; polyp of uterine cervix; cervix uteri adenomatous polyp; polyp of the cervix; adenomatous polyp of the cervix + A polyp that arises from the surface of the cervix. [Definition Source: NCI] + Cervical Polyp + Cervicale Poliep + Polipo Cervicale + + + M768002 + M768003 + + + + + + + + + + + + atrophy of vulva; atrophic vulva + atrophic vulvitis + Vaginal atrophy (atrophic vaginitis) is thinning, drying and inflammation of the vaginal walls that may occur when your body has less estrogen. Vaginal atrophy occurs most often after menopause. + +For many women, vaginal atrophy not only makes intercourse painful but also leads to distressing urinary symptoms. Because the condition causes both vaginal and urinary symptoms, doctors use the term "genitourinary syndrome of menopause (GSM)" to describe vaginal atrophy and its accompanying symptoms. + Atrofische Vulva + Atrophic Vulva + Vulva Atrofica + + + M580000 + + + + + + + + + + + + A carcinoma that arises from epithelial cells of the colon [Definition Source: https://orcid.org/0000-0002-6601-2165] + Carcinoma del Colon + Colon Carcinoma + Coloncarcinoom + + + + + + + + + + + + + + lymph gland infection + inflammation of lymph node; acute adenitis; chronic lymphadenitis; lymphadenitis; Inflammation of lymph node; acute lymphadenitis; adenitis; lymph node inflammation; chronic adenitis; lymph nodeitis + Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. [Definition Source: NCI] + Linfoadenite + Lymfadenitis + Lymphadenitis + + + M400000 + + + + + + + + + + + + cervical neoplasm; tumor of the cervix uteri; uterine cervical neoplasm + malignant tumor of uterine cervix; uterine cervix cancer; malignant neoplasm of cervix; malignant neoplasm of uterine cervix; malignant tumor of the uterine cervix; malignant tumor of cervix uteri; malignant cervical neoplasm; cervix cancer; malignant neoplasm of cervix uteri; neoplasm of uterine cervix; malignant neoplasm of the uterine cervix; malignant cervix uteri neoplasm; malignant uterine cervix neoplasm; malignant tumor of cervix; malignant cervix neoplasm; malignant tumor of the cervix uteri; malignant neoplasm of the cervix uteri; malignant cervix uteri tumor; malignant cervix tumor; malignant uterine cervix tumor; cancer of uterine cervix; cervix uteri cancer; malignant cervical tumor; malignant tumor of the cervix; malignant neoplasm of the cervix + A primary or metastatic malignant neoplasm involving the cervix. [Definition Source: NCI] + Baarmoederhalskanker + Cancro Cervicale + Cervical Cancer + + + + + + + + + + + + + + + + squamous carcinoma in situ; cervical intraepithelial neoplasia grade III with severe dysplasia; stage 0 uterine cervix carcinoma; severe dysplasia of the cervix uteri; stage 0 squamous cell carcinoma; CIN III - carcinoma in situ of cervix; squamous cell carcinoma in-situ; epidermoid cell carcinoma in situ; CIN III - severe dyskaryosis; grade III SIN; carcinoma in situ of uterine cervix; carcinoma, squamous cell, in situ, malignant; grade 3 SIN; uterine cervix in situ carcinoma; squamous intraepithelial neoplasia, grade III; carcinoma in situ of cervix; CIN III; intraepithelial squamous cell carcinoma; grade 3 squamous intraepithelial neoplasia; squamous cell carcinoma in situ; epidermoid carcinoma in situ; grade III squamous intraepithelial neoplasia; severe dysplasia of cervix; cervix Ca in situ + squamous carcinoma in situ + A malignant epithelial neoplasm confined to the squamous epithelium, without invasion of the underlying tissues. [Definition Source: NCI] + Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 3 + Neoplasia Cervicale Squamosa Intraepiteliale di Grado 3 + Squamous Carcinoma in Situ + + + M740080 + M801020 + + originally the SNOMED code was M74008* + + + + + + + + + + + coeliac disease; non tropical sprue; idiopathic steatorrhea; gluten-induced enteropathy; celiac sprue + An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. [Definition Source: NCI] + Celiac disease + Celiachia + Coeliakie + + + + + + + + + + + + + + cervix cancer; cervical cancer, NOS; cervical cancer; cancer of cervix; uterine cervix cancer + cancer of the uterine cervix; carcinoma of the cervix; carcinoma of cervix; carcinoma of the cervix uteri; carcinoma cervix uteri; cancer of uterine cervix; cervical carcinoma; carcinoma of uterine cervix; cervix carcinoma; uterine cervix carcinoma; carcinoma of cervix uteri; cancer of the cervix; cervix uteri carcinoma; carcinoma of the uterine cervix; cancer of cervix + A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are: squamous carcinoma, adenocarcinoma, adenosquamous carcinoma, adenoid cystic carcinoma and undifferentiated carcinoma. [Definition Source: NCI] + Carcinoma Cervicale + Cervicaal Carcinoom + Cervical Carcinoma + + + M801030 + + + + + + + + + + + + A cervix disease may present or not the human papilloma virus. + An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. [Definition Source: NCI] + Humaan Papillomavirus-Infectie + Human Papilloma Virus Infection + Infezione da Papillomavirus Umano + + presence of code D0445** in field 'Diagnosi' + + Human papilloma Virus infection; Human papillomavirus disease or disorder; Human Papillomavirus infection; Human papillomavirus infectious disease; Human papillomavirus caused disease or disorder + D044500 + + original SNOMED D0445 + + + + + + + + + + + + cervical intraepithelial neoplasia grade 2/3; high grade dysplasia; moderate or severe dysplasia + A neoplastic process in the cervix characterized by morphologic features of both moderate and severe intraepithelial neoplasia. [Definition Source: NCI] + Cervical Intraepithelial Neoplasia Grade 2/3 + Cervicale Intra-Epitheliale Neoplasie Graad 2/3 + Neoplasia Intraepiteliale Cervicale di Grado 2/3 + + + + + + + + + + + + + + + squamous cervical cancer; cervical squamous cell cancer; squamous cell carcinoma of cervix uteri; squamous cell carcinoma of cervix; squamous cell carcinoma of the uterine cervix; cervix uteri squamous cell carcinoma; uterine cervix squamous cell carcinoma; cervical squamous cell carcinoma; cervix squamous cell carcinoma; squamous cell carcinoma of the cervix uteri; squamous cell carcinoma of the cervix; squamous cell carcinoma of uterine cervix +has_related_synonym: cervical squamous cell carcinoma, NOS; CESC; cervical squamous cell carcinoma, not otherwise specified + A squamous cell carcinoma arising from the cervical epithelium. It usually evolves from a precancerous cervical lesion. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors for cervical squamous cell carcinoma. The following histologic patterns have been described: conventional squamous cell carcinoma, papillary squamous cell carcinoma, transitional cell carcinoma, lymphoepithelioma-like carcinoma, verrucous carcinoma, condylomatous carcinoma and spindle cell carcinoma. Survival is most closely related to the stage of disease at the time of diagnosis. [Definition Source: NCI] + Carcinoma a Cellule Squamose Cervicali + Cervicaal Plaveiselcelcarcinoom + Cervical Squamous Cell Carcinoma + + + M807030 + + previous SNOMED M80703* + + + + + + + + + + + malignant neoplasm of the lung; lung cancer; malignant lung neoplasm; cancer of lung; malignant tumor of the lung; malignant tumor of lung; malignant neoplasm of lung; malignant lung tumor. + lung neoplasm; Nonsmall cell lung cancer; alveolar cell carcinoma; lung cancer, protection against. + A malignant neoplasm involving the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165] + Cancro ai Polmoni + Longkanker + Lung cancer + + + + + + + + + + + + + + benign lymphogranulomatosis of Schaumann; lupus pernio of Besnier; miliary lupoid of boeck + besnier-Boeck-Schaumann syndrome; sarcoid; Darier-Roussy sarcoid; Boeck's sarcoid; Besnier-Boeck-Schaumann disease; Boeck's sarcoidosis; lymphogranulomatosis; sarcoidosis; Boeck sarcoid + Sarcoidosis is a multisystemic disorder of unknown cause characterized by the formation of immune granulomas in involved organs. [Definition Source: Orhpanet 797] + Sarcoidosi + Sarcoidosis + Sarcoïdose + + + D028280 + + + + + + + + + + + + cervical intraepithelial neoplasia + Intraepithelial Neoplasia of the Uterine Cervix; Intraepithelial Neoplasms, Cervical; Neoplasm, Cervical Intraepithelial; Intraepithelial Neoplasm, Cervical; Cervix Intraepithelial Neoplasia; Cervical Intraepithelial Neoplasms; Intraepithelial Neoplasia of the Cervix Uteri; Neoplasms, Cervical Intraepithelial; Intraepithelial Neoplasia of Uterine Cervix; Neoplasia, Cervical Intraepithelial; Cervical Intraepithelial Neoplasm; Intraepithelial Neoplasia, Cervical; Cervical intraepithelial neoplasia; NEOPL CERVICAL INTRAEPITHELIAL; Uterine Cervix Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix Uteri; Intraepithelial Neoplasia of the Cervix; Cervix Uteri Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix; Cervical Dysplasia; Cervical Intraepithelial Neoplasia + Squamous or glandular intraepithelial neoplasia that affects the cervical mucosal epithelium. There is no evidence of stromal invasion. According to the degree of cellular atypia and the associated architectural changes, it is classified as low or high grade. [Definition Source: NCI] + Cervical Intraepithelial Neoplasia + Cervicale intra-epitheliale neoplasie + Neoplasia Intraepiteliale Cervicale + + + + + + + + + + + + + + + + severe dysplasia of the cervix uteri aJCC v6; uterine cervix intraepithelial neoplasia grade 3 aJCC v6; intraepithelial neoplasia of the cervix grade 3 aJCC v6; carcinoma in situ of the uterine cervix aJCC v6; intraepithelial neoplasia of the cervix uteri grade 3 aJCC v6; severe dysplasia of cervix aJCC v6; severe dysplasia of cervix; intraepithelial neoplasia of uterine cervix grade 3 aJCC v6; cervical intraepithelial neoplasia grade 3 aJCC v6; uterine cervix carcinoma in situ aJCC v6; carcinoma in situ of the cervix aJCC v6; FIGO stage 0 carcinoma of uterine cervix; severe dysplasia of cervix uteri aJCC v6; cervix uteri intraepithelial neoplasia grade 3 aJCC v6; grade 3 cervical intraepithelial neoplasia aJCC v6; stage 0 uterine cervix carcinoma; carcinoma in situ of uterine cervix aJCC v6; CIN III - severe dyskaryosis; cervix uteri Severe dysplasia aJCC v6; FIGO stage 0 cervical carcinoma; cervix uteri carcinoma in situ aJCC v6; stage 0 cervical cancer aJCC v6; FIGO stage 0 carcinoma of the cervix uteri; cervical carcinoma in situ aJCC v6; uterine cervix Severe dysplasia aJCC v6; carcinoma in situ of the cervix uteri aJCC v6; severe cervical dysplasia aJCC v6; FIGO stage 0 carcinoma of cervix uteri; carcinoma in situ of cervix aJCC v6; carcinoma in situ of uterine cervix; carcinoma in situ of cervix uteri aJCC v6; cervix intraepithelial neoplasia grade 3 aJCC v6; FIGO stage 0 carcinoma of the uterine cervix; CIN III; cervical intraepithelial neoplasia grade III with severe dysplasia; cervical Severe dysplasia aJCC v6; CIN III - carcinoma in situ of cervix; FIGO stage 0 uterine cervix carcinoma; CIN 3 aJCC v6; severe dysplasia of the uterine cervix aJCC v6; carcinoma of cervix stage 0; intraepithelial neoplasia of cervix uteri grade 3 aJCC v6; squamous intraepithelial neoplasia, grade III; stage 0 cervical cancer; cervix Severe dysplasia aJCC v6; FIGO stage 0 carcinoma of the cervix; carcinoma in situ of cervix; CIN grade 3 aJCC v6; cervical cancer stage 0 aJCC v6; intraepithelial neoplasia of cervix grade 3 aJCC v6; intraepithelial neoplasia of the uterine cervix grade 3 aJCC v6; FIGO stage 0 carcinoma of cervix; cervix carcinoma in situ aJCC v6; severe dysplasia of the cervix aJCC v6; severe dysplasia of uterine cervix aJCC v6; cervix Ca in situ; FIGO stage 0 cervix carcinoma; severe dysplasia of the cervix uteri; FIGO stage 0 cervix uteri carcinoma + cervix uteri carcinoma in situ + uterine cervix carcinoma in situ + Slightly abnormal cells are found on the surface of the cervix. Cervical squamous intraepithelial neoplasia 1 is usually caused by infection with certain types of human papillomavirus (HPV) and is found when a cervical biopsy is done. Cervical squamous intraepithelial neoplasia 1 is not cancer and usually goes away on its own without treatment, but sometimes it can become cancer and spread into nearby tissue. Cervical squamous intraepithelial neoplasia 1 is sometimes called low-grade or mild dysplasia. Also called CIN 1. + Neoplasia Intraepiteliale Squamosa + Squameuze Intra-Epitheliale Neoplasie + Squamous Intraepithelial Neoplasia + + + + + + + + + + + + + intestinal synechia; intestinal adhesions + Formation of fibrous tissue in any part of the intestine as a result of repair or a reactive process. + Fibrosi Intestinale + Intestinal Fibrosis + Intestinale Fibrose + + fibrosi + + + + + + + + + + + + Inadequate absorption of nutrients in the small intestine. [Definition Source: NCI] + Malabsorptie + Malabsorption + Malassorbimento + + malassorbimento + + + + + + + + + + + + + Mainstem bronchus; Main Bronchus + The left and right main bronchi considered as a group. + Belangrijkste Bronchus + Bronco Principale + Main Bronchus + + + + + + + + + + + + + MSH: The mucous membrane lining of the uterine cavity that is hormonally responsive during the MENSTRUAL CYCLE and PREGNANCY. The endometrium undergoes cyclic changes that characterize MENSTRUATION. After successful FERTILIZATION, it serves to sustain the developing embryo.,CSP: tissue lining the uterus, it is sloughed off during the woman's menstrual period, and afterward grows back and slowly gets thicker and thicker until the next period.,NCI: The layer of tissue that lines the uterus.,NCI: The endometrium, or tunica mucosa, is the mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle.,NCI: The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thicknes + The layer of tissue that lines the uterus.; The mucous membrane comprising the inner layer of the uterine wall. + + + The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle. [Definition Source: NCI] + Baarmoederslijmvlies + Endometrio + Endometrium + + + M793100 + + + + + + + + + + + + Blood cells that are devoid of hemoglobin, capable of ameboid motion and phagocytosis, and act as the principal components of the immune system. [Definition Source: NCI] + Leucocita + Leukocyt + Leukocyte + + "leucocitario" + + + + + + + + + + + + polymorphonuclear leukocyte; granular leucocyte; granular leukocyte + A type of leukocyte with a multilobed nucleus and cytoplasmic granules. The unique morphology of the nucleus has led to their also being known as polymorphonuclear leukocytes (PMLs or PMNs). Granulocytes are subdivided according to the staining properties of their granules into eosinophils (red with acidic dye), basophils (blue with basic dye), and neutrophils (not amenable to staining with either acidic or basic dyes). [Definition Source: NCI] + Granulocita + Granulocyte + Granulocyte + + “infiltrato” + “granulociti”/“granulocitario" + + + + + + + + + + + + + + Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin. [Definition Source: NCI] + Eosinofiel + Eosinofilo + Eosinophil + + eosinofili, eosinofilo + + + + + + + + + + + + + + Granular leukocytes having a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. [Definition Source: NCI] + Neutrofiel + Neutrofilo + Neutrophil + + neutrofilo + + + + + + + + + + + + White blood cells formed in the body's lymphoid tissue. The nucleus is round or ovoid with coarse, irregularly clumped chromatin while the cytoplasm is typically pale blue with azurophilic (if any) granules. Most lymphocytes can be classified as either T or B (with subpopulations of each); those with characteristics of neither major class are called null cells. [Definition Source: NCI] + Linfocita + Lymfocyt + Lymphocyte + + “infiltrato” + “linfociti”/“linfocitario" + + + + + + + + + + + + A type of epithelial cell that lines the intestines and colon. It participates in the absorption of water and nutrients from the intestinal lumen, and in the secretion of digestive enzymes. [Definition Source: NCI] + Enterocita + Enterocyt + Enterocyte + + enterociti + + + + + + + + + + + The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). + + Mucosal; MUCOSA; Mucous Membrane; mucous membrane; Mucosa; mucosa + The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). [Definition Source: NCI] + Mucosa + Mucosa + Slijmvlies + + + + + + + + + + + + Pathologic Function + + A rare hyperplastic lesion of Brunner's gland in the duodenum. Although it is usually asymptomatic and discovered incidentally during upper gastrointestinal endoscopy, it may cause hemorrhage. [Definition Source: NCI] + Brunner's Gland Hyperplasia + Hyperplasie van de Klier van Brunner + Iperplasia della Ghiandola di Brunner + + “Brunner” + “iperplasia” + “ghiandole” + Usually hyperplasia of Brunner’s glands. NB: the mere Presence of Brunner’s glands is not automatically an hyperplasia. Rather, hyperplasia Is something the glands may have or not. If they have it, it may be a problem + + + + + + + + + + + Location; Anatomic Site + Anatomical Location + Anatomische Locatie + Posizione Anatomica + Named locations of or within the body. [Definition Source: NCI] + + + + + + + + + + The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation. [Definition Source: NCI] + Diagnose + Diagnosi + Diagnosis + + + + + + + + + + Surgery to remove the uterus and, sometimes, the cervix. When the uterus and the cervix are removed, it is called a total hysterectomy. When only the uterus is removed, it is called a partial hysterectomy. + + A surgical procedure to remove the uterine body (partial hysterectomy) or the uterine body and cervix (total hysterectomy). [Definition Source: NCI] + Hysterectomie + Hysterectomy + Isterectomia + + + + + + + + + + + + + Diagnostic Procedure + + Endoscopy and Biopsy; Endoscopic Biopsy + The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. In the case of an endoscopic biopsy, an endoscope is used to obtain the sample. [Definition Source: NCI] + Biopsia Endoscopica + Endoscopic Biopsy + Endoscopische Biopsie + + + P410000 + + previous SNOMED P41 + + + + + + + + + + + cone biopsy; LEEP + Bx; BIOPSY; biopsy; Biopsy + Surgical removal of a cone-shaped portion of tissue from the uterine cervix. [Definition Source: NCI] + Conization + Conization + Conizzazione + + + + + + + + + + + + Diagnostic Procedure + A procedure in which the mucous membrane of the cervical canal is scraped using a spoon-shaped instrument called a curette. + + A procedure in which the mucous membrane of the cervical canal is scraped using a curette. [Definition Source: NCI] + Curettage Endocervicale + Endocervical Curettage + Endocervicale Curettage + + + + + + + + + + + + Finding + + A subjective characterization of the phenomenon of dysplasia, based on microscopic examination of the architectural and/or cytological changes in a tissue sample, that is determined to be high. [Definition Source: NCI] + Displasia di Alto Grado + High Grade Dysplasia + Hoogwaardige Dysplasie + + + + + + + + + + + + Therapeutic or Preventive Procedure + A procedure to connect healthy sections of tubular structures in the body after the diseased portion has been surgically removed.; A natural or surgically-induced connection between tubular structures in the body. + + A natural or surgically-induced connection between tubular structures in the body. [Definition Source: NCI] + Anastomose + Anastomosi + Anastomosis + + M182000 + + previous snomed was M18200 + + + + + + + + + + + Removal Technique; Resection; Surgical Resection + A surgical procedure in which tissue is removed from the body. [Definition Source: NCI] + Resectie + Resection + Resezione + + P110000 + + previous SNOMED was P11000 + + + + + + + + + + + + + An adenocarcinoma that arises from the colon and has metastasized to another anatomic site. [Definition Source: NCI] + Adenocarcinoma Metastatico del Colon + Gemetastaseerd Colon Adenocarcinoom + Metastatic Colon Adenocarcinoma + + + + + + + + + + + + + Female Gender, Self Reported; Female Gender, Self Report; Female; Female Gender + A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. [Definition Source: NCI] + Female Gender + Genere Femminile + Vrouwlijk Geslacht + + + + + + + + + + + + + An inflammatory process characterized by the presence of lymphocytes and plasma cells and the absence of polymorphonuclear neutrophils. [Definition Source: NCI] + Chronic Inflammation + Chronische Ontsteking + Infiammazione Cronica + + flogosi cronica, flogosi cronica non attiva + + + + + + + + + + + + The spread of cancer from one part of the body to another. A tumor formed by cells that have spread is called a "metastatic tumor" or a "metastasis." The metastatic tumor contains cells that are like those in the original (primary) tumor. [Definition Source: NCI] + Metastase + Metastasi + Metastasis + + + + + + + + + + + + Qualitative Concept + + Male Gender, Self Report; Male; Male Gender; Male Gender, Self Reported + A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. [Definition Source: NCI] + Genere Maschile + Male Gender + Mannelijk Geslacht + + + + + + + + + + + + + Polypectomy + Complete or partial removal of a polypoid lesion from the mucosal surface. [Definition Source: NCI] + Polipectomia + Polypectomie + Polypectomy + Presence of jeyword "polipectomia" in "Materiali" + + + Complete or partial removal of a polypoid lesion from the mucosal surface. + + + + + + + + + + Disease or Syndrome + + + Cervicitis + An acute or chronic inflammatory process that affects the cervix. Causes include sexually transmitted diseases and bacterial infections. Clinical manifestations include abnormal vaginal bleeding and vaginal discharge. [Definition Source: NCI] + Cervicite + Cervicitis + Cervicitis + + M400000 + M430000 + + Previously, this class presented SNOMED coded M40000 and M30000* + + + + + + + + + + + Lymphadenitis; colitis; colon inflammation; inflammation of colon + Inflammation of the colon. [Defintion Source: NCI] + Colite + Colitis + Colitis + + M400000 + M400700 + + previously it had snomed codes M40000 and M40070 + + + + + + + + + + + + Chronic inflammation of the cervix. [Definition Source: NCI] + Cervicite Cronica + Chronic Cervicitis + Chronische Cervicitis + + + + + + + + + + + + + A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma. [Definition Source: NCI] + Adenocarcinoma + Adenocarcinoma + adenocarcinoom + + + + + + + + + + + A raised growth on the surface of the genitals caused by human papillomavirus (HPV) infection. The HPV in genital warts is very contagious and can be spread by skin-to-skin contact, usually during oral, anal, or genital sex with an infected partner.; A wart of the perianal region or genitalia that is caused by sexual transmission of the human papillomavirus. + + genital wart; condyloma; Genital Warts; Condyloma Acuminatum; Condyloma Acuminata; Genital Wart; Condyloma; Venereal Wart + A sexually transmitted papillary growth caused by the human papillomavirus. It usually arises in the skin and mucous membranes of the perianal region and external genitalia. [Definition Source: NCI] + Condiloma + Condyloma + Condyloma + + M767000 + + previous SNOMED was M76700 + + + + + + + + + + + A gastrointestinal disorder characterized by chronic inflammation involving all layers of the intestinal wall, noncaseating granulomas affecting the intestinal wall and regional lymph nodes, and transmural fibrosis. Crohn disease most commonly involves the terminal ileum; the colon is the second most common site of involvement. [Definition Source: NCI] + Crohn Disease + Morbo di Crohn + Ziekte van Crohn + + Crohn + + + + + + + + + + + + Accumulation of an excessive amount of fluid in cells or intercellular tissues. [Definition Source: NCI] + Edema + Edema + Oedeem + + Edema + + + + + + + + + + + + An inflammation AE that shows localized nodular inflammation found in tissues. + Granuloma + Granuloma + Granuloom + + + + M440000 + + old SNOMED M44000 + + + + + + + + + + + A finding of a localized protective response resulting from injury or destruction of tissues. Inflammation serves to destroy, dilute, or wall off both the injurious agent and the injured tissue. In the acute phase, inflammation is characterized by the signs of pain, heat, redness, swelling, and loss of function. Histologically, inflammation involves a complex series of events, including dilatation of arterioles, capillaries, and venules, with increased permeability and blood flow; exudation of fluids, including plasma proteins; and leukocyte migration into the site of inflammation. [Definition Source: NCI] + Infiammazione + Inflammation + Ontsteking + + flogosi + + + + + + + + + + + Conversion of a mature, normal cell or groups of mature cells to other forms of mature cells.; A change of cells to a form that does not normally occur in the tissue in which it is found. + + Metaplasia; METAPLASIA; Metaplastic Change; metaplasia + Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy. [Definition Source: NCI] + Metaplasia + Metaplasia + Metaplasie + + MSH: A condition in which there is a change of one adult cell type to another similar adult cell type.,CSP: transformation of a normal to a similar but abnormal mature cell type.,NCI: A change of cells to a form that does not normally occur in the tissue in which it is found.,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,NCI: Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy. + M730000 + + + + + + + + + + + + + A morphologic finding indicating the transformation of glandular or transitional epithelial cells to, usually, mature squamous epithelial cells. Representative examples include squamous metaplasia of bronchial epithelium, cervix, urinary bladder, and prostate gland. [Definition Source: NCI] + Metaplasia Squamosa + Plaveiselcelmetaplasie + Squamous Metaplasia + + M732200 + + + + + + + + + + + + + cassock + The connective tissue coat of a mucous membrane including the epithelium and basement membrane. [Definition Source: NCI] + Lamina Propria + Lamina Propria + Lamina Propria + + A type of connective tissue found under the thin layer of tissues covering a mucous membrane.,NCI: The connective tissue coat of a mucous membrane including the epithelium and basement membrane. [Definition Source: NCI] + + + + + + + + + + + + + MAIN BRONCHUS, LEFT; Left Main Bronchus + One of the two main bronchi. It is narrower but longer than the right main bronchus and connects to the left lung. [Definition Source: NCI] + Bronco Principale Sinistro + Left Main Bronchus + Linker Hoofdbronchus + + + + + + + + + + + + + + Lobar Bronchus; Secondary Bronchus + A part the bronchial tree, arising from the primary bronchi, with each one serving as the airway to a specific lobe of the lung. [Definition Source: NCI] + Bronco Lobare + Lobaire Bronchus + Lobar Bronchus + + + + + + + + + + + + + + Right Main Bronchus; MAIN BRONCHUS, RIGHT + One of the two main bronchi. It is wider but shorter than the left main bronchus and connects to the right lung. [Definition Source: NCI] + Bronco Principale Destro + Rechter Hoofdbronchus + Right Main Bronchus + + + + + + + + + + + + + + Simple Epithelium + Unilaminar epithelium + Epithelium composed of a single layer of cells attached to a basement membrane. [Definition Source: NCI] + Eenlagig Epitheel + Epitelio Semplice + Simple Epithelium + + + + + + + + + + + + + A circumscribed loss of integrity of the skin or mucous membrane.; Destruction of an epithelial surface extending into or beyond the basement membrane. + + Ulcerative Inflammation; Ulcer; Ulceration; Ulcers; Ulcerated; ulcer; ULCER; Ulcerative + A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. [Definition Source: NCI] + Ulcer + Ulcera + Zweer + + + ulcerativa, ulcerata + 400300 + + previous SNOMED was M40030 + + + + + + + + + + + Diffuse hypertrophy of the stratum spinosum layer of the epidermis. [Definition Source: NCI] + Acanthosis + Acanthosis + Acantosi + + G000900 + M727100 + + previous SNOMED G0009 + + + + + + + + + + Thickening of the outermost layer of stratified squamous epithelium.; A condition marked by thickening of the outer layer of the skin, which is made of keratin (a tough, protective protein). It can result from normal use (corns, calluses), chronic inflammation (eczema), or genetic disorders (X-linked ichthyosis, ichthyosis vulgaris). + + Hypertrophy of the outermost layer of the epidermis. It may be caused by physical or chemical irritants, irradiation, infection, or neoplastic processes. [Definition Source: NCI] + Hyperkeratose + Hyperkeratosis + Ipercheratosi + + + + + + + + + + + + + Koilocyte; Koilocytotic Squamous Cell + Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031] + Cellula Squamosa Cilocitotica + Koilocytotic Squamous Cell + Koilocytotische Plaveiselcel + + + + + + + + + + + + + + Mild Squamous Dysplasia of the Cervix; Low Grade Cervical Squamous Intraepithelial Neoplasia; Low-Grade Cervical SIL; Low-Grade Cervical Squamous Intraepithelial Lesion; Low Grade Cervical Squamous Intraepithelial Lesion; Low-Grade CIN; Cervical Squamous Intraepithelial Neoplasia 1; Low Grade Cervical Squamous Intraepithelial Neoplasia; LSIL; low grade dysplasia; mild dysplasia + A precancerous neoplastic process that affects the cervical squamous epithelium without evidence of invasion. It is usually associated with human papillomavirus infection. It is characterized by the presence of mild atypia in the superficial epithelial layer that may be associated with koilocytosis. Maturation is present in the upper two thirds of the epithelium. Mitotic figures are not numerous and are present in the basal third of the epithelium. [Definition Source: NCI] + Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 1 + Low Grade Cervical Squamous Intraepithelial Neoplasia + Neoplasia Cervicale Squamosa Intraepiteliale di Grado 1 + + M740060 + + old SNOMED M74006* + + + + + + + + + + + + CIN 2; Cervical Squamous Intraepithelial Neoplasia 2; Moderate Squamous Dysplasia of the Cervix; cervical squamous intraepithelial neoplasia 2 + Cervical squamous intraepithelial neoplasia characterized by the presence of maturation in the upper half of the squamous epithelium and conspicuous nuclear atypia which is present in all epithelial layers. Mitotic figures are present in the basal two thirds of the epithelium. [Definition Source: NCI] + Cervical Squamous Intraepithelial Neoplasia 2 + Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 2 + Neoplasia Cervicale Squamosa Intraepiteliale di Grado 2 + + M740070 + + original SNOMED M74007* + + + + + + + + + + + + adenocarcinoma of the uterine cervix; uterine cervix adenocarcinoma; adenocarcinoma of cervix; adenocarcinoma of cervix uteri; adenocarcinoma - cervix; cervix adenocarcinoma; adenocarcinoma of the cervix; adenocarcinoma of the cervix uteri; adenocarcinoma cervix uteri; adenocarcinoma of uterine cervix; cervix uteri adenocarcinoma; cervical adenocarcinoma + cervical adenocarcinoma, NOS; cervical adenocarcinoma, not otherwise specified + An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type. [Definition Source: NCI] + Adenocarcinoma Cervicale + Cervicaal Adenocarcinoom + Cervical Adenocarcinoma + + + + + + + + + + + + + + + Metastatic Adenocarcinoma + An adenocarcinoma which has spread from its original site of growth to another anatomic site. [Definition Source: NCI] + Adenocarcinoma Metastatico + Gemetastaseerd Adenocarcinoom + Metastatic Adenocarcinoma + + M80106 + M814060 + + old SNOMED M81406 + + + + + + + + + + + A benign, slow-growing tumor arising from the soft tissues usually in the mid-thoracic region of the elderly. It is characterized by the presence of paucicellular collagenous tissue, adipocytes and a predominance of large coarse elastic fibers arranged in globules. [Definition Source: NCI] + Elastofibroma + Elastofibroma + Elastofibroma + + + + + + + + + + + + + + colonic adenocarcinoma; adenocarcinoma of the colon; colon adenocarcinoma; adenocarcinoma of colon; adenocarcinoma - colon + COAD + An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well, moderately, and poorly differentiated. Histologic variants include mucinous adenocarcinoma, signet ring cell carcinoma, medullary carcinoma, serrated adenocarcinoma, cribriform comedo-type adenocarcinoma, and micropapillary adenocarcinoma. [Definition Source: NCI] + Adenocarcinoma del Colon + Colon Adenocarcinoma + Colon Adenocarcinoom + + M80102 + M814030 + + + + + + + + + + + + Neoplastic Process + + Uterine Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of the Uterine Cervix; Cervix Uteri Adenocarcinoma in situ; Adenocarcinoma in situ of Uterine Cervix; Cervical Adenocarcinoma In Situ AJCC v7; Adenocarcinoma in situ of the Cervix; Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of Cervix Uteri; Adenocarcinoma in situ of Cervix; Adenocarcinoma in situ of the Cervix Uteri; Cervical Adenocarcinoma In Situ + Adenocarcinoma in situ (AIS) represents a pre-cancerous condition that can progress to cervical adenocarcinoma. Cervical adenocarcinoma in situ occurs in the glandular tissue of the cervix and is the condition which leads to invasive adenocarcinoma. [Definition Source: NCI] + Adenocarcinoma Cervicale in Situ + Cervicaal Adenocarcinoom in Situ + Cervical Adenocarcinoma in Situ + + tage 0 includes: (Tis, N0, M0). Tis: Carcinoma in situ. N0: No regional lymph node metastasis. M0: No distant metastasis. FIGO no longer includes stage 0. + + + + + + + + + + + Finding + + Dysplasia of the Colon; Colonic Dysplasia; Dysplasia of Colon; Colon Dysplasia + A morphologic finding indicating the presence of dysplastic glandular epithelial cells in the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI] + Colon Dysplasia + Colon Dysplasie + Displasia del Colon + + + + + + + + + + + + + + + Low Grade Dysplasia of the Colon; Low-Grade Dysplasia of Colon; Low-Grade Dysplasia of the Colon; Mild Dysplasia of Colon; Low-Grade Colon Dysplasia; Mild Colon Dysplasia; Low-Grade Colonic Dysplasia; Mild Colonic Dysplasia; Mild Dysplasia of the Colon; Low Grade Colon Dysplasia; Low Grade Colonic Dysplasia; Low Grade Dysplasia of Colon + A morphologic finding indicating the presence of mild dysplastic cellular changes and mild architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI] + Displasia del Colon Lieve + Mild Colon Dysplasia + Milde Colondysplasie + + + + + + + + + + + + + + Finding + + Moderate Dysplasia of the Colon; Moderate Colonic Dysplasia; Moderate Colon Dysplasia; Moderate Dysplasia of Colon + A morphologic finding indicating the presence of moderate dysplastic cellular changes and moderate architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI] + Displasia Moderata del colon + Matige Colondysplasie + Moderate Colon Dysplasia + + + + + + + + + + + + + An eating away or breakdown of any type of external or internal human tissue including but not limited to skin, teeth, mucosa, or somatic, which involves only the outer tissue layer. When tissue surrounds an implanted device, the tissue breakdown may result in migration and loss of the implant material and may result in further complications such as infection or abscess. [Definition Source: NCI] + Erosie + Erosion + Erosione + + erosioni, erosivo, erosiva + + + + + + + + + + + + hyperaemia; hyperemic + The presence of an increased amount of blood in a part or organ; engorgement. [Definition Source: NCI] + Hyperemia + Hyperemie + Iperemia + + iperemia + + + + + + + + + + + + + Removal of tissue from the small intestine for microscopic examination, using an endoscope. [Definition Source: NCI] + Biopsia dell'Intestino Tenue + Biopsie van de Dunne Darm + Biopsy of Small Intestine + + + + + + + + + + + + Diagnostic Procedure + + Biopsy (cervical); Other method, specify: ECC + Removal of tissue from the cervix for microscopic examination. [Definition Source: NCI] + Biopsia Cervicale + Cervical Biopsy + Cervicale Biopsie + + + + + + + + + + + + + + Colonoscopic Biopsy; Colonoscopy and Biopsy; Biopsy of Colon + Removal of tissue from the colon for microscopic examination, using an endoscope. [Definition Source: NCI] + Biopsia del Colon + Biopsie van de Dikke Darm + Biopsy of Colon + + P114000 + P400000 + + previous SNOMED was P11400, P40 + + + + + + + + + + + Diagnostic Procedure + + Endoscopic Biopsy of Duodenum; Duodenal Biopsy; Biopsy of Duodenum + Removal of tissue from the duodenum for microscopic examination, using an endoscope. [Definition Source: NCI] + Biopsia del Duodeno + Biopsie van de Twaalfvingerige Darm + Biopsy of Duodenum + + Biopsia duodeno + + + + + + + + + + + + + + + Colonoscopic Polypectomy; Colonic Polypectomy + Complete or partial removal of a polypoid lesion from the mucosal surface of the large intestine. [Definition Source: NCI] + Colonoscopic Polypectomy + Colonoscopische Polypectomie + Polipectomia Colonscopica + + + + + + + + + + + + + Therapeutic or Preventive Procedure + + Surgical removal of all of the uterus, via an abdominal approach. [Definition Source: NCI] + Isterectomia Addominale Totale + Total Abdominal Hysterectomy + Totale Abdominale Hysterectomie + Other method, specify: total Abdominal Hysterectomy + + + + + + + + + + + + Diagnostic Procedure + Removal of tissue from the lung, for microscopic examination. + + The removal of a small piece of lung tissue to be checked by a pathologist for cancer or other diseases. The tissue may be removed using a bronchoscope (a thin, lighted, tube-like instrument that is inserted through the trachea and into the lung). It may also be removed using a fine needle inserted through the chest wall, by surgery guided by a video camera inserted through the chest wall, or by an open biopsy. In an open biopsy, a doctor makes an incision between the ribs, removes a sample of lung tissue, and closes the wound with stitches. [Definition Source: NCI] + Biopsia Polmonare + Long Biopsie + Lung Biopsy + + + + + + + + + + + + + Uses a thin, low-voltage electrified wire loop to cut out a thin layer of abnormal tissue; generally used to remove abnormal cells on the surface of the cervix. [Definition Source: NCI] + Cervicale Sprong + Leep Cervicale + Loop Electrosurgical Excision + + + + + + + + + + + + Diagnostic Procedure + + Bronchial Biopsy; Biopsy of Bronchus + Removal of tissue from the bronchus for microscopic examination. [Definition Source: NCI] + Biopsia Bronchiale + Bronchial Biopsy + Bronchiale Biopsie + + Removal of tissue from the bronchus for microscopic examination. + + + + + + + + + + + + + Removal of tissue from the jujunum for microscopic examination, using an endoscope. [Definition Source: NCI] + Biopsia del Digiuno + Biopsie van Jejunum + Biopsy of Jejunum + + + + + + + + + + + + + Dyskeratosis is abnormal keratinization occurring prematurely within individual cells or groups of cells below the stratum granulosum.[Defintion Source: ISBN 0-7216-0187-1] + +Dyskeratosis congenita is congenital disease characterized by reticular skin pigmentation, nail degeneration, and leukoplakia on the mucous membranes associated with short telomeres. [Defintion Source: PMID 22285015] + Discheratosi + Dyskeratose + Dyskeratosis + + M740100 + + + + + + + + + + + + Gastric heterotopia (GH) is a rare, congenital condition where gastric tissue is found outside of its normal location in the gastric mucosa. It is usually benign and can be found throughout the gastrointestinal (GI) tract. In the duodenum, it is usually seen as multiple polyps, specifically in the duodenal bulb. [Definition Source: PMID 35607542] + Eterotopia Gastrica + Gastric Heterotopia of the Small Intestine + Maag Heterotopie van de Dunne Darm + + eterotopia + + + + + + + + + + + + + The coexistence of a chronic inflammatory process with a superimposed polymorphonuclear neutrophilic infiltration. [Definition Source: NCI] + Chronic Active Inflammation + Chronische Actieve Ontsteking + Infiammazione Cronica Attiva + + flogosi cronica attiva + + + + + + + + + + + + An inflammatory process characterized by the localized collection of polymorphonuclear neutrophils. [Definition Source: NCI] + Focal Acute Inflammation + Focale Acute Ontsteking + Infiammazione Acuta Focale + + M410000 + + old SNOMED M41000 + + + + + + + + + + + A finding indicating the presence of increased blood volume in the vascular lumen. [Definition Source: NCI] + Congestione + Tissue Congestion + Weefsel Congestie + + congestione + + + + + + + + + + + + A morphologic finding indicating the replacement of epithelial tissue outside the intestines by intestinal-type epithelium. [Definition Source: NCI] + Intestinal Metaplasia + Intestinale Metaplasie + Metaplasia Intestinale + + metaplasia intestinale + + + + + + + + + + + + Precancerous change of the mucosa of the stomach with intestinal epithelium, and is associated with an increased risk of dysplasia and cancer. [Definition Source: PMID 29606921] + Gastric Metaplasia + Maagmetaplasie + Metaplasia Gastrica + + metaplasia gastrica + + + + + + + + + + + + CIN 1; DYSPLASIA, MILD; MILD DYSPLASIA, CIN 1 + A morphologic finding indicating the presence of mild cellular atypia associated with mild architectural changes in a tissue sample. [Definition Source: NCI] + Displasia Lieve + Mild Dysplasia + Milde Dysplasie + + M740060 + + original SNOMED M74006 + + + + + + + + + + + + Moderate Dysplasia; CIN 2; DYSPLASIA, MODERATE; MODERATE DYSPLASIA, CIN 2 + A morphologic finding indicating the presence of moderate cellular atypia associated with moderate architectural changes in a tissue sample. [Definition Source: NCI] + Displasia Moderata + Matige Dysplasie + Moderate Dysplasia + + M740070 + + + + + + + + + + + + Finding + + Severe Dysplasia; CIN 3; DYSPLASIA, SEVERE; SEVERE DYSPLASIA, CIN 3 + A morphologic finding indicating the presence of severe cellular atypia associated with severe architectural changes in a tissue sample. [Definition Source: NCI] + Displasia Grave + Ernstige Dysplasie + Severe Dysplasia + + + + + + + + + + + + + Hemicolectomy + Surgical removal of approximately half of the colon. [Definition Source: NCI] + Emicolectomia + Hemicolectomie + Hemicolectomy + + P111500 + + old SNOMED P11150 + + + + + + + + + + + + Radical hysterectomy refers to the excision of the uterus en bloc with the parametrium (ie, round, broad, cardinal, and uterosacral ligaments) and the upper one-third to one-half of the vagina. The surgeon usually also performs a bilateral pelvic lymph node dissection. The procedure requires a thorough knowledge of pelvic anatomy, meticulous attention to sharp dissection, and careful technique to allow dissection of the ureters and mobilization of both bladder and rectum from the vagina. Particular care must be taken with the vasculature of the pelvic side walls and the venous plexuses at the lateral corners of the bladder to avoid excessive blood loss. Removal of the ovaries and fallopian tubes is not part of a radical hysterectomy; they may be preserved if clinically appropriate. + Isterectomia Radicale + Radical Hysterectomy + Radicale Hysterectomie + + + + + + + + + + + + + + cervix mucus + A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation [WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. + Baarmoederhalsslijm + Cervical Mucus + Muco Cervicale + + + + + + + + + + + + + + doudenal mucosa; mucosa of duodenum; mucous membrane of duodenum; duodenal mucous membrane + duodenum mucosa + The inner lining of the duodenum. [Definition Source: NCI] + Duodenal Mucosa + Mucosa Duodenale + Slijmvlies van de Twaalfvingerige Darm + + + mucosa duodenale + + + + + + + + + + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + + abdominopelvis; abdominopelvic region + belly; celiac region; adult abdomen + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. [Definition Source: http://orcid.org/0000-0002-6601-2165] + Abdomen + Addome + Buik + + + TY4100 + + original SNOMED TY4100 + + + + + + + + + + A thin layer of tissue that covers the lungs and lines the interior wall of the chest cavity. It protects and cushions the lungs. This tissue secretes a small amount of fluid that acts as a lubricant, allowing the lungs to move smoothly in the chest cavity while breathing.; The serous membrane that lines the wall of the thoracic cavity and the surface of the lungs. [Definition Source: NCI] + + The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). + Borstvlies + Pleura + Pleura + + + T29000 + + + + + + + + + + + he hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. + + Uterus + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. + Baarmoeder, Niet Anders Gespecificeerd + Utero, Non Altrimenti Specificato + Uterus, NOS + + + + Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. + + + + + + + + + + + + terminal portion of intestine + terminal portion of large intestine; rectal sac; intestinum rectum + Rectum, Not Otherwise Specified (NOS) + Rectum, NOS + Rectum, Niet Anders Gespecificeerd + Retto, Non Altrimenti Specificato + + Presence of keyword "Rectum NOS" in "Materiali" field in AOEC Database. + + The terminal portion of the intestinal tube, terminating with the anus. [Definition Source: NCI] + T680000 + + original SNOMED T68000 + + + + + + + + + + + + caecum; cecum; intestinum crassum caecum + intestinum crassum cecum; intestinum caecum; blindgut; blind intestine + A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. + Blinde Darm + Caecum + Cieco + + Keyword Caecum in "Materiali" field + + T671000 + + original SNOMED T67100 + + + + + + + + + + + + large bowel + hindgut + Colon, Not Otherwise Specified (NOS) + Colon, NOS + Colon, Non Altrimenti Specificato + Dikke Darm, Niet Anders Gespecificeerd + + + Last portion of the large intestine before it becomes the rectum. + T670000 + + original SNOMED T67000 + + + + + + + + + + + + + colon ascendens + spiral colon + Section of colon which is distal to the cecum and proximal to the transversecolon. + Ascending Colon + Colon Ascendente + Oplopende Dubbele Punt + + + T672000 + + original SNOMED T67200 + + + + + + + + + + + + colon transversum + The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon. + Colon Trasverso + Dwars Dubbele Punt + Transverse Colon + + Keyword "trasverso" in "Materiali" field. + + T674000 + + original SNOMED T67400 + + + + + + + + + + + + colon descendens + The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. + Aflopende Dubbele Punt + Colon Discendente + Descending Colon + + + T676000 + + + + + + + + + + + + + colon sigmoideum; pelvic colon; sigmoid colon; sigmoid flexure + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. + Colon Sigmoideo + Sigmoid Colon + Sigmoid Colon + + + T677000 + + original SNOMED T67700 + + + + + + + + + + + stomach greater curvature + The lateral and inferior border of the stomach. Attached to it is the greater omentum. [Definition Source: NCI] + Curvatura Maggiore dello Stomaco + Greater Curvature of Stomach + Grotere Kromming van de Maag + + + Corpo + + + + + + + + + + + + antrum + antrum of stomach; stomach pyloric antrum + antrum pyloricum; antrum of Willis; stomach antrum; antrum pylori; gastric antrum + The initial part of the pyloric canal of the stomach. This site contains endocrine cells that produce gastrin and somatostatin. [Definition Source: NCI] + Antro Pilorico + Antrum Pylori + Pylorus Antrum + + + Antro + + + + + + + + + + + + + Compound, tubular, submucosal glands located in the duodenum proximal to the sphincter of Oddi; these glands produce alkaline-rich secretions that function to both protect the duodenum from the acidic content of the stomach and to enable intestinal enzymes to activate, thus enabling absorption to start. [Definition Source: NCI] + Duodenal Gland + Duodenale Klier + Ghiandola Duodenale + + + editor note: currently defined as equivalent to any submucosal gland in the duodenum. +database_cross_reference: EMAPA:36522; GAID:314; NCIT:C13010; FMA:15060; http://www.snomedbrowser.com/Codes/Details/41298001; http://en.wikipedia.org/wiki/Brunner's_glands; MESH:A03.492.411.620.270.322; UMLS:C0006323; MA:0001551; http://linkedlifedata.com/resource/umls/id/C0006323; BTO:0002376 +has_exact_synonym: submucosal gland of duodenum; Brunner's gland; gland of Brunner +has_obo_namespace: uberon +has_related_synonym: glandula duodenales Brunneri; glandula duodenales +http://www.geneontology.org/formats/oboInOwl#id: UBERON:0001212 +in_subset: http://purl.obolibrary.org/obo/uberon/core#organ_slim; http://purl.obolibrary.org/obo/uberon/core#pheno_slim; http://purl.obolibrary.org/obo/uberon/core#uberon_slim +taxon_notes: Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds + + + + + + + + + + + Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air. + + pulmo + Respiration organ that develops as an oupocketing of the esophagus. + Long + Lung + Polmone + + + T280000 + + original SNOMED T28000 + respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi + + + + + + + + + + + The section of the intestines between the pylorus and cecum. The small intestine is approximately 20 feet long and consists of the duodenum, the jejunum, and the ileum. Its main function is to absorb nutrients from food as the food is transported to the large intestine. [Definition Source: NCI] + Dunne Darm + Intestino Tenue + Small Intestine + + + + + + + + + + + + + The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. + + upper intestine; proximal intestine + A jointed tube 25-30 cm long that connects the stomach to the jejunum. [Definition Source: NCI] + Duodeno + Duodenum + Twaalfvingerige darm + + + T643000 + + original SNOMED T-64300 + In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.; In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. + + + + + + + + + + + The portion of the small intestine that extends from the duodenum to the ileum. [Definition Source: NCI] + Digiuno + Jejunum + Jejunum + + + + + + + + + + + + + + intestinum ileum; lower intestine; posterior intestine; distal intestine + The portion of the small intestine that extends from the jejunum to the colon + Ileo + Ileum + Ileum + + + T65200 + T679210 + + The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum. + + + + + + + + + + + bronchi; bronchial trunk + bronchial tissue + The upper conducting airways of the lung; these airways arise from the terminus of the trachea + Bronchus + Bronchus + Bronco + + + T260000 + + original SNOMED T26000 + In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue + + + + + + + + + + + + mucous membrane of rectum; rectum mucous membrane; mucosa of organ of rectum; rectal mucosa; rectum mucosa; rectal mucous membrane; rectum mucosa of organ; organ mucosa of rectum; rectum organ mucosa + A mucosa that is part of a rectum + Membrana Mucosa Rettale + Rectaal Slijmvlies + Rectal Mucous Membrane + + T680100 + + + + + + + + + + + + mediastinal part of chest + The central part of the thoracic cavity enclosed by the left and right pleurae. + Mediastino + Mediastinum + Mediastinum + + + TY2300 + + original SNOMED TY2300, I decided to left it untouched since it is quite peculiar + + + + + + + + + + The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium. + + cervical epithelium; epithelium of cervix; cervix epithelial tissue; cervical canal epithelial tissue; cervical canal epithelium + An epithelium that is part of a uterine cervix + Cervix Epitheel + Cervix Epithelium + Epitelio della Cervice + + + + + + + + + + + + + + + cervical squamous epithelium + The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. + Cervix Plaveiselepitheel + Cervix Squamous Epithelium + Epitelio Squamoso della Cervice + + + + + + + + + + + + + + lymph node of thorax + deep thoracic lymph node + A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes + Linfonodo Toracico + Thoracale Lymfeknoop + Thoracic Lymph Node + + + T083000 + + + + + + + + + + + + + An intestinal villus in the duodenum. + Intestinal Villus of Duodenum + Intestinale Villus van de Twaalfvingerige Darm + Villi Intestinali del Duodeno + + + + + + + + + + + + + + epithelium of duodenum + An epithelium that is part of a duodenum. + Duodenaal Epitheel + Duodenal Epithelium + Epitelio Duodenale + + + + + + + + + + + + + + distal colon + The distal portion of the colon; it develops embryonically from the hindgut and functions in the storage and elimination of waste. + Colon Sinistro + Left Colon + Linker Dubbele Punt + + + T679950 + + previous SNOMED T67995 + + + + + + + + + + + + proximal colon + The proximal portion of the colon, extending from the ileocecal valve usually to a point proximal to the left colic flexure; it develops embryonically from the terminal portion of the midgut and functions in absorption. + Colon Destro + Rechter Dubbele Punt + Right Colon + + + T679650 + + original SNOMED T67965 + + + + + + + + + + + The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. + + cervix columnar epithelium + A glandular epithelium that is part of a uterine cervix. + Cervix Glandulair Epitheel + Cervix Glandular Epithelium + Epitelio Ghiandolare della Cervice + + + + + + + + + + + + + + + ectocervical epithelium; exocervical epithelium + A epithelium that is part of a ectocervix. + Epitelio Esocervicale + Exocervicaal Epitheel + Exocervical Epithelium + + + + + + + + + + + + + + squamocolumnar junction + squamocolumnar junction of uterine cervix; squamo-columnar junction of uterine cervix + Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet + Cervical Squamo-Columnar Junction + Cervicale Squamocolumnaire Overgang + Giunzione Squamocolonnare Cervicale + + + + + + + + + + + + + + The subdivision of the digestive tract that consists of the colon and the rectum + Colorectum + Colorectum + Coloretto + + + + + + + + + + + + + + + duodenal crypt; duodenal crypt of Lieberkuhn + An intestinal crypt that is located in the duodenum. [Definition Source: http://orcid.org/0000-0002-6601-2165] + Cripta di Lieberkuhn del Duodeno + Crypt of Lieberkuhn of Duodenum + Crypte van Lieberkuhn van de Twaalfvingerige Darm + + + database_cross_reference: EMAPA:37838; FMA:269063 +has_exact_synonym: duodenal crypt; duodenal crypt of Lieberkuhn +has_obo_namespace: uberon +http://www.geneontology.org/formats/oboInOwl#id: UBERON:0013482 +in_subset: http://purl.obolibrary.org/obo/uberon/core#pheno_slim + + + + + + + + + + + + + duodenal cap; bulbus (duodenum); ampulla duodeni; duodenal cap viewed radiologically; bulbus duodeni; ampulla (duodenum); ampulla of duodenum + The very first part of the duodenum which is slightly dilated. + Ampolla Duodenale + Duodenal Ampulla + Duodenale Ampulla + + + + + + + + + + + + + + lamina propria of duodenum; duodenal lamina propria; lamina propria mucosae of duodenum + A lamina propria that is part of a duodenum. + Duodenal Lamina Propria + Duodenal Lamina Propria + Lamina Propria del Duodeno + + + + + + + + + + + + + Pulmonary lymph nodes are a common and underrecognized cause of a peripheral SPN. These lymph nodes are usually found at the bifurcation of the bronchi, before the fourth branch, where they are referred to as peribronchial lymph nodes. Lymph nodes are occasionally present within the lung parenchyma, where they are designated intrapulmonary lymph nodes (IPLNs) or perifissural nodules (PFNs). + Linfonodo Polmonare + Pulmonale Lymfeknoop + Pulmonary Lymph Node + + T080000 + T083110 + T083120 + T083200 + T083210 + + previous SNOMED was T08311, T08312, T08320, T08321, T08000 + + + + + + + + + + + + rectosigmoid region + An anatomical junction that is between the sigmoid colon and rectum. + Giunzione Rettosigmoidea + Rectosigmoid Junctie + Rectosigmoid Junction + + + T679210 + + + + + + + + + + + + Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. [Defintion Source: HPO probison] + Adult Onset + Gruppo d'Età Adulta + Volwassen Aanvang + + + + + + + + + + + + + A type of adult onset with onset of symptoms after the age of 60 years. [Defintion Source: HPO probison] + Gruppo d'Età Tarda + Laat Begin + Late Onset + + + + + + + + + + + + + A type of adult onset with onset of symptoms at the age of 40 to 60 years. [Defintion Source: HPO probison] + Begin op Middelbare Leeftijd + Gruppo d'Età della Mezza Età + Midlle Age Onset + + + + + + + + + + + + + Onset of disease at the age of between 16 and 40 years. [Defintion Source: HPO DDD:hfirth] + Begin bij Jonge Volwassenen + Gruppo d'Età Giovane Adulto + Young Adult Onset + + + + + + + + + + Dennis Dosso + Dennis Dosso + + + + + + + + + Laura Menotti + Laura Menotti + + + + + + + + + Stefano Marchesin + Stefano Marchesin + + + + + + + + + Gianmaria Silvello + Gianmaria Silvello + + + + + + + + + + + Biopsy executed in the pyloric antrum, a form of endoscopic biopsy. + Biopsia dell'Antro Pilorico + Biopsie van Het Pylorusantrum + Biopsy of the Pyloric Antrum + + “Biopsia” + “STOMACO” + “Antro” + + + + + + + + + + Entity representing the Cannizzaro Hospital as producer of medical report + Cannizzaro Hospital + Ospedale Cannizzaro + Ziekenhuis Cannizzaro + + + + + + + + + + + + Biopsy produced in the greater curvature area, a region in the stomach. + Biopsia della Grande Curvatura + Biopsie van de Grotere Kromming + Biopsy of the Greater Curvature + + Biopsia + Stomaco + Corpo + + + + + + + + + + + + + + Severe Colon Dysplasia; Severe dysplasia of colon + Dysplasia is a term that describes how much your polyp looks like cancer under the microscope. Polyps that are more abnormal and look more like cancer are said to have high-grade (severe) dysplasia. + Ernstige Colondysplasie + Grave Displasia del Colon + Severe Colon Dysplasia + + + + + + + + + + + + + Campione Insoddisfacente per la Diagnosi + Specimen Onbevredigend voor Diagnose + Specimen Unsatisfactory for Diagnosis + M090000 + + + + + + + + + + In this ontology there are different semantic areas. These are: diagnosis, procedure, test, anatomical location, and general. +General is the area of entities that are common to all clinical cases. Organization, clinical case reports, diseases, are classes with entities that do not belong to the other 4 semantic areas, therefore we classified them in general. These are the classes that, in our documentation, are contained in the green box. + Algemene Entiteit + Entità Generica + General Entity + + + + + + + + + + + Atrofia Ghiandolare + Glandulaire Atrofie + Glandular Atrophy + + + + + + + + + + + + + Inconclusive outcome where not enough material was present for the diagnosis. + Insufficient Material + Materiale Insufficiente + Onvoldoende Materiaal + M010100 + + + + + + + + + + Intervention + Semantic class to describe the semantic area of the interventions. We defined our own class (and not used the ncit one) because we wanted to keep the two separated to not entangle too much queries and also because here we are using it with a slightly different semantic meaning. + Procedura + Procedure + Procedure + + + + + + + + + Test is a semantic area encompassing all those entities representing one test. One example are the immunistochemical tests like the immunoprecipitation. These tests may have different outcome, like being true or false, or a non-negative integer. + Test + Test + Test + + + + + + + + + ExaMode Consortium + + diff --git a/sket/ont_proc/ontology_processing.py b/sket/ont_proc/ontology_processing.py index a9f792b..87ef4b4 100644 --- a/sket/ont_proc/ontology_processing.py +++ b/sket/ont_proc/ontology_processing.py @@ -1,9 +1,12 @@ import owlready2 import itertools import pandas as pd +import rdflib from collections import defaultdict from copy import deepcopy +from rdflib import URIRef +from rdflib.namespace import RDFS from owlready2 import IRIS from ..utils import utils @@ -22,15 +25,17 @@ def __init__(self, ontology_path=None, hierarchies_path=None): Returns: None """ + self.ontology = rdflib.Graph() if ontology_path: # custom ontology path - self.ontology = owlready2.get_ontology(ontology_path).load() + #self.ontology = owlready2.get_ontology(ontology_path).load() + self.ontology.parse(ontology_path) else: # default ontology path - self.ontology = owlready2.get_ontology('./sket/ont_proc/ontology/examode.owl').load() + self.ontology.parse('./sket/ont_proc/ontology/examode.owl') if hierarchies_path: # custom hierarchy relations path self.hrels = utils.read_hierarchies(hierarchies_path) else: # default hierarchy relations path self.hrels = utils.read_hierarchies('./sket/ont_proc/rules/hierarchy_relations.txt') - self.disease = {'colon': 'colon carcinoma', 'lung': 'lung cancer', 'cervix': 'cervical cancer', 'celiac': 'celiac disease'} + self.disease = {'colon': '0002032', 'lung': '0008903', 'cervix': '0002974', 'celiac': '0005130'} def restrict2use_case(self, use_case, limit=1000): """ @@ -40,41 +45,56 @@ def restrict2use_case(self, use_case, limit=1000): use_case (str): use case considered (colon, lung, cervix, celiac) limit (int): max number of returned elements - Returns: a pandas DataFrame containng concepts information + Returns: a pandas DataFrame containing concepts information """ disease = self.disease[use_case] sparql = "PREFIX exa: " \ "PREFIX rdfs: " \ + "PREFIX mondo: " \ + "PREFIX dcterms: "\ "select ?iri ?iri_label ?iri_SNOMED_code ?iri_UMLS_code ?semantic_area ?semantic_area_label where { " \ - "?iri rdfs:label ?iri_label ; exa:AssociatedDisease ?disease . " \ + "?iri rdfs:label ?iri_label ; exa:associatedDisease mondo:" + disease + ". " \ "filter (langMatches( lang(?iri_label), 'en')). " \ - "?disease rdfs:label '" + disease + "'@en . " \ "OPTIONAL {?iri exa:hasSNOMEDCode ?iri_SNOMED_code .} " \ - "OPTIONAL {?iri exa:hasUMLS ?iri_UMLS_code .} " \ + "OPTIONAL {?iri dcterms:conformsTo ?iri_UMLS_code .} " \ "OPTIONAL {?iri exa:hasSemanticArea ?semantic_area . " \ "?semantic_area rdfs:label ?semantic_area_label . " \ "filter (langMatches( lang(?semantic_area_label), 'en')).} " \ "} " \ "limit " + str(limit) - # get ontology graph as in rdflib - ontology_graph = self.ontology.world.as_rdflib_graph() # issue sparql query - r = ontology_graph.query(query_object=sparql) + resultSet = self.ontology.query(query_object=sparql) # convert query output to DataFrame ontology_dict = defaultdict(list) - for e in r: + for row in resultSet: # store entity as IRI - if self.ontology[e[0]]: # entity belongs to the ExaMode ontology - ontology_dict['iri'].append(self.ontology[e[0]].iri) - else: # entity belongs to external ontologies - ontology_dict['iri'].append(e[0].toPython() if e[0] else None) + ontology_dict['iri'].append(str(row.iri)) # store additional information associated w/ entity - ontology_dict['label'].append(e[1].toPython() if e[1] else None) - ontology_dict['SNOMED'].append(e[2].toPython().replace('*', '') if e[2] else None) - ontology_dict['UMLS'].append(e[3].toPython() if e[3] else None) - ontology_dict['semantic_area'].append(e[4].toPython() if e[4] else None) - ontology_dict['semantic_area_label'].append(e[5].toPython() if e[5] else None) + ontology_dict['label'].append(str(row.iri_label)) + ontology_dict['SNOMED'].append(str(row.iri_SNOMED_code) if row.iri_SNOMED_code is not None else None) + ontology_dict['UMLS'].append(str(row.iri_UMLS_code)if row.iri_UMLS_code is not None else None) + ontology_dict['semantic_area'].append(str(row.semantic_area)) + ontology_dict['semantic_area_label'].append(str(row.semantic_area_label)) + if use_case == 'celiac': + # Add negative result + # store entity as IRI + ontology_dict['iri'].append('https://w3id.org/examode/ontology/NegativeResult') + # store additional information associated w/ entity + ontology_dict['label'].append('Negative Result') + ontology_dict['SNOMED'].append('M-010100') + ontology_dict['UMLS'].append(None) + ontology_dict['semantic_area'].append('http://purl.obolibrary.org/obo/NCIT_C15220') + ontology_dict['semantic_area_label'].append('Diagnosis') + # Add inconclusive result + # store entity as IRI + ontology_dict['iri'].append('https://w3id.org/examode/ontology/InconclusiveOutcome') + # store additional information associated w/ entity + ontology_dict['label'].append('Inconclusive Outcome') + ontology_dict['SNOMED'].append(None) + ontology_dict['UMLS'].append(None) + ontology_dict['semantic_area'].append('http://purl.obolibrary.org/obo/NCIT_C15220') + ontology_dict['semantic_area_label'].append('Diagnosis') return pd.DataFrame(ontology_dict) @staticmethod @@ -103,7 +123,7 @@ def get_ancestors(self, concepts, include_self=False): Returns the list of ancestor concepts given target concept and hierachical relations Params: - concepts (list(owlready2.entity.ThingClass/examode.DiseaseAnnotation)): list of concepts from ontology + concepts (list(str)): list of concepts from ontology include_self (bool): whether to include current concept in the list of ancestors Returns: the list of ancestors for target concept @@ -113,45 +133,76 @@ def get_ancestors(self, concepts, include_self=False): # get latest concept within concepts concept = concepts[-1] - # the get_properties class depends on concept type - if type(concept) == owlready2.entity.ThingClass: # class level - rely on ancestors() property (recursively return all parent classes) - return concept.ancestors(include_self=include_self) - else: # instance level - navigate through instance-instance relations - rels = [rel for rel in concept.get_properties() if rel.name in self.hrels] - if rels: # concept hierarchically related w/ ancestor - assert len(rels) == 1 - # append ancestor to list - concepts.append(rels[0][concept][0]) - # recursively search for ancestors - return self.get_ancestors(concepts) - else: # base case - return set(concepts[1:]) - - def get_higher_concept(self, iri1, iri2, include_self=False): + + # Query to return ancestors (both for classes or individuals + txtQuery = "PREFIX rdfs: " \ + "PREFIX skos: " \ + "select ?ancestor where { " \ + "<" + concept + "> (rdfs:subClassOf|skos:broaderTransitive)+ ?ancestor. " \ + "}" + + # issue sparql query + resultSet = self.ontology.query(query_object=txtQuery) + ancestors = [] + for r in resultSet: + ancestors.append(str(r.ancestor)) + # if include_self include concept + if include_self: + ancestors.append(concept) + + return ancestors + + def check_individual_type(self, individual, classURI): + """ + Checks if an individual belongs to a specified class. + + Params: + individual (str): URI of the individual. + classURI (str): URI of the class. + + Returns: boolean value asserting whether individual belongs to classURI. + """ + + # Query to return classes of individual + txtQuery = "select ?type { <" + individual + "> a ?type.}" + + # issue sparql query + resultSet = self.ontology.query(query_object=txtQuery) + classes = [] + for r in resultSet: + classes.append(str(r.type)) + # if include_self include concept + if classURI in classes: + return True + else: + return False + + def get_higher_concept(self, iri1, iris, include_self=False): """ Return the ontology concept that is more general (hierarchically higher) Params: iri1 (str): the first iri considered - iri2 (str): the second iri considered + iris (list(str)): list of the second iris considered include_self (bool): whether to include current concept in the list of ancestors Returns: the hierarchically higher concept's iri """ - - # convert iris into full ontology concepts - concept1 = IRIS[iri1] - concept2 = IRIS[iri2] # get ancestors for both concepts - ancestors1 = self.get_ancestors([concept1], include_self) - ancestors2 = self.get_ancestors([concept2], include_self) - if concept2 in ancestors1: # concept1 is a descendant of concept2 - return iri2 - elif concept1 in ancestors2: # concept1 is an ancestor of concept2 + ancestors1 = self.get_ancestors([iri1], include_self) + ancestors2 = self.get_ancestors([iris[0]], include_self) + if iris[0] in ancestors1: # concept1 is a descendant of concept2 + return iris[0] + elif iri1 in ancestors2: # concept1 is an ancestor of concept2 return iri1 - else: # concept1 and concept2 are not hierarchically related + else: # concept1 and concept2 are not hierarchically related, check if there is another concept + if len(iris) == 2: + poType = self.check_individual_type(iri1, iris[1]) + if poType: # concept1 is an individual of type concept3 + return iris[1] return None + def merge_nlp_and_struct(self, nlp_concepts, struct_concepts): """ Merge the information extracted from 'nlp' and 'struct' sections diff --git a/sket/ont_proc/rules/hierarchy_relations.txt b/sket/ont_proc/rules/hierarchy_relations.txt index 752cb5e..2a5af10 100644 --- a/sket/ont_proc/rules/hierarchy_relations.txt +++ b/sket/ont_proc/rules/hierarchy_relations.txt @@ -1,2 +1 @@ -partOf -isSpecificationOf \ No newline at end of file +hasBroaderTransitive \ No newline at end of file diff --git a/sket/rdf_proc/rdf_processing.py b/sket/rdf_proc/rdf_processing.py index 195ae60..b702800 100644 --- a/sket/rdf_proc/rdf_processing.py +++ b/sket/rdf_proc/rdf_processing.py @@ -4,7 +4,7 @@ import itertools from rdflib import Namespace, URIRef, Literal, Graph -from rdflib.namespace import DC, RDF +from rdflib.namespace import DC, RDF, XSD class RDFProc(object): @@ -21,11 +21,12 @@ def __init__(self): # @smarchesin TODO: add Test outcome to predicate2literal l # set base IRI, namespace, gender, and age information self.base_iri = 'https://w3id.org/examode/' self.namespace = {'exa': Namespace('https://w3id.org/examode/ontology/'), 'dc': DC} - self.gender = {'M': 'http://purl.obolibrary.org/obo/NCIT_C46109', 'F': 'http://purl.obolibrary.org/obo/NCIT_C46110'} + self.gender = {'M': URIRef('http://purl.obolibrary.org/obo/NCIT_C20197'), + 'F': URIRef('http://purl.obolibrary.org/obo/NCIT_C16576')} self.age_set = { - 'young': 'https://hpo.jax.org/app/browse/term/HP:0011462', - 'middle': 'https://hpo.jax.org/app/browse/term/HP:0003596', - 'late': 'https://hpo.jax.org/app/browse/term/HP:0003584' + 'young': URIRef('https://hpo.jax.org/app/browse/term/HP:0011462'), + 'middle': URIRef('https://hpo.jax.org/app/browse/term/HP:0003596'), + 'late': URIRef('https://hpo.jax.org/app/browse/term/HP:0003584') } # set predicates that associate Resource w/ Literal @@ -35,7 +36,7 @@ def __init__(self): # @smarchesin TODO: add Test outcome to predicate2literal l self.namespace['exa']['hasImage'], self.namespace['exa']['hasBlockNumber'], self.namespace['exa']['hasSlideId'], - self.namespace['exa']['detectedHumanPapillomaVirus'], + self.namespace['exa']['detectedHPV'], self.namespace['exa']['koylociteDetected'] ] @@ -63,56 +64,64 @@ def compute_age(birth_date, visit_date): return age @staticmethod - def associate_polyp2dysplasia(outcomes, mask_outcomes, debug=False): # @smarchesin TODO: needs to be part of a dict of functions that are use-case dependants + def associate_outcome2annotation(outcomes, mask_outcomes, use_case, debug=False): # @smarchesin TODO: needs to be part of a dict of functions that are use-case dependants """ Associate polyp-type outcomes w/ dysplasia mentions (colon-related function) Params: outcomes (list(pair(str))): the list of report outcomes mask_outcomes (str): the string representing masked outcomes - 0 for dysplasia and 1 for polyp (sub)classes + use_case (str): use_case we are considering. debug (bool): whether to keep flags for debugging Returns: a list of associated polyp-dysplasia pairs, when possible, or single polyp mentions """ - + general_outcome = { + 'colon': 'https://w3id.org/examode/ontology/ColonPolyp', + 'lung': 'https://w3id.org/examode/ontology/LungCarcinomaFinding' + } + outcome_class = { + 'colon': 'https://w3id.org/examode/ontology/ColonOutcome', + 'lung': 'https://w3id.org/examode/ontology/LungOutcome' + } pairs = list() if len(mask_outcomes) == 1: # there is one outcome only - if mask_outcomes == '1': # outcome is subclass of polyp class - pairs.append([outcomes[0][0]]) + if mask_outcomes == '1': # outcome is subclass of general outcome class + pairs.append([outcomes[0][0], outcome_class[use_case]]) return pairs - else: # outcome is a dysplasia mention - append it w/ the general 'Polyp of Colon' concept + else: # outcome is an annotation mention - append it w/ the general outcome concept if debug: - print('decoupled dysplasia mention') - pairs.append(['http://purl.obolibrary.org/obo/MONDO_0021400', outcomes[0][0]]) + print('decoupled annotation mention') + pairs.append([general_outcome[use_case], outcomes[0][0]]) return pairs # group masked_outcomes by '0' -- e.g., 000111001000 --> ['000', '1', '1', '1', '00', '1', '000'] mask_outcomes = [["".join(g)] if k == '0' else list(g) for k, g in itertools.groupby(mask_outcomes)] mask_outcomes = [item for sublist in mask_outcomes for item in sublist] for ix, out in enumerate(mask_outcomes): # multiple outcomes available if ix == 0: # first outcome - if out[0] == '0': # first outcome is a dysplasia mention + if out[0] == '0': # first outcome is an annotation mention if debug: - print('decoupled dysplasia mention(s)') - dysplasia_outcomes = [outcomes[ix+oix][0] for oix in range(len(out))] - pairs.append(['http://purl.obolibrary.org/obo/MONDO_0021400'] + dysplasia_outcomes) - else: # first outcome is subclass of polyp class - if mask_outcomes[ix+1][0] == '0': # the second outcome is a dysplasia mention - dysplasia_outcomes = [outcomes[ix+1+oix][0] for oix in range(len(mask_outcomes[ix+1]))] - pairs.append([outcomes[ix][0]] + dysplasia_outcomes) - else: # the second outcome is another subclass of polyp class - pairs.append([outcomes[ix][0]]) + print('decoupled annotation mention(s)') + annotation_outcomes = [outcomes[ix+oix][0] for oix in range(len(out))] + pairs.append([general_outcome[use_case]] + annotation_outcomes) + else: # first outcome is subclass of general outcome class + if mask_outcomes[ix+1][0] == '0': # the second outcome is an annotation mention + annotation_outcomes = [outcomes[ix+1+oix][0] for oix in range(len(mask_outcomes[ix+1]))] + pairs.append([outcomes[ix][0]] + annotation_outcomes) + else: # the second outcome is another subclass of general outcome class + pairs.append([outcomes[ix][0], outcome_class[use_case]]) else: - if out[0] == '0': # outcome is a dysplasia mention - skip it + if out[0] == '0': # outcome is an annotation mention - skip it continue else: # outcome is subclass of polyp class if ix+1 < len(mask_outcomes): # ix != last - if mask_outcomes[ix+1][0] == '0': # succeeding outcome is a dysplasia mention - dysplasia_outcomes = [outcomes[ix+1+oix][0] for oix in range(len(mask_outcomes[ix+1]))] - pairs.append([outcomes[ix][0]] + dysplasia_outcomes) - else: # the succeeding outcome is another subclass of polyp class - pairs.append([outcomes[ix][0]]) + if mask_outcomes[ix+1][0] == '0': # succeeding outcome is an annotation mention + annotation_outcomes = [outcomes[ix+1+oix][0] for oix in range(len(mask_outcomes[ix+1]))] + pairs.append([outcomes[ix][0]] + annotation_outcomes) + else: # the succeeding outcome is another subclass of general outcome class + pairs.append([outcomes[ix][0], outcome_class[use_case]]) else: # ix == last - pairs.append([outcomes[ix][0]]) + pairs.append([outcomes[ix][0], outcome_class[use_case]]) return pairs def serialize_report_graphs(self, graphs, output='stream', rdf_format='turtle'): @@ -134,6 +143,8 @@ def serialize_report_graphs(self, graphs, output='stream', rdf_format='turtle'): # loop over graphs and convert them into rdflib classes for graph in graphs: for triple in graph: + g.add(triple) + """ s = URIRef(triple[0]) p = triple[1] if triple[1] in self.predicate2literal: @@ -141,6 +152,7 @@ def serialize_report_graphs(self, graphs, output='stream', rdf_format='turtle'): else: o = URIRef(triple[2]) g.add((s, p, o)) + """ if output == 'stream': # stream rdf graph to output # serialize graphs into predefined rdf format return g.serialize(format=rdf_format) @@ -181,30 +193,34 @@ def aoec_create_graph(self, rid, report_data, report_concepts, onto_proc, use_ca resource = self.base_iri + 'resource/' # build the IRI for the given report - report = resource + 'report/' + hrid - struct_graph['ReportURL'] = report + report_uri = URIRef(resource + 'report/' + hrid) + struct_graph['ReportURL'] = str(report_uri) # build the IRI for the use-case ClinicalCaseReport - use_case_ccreport = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] - struct_graph['ClinicalCase'] = use_case_ccreport + use_case_report_uri = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] + struct_graph['ClinicalCase'] = str(use_case_report_uri) # generate report data-related triples - rdf_graph.append((report, RDF.type, use_case_ccreport)) - rdf_graph.append((report, self.namespace['dc']['identifier'], hrid)) + rdf_graph.append((report_uri, RDF.type, use_case_report_uri)) + rdf_graph.append((report_uri, self.namespace['dc']['identifier'], Literal(hrid, datatype=XSD.string))) if report_data['diagnosis_nlp']: # textual diagnosis is present within report data - rdf_graph.append((report, self.namespace['exa']['hasDiagnosisText'], report_data['diagnosis_nlp'])) + rdf_graph.append((report_uri, self.namespace['exa']['hasDiagnosisText'], + Literal(report_data['diagnosis_nlp'], datatype=XSD.string))) struct_graph['hasDiagnosisText'] = report_data['diagnosis_nlp'] if 'image' in report_data: # report belongs to v2 - rdf_graph.append((report, self.namespace['exa']['hasImage'], report_data['image'])) + rdf_graph.append((report_uri, self.namespace['exa']['hasImage'], + Literal(report_data['image'], datatype=XSD.string))) if 'internalid' in report_data: # report belongs to v2 - rdf_graph.append((report, self.namespace['exa']['hasBlockNumber'], report_data['internalid'])) + rdf_graph.append((report_uri, self.namespace['exa']['hasBlockNumber'], + Literal(int(report_data['internalid']), datatype=XSD.integer))) struct_graph['hasBlockNumber'] = report_data['internalid'] else: # report belongs to v1 - if len(rid.split('_')) == 1: # no internalid specified - set to 1 - rdf_graph.append((report, self.namespace['exa']['hasBlockNumber'], '1')) + if len(rid.split('_')) == 1 or use_case == 'celiac': # no internalid specified - set to 1 + rdf_graph.append((report_uri, self.namespace['exa']['hasBlockNumber'], Literal(1, datatype=XSD.integer))) struct_graph['hasBlockNumber'] = '1' else: - rdf_graph.append((report, self.namespace['exa']['hasBlockNumber'], rid.split('_')[1])) + rdf_graph.append((report_uri, self.namespace['exa']['hasBlockNumber'], + Literal(int(rid.split('_')[1]), datatype=XSD.integer))) struct_graph['hasBlockNumber'] = rid.split('_')[1] # create patient-related triples @@ -214,53 +230,83 @@ def aoec_create_graph(self, rid, report_data, report_concepts, onto_proc, use_ca # generate patient id hashing the first part of the 'rid' field pid = hashlib.md5(rid.split('_')[0].encode()).hexdigest() # build the IRI for the patient - patient = self.base_iri + 'resource/patient/' + pid - struct_graph['patient']['PatientURL'] = patient + patient_uri = URIRef(self.base_iri + 'resource/patient/' + pid) + struct_graph['patient']['PatientURL'] = str(patient_uri) # generate patient-related triples - rdf_graph.append((patient, RDF.type, 'http://purl.obolibrary.org/obo/IDOMAL_0000603')) - struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/IDOMAL_0000603' + rdf_graph.append((patient_uri, RDF.type, URIRef('http://purl.obolibrary.org/obo/NCIT_C16960'))) + struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/NCIT_C16960' # associate report to patient - rdf_graph.append((patient, self.namespace['exa']['hasClinicalCaseReport'], report)) + rdf_graph.append((patient_uri, self.namespace['exa']['hasClinicalCaseReport'], report_uri)) # associate age to patient age = None if 'age' in report_data: # age data is present within report_data age = report_data['age'] elif report_data['birth_date'] and report_data['visit_date']: # birth date and visit date are present - compute age - age = self.compute_age(report_data['birth_date'], report_data['visit_date']) - if age: # age found within current report + age = self.compute_age(str(report_data['birth_date']), str(report_data['visit_date'])) + if age and age > 0: # age found within current report # associate age to report - rdf_graph.append((patient, self.namespace['exa']['hasAge'], age)) + rdf_graph.append((patient_uri, self.namespace['exa']['hasAge'], Literal(age, datatype=XSD.integer))) struct_graph['patient']['hasAge'] = age - # convert age to age set and associate to report - if age < 40: # young - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['young'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['young'] + if age < 40: # young + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['young'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['young']) elif 40 <= age < 60: # middle - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['middle'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['middle'] + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['middle'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['middle']) else: # late - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['late'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['late'] + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['late'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['late']) # associate gender to patient - if report_data['gender']: # gender data is present within report_data - rdf_graph.append((patient, self.namespace['exa']['hasGender'], self.gender[report_data['gender']])) - struct_graph['patient']['hasGender'] = self.gender[report_data['gender']] + if 'gender' in report_data and report_data['gender']: # gender data is present within report_data + rdf_graph.append((patient_uri, self.namespace['exa']['hasGender'], self.gender[report_data['gender']])) + struct_graph['patient']['hasGender'] = str(self.gender[report_data['gender']]) struct_graph['patient']['hasGenderLiteral'] = report_data['gender'] # create report concept-related triples # set ontology 'Outcome' IRI to identify its descendants within the 'Diagnosis' section - ontology_outcome = 'http://purl.obolibrary.org/obo/NCIT_C20200' + ontology_outcomes = [str(self.namespace['exa'][use_case.capitalize() + 'Outcome']), + str(self.namespace['exa'][use_case.capitalize() + 'POType'])] if use_case == 'colon': # set ontology 'Polyp' IRI to identify its descendants within the 'Diagnosis' section - ontology_polyp = 'http://purl.obolibrary.org/obo/MONDO_0021400' + ontology_annotation = str(self.namespace['exa']['ColonPolyp']) elif use_case == 'cervix': # set ontology 'Human Papilloma Virus Infection' and 'Koilocytotic Squamous Cell' IRIs to identify such outcomes within 'Diagnosis' - ontology_hpv = 'http://purl.obolibrary.org/obo/MONDO_0005161' - ontology_koilocyte = 'http://purl.obolibrary.org/obo/NCIT_C36808' + ontology_hpv = ['http://purl.obolibrary.org/obo/MONDO_0005161', + 'https://w3id.org/examode/ontology/HPVInfection'] + ontology_koilocyte = ['http://purl.obolibrary.org/obo/NCIT_C36808', + 'https://w3id.org/examode/ontology/Koilocyte'] + elif use_case == 'lung': + # set ontology 'Lung Carcinoma' IRI to identify its descendants within the 'Diagnosis' section + ontology_annotation = str(self.namespace['exa']['LungCarcinoma']) + + elif use_case == 'celiac': + ontology_outcomes = [str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['Duodenitis']), + str(self.namespace['exa']['NegativeResult']), + str(self.namespace['exa']['InconclusiveResult'])] + ontology_annotations = [str(self.namespace['exa']['IntestinalAbnormality']), + str(self.namespace['exa']['CeliacDiseaseFinding'])] + valued_props = { + str(self.namespace['exa']['MarshStage']): str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['duodenitisSeverity']): str(self.namespace['exa']['Duodenitis']), + } + lab_props = { + str(self.namespace['exa']['mitosisPerCrypt']): str(self.namespace['exa']['OtherFinding']), + str(self.namespace['exa']['hasIEL']): str(self.namespace['exa']['OtherFinding']) + } + villi_props = { + str(self.namespace['exa']['villiAtrophy']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiStatus']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['hasVillusCryptRatio']): str(self.namespace['exa']['VilliFinding']) + } + boolean_props = { + str(self.namespace['exa']['hasFlatVilli']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiAbsence']): str(self.namespace['exa']['VilliFinding']) + } # identify report procedures report_procedures = [procedure[0] for procedure in report_concepts['Procedure']] @@ -275,30 +321,82 @@ def aoec_create_graph(self, rid, report_data, report_concepts, onto_proc, use_ca # identify report tests report_tests = [test[0] for test in report_concepts['Test']] - # identify report outcomes - report_outcomes = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_outcome)) for diagnosis in report_concepts['Diagnosis']] - if use_case == 'colon': - # identify report polyps - report_polyps = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_polyp, include_self=True)) + if use_case != 'celiac': + # identify report outcomes + report_outcomes = [ + (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_outcomes)) for diagnosis in report_concepts['Diagnosis']] - # restrict report_polyps/report_outcomes to those polyp-related/non polyp-related and mask concepts that are sublcass of Polyp w/ 1 and 0 otherwise (dysplasia-related concepts) - for ix, (outcome, polyp) in enumerate(zip(report_outcomes, report_polyps)): - if (outcome[1] is not None) and (polyp[1] is None): # non-polyp outcome - report_polyps.pop(ix) - elif (outcome[1] is not None) and (polyp[1] is not None): # polyp outcome - report_outcomes.pop(ix) - else: # dysplasia outcome - report_outcomes.pop(ix) - # mask report_polyps w/ 1 for concepts that are subclass of Polyp and 0 for other - masked_outcomes = ''.join(['0' if report_outcome[1] is None else '1' for report_outcome in report_polyps]) - # associate polyp-related mentions w/ dysplasia ones - restricted to colon disease only - paired_outcomes = self.associate_polyp2dysplasia(report_polyps, masked_outcomes, debug=debug) - # concatenate the non-polyp outcomes to paired_outcomes - paired_outcomes += [[outcome[0]] for outcome in report_outcomes] + if use_case == 'cervix': + paired_outcomes = [] + for outcome in report_outcomes: + if outcome[0] in ontology_hpv or outcome[0] in ontology_koilocyte: + paired_outcomes.append([str(self.namespace['exa']['CervixOutcome']), outcome[0]]) + else: + paired_outcomes.append([outcome[0], outcome[1]]) + elif use_case in ['colon', 'lung']: + # Identify report for subclasses of outcome where there are additional annotations + # i.e, colon -> polyp, lung -> lung carcinoma + report_annotation = [ + (diagnosis[0], + onto_proc.get_higher_concept(iri1=diagnosis[0], iris=[ontology_annotation], include_self=True)) + for diagnosis in report_concepts['Diagnosis']] + # restrict report_outcomes to those polyp-related and mask concepts that are sublcass of Polyp w/ 1 and 0 otherwise (dysplasia-related) + removed_annotations = [] + removed_outcomes = [] + for ix, (outcome, annotation) in enumerate(zip(report_outcomes, report_annotation)): + if (outcome[1] is not None) and (annotation[1] is None): # outcome without annotations + removed_annotations.append(annotation) + elif (outcome[1] is not None) and (annotation[1] is not None): # outcome with additional annotation + removed_outcomes.append(outcome) + else: # additional annotation for outcome + removed_outcomes.append(outcome) + # Remove outcomes reports based on previous check + for o in removed_outcomes: + report_outcomes.remove(o) + # Remove annotation reports based on previous check + for a in removed_annotations: + report_annotation.remove(a) + # mask report_annotation w/ 1 for concepts that are subclass of outcome with additional annotation and 0 for other + masked_outcomes = ''.join( + ['0' if report_outcome[1] is None else '1' for report_outcome in report_annotation]) + # associate outcome-related mentions w/ annotation ones - restricted to use-case disease only + paired_outcomes = self.associate_outcome2annotation(report_annotation, masked_outcomes, use_case, + debug=debug) + # concatenate the non-annotation outcomes to paired_outcomes + paired_outcomes += [[outcome[0], outcome[1]] for outcome in report_outcomes] + elif use_case == 'celiac': + # identify report outcomes + report_outcomes = [diagnosis[0] for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in ontology_outcomes] + diagnosis_uris = [d for d in report_outcomes] + # Data properties related to the outcome + data_props = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in valued_props.keys()] + diagnosis_uris += [d[0] for d in data_props] + # Other finding data properties + lab_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in lab_props.keys()] + diagnosis_uris += [d[0] for d in lab_findings] + # Villi finding data properties + villi_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in villi_props.keys()] + villi_findings += [(diagnosis[0], True) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in boolean_props.keys()] + diagnosis_uris += [d[0] for d in villi_findings] + # identify report annotations + report_finding = [(diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_annotations, + include_self=True)) + for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] not in diagnosis_uris] + removed_annotations = [finding for finding in report_finding if finding[1] is None] + # Remove annotation reports based on previous check + for f in removed_annotations: + report_finding.remove(f) + # Default outcome is Celiac Outcome + if len(report_outcomes) == 0: + report_outcomes = ['https://w3id.org/examode/ontology/CeliacOutcome'] + paired_outcomes = [[report_outcomes[0], data_props, report_finding, lab_findings, villi_findings]] else: # @smarchesin TODO: the 'else' will probably be replaced with use-case dependants if conditions - paired_outcomes = [[outcome[0]] for outcome in report_outcomes] + paired_outcomes = [[outcome[0], outcome[1]] for outcome in report_outcomes] # set the counter for outcomes identified from report report_outcome_n = 0 @@ -314,61 +412,130 @@ def aoec_create_graph(self, rid, report_data, report_concepts, onto_proc, use_ca # 'Diagnosis'-related triples # build the IRI for the identified outcome - resource_outcome = resource + hrid + '/' + str(report_outcome_n) - outcomes_struct['OutcomeURL'] = resource_outcome + outcome_uri = URIRef(resource + hrid + '/' + str(report_outcome_n)) + outcomes_struct['OutcomeURL'] = str(outcome_uri) # attach outcome instance to graph - rdf_graph.append((report, self.namespace['exa']['hasOutcome'], resource_outcome)) - # specify what the resource_outcome is - if use_case == 'cervix': - if pair[0] == ontology_hpv: # outcome is hpv infection - rdf_graph.append((resource_outcome, self.namespace['exa']['detectedHumanPapillomaVirus'], pair[0])) - outcomes_struct['detectedHumanPapillomaVirus'] = pair[0] - if pair[0] == ontology_koilocyte: # outcome is koilocyte - rdf_graph.append((resource_outcome, self.namespace['exa']['koylociteDetected'], pair[0])) - outcomes_struct['koylociteDetected'] = pair[0] - else: # regular outcome - rdf_graph.append((resource_outcome, RDF.type, pair[0])) - outcomes_struct['a'] = pair[0] - - if use_case == 'colon' and len(pair) > 1: # target outcome has associated dysplasia + rdf_graph.append((report_uri, self.namespace['exa']['hasOutcome'], outcome_uri)) + # specify the type of outcome + if use_case != 'celiac' and pair[1] == ontology_outcomes[1]: + # outcome type is an individual + rdf_graph.append( + (outcome_uri, RDF.type, self.namespace['exa'][use_case.capitalize() + 'PositiveOutcome'])) + rdf_graph.append((outcome_uri, self.namespace['exa']['positiveType'], URIRef(pair[0]))) + else: + # outcome type is the belonging class + rdf_graph.append((outcome_uri, RDF.type, URIRef(pair[0]))) + # outcome type in json graph + outcomes_struct['a'] = pair[0] + # Handle specifics based on the use-case + if use_case == 'colon' and pair[1] not in ontology_outcomes: # target outcome has associated dysplasia outcomes_struct['hasDysplasia'] = [] - for dysplasia_outcome in pair[1:]: # specify the associated dysplasia - rdf_graph.append((resource_outcome, self.namespace['exa']['hasDysplasia'], dysplasia_outcome)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasDysplasia'], URIRef(dysplasia_outcome))) outcomes_struct['hasDysplasia'].append(dysplasia_outcome) + if use_case == 'cervix': + # check if target outcome is hpv/koilocyte + if pair[1] in ontology_hpv: # outcome is hpv infection + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedHPV'], + URIRef(ontology_hpv[0]))) + outcomes_struct['detectedHumanPapillomaVirus'] = ontology_hpv[0] + if pair[1] in ontology_koilocyte: # outcome is koilocyte + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedKoilocyte'], + URIRef(ontology_koilocyte[0]))) + outcomes_struct['koylociteDetected'] = ontology_koilocyte[0] + if use_case == 'lung' and pair[1] not in ontology_outcomes: # target outcome has associated necrosis/metastasis + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[1:]: + # specify the associated dysplasia + rdf_graph.append((outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome))) + outcomes_struct['presenceOf'].append(annotation_outcome) + if use_case == 'celiac': + # Add outcome data properties, if any + if len(pair[1]) > 0: + outcome_property = pair[1][0] + rdf_graph.append( + (outcome_uri, URIRef(outcome_property[0]), Literal(outcome_property[1], datatype=XSD.string))) + outcomes_struct['outcomeProperty'] = outcome_property[1] + # Add annotations, if any + if len(pair[2]) > 0: + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[2]: + if annotation_outcome[1] == str(self.namespace['exa']['CeliacDiseaseFinding']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + elif annotation_outcome[1] == str(self.namespace['exa']['intestinalAbnormality']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOfIntestinalAbnormality'], + URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + # Add lab finding, if any + if any([len(pair[3]) > 0, len(pair[4]) > 0]): + outcomes_struct['labFinding'] = [] + # Add laboratory finding, if any + if len(pair[3]) > 0: + # Instantiate other finding + finding_uri = URIRef(resource + hrid + '/' + 'other_finding_' + str(report_outcome_n)) + rdf_graph.append((finding_uri, RDF.type, self.namespace['exa']['OtherFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], finding_uri)) + outcomes_struct['hasLabFinding'] = str(finding_uri) + for finding in pair[3]: + rdf_graph.append((finding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) + # Add villi finding, if any + if len(pair[4]) > 0: + # Instantiate other finding + villifinding_uri = URIRef(resource + hrid + '/' + 'villi_finding_' + str(report_outcome_n)) + rdf_graph.append((villifinding_uri, RDF.type, self.namespace['exa']['VilliFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], villifinding_uri)) + outcomes_struct['hasLabFinding'] = str(villifinding_uri) + for finding in pair[4]: + if isinstance(finding[1], str): + rdf_graph.append( + (villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + else: + rdf_graph.append( + (villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.boolean))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) # 'Anatomical'-related triples outcomes_struct['hasLocation'] = [] # specify the anatomical location associated to target outcome for location in report_locations: # @smarchesin TODO: correct? we might link multiple locations to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasLocation'], location)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLocation'], URIRef(location))) outcomes_struct['hasLocation'].append(location) # 'Procedure'-related triples outcomes_struct['hasIntervention'] = [] # loop over procedures and build 'Procedure'-related triples - for ix, procedure in enumerate(report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes + for ix, procedure in enumerate( + report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes intervention_struct = {} # build the IRI for the identified procedure - resource_procedure = resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix+1) + procedure_uri = URIRef( + resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix + 1)) # attach procedure instance to graph - rdf_graph.append((resource_outcome, self.namespace['exa']['hasIntervention'], resource_procedure)) - intervention_struct['InterventionURL'] = resource_procedure + rdf_graph.append((outcome_uri, self.namespace['exa']['hasIntervention'], procedure_uri)) + rdf_graph.append((procedure_uri, RDF.type, + self.namespace['exa'][use_case.capitalize() + 'Intervention'])) + intervention_struct['InterventionURL'] = str(procedure_uri) # specify what the resource_procedure is - rdf_graph.append((resource_procedure, RDF.type, procedure)) + rdf_graph.append((procedure_uri, self.namespace['exa']['hasInterventionType'], URIRef(procedure))) intervention_struct['a'] = procedure - intervention_struct['hasTopography'] = [] + intervention_struct['hasLocation'] = [] # specify the anatomical location associated to target procedure for location in report_locations: # @smarchesin TODO: correct? we might associate multiple locations to the same procedure - rdf_graph.append((resource_procedure, self.namespace['exa']['hasTopography'], location)) - intervention_struct['hasTopography'].append(location) + rdf_graph.append((procedure_uri, self.namespace['exa']['haslocation'], URIRef(location))) + intervention_struct['hasLocation'].append(location) outcomes_struct['hasIntervention'].append(intervention_struct) @@ -377,7 +544,7 @@ def aoec_create_graph(self, rid, report_data, report_concepts, onto_proc, use_ca outcomes_struct['hasTest'] = [] if use_case != 'cervix': for test in report_tests: # @smarchesin TODO: is it correct? in this way we can associate multiple tests to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasTest'], test)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasTest'], URIRef(test))) outcomes_struct['hasTest'].append(test) struct_graph['hasOutcome'].append(outcomes_struct) @@ -415,105 +582,212 @@ def radboud_create_graph(self, rid, report_data, report_concepts, onto_proc, use resource = self.base_iri + 'resource/' # build the IRI for the given report - report = resource + 'report/' + hrid - struct_graph['ReportURL'] = report + report_uri = URIRef(resource + 'report/' + hrid) + struct_graph['ReportURL'] = str(report_uri) # build the IRI for the use-case ClinicalCaseReport - use_case_ccreport = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] - struct_graph['ClinicalCase'] = use_case_ccreport + use_case_report_uri = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] + struct_graph['ClinicalCase'] = str(use_case_report_uri) # generate report data-related triples - rdf_graph.append((report, RDF.type, use_case_ccreport)) - rdf_graph.append((report, self.namespace['dc']['identifier'], hrid)) + rdf_graph.append((report_uri, RDF.type, use_case_report_uri)) + rdf_graph.append((report_uri, self.namespace['dc']['identifier'], Literal(hrid, datatype=XSD.string))) # store conclusion text from radboud report diagnosis = report_data['diagnosis'] if diagnosis: # textual diagnosis is present within conclusions - rdf_graph.append((report, self.namespace['exa']['hasDiagnosisText'], diagnosis)) + rdf_graph.append((report_uri, self.namespace['exa']['hasDiagnosisText'], Literal(diagnosis, datatype=XSD.string))) struct_graph['hasDiagnosisText'] = diagnosis if 'slide_ids' in report_data: struct_graph['slides'] = [] # set ontology 'Slide Device' - ontology_slide = 'http://purl.obolibrary.org/obo/NCIT_C50178' + ontology_slide = self.namespace['exa']['SlideDevice'] # generate report slide-related triples for slide_id in report_data['slide_ids']: slide = {} - rdf_graph.append((report + '/slide/' + slide_id, RDF.type, ontology_slide)) - slide['a'] = ontology_slide - rdf_graph.append((report + '/slide/' + slide_id, self.namespace['exa']['hasSlideId'], slide_id)) + slide_uri = URIRef(report_uri + '/slide/' + slide_id) + rdf_graph.append((slide_uri, RDF.type, ontology_slide)) + slide['a'] = str(ontology_slide) + rdf_graph.append((slide_uri, self.namespace['exa']['hasSlideId'], Literal(slide_id, datatype=XSD.string))) slide['hasSlideId'] = slide_id - rdf_graph.append((report, self.namespace['exa']['hasSlide'], report + '/slide/' + slide_id)) - slide['hasSlide'] = report + '/slide/' + slide_id + rdf_graph.append((report_uri, self.namespace['exa']['hasSlide'], slide_uri)) + slide['hasSlide'] = str(slide_uri) struct_graph['slides'].append(slide) # create patient-related triples struct_graph['patient'] = {} - # generate patient id hashing the first part of the 'rid' field (up to P00000###) - pid = hashlib.md5('_'.join(rid.split('_')[0:3]).encode()).hexdigest() + # generate patient id + pid = 'p_' + str(rid) # build the IRI for the patient - patient = self.base_iri + 'resource/patient/' + pid - struct_graph['patient']['PatientURL'] = patient + patient_uri = URIRef(self.base_iri + 'resource/patient/' + pid) + struct_graph['patient']['PatientURL'] = str(patient_uri) # generate patient-related triples - rdf_graph.append((patient, RDF.type, 'http://purl.obolibrary.org/obo/IDOMAL_0000603')) - struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/IDOMAL_0000603' + rdf_graph.append((patient_uri, RDF.type, URIRef('http://purl.obolibrary.org/obo/NCIT_C16960'))) + struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/NCIT_C16960' # associate report to patient - rdf_graph.append((patient, self.namespace['exa']['hasClinicalCaseReport'], report)) + rdf_graph.append((patient_uri, self.namespace['exa']['hasClinicalCaseReport'], report_uri)) + if 'age' in report_data: + # associate age to patient + age = report_data['age'] + if age and age > 0: # age found within current report + # associate age to report + rdf_graph.append((patient_uri, self.namespace['exa']['hasAge'], Literal(age, datatype=XSD.integer))) + struct_graph['patient']['hasAge'] = age + # convert age to age set and associate to report + if age < 40: # young + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['young'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['young']) + elif 40 <= age < 60: # middle + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['middle'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['middle']) + else: # late + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['late'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['late']) + # associate gender to patient + if 'gender' in report_data and report_data['gender']: + # gender data is present within report_data + rdf_graph.append((patient_uri, self.namespace['exa']['hasGender'], self.gender[report_data['gender']])) + struct_graph['patient']['hasGender'] = str(self.gender[report_data['gender']]) + struct_graph['patient']['hasGenderLiteral'] = report_data['gender'] # create report concept-related triples # set ontology 'Outcome' IRI to identify its descendants within the 'Diagnosis' section - ontology_outcome = 'http://purl.obolibrary.org/obo/NCIT_C20200' + ontology_outcomes = [str(self.namespace['exa'][use_case.capitalize() + 'Outcome']), + str(self.namespace['exa'][use_case.capitalize() + 'POType'])] if use_case == 'colon': # set ontology 'Polyp' IRI to identify its descendants within the 'Diagnosis' section - ontology_polyp = 'http://purl.obolibrary.org/obo/MONDO_0021400' + ontology_annotation = str(self.namespace['exa']['ColonPolyp']) elif use_case == 'cervix': # set ontology 'Human Papilloma Virus Infection' and 'Koilocytotic Squamous Cell' IRIs to identify such outcomes within 'Diagnosis' - ontology_hpv = 'http://purl.obolibrary.org/obo/MONDO_0005161' - ontology_koilocyte = 'http://purl.obolibrary.org/obo/NCIT_C36808' + ontology_hpv = ['http://purl.obolibrary.org/obo/MONDO_0005161', + 'https://w3id.org/examode/ontology/HPVInfection'] + ontology_koilocyte = ['http://purl.obolibrary.org/obo/NCIT_C36808', + 'https://w3id.org/examode/ontology/Koilocyte'] + elif use_case == 'lung': + # set ontology 'Lung Carcinoma' IRI to identify its descendants within the 'Diagnosis' section + ontology_annotation = str(self.namespace['exa']['LungCarcinoma']) + elif use_case == 'celiac': + ontology_outcomes = [str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['Duodenitis']), + str(self.namespace['exa']['NegativeResult']), + str(self.namespace['exa']['InconclusiveResult'])] + ontology_annotations = [str(self.namespace['exa']['IntestinalAbnormality']), + str(self.namespace['exa']['CeliacDiseaseFinding'])] + valued_props = { + str(self.namespace['exa']['MarshStage']): str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['duodenitisSeverity']): str(self.namespace['exa']['Duodenitis']), + } + lab_props = { + str(self.namespace['exa']['mitosisPerCrypt']): str(self.namespace['exa']['OtherFinding']), + str(self.namespace['exa']['hasIEL']): str(self.namespace['exa']['OtherFinding']) + } + villi_props = { + str(self.namespace['exa']['villiAtrophy']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiStatus']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['hasVillusCryptRatio']): str(self.namespace['exa']['VilliFinding']) + } + boolean_props = { + str(self.namespace['exa']['hasFlatVilli']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiAbsence']): str(self.namespace['exa']['VilliFinding']) + } # identify report procedures - report_procedures = [procedure[0] for procedure in report_concepts['concepts']['Procedure']] + report_procedures = [procedure[0] for procedure in report_concepts['Procedure']] # identify report anatomical locations - report_locations = [location[0] for location in report_concepts['concepts']['Anatomical Location']] + report_locations = [location[0] for location in report_concepts['Anatomical Location']] if not report_locations: # @smarchesin TODO: decide how to handle cervix when location is absent if use_case == 'colon': # add 'Colon, NOS' IRI as default report_locations += ['http://purl.obolibrary.org/obo/UBERON_0001155'] if use_case != 'cervix': # @smarchesin TODO: this might be updated depending on the other use cases # identify report tests - report_tests = [test[0] for test in report_concepts['concepts']['Test']] + report_tests = [test[0] for test in report_concepts['Test']] - # identify report outcomes - report_outcomes = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_outcome)) - for diagnosis in report_concepts['concepts']['Diagnosis']] - if use_case == 'colon': - # identify report polyps - report_polyps = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_polyp, include_self=True)) - for diagnosis in report_concepts['concepts']['Diagnosis']] + if use_case != 'celiac': + # identify report outcomes + report_outcomes = [ + (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_outcomes)) + for diagnosis in report_concepts['Diagnosis']] + if use_case == 'cervix': + paired_outcomes = [] + for outcome in report_outcomes: + if outcome[0] in ontology_hpv or outcome[0] in ontology_koilocyte: + paired_outcomes.append([str(self.namespace['exa']['CervixOutcome']), outcome[0]]) + else: + paired_outcomes.append([outcome[0], outcome[1]]) + + elif use_case in ['colon', 'lung']: + # Identify report for subclasses of outcome where there are additional annotations + # i.e, colon -> polyp, lung -> lung carcinoma + report_annotation = [ + (diagnosis[0], + onto_proc.get_higher_concept(iri1=diagnosis[0], iris=[ontology_annotation], include_self=True)) + for diagnosis in report_concepts['Diagnosis']] # restrict report_outcomes to those polyp-related and mask concepts that are sublcass of Polyp w/ 1 and 0 otherwise (dysplasia-related) - for ix, (outcome, polyp) in enumerate(zip(report_outcomes, report_polyps)): - if (outcome[1] is not None) and (polyp[1] is None): # non-polyp outcome - report_polyps.pop(ix) - elif (outcome[1] is not None) and (polyp[1] is not None): # polyp outcome - report_outcomes.pop(ix) - else: # dysplasia outcome - report_outcomes.pop(ix) - # mask report_polyps w/ 1 for concepts that are subclass of Polyp and 0 for other - masked_outcomes = ''.join(['0' if report_outcome[1] is None else '1' for report_outcome in report_polyps]) - # associate polyp-related mentions w/ dysplasia ones - restricted to colon disease only - paired_outcomes = self.associate_polyp2dysplasia(report_polyps, masked_outcomes, debug=debug) - # concatenate the non-polyp outcomes to paired_outcomes - paired_outcomes += [[outcome[0]] for outcome in report_outcomes] + removed_annotations = [] + removed_outcomes = [] + for ix, (outcome, annotation) in enumerate(zip(report_outcomes, report_annotation)): + if (outcome[1] is not None) and (annotation[1] is None): # outcome without annotations + removed_annotations.append(annotation) + elif (outcome[1] is not None) and (annotation[1] is not None): # outcome with additional annotation + removed_outcomes.append(outcome) + else: # additional annotation for outcome + removed_outcomes.append(outcome) + # Remove outcomes reports based on previous check + for o in removed_outcomes: + report_outcomes.remove(o) + # Remove annotation reports based on previous check + for a in removed_annotations: + report_annotation.remove(a) + # mask report_annotation w/ 1 for concepts that are subclass of outcome with additional annotation and 0 for other + masked_outcomes = ''.join( + ['0' if report_outcome[1] is None else '1' for report_outcome in report_annotation]) + # associate outcome-related mentions w/ annotation ones - restricted to use-case disease only + paired_outcomes = self.associate_outcome2annotation(report_annotation, masked_outcomes, use_case, + debug=debug) + # concatenate the non-annotation outcomes to paired_outcomes + paired_outcomes += [[outcome[0], outcome[1]] for outcome in report_outcomes] + + elif use_case == 'celiac': + # identify report outcomes + report_outcomes = [diagnosis[0] for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in ontology_outcomes] + diagnosis_uris = [d for d in report_outcomes] + # Data properties related to the outcome + data_props = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in valued_props.keys()] + diagnosis_uris += [d[0] for d in data_props] + # Other finding data properties + lab_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in lab_props.keys()] + diagnosis_uris += [d[0] for d in lab_findings] + # Villi finding data properties + villi_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in villi_props.keys()] + villi_findings += [(diagnosis[0], True) for diagnosis in report_concepts['Diagnosis'] if + diagnosis[0] in boolean_props.keys()] + diagnosis_uris += [d[0] for d in villi_findings] + # identify report annotations + report_finding = [(diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_annotations, + include_self=True)) + for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] not in diagnosis_uris] + removed_annotations = [finding for finding in report_finding if finding[1] is None] + # Remove annotation reports based on previous check + for f in removed_annotations: + report_finding.remove(f) + # Default outcome is Celiac Outcome + if len(report_outcomes) == 0: + report_outcomes = ['https://w3id.org/examode/ontology/CeliacOutcome'] + paired_outcomes = [[report_outcomes[0], data_props, report_finding, lab_findings, villi_findings]] else: # @smarchesin TODO: the 'else' will probably be replaced with use-case dependants if conditions - paired_outcomes = [[outcome[0]] for outcome in report_outcomes] + paired_outcomes = [[outcome[0], outcome[1]] for outcome in report_outcomes] # set the counter for outcomes identified from report report_outcome_n = 0 @@ -529,61 +803,134 @@ def radboud_create_graph(self, rid, report_data, report_concepts, onto_proc, use # 'Diagnosis'-related triples # build the IRI for the identified outcome - resource_outcome = resource + hrid + '/' + str(report_outcome_n) - outcomes_struct['OutcomeURL'] = resource_outcome + outcome_uri = URIRef(resource + hrid + '/' + str(report_outcome_n)) + outcomes_struct['OutcomeURL'] = str(outcome_uri) # attach outcome instance to graph - rdf_graph.append((report, self.namespace['exa']['hasOutcome'], resource_outcome)) - # specify what the resource_outcome is - if use_case == 'cervix': - if pair[0] == ontology_hpv: # outcome is hpv infection - rdf_graph.append((resource_outcome, self.namespace['exa']['detectedHumanPapillomaVirus'], pair[0])) - outcomes_struct['detectedHumanPapillomaVirus'] = pair[0] - if pair[0] == ontology_koilocyte: # outcome is koilocyte - rdf_graph.append((resource_outcome, self.namespace['exa']['koylociteDetected'], pair[0])) - outcomes_struct['koylociteDetected'] = pair[0] - else: # regular outcome - rdf_graph.append((resource_outcome, RDF.type, pair[0])) - outcomes_struct['a'] = pair[0] - - if use_case == 'colon' and len(pair) > 1: # target outcome has associated dysplasia - outcomes_struct['hasDysplasia'] = [] + rdf_graph.append((report_uri, self.namespace['exa']['hasOutcome'], outcome_uri)) + # specify the type of outcome + if use_case != 'celiac' and pair[1] == ontology_outcomes[1]: + # outcome type is an individual + rdf_graph.append( + (outcome_uri, RDF.type, self.namespace['exa'][use_case.capitalize() + 'PositiveOutcome'])) + rdf_graph.append((outcome_uri, self.namespace['exa']['positiveType'], URIRef(pair[0]))) + else: + # outcome type is the belonging class + rdf_graph.append((outcome_uri, RDF.type, URIRef(pair[0]))) + # outcome type in json graph + outcomes_struct['a'] = pair[0] + # Handle specifics based on the use-case + if use_case == 'colon' and pair[1] not in ontology_outcomes: # target outcome has associated dysplasia + outcomes_struct['hasDysplasia'] = [] for dysplasia_outcome in pair[1:]: # specify the associated dysplasia - rdf_graph.append((resource_outcome, self.namespace['exa']['hasDysplasia'], dysplasia_outcome)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasDysplasia'], URIRef(dysplasia_outcome))) outcomes_struct['hasDysplasia'].append(dysplasia_outcome) + if use_case == 'cervix': + # check if target outcome is hpv/koilocyte + if pair[1] in ontology_hpv: # outcome is hpv infection + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedHPV'], + URIRef(ontology_hpv[0]))) + outcomes_struct['detectedHumanPapillomaVirus'] = ontology_hpv[0] + if pair[1] in ontology_koilocyte: # outcome is koilocyte + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedKoilocyte'], + URIRef(ontology_koilocyte[0]))) + outcomes_struct['koylociteDetected'] = ontology_koilocyte[0] + + if use_case == 'lung' and pair[ + 1] not in ontology_outcomes: # target outcome has associated necrosis/metastasis + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[1:]: + # specify the associated dysplasia + rdf_graph.append((outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome))) + outcomes_struct['presenceOf'].append(annotation_outcome) + + if use_case == 'celiac': + # Add outcome data properties, if any + if len(pair[1]) > 0: + outcome_property = pair[1][0] + rdf_graph.append( + (outcome_uri, URIRef(outcome_property[0]), Literal(outcome_property[1], datatype=XSD.string))) + outcomes_struct['outcomeProperty'] = outcome_property[1] + # Add annotations, if any + if len(pair[2]) > 0: + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[2]: + if annotation_outcome[1] == str(self.namespace['exa']['CeliacDiseaseFinding']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + elif annotation_outcome[1] == str(self.namespace['exa']['intestinalAbnormality']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOfIntestinalAbnormality'], + URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + # Add lab finding, if any + if any([len(pair[3]) > 0, len(pair[4]) > 0]): + outcomes_struct['labFinding'] = [] + # Add laboratory finding, if any + if len(pair[3]) > 0: + # Instantiate other finding + finding_uri = URIRef(resource + hrid + '/' + 'other_finding_' + str(report_outcome_n)) + rdf_graph.append((finding_uri, RDF.type, self.namespace['exa']['OtherFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], finding_uri)) + outcomes_struct['hasLabFinding'] = str(finding_uri) + for finding in pair[3]: + rdf_graph.append((finding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) + # Add villi finding, if any + if len(pair[4]) > 0: + # Instantiate other finding + villifinding_uri = URIRef(resource + hrid + '/' + 'villi_finding_' + str(report_outcome_n)) + rdf_graph.append((villifinding_uri, RDF.type, self.namespace['exa']['VilliFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], villifinding_uri)) + outcomes_struct['hasLabFinding'] = str(villifinding_uri) + for finding in pair[4]: + if isinstance(finding[1], str): + rdf_graph.append( + (villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + else: + rdf_graph.append( + (villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.boolean))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) + # 'Anatomical'-related triples outcomes_struct['hasLocation'] = [] # specify the anatomical location associated to target outcome for location in report_locations: # @smarchesin TODO: correct? we might link multiple locations to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasLocation'], location)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLocation'], URIRef(location))) outcomes_struct['hasLocation'].append(location) # 'Procedure'-related triples outcomes_struct['hasIntervention'] = [] # loop over procedures and build 'Procedure'-related triples - for ix, procedure in enumerate(report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes + for ix, procedure in enumerate( + report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes intervention_struct = {} # build the IRI for the identified procedure - resource_procedure = resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix+1) + procedure_uri = URIRef(resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix + 1)) # attach procedure instance to graph - rdf_graph.append((resource_outcome, self.namespace['exa']['hasIntervention'], resource_procedure)) - intervention_struct['InterventionURL'] = resource_procedure + rdf_graph.append((outcome_uri, self.namespace['exa']['hasIntervention'], procedure_uri)) + rdf_graph.append((procedure_uri, RDF.type, + self.namespace['exa'][use_case.capitalize() + 'Intervention'])) + intervention_struct['InterventionURL'] = str(procedure_uri) # specify what the resource_procedure is - rdf_graph.append((resource_procedure, RDF.type, procedure)) + rdf_graph.append((procedure_uri, self.namespace['exa']['hasInterventionType'], URIRef(procedure))) intervention_struct['a'] = procedure - intervention_struct['hasTopography'] = [] + intervention_struct['hasLocation'] = [] # specify the anatomical location associated to target procedure - for location in report_locations: # @smarchesin TODO: correct? we might link multiple locations to the same procedure - rdf_graph.append((resource_procedure, self.namespace['exa']['hasTopography'], location)) - intervention_struct['hasTopography'].append(location) + for location in report_locations: # @smarchesin TODO: correct? we might associate multiple locations to the same procedure + rdf_graph.append((procedure_uri, self.namespace['exa']['haslocation'], URIRef(location))) + intervention_struct['hasLocation'].append(location) outcomes_struct['hasIntervention'].append(intervention_struct) @@ -592,7 +939,7 @@ def radboud_create_graph(self, rid, report_data, report_concepts, onto_proc, use outcomes_struct['hasTest'] = [] if use_case != 'cervix': for test in report_tests: # @smarchesin TODO: correct? we might link multiple tests to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasTest'], test)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasTest'], URIRef(test))) outcomes_struct['hasTest'].append(test) struct_graph['hasOutcome'].append(outcomes_struct) @@ -630,20 +977,20 @@ def create_graph(self, rid, report_data, report_concepts, onto_proc, use_case, d resource = self.base_iri + 'resource/' # build the IRI for the given report - report = resource + 'report/' + hrid - struct_graph['ReportURL'] = report + report_uri = URIRef(resource + 'report/' + hrid) + struct_graph['ReportURL'] = str(report_uri) # build the IRI for the use-case ClinicalCaseReport - use_case_ccreport = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] - struct_graph['ClinicalCase'] = use_case_ccreport + use_case_report_uri = self.namespace['exa'][use_case.capitalize() + 'ClinicalCaseReport'] + struct_graph['ClinicalCase'] = str(use_case_report_uri) # generate report data-related triples - rdf_graph.append((report, RDF.type, use_case_ccreport)) - rdf_graph.append((report, self.namespace['dc']['identifier'], hrid)) + rdf_graph.append((report_uri, RDF.type, use_case_report_uri)) + rdf_graph.append((report_uri, self.namespace['dc']['identifier'], Literal(hrid, datatype=XSD.string))) # store text from report diagnosis = report_data['text'] if diagnosis: # textual diagnosis is present within conclusions - rdf_graph.append((report, self.namespace['exa']['hasDiagnosisText'], diagnosis)) + rdf_graph.append((report_uri, self.namespace['exa']['hasDiagnosisText'], Literal(diagnosis, datatype=XSD.string))) struct_graph['hasDiagnosisText'] = diagnosis # create patient-related triples @@ -653,49 +1000,80 @@ def create_graph(self, rid, report_data, report_concepts, onto_proc, use_case, d # generate patient id pid = 'p_' + str(rid) # build the IRI for the patient - patient = self.base_iri + 'resource/patient/' + pid - struct_graph['patient']['PatientURL'] = patient + patient_uri = URIRef(self.base_iri + 'resource/patient/' + pid) + struct_graph['patient']['PatientURL'] = str(patient_uri) # generate patient-related triples - rdf_graph.append((patient, RDF.type, 'http://purl.obolibrary.org/obo/IDOMAL_0000603')) - struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/IDOMAL_0000603' + rdf_graph.append((patient_uri, RDF.type, URIRef('http://purl.obolibrary.org/obo/NCIT_C16960'))) + struct_graph['patient']['a'] = 'http://purl.obolibrary.org/obo/NCIT_C16960' # associate report to patient - rdf_graph.append((patient, self.namespace['exa']['hasClinicalCaseReport'], report)) - # associate age to patient - age = report_data['age'] - if age: # age found within current report - # associate age to report - rdf_graph.append((patient, self.namespace['exa']['hasAge'], age)) - struct_graph['patient']['hasAge'] = age + rdf_graph.append((patient_uri, self.namespace['exa']['hasClinicalCaseReport'], report_uri)) - # convert age to age set and associate to report - if age < 40: # young - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['young'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['young'] - elif 40 <= age < 60: # middle - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['middle'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['middle'] - else: # late - rdf_graph.append((patient, self.namespace['exa']['hasAgeOnset'], self.age_set['late'])) - struct_graph['patient']['hasAgeOnset'] = self.age_set['late'] + if 'age' in report_data: + # associate age to patient + age = report_data['age'] + if age and age > 0: # age found within current report + # associate age to report + rdf_graph.append((patient_uri, self.namespace['exa']['hasAge'], Literal(age, datatype=XSD.integer))) + struct_graph['patient']['hasAge'] = age + # convert age to age set and associate to report + if age < 40: # young + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['young'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['young']) + elif 40 <= age < 60: # middle + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['middle'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['middle']) + else: # late + rdf_graph.append((patient_uri, self.namespace['exa']['hasAgeOnset'], self.age_set['late'])) + struct_graph['patient']['hasAgeOnset'] = str(self.age_set['late']) # associate gender to patient - if report_data['gender']: # gender data is present within report_data - rdf_graph.append((patient, self.namespace['exa']['hasGender'], self.gender[report_data['gender']])) - struct_graph['patient']['hasGender'] = self.gender[report_data['gender']] + if 'gender' in report_data and report_data['gender']: # gender data is present within report_data + rdf_graph.append((patient_uri, self.namespace['exa']['hasGender'], self.gender[report_data['gender']])) + struct_graph['patient']['hasGender'] = str(self.gender[report_data['gender']]) struct_graph['patient']['hasGenderLiteral'] = report_data['gender'] # create report concept-related triples # set ontology 'Outcome' IRI to identify its descendants within the 'Diagnosis' section - ontology_outcome = 'http://purl.obolibrary.org/obo/NCIT_C20200' + ontology_outcomes = [str(self.namespace['exa'][use_case.capitalize() + 'Outcome']), + str(self.namespace['exa'][use_case.capitalize() + 'POType'])] if use_case == 'colon': # set ontology 'Polyp' IRI to identify its descendants within the 'Diagnosis' section - ontology_polyp = 'http://purl.obolibrary.org/obo/MONDO_0021400' + ontology_annotation = str(self.namespace['exa']['ColonPolyp']) elif use_case == 'cervix': # set ontology 'Human Papilloma Virus Infection' and 'Koilocytotic Squamous Cell' IRIs to identify such outcomes within 'Diagnosis' - ontology_hpv = 'http://purl.obolibrary.org/obo/MONDO_0005161' - ontology_koilocyte = 'http://purl.obolibrary.org/obo/NCIT_C36808' + ontology_hpv = ['http://purl.obolibrary.org/obo/MONDO_0005161', + 'https://w3id.org/examode/ontology/HPVInfection'] + ontology_koilocyte = ['http://purl.obolibrary.org/obo/NCIT_C36808', + 'https://w3id.org/examode/ontology/Koilocyte'] + elif use_case == 'lung': + # set ontology 'Lung Carcinoma' IRI to identify its descendants within the 'Diagnosis' section + ontology_annotation = str(self.namespace['exa']['LungCarcinoma']) + elif use_case == 'celiac': + ontology_outcomes = [str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['Duodenitis']), + str(self.namespace['exa']['NegativeResult']), + str(self.namespace['exa']['InconclusiveResult'])] + ontology_annotations = [str(self.namespace['exa']['IntestinalAbnormality']), + str(self.namespace['exa']['CeliacDiseaseFinding'])] + valued_props = { + str(self.namespace['exa']['MarshStage']): str(self.namespace['exa']['PositiveToCeliacDisease']), + str(self.namespace['exa']['duodenitisSeverity']): str(self.namespace['exa']['Duodenitis']), + } + lab_props = { + str(self.namespace['exa']['mitosisPerCrypt']): str(self.namespace['exa']['OtherFinding']), + str(self.namespace['exa']['hasIEL']): str(self.namespace['exa']['OtherFinding']) + } + villi_props = { + str(self.namespace['exa']['villiAtrophy']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiStatus']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['hasVillusCryptRatio']): str(self.namespace['exa']['VilliFinding']) + } + boolean_props = { + str(self.namespace['exa']['hasFlatVilli']): str(self.namespace['exa']['VilliFinding']), + str(self.namespace['exa']['villiAbsence']): str(self.namespace['exa']['VilliFinding']) + } # identify report procedures report_procedures = [procedure[0] for procedure in report_concepts['Procedure']] @@ -710,31 +1088,74 @@ def create_graph(self, rid, report_data, report_concepts, onto_proc, use_case, d # identify report tests report_tests = [test[0] for test in report_concepts['Test']] - # identify report outcomes - report_outcomes = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_outcome)) - for diagnosis in report_concepts['Diagnosis']] - if use_case == 'colon': - # identify report polyps - report_polyps = [ - (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iri2=ontology_polyp, include_self=True)) + if use_case != 'celiac': + # identify report outcomes + report_outcomes = [ + (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_outcomes)) + for diagnosis in report_concepts['Diagnosis']] + if use_case == 'cervix': + paired_outcomes = [] + for outcome in report_outcomes: + if outcome[0] in ontology_hpv or outcome[0] in ontology_koilocyte: + paired_outcomes.append([str(self.namespace['exa']['CervixOutcome']), outcome[0]]) + else: + paired_outcomes.append([outcome[0], outcome[1]]) + elif use_case in ['colon', 'lung']: + # Identify report for subclasses of outcome where there are additional annotations + # i.e, colon -> polyp, lung -> lung carcinoma + report_annotation = [ + (diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=[ontology_annotation], include_self=True)) for diagnosis in report_concepts['Diagnosis']] # restrict report_outcomes to those polyp-related and mask concepts that are sublcass of Polyp w/ 1 and 0 otherwise (dysplasia-related) - for ix, (outcome, polyp) in enumerate(zip(report_outcomes, report_polyps)): - if (outcome[1] is not None) and (polyp[1] is None): # non-polyp outcome - report_polyps.pop(ix) - elif (outcome[1] is not None) and (polyp[1] is not None): # polyp outcome - report_outcomes.pop(ix) - else: # dysplasia outcome - report_outcomes.pop(ix) - # mask report_polyps w/ 1 for concepts that are subclass of Polyp and 0 for other - masked_outcomes = ''.join(['0' if report_outcome[1] is None else '1' for report_outcome in report_polyps]) - # associate polyp-related mentions w/ dysplasia ones - restricted to colon disease only - paired_outcomes = self.associate_polyp2dysplasia(report_polyps, masked_outcomes, debug=debug) - # concatenate the non-polyp outcomes to paired_outcomes - paired_outcomes += [[outcome[0]] for outcome in report_outcomes] + removed_annotations = [] + removed_outcomes = [] + for ix, (outcome, annotation) in enumerate(zip(report_outcomes, report_annotation)): + if (outcome[1] is not None) and (annotation[1] is None): # outcome without annotations + removed_annotations.append(annotation) + elif (outcome[1] is not None) and (annotation[1] is not None): # outcome with additional annotation + removed_outcomes.append(outcome) + else: # additional annotation for outcome + removed_outcomes.append(outcome) + # Remove outcomes reports based on previous check + for o in removed_outcomes: + report_outcomes.remove(o) + # Remove annotation reports based on previous check + for a in removed_annotations: + report_annotation.remove(a) + # mask report_annotation w/ 1 for concepts that are subclass of outcome with additional annotation and 0 for other + masked_outcomes = ''.join(['0' if report_outcome[1] is None else '1' for report_outcome in report_annotation]) + # associate outcome-related mentions w/ annotation ones - restricted to use-case disease only + paired_outcomes = self.associate_outcome2annotation(report_annotation, masked_outcomes, use_case, debug=debug) + # concatenate the non-annotation outcomes to paired_outcomes + paired_outcomes += [[outcome[0], outcome[1]] for outcome in report_outcomes] + elif use_case == 'celiac': # TODO handle data properties (list: valued_props) value in position [2] + # identify report outcomes + report_outcomes = [diagnosis[0] for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] in ontology_outcomes] + diagnosis_uris = [d for d in report_outcomes] + # Data properties related to the outcome + data_props = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] in valued_props.keys()] + diagnosis_uris += [d[0] for d in data_props] + # Other finding data properties + lab_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] in lab_props.keys()] + diagnosis_uris += [d[0] for d in lab_findings] + # Villi finding data properties + villi_findings = [(diagnosis[0], diagnosis[2]) for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] in villi_props.keys()] + villi_findings += [(diagnosis[0], True) for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] in boolean_props.keys()] + diagnosis_uris += [d[0] for d in villi_findings] + # identify report annotations + report_finding = [(diagnosis[0], onto_proc.get_higher_concept(iri1=diagnosis[0], iris=ontology_annotations, + include_self=True)) + for diagnosis in report_concepts['Diagnosis'] if diagnosis[0] not in diagnosis_uris] + removed_annotations = [finding for finding in report_finding if finding[1] is None] + # Remove annotation reports based on previous check + for f in removed_annotations: + report_finding.remove(f) + # Default outcome is Celiac Outcome + if len(report_outcomes) == 0: + report_outcomes = ['https://w3id.org/examode/ontology/CeliacOutcome'] + paired_outcomes = [[report_outcomes[0], data_props, report_finding, lab_findings, villi_findings]] else: # @smarchesin TODO: the 'else' will probably be replaced with use-case dependants if conditions - paired_outcomes = [[outcome[0]] for outcome in report_outcomes] + paired_outcomes = [[outcome[0], outcome[1]] for outcome in report_outcomes] # set the counter for outcomes identified from report report_outcome_n = 0 @@ -750,61 +1171,125 @@ def create_graph(self, rid, report_data, report_concepts, onto_proc, use_case, d # 'Diagnosis'-related triples # build the IRI for the identified outcome - resource_outcome = resource + hrid + '/' + str(report_outcome_n) - outcomes_struct['OutcomeURL'] = resource_outcome + outcome_uri = URIRef(resource + hrid + '/' + str(report_outcome_n)) + outcomes_struct['OutcomeURL'] = str(outcome_uri) # attach outcome instance to graph - rdf_graph.append((report, self.namespace['exa']['hasOutcome'], resource_outcome)) - # specify what the resource_outcome is - if use_case == 'cervix': - if pair[0] == ontology_hpv: # outcome is hpv infection - rdf_graph.append((resource_outcome, self.namespace['exa']['detectedHumanPapillomaVirus'], pair[0])) - outcomes_struct['detectedHumanPapillomaVirus'] = pair[0] - if pair[0] == ontology_koilocyte: # outcome is koilocyte - rdf_graph.append((resource_outcome, self.namespace['exa']['koylociteDetected'], pair[0])) - outcomes_struct['koylociteDetected'] = pair[0] - else: # regular outcome - rdf_graph.append((resource_outcome, RDF.type, pair[0])) - outcomes_struct['a'] = pair[0] - - if use_case == 'colon' and len(pair) > 1: # target outcome has associated dysplasia + rdf_graph.append((report_uri, self.namespace['exa']['hasOutcome'], outcome_uri)) + # specify the type of outcome + if use_case != 'celiac' and pair[1] == ontology_outcomes[1]: + # outcome type is an individual + rdf_graph.append((outcome_uri, RDF.type, self.namespace['exa'][use_case.capitalize() + 'PositiveOutcome'])) + rdf_graph.append((outcome_uri, self.namespace['exa']['positiveType'], URIRef(pair[0]))) + else: + # outcome type is the belonging class + rdf_graph.append((outcome_uri, RDF.type, URIRef(pair[0]))) + # outcome type in json graph + outcomes_struct['a'] = pair[0] + # Handle specifics based on the use-case + if use_case == 'colon' and pair[1] not in ontology_outcomes: # target outcome has associated dysplasia outcomes_struct['hasDysplasia'] = [] - for dysplasia_outcome in pair[1:]: # specify the associated dysplasia - rdf_graph.append((resource_outcome, self.namespace['exa']['hasDysplasia'], dysplasia_outcome)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasDysplasia'], URIRef(dysplasia_outcome))) outcomes_struct['hasDysplasia'].append(dysplasia_outcome) + if use_case == 'cervix': + # check if target outcome is hpv/koilocyte + if pair[1] in ontology_hpv: # outcome is hpv infection + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedHPV'], + URIRef(ontology_hpv[0]))) + outcomes_struct['detectedHumanPapillomaVirus'] = ontology_hpv[0] + if pair[1] in ontology_koilocyte: # outcome is koilocyte + rdf_graph.append((outcome_uri, self.namespace['exa']['detectedKoilocyte'], + URIRef(ontology_koilocyte[0]))) + outcomes_struct['koylociteDetected'] = ontology_koilocyte[0] + if use_case == 'lung' and pair[1] not in ontology_outcomes: # target outcome has associated necrosis/metastasis + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[1:]: + # specify the associated dysplasia + rdf_graph.append((outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome))) + outcomes_struct['presenceOf'].append(annotation_outcome) + + if use_case == 'celiac': + # Add outcome data properties, if any + if len(pair[1]) > 0: + outcome_property = pair[1][0] + rdf_graph.append((outcome_uri, URIRef(outcome_property[0]), Literal(outcome_property[1], datatype=XSD.string))) + outcomes_struct['outcomeProperty'] = outcome_property[1] + # Add annotations, if any + if len(pair[2]) > 0: + outcomes_struct['presenceOf'] = [] + for annotation_outcome in pair[2]: + if annotation_outcome[1] == str(self.namespace['exa']['CeliacDiseaseFinding']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOf'], URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + elif annotation_outcome[1] == str(self.namespace['exa']['intestinalAbnormality']): + rdf_graph.append( + (outcome_uri, self.namespace['exa']['presenceOfIntestinalAbnormality'], URIRef(annotation_outcome[0]))) + outcomes_struct['presenceOf'].append(annotation_outcome) + # Add lab finding, if any + if any([len(pair[3]) > 0, len(pair[4]) > 0]): + outcomes_struct['labFinding'] = [] + # Add laboratory finding, if any + if len(pair[3]) > 0: + # Instantiate other finding + finding_uri = URIRef(resource + hrid + '/' + 'other_finding_' + str(report_outcome_n)) + rdf_graph.append((finding_uri, RDF.type, self.namespace['exa']['OtherFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], finding_uri)) + outcomes_struct['hasLabFinding'] = str(finding_uri) + for finding in pair[3]: + rdf_graph.append((finding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) + # Add villi finding, if any + if len(pair[4]) > 0: + # Instantiate other finding + villifinding_uri = URIRef(resource + hrid + '/' + 'villi_finding_' + str(report_outcome_n)) + rdf_graph.append((villifinding_uri, RDF.type, self.namespace['exa']['VilliFinding'])) + # Link lab finding and outcome + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLabFinding'], villifinding_uri)) + outcomes_struct['hasLabFinding'] = str(villifinding_uri) + for finding in pair[4]: + if isinstance(finding[1], str): + rdf_graph.append((villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.string))) + else: + rdf_graph.append( + (villifinding_uri, URIRef(finding[0]), Literal(finding[1], datatype=XSD.boolean))) + outcomes_struct['labFinding'].append([finding[0], finding[1]]) # 'Anatomical'-related triples - outcomes_struct['hasLocation'] = [] # specify the anatomical location associated to target outcome for location in report_locations: # @smarchesin TODO: correct? we might link multiple locations to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasLocation'], location)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasLocation'], URIRef(location))) outcomes_struct['hasLocation'].append(location) # 'Procedure'-related triples outcomes_struct['hasIntervention'] = [] # loop over procedures and build 'Procedure'-related triples - for ix, procedure in enumerate(report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes + for ix, procedure in enumerate( + report_procedures): # @smarchesin TODO: correct? we might link the same procedure to multiple outcomes intervention_struct = {} # build the IRI for the identified procedure - resource_procedure = resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix+1) + procedure_uri = URIRef(resource + 'procedure/' + hrid + '/' + str(report_outcome_n) + '.' + str(ix + 1)) # attach procedure instance to graph - rdf_graph.append((resource_outcome, self.namespace['exa']['hasIntervention'], resource_procedure)) - intervention_struct['InterventionURL'] = resource_procedure + rdf_graph.append((outcome_uri, self.namespace['exa']['hasIntervention'], procedure_uri)) + rdf_graph.append((procedure_uri, RDF.type, + self.namespace['exa'][use_case.capitalize() + 'Intervention'])) + intervention_struct['InterventionURL'] = str(procedure_uri) # specify what the resource_procedure is - rdf_graph.append((resource_procedure, RDF.type, procedure)) + rdf_graph.append((procedure_uri, self.namespace['exa']['hasInterventionType'], URIRef(procedure))) intervention_struct['a'] = procedure - intervention_struct['hasTopography'] = [] + intervention_struct['hasLocation'] = [] # specify the anatomical location associated to target procedure - for location in report_locations: # @smarchesin TODO: correct? we might link multiple locations to the same procedure - rdf_graph.append((resource_procedure, self.namespace['exa']['hasTopography'], location)) - intervention_struct['hasTopography'].append(location) + for location in report_locations: # @smarchesin TODO: correct? we might associate multiple locations to the same procedure + rdf_graph.append((procedure_uri, self.namespace['exa']['haslocation'], URIRef(location))) + intervention_struct['hasLocation'].append(location) outcomes_struct['hasIntervention'].append(intervention_struct) @@ -813,7 +1298,7 @@ def create_graph(self, rid, report_data, report_concepts, onto_proc, use_case, d outcomes_struct['hasTest'] = [] if use_case != 'cervix': for test in report_tests: # @smarchesin TODO: correct? we might link multiple tests to the same outcome - rdf_graph.append((resource_outcome, self.namespace['exa']['hasTest'], test)) + rdf_graph.append((outcome_uri, self.namespace['exa']['hasTest'], URIRef(test))) outcomes_struct['hasTest'].append(test) struct_graph['hasOutcome'].append(outcomes_struct) diff --git a/sket/rep_proc/report_processing.py b/sket/rep_proc/report_processing.py index e12cdd7..78c5f3c 100644 --- a/sket/rep_proc/report_processing.py +++ b/sket/rep_proc/report_processing.py @@ -11,6 +11,7 @@ from copy import deepcopy from collections import defaultdict from transformers import MarianMTModel, MarianTokenizer +from datetime import datetime from ..utils import utils @@ -129,6 +130,7 @@ def load_dataset(self, reports_path, sheet, header): dataset = pd.read_excel(io=reports_path, sheet_name=sheet, header=header) # remove rows w/ na dataset.dropna(axis=0, how='all', inplace=True) + # dataset.dropna(axis=0, how='all', subset=dataset.columns[1:], inplace=True) return dataset @@ -171,7 +173,7 @@ def aoec_process_data(self, dataset): 'procedure': report.Procedura if type(report.Procedura) == str else '', 'topography': report.Topografia if type(report.Topografia) == str else '', 'diagnosis_struct': report._5 if type(report._5) == str else '', - 'age': int(report.Età) if not math.isnan(report.Età) else 0, + 'age': int(report.Età) if not math.isnan(report.Età) else None, 'gender': report.Sesso if type(report.Sesso) == str else '' } return reports @@ -243,22 +245,51 @@ def aoec_process_data_v2(self, dataset, debug=False): print('acquire data and split it based on diagnoses') # acquire data and split it based on diagnoses for report in tqdm(dataset.itertuples()): - rid = str(report.FILENAME).strip() + '_' + str(report.IDINTERNO).strip() - reports[rid] = { - 'diagnosis_nlp': self.aoec_split_diagnoses(report.TESTODIAGNOSI, report.IDINTERNO, debug=debug), - 'materials': report.MATERIALE, - 'procedure': report.SNOMEDPROCEDURA if type(report.SNOMEDPROCEDURA) == str else '', - 'topography': report.SNOMEDTOPOGRAFIA if type(report.SNOMEDTOPOGRAFIA) == str else '', - 'diagnosis_struct': report.SNOMEDDIAGNOSI if type(report.SNOMEDDIAGNOSI) == str else '', - 'birth_date': report.NATOIL if report.NATOIL else '', - 'visit_date': report.DATAORAFINEVALIDAZIONE if report.DATAORAFINEVALIDAZIONE else '', - 'gender': report.SESSO if type(report.SESSO) == str else '', - 'image': report.FILENAME, - 'internalid': report.IDINTERNO - } + if 'IDINTERNO' in dataset.columns: + rid = str(report.FILENAME).strip() + '_' + str(report.IDINTERNO).strip() + if type(report.TESTODIAGNOSI) == str: + reports[rid] = { + 'diagnosis_nlp': self.aoec_split_diagnoses(report.TESTODIAGNOSI, report.IDINTERNO, debug=debug) + if type(report.IDINTERNO) == str else report.TESTODIAGNOSI, + 'materials': report.MATERIALE, + 'procedure': report.SNOMEDPROCEDURA if type(report.SNOMEDPROCEDURA) == str else '', + 'topography': report.SNOMEDTOPOGRAFIA if type(report.SNOMEDTOPOGRAFIA) == str else '', + 'diagnosis_struct': report.SNOMEDDIAGNOSI if type(report.SNOMEDDIAGNOSI) == str else '', + 'birth_date': report.NATOIL if report.NATOIL else '', + 'visit_date': report.DATAORAFINEVALIDAZIONE if report.DATAORAFINEVALIDAZIONE else '', + 'gender': report.SESSO if type(report.SESSO) == str else '', + 'image': report.FILENAME, + 'internalid': report.IDINTERNO + } + else: + # process_data_v3, no IDINTERNO and MATERIALI + rid = str(int(report.FILENAME)).strip() + if type(report.TESTODIAGNOSI) == str: + reports[rid] = { + 'diagnosis_nlp': report.TESTODIAGNOSI, + 'procedure': report.SNOMEDPROCEDURA if type(report.SNOMEDPROCEDURA) == str else '', + 'topography': report.SNOMEDTOPOGRAFIA if type(report.SNOMEDTOPOGRAFIA) == str else '', + 'diagnosis_struct': report.SNOMEDDIAGNOSI if type(report.SNOMEDDIAGNOSI) == str else '', + 'birth_date': report.NATOIL.to_pydatetime().strftime("%Y%m%d")+"000000" if report.NATOIL else '', + 'visit_date': report.DATAORAFINEVALIDAZIONE.to_pydatetime().strftime("%Y%m%d")+"000000" if report.DATAORAFINEVALIDAZIONE else '', + 'gender': report.SESSO if type(report.SESSO) == str else '', + 'image': int(report.FILENAME) + } return reports + @staticmethod + def date_formatter(raw_date): + """ + Returns date in the correct format. + + Params: + raw_date (timestamp): date to format + Return string with correctly formatted date. + """ + date = datetime.strptime(raw_date, '%d/%m/%Y') + return date.strftime("%Y%m%d")+"000000" + def aoec_translate_reports(self, reports): """ Translate processed reports @@ -274,7 +305,8 @@ def aoec_translate_reports(self, reports): # translate text for rid, report in tqdm(trans_reports.items()): trans_reports[rid]['diagnosis_nlp'] = self.translate_text(report['diagnosis_nlp']) - trans_reports[rid]['materials'] = self.translate_text(report['materials']) + if 'materials' in report: + trans_reports[rid]['materials'] = self.translate_text(report['materials']) if report['materials'] != '' else '' return trans_reports # RADBOUD SPECIFIC FUNCTIONS @@ -542,6 +574,103 @@ def radboud_process_data_v2(self, dataset): proc_reports[bid]['diagnosis'] = conclusions[cid] return proc_reports + def radboud_process_celiac_data(self, dataset): + """ + Read Radboud reports and extract the required fields (used for celiac datasets) + + Params: + dataset (pandas DataFrame): target dataset + + Returns: a dict containing the required report fields + """ + + proc_reports = dict() + for report in tqdm(dataset.itertuples()): + rid = str(report.Studynumber).strip() + if type(report._7) == str: + if any(report._6.strip() == k for k in ['alle', 'aIle', 'aI', 'al', 'a', '?']): # single conclusion + + # create dict to store block diagnosis + proc_reports[rid] = dict() + # store conclusion - i.e., the final diagnosis + proc_reports[rid]['diagnosis'] = utils.nl_sanitize_record(report._7.lower(), self.use_case) + # Add other fields + proc_reports[rid]['tissue'] = report._8 if type(report._8) == str else '' + proc_reports[rid]['procedure'] = report._9 if type(report._9) == str else '' + proc_reports[rid]['short'] = [] + for short in [report.short1, report.short2, report.short3]: + if type(short) == str: + proc_reports[rid]['short'].append(short) + proc_reports[rid]['slide_ids'] = [rid.lstrip(report.block).split('_')[1].lstrip(report.block.split('_')[3])] + else: # split conclusions and associate to each block the corresponding conclusion + # split conclusions into sections + conclusions = self.radboud_split_conclusions(utils.nl_sanitize_record(report._7.lower(), self.use_case)) + + if 'whole' in conclusions: # unable to split conclusions - either single conclusion or not appropriately specified + # create dict to store block diagnosis + proc_reports[rid] = dict() + # store conclusion - i.e., the final diagnosis + proc_reports[rid]['diagnosis'] = conclusions['whole'] + # Add other fields + proc_reports[rid]['tissue'] = report._8 if type(report._8) == str else '' + proc_reports[rid]['procedure'] = report._9 if type(report._9) == str else '' + proc_reports[rid]['short'] = [] + for short in [report.short1, report.short2, report.short3]: + if type(short) == str: + proc_reports[rid]['short'].append(short) + proc_reports[rid]['slide_ids'] = [rid.lstrip(report.block).split('_')[1].lstrip( + report.block.split('_')[3])] + + else: + # get conclusions IDs + cid2ix = {cid: roman.fromRoman(cid) for cid in conclusions.keys()} + for cid, cix in cid2ix.items(): + numbers = [n.strip() for n in report._6.split('&')] + if cid in numbers: + # create block id + bid = rid + '_' + str(cix) + # create dict to store block diagnosis + proc_reports[bid] = dict() + # store conclusion - i.e., the final diagnosis + proc_reports[bid]['diagnosis'] = conclusions[cid] + # Add other fields + proc_reports[bid]['tissue'] = report._8 if type(report._8) == str else '' + proc_reports[bid]['procedure'] = report._9 if type(report._9) == str else '' + proc_reports[bid]['short'] = [] + for short in [report.short1, report.short2, report.short3]: + if type(short) == str: + proc_reports[bid]['short'].append(short) + proc_reports[bid]['slide_ids'] = [rid.lstrip(report.block).split('_')[1].lstrip( + report.block.split('_')[3])] + + return proc_reports + + def radboud_translate_celiac_reports(self, reports): + """ + Translate processed reports for celiac use-case + + Params: + reports (dict): processed reports + + Returns: translated reports + """ + + trans_reports = copy.deepcopy(reports) + print('translate text') + # translate text + for rid, report in tqdm(trans_reports.items()): + trans_reports[rid]['diagnosis'] = self.translate_text(report['diagnosis']) + if report['tissue'] != '': + trans_reports[rid]['tissue'] = self.translate_text(report['tissue']) + if report['procedure'] != '': + trans_reports[rid]['procedure'] = self.translate_text(report['procedure']) + # List of translated shorts + tmp = [] + for short in report['short']: + tmp.append(self.translate_text(short)) + trans_reports[rid]['short'] = tmp + return trans_reports + def radboud_translate_reports(self, reports): """ Translate processed reports @@ -582,6 +711,24 @@ def read_xls_reports(self, dataset): # return report(s) return reports + def read_csv_reports(self, dataset): + """ + Read reports from csv file + + Params: + dataset (str): target dataset + + Returns: a list containing dataset report(s) + """ + # read input file as csv object + ds = pd.read_csv(filepath_or_buffer=dataset, sep=' ', header=0) + + reports = [] + for report in tqdm(ds.itertuples(index=False)): # convert raw dataset into list containing report(s) + reports.append({field: report[ix] for ix, field in enumerate(report._fields)}) + # return report(s) + return reports + def read_json_reports(self, dataset): """ Read reports from JSON file @@ -635,8 +782,10 @@ def process_data(self, dataset, debug=False): reports = self.read_json_reports(dataset) elif dataset.split('.')[-1] == 'xlsx' or dataset.split('.')[-1] == 'xls': # read input file as xlsx or xls object reports = self.read_xls_reports(dataset) + elif dataset.split('.')[-1] == 'csv': # read input file as csv or csv object + reports = self.read_csv_reports(dataset) else: # raise exception - print('Format required for input: JSON, xls, or xlsx.') + print('Format required for input: JSON, xls, xlsx or csv.') raise Exception else: # dataset passed as stream dict reports = self.read_stream_reports(dataset) diff --git a/sket/rep_proc/rules/report_fields.txt b/sket/rep_proc/rules/report_fields.txt index 8b13789..f3a3485 100644 --- a/sket/rep_proc/rules/report_fields.txt +++ b/sket/rep_proc/rules/report_fields.txt @@ -1 +1 @@ - +text \ No newline at end of file diff --git a/sket/sket.py b/sket/sket.py index 30bf9fe..662e6fa 100644 --- a/sket/sket.py +++ b/sket/sket.py @@ -64,7 +64,9 @@ def __init__( 'original': utils.aoec_cervix_concepts2labels, 'custom': utils.aoec_cervix_labels2aggregates}, 'lung': { - 'original': utils.aoec_lung_concepts2labels} + 'original': utils.aoec_lung_concepts2labels}, + 'celiac': { + 'original': utils.aoec_celiac_concepts2labels} }, 'radboud': { 'colon': { @@ -72,7 +74,9 @@ def __init__( 'custom': utils.radboud_colon_labels2binary}, 'cervix': { 'original': utils.radboud_cervix_concepts2labels, - 'custom': utils.radboud_cervix_labels2aggregates} + 'custom': utils.radboud_cervix_labels2aggregates}, + 'celiac': { + 'original': utils.radboud_celiac_concepts2labels} } } @@ -87,6 +91,9 @@ def __init__( }, 'lung': { 'original': utils.lung_concepts2labels + }, + 'celiac': { + 'original': utils.celiac_concepts2labels } } @@ -133,8 +140,8 @@ def update_usecase(self, use_case): Returns: None """ - if use_case not in ['colon', 'cervix', 'lung']: # raise exception - print('current supported use cases are: "colon", "cervix", and "lung"') + if use_case not in ['colon', 'cervix', 'lung', 'celiac']: # raise exception + print('current supported use cases are: "colon", "cervix", "lung" and "celiac"') raise Exception # set use case self.use_case = use_case @@ -283,6 +290,7 @@ def prepare_exa_dataset(self, ds_fpath, sheet, header, hospital, ver, ds_name=No header (int): row index used as header hospital (str): considered hospital ver (int): data format version + use_case (str): considered use case ds_name (str): dataset name debug (bool): whether to keep flags for debugging @@ -307,8 +315,12 @@ def prepare_exa_dataset(self, ds_fpath, sheet, header, hospital, ver, ds_name=No # translate reports trans_reports = self.rep_proc.aoec_translate_reports(proc_reports) elif hospital == 'radboud': - # translate reports - trans_reports = self.rep_proc.radboud_translate_reports(proc_reports) + if self.use_case == 'celiac': + # translate celiac reports + trans_reports = self.rep_proc.radboud_translate_celiac_reports(proc_reports) + else: + # translate reports + trans_reports = self.rep_proc.radboud_translate_reports(proc_reports) else: # raise exception print('provide correct hospital info: "aoec" or "radboud"') raise Exception @@ -332,13 +344,18 @@ def prepare_exa_dataset(self, ds_fpath, sheet, header, hospital, ver, ds_name=No # translate reports trans_reports = self.rep_proc.aoec_translate_reports(proc_reports) elif hospital == 'radboud': - if ver == 1: # process data using method v1 + if self.use_case == 'celiac': + proc_reports = self.rep_proc.radboud_process_celiac_data(dataset) + elif ver == 1: # process data using method v1 proc_reports = self.rep_proc.radboud_process_data(dataset, debug=debug) else: # process data using method v2 proc_reports = self.rep_proc.radboud_process_data_v2(dataset) - - # translate reports - trans_reports = self.rep_proc.radboud_translate_reports(proc_reports) + if self.use_case == 'celiac': + # translate reports + trans_reports = self.rep_proc.radboud_translate_celiac_reports(proc_reports) + else: + # translate reports + trans_reports = self.rep_proc.radboud_translate_reports(proc_reports) else: # raise exception print('provide correct hospital info: "aoec" or "radboud"') raise Exception @@ -593,7 +610,7 @@ def create_med_graphs(self, reports, concepts, struct=False, debug=False): else: return rdf_graphs - def med_pipeline(self, ds, src_lang=None, use_case=None, sim_thr=0.7, store=False, rdf_format='all', raw=False, debug=False): + def med_pipeline(self, ds, preprocess, src_lang=None, use_case=None, sim_thr=0.7, store=False, rdf_format='all', raw=False, debug=False): """ Perform the complete SKET pipeline over generic data: - (i) Process dataset @@ -608,6 +625,7 @@ def med_pipeline(self, ds, src_lang=None, use_case=None, sim_thr=0.7, store=Fals Params: ds (dict): dataset + preprocess (boolean): whether to preprocess data or not. src_lang (str): considered language use_case (str): considered use case hosp (str): considered hospital @@ -635,10 +653,23 @@ def med_pipeline(self, ds, src_lang=None, use_case=None, sim_thr=0.7, store=Fals rdf_graphs_out = './outputs/graphs/rdf/' + self.use_case + '/' struct_graphs_out = './outputs/graphs/json/' + self.use_case + '/' - # set dataset name - ds_name = str(uuid.uuid4()) - # prepare dataset - reports = self.prepare_med_dataset(ds, ds_name, src_lang, store, debug=debug) + if preprocess: + if type(ds) == str: + # set dataset name as input file name + ds_name = ds.split('/')[-1].split('.')[0] + else: + # set dataset name with random identifier + ds_name = str(uuid.uuid4()) + # prepare dataset + reports = self.prepare_med_dataset(ds, ds_name, src_lang, store, debug=debug) + else: + if type(ds) == str and ds.split('.')[-1] == 'json': + # set dataset name as input file name + ds_name = ds.split('/')[-1].split('.')[0] + reports = self.load_reports(ds) + else: # raise exception + print('Format required for input without preprocess step: JSON.') + raise Exception # perform entity linking concepts = self.med_entity_linking(reports, sim_thr, raw, debug=debug) diff --git a/sket/utils/utils.py b/sket/utils/utils.py index 25c28d1..760e991 100644 --- a/sket/utils/utils.py +++ b/sket/utils/utils.py @@ -88,6 +88,52 @@ def en_sanitize_record(record, use_case): # @smarchesin TODO: define sanitize u record = record.replace('ii cin', 'cin2') record = record.replace('i cin', 'cin1') record = record.replace('port biopsy', 'portio biopsy') + if use_case == 'celiac': + record = record.replace('villas', 'villi') + record = record.replace('duodonitis', 'duodenitis') + record = record.replace('duodoneitis', 'duodenitis') + record = record.replace('duodonia', 'duodenitis') + record = record.replace('duedenitis', 'duodenitis') + record = record.replace('mucosae', 'mucosa') + record = record.replace('mucous', 'mucosa') + record = record.replace('oedema', 'edema') + record = record.replace('leucocyte', 'leukocyte') + record = record.replace('granulocytes', 'granulocyte') + record = record.replace('eosinophiles', 'eosinophil') + record = record.replace('neutrophiles', 'neutrophil') + record = record.replace('leukocytes', 'leukocyte') + record = record.replace('lymphocytes', 'lymphocyte') + record = record.replace('lymphocytosis', 'lymphocyte') + record = record.replace('enterocytes', 'enterocyte') + record = record.replace('vills', 'villi') + record = record.replace('villous', 'villi') + record = record.replace('villuse', 'villi') + record = record.replace('villus', 'villi') + record = record.replace('cryptes', 'crypts') + record = record.replace('hyperaemia', 'hyperemia') + record = record.replace('antro', 'antrum') + record = record.replace('biopt', 'biopsy') + record = record.replace('biopsys', 'biopsy') + record = record.replace('geen afwijking', 'no abnormalities') + record = record.replace('no deviation', 'no abnormalities') + record = record.replace('no abnormality', 'no abnormalities') + record = record.replace('bioptes', 'biopsy') + record = record.replace('biopsie', 'biopsy') + record = record.replace('duedenum', 'duodenum') + record = record.replace('duodenium', 'duodenum') + record = record.replace('biopsies', 'biopsy') + record = record.replace('coeliac', 'celiac') + record = record.replace('coeliakie', 'celiac disease') + record = record.replace('ontsteking', 'inflammation') + record = record.replace('anthrum', 'antrum') + record = record.replace('corpusbiopts', 'corpus biopsy') + record = record.replace('flokatrophy', 'villi atrophy') + record = record.replace('flocatrophy', 'villi atrophy') + record = record.replace('flake', 'villi') + record = record.replace('bulbus duodeni', 'duodenal bulb') + record = record.replace('eosinophilia', 'eosinophil') + record = record.replace('theduodenum', 'the duodenum') + return record @@ -519,6 +565,40 @@ def aoec_lung_concepts2labels(report_concepts): return report_labels +def aoec_celiac_concepts2labels(report_concepts): + """ + Convert the concepts extracted from celiac reports to the set of pre-defined labels used for classification + + Params: + report_concepts (dict(list)): the dict containing for each celiac report the extracted concepts + + Returns: a dict containing for each celiac report the set of pre-defined labels where 0 = absence and 1 = presence + """ + + report_labels = dict() + # loop over reports + for rid, rconcepts in report_concepts.items(): + # assign pre-defined set of labels to current report + report_labels[rid] = { + 'celiac_disease': 0, 'duodenitis': 0, 'inconclusive': 0, 'normal': 0} + # make diagnosis section a set + diagnosis = set([concept[1].lower() for concept in rconcepts['Diagnosis']]) + # update pre-defined labels w/ 1 in case of label presence + for d in diagnosis: + if 'positive to celiac disease' == d: + report_labels[rid]['celiac_disease'] = 1 + if 'duodenitis' == d: + report_labels[rid]['duodenitis'] = 1 + if 'inconclusive outcome' == d: + report_labels[rid]['inconclusive'] = 1 + if 'negative result' == d: + report_labels[rid]['normal'] = 1 + # update when no label has been set to 1 + if sum(report_labels[rid].values()) == 0: + report_labels[rid]['normal'] = 1 + return report_labels + + # RADBOUD RELATED FUNCTIONS def radboud_colon_concepts2labels(report_concepts): @@ -538,7 +618,7 @@ def radboud_colon_concepts2labels(report_concepts): # assign pre-defined set of labels to current report report_labels[rid]['labels'] = {'cancer': 0, 'hgd': 0, 'lgd': 0, 'hyperplastic': 0, 'ni': 0} # textify diagnosis section - diagnosis = ' '.join([concept[1].lower() for concept in rconcepts['concepts']['Diagnosis']]) + diagnosis = ' '.join([concept[1].lower() for concept in rconcepts['Diagnosis']]) # update pre-defined labels w/ 1 in case of label presence if 'colon adenocarcinoma' in diagnosis: # update cancer report_labels[rid]['labels']['cancer'] = 1 @@ -597,41 +677,42 @@ def radboud_cervix_concepts2labels(report_concepts): report_labels = dict() # loop over reports for rid, rconcepts in report_concepts.items(): + report_labels[rid] = dict() # assign pre-defined set of labels to current report - report_labels[rid] = { + report_labels[rid]['labels'] = { 'cancer_scc_inv': 0, 'cancer_scc_insitu': 0, 'cancer_adeno_inv': 0, 'cancer_adeno_insitu': 0, 'lgd': 0, 'hgd': 0, 'hpv': 0, 'koilocytes': 0, 'glands_norm': 0, 'squamous_norm': 0 } # make diagnosis section a set - diagnosis = set([concept[1].lower() for concept in rconcepts['concepts']['Diagnosis']]) + diagnosis = set([concept[1].lower() for concept in rconcepts['Diagnosis']]) # update pre-defined labels w/ 1 in case of label presence for d in diagnosis: if 'cervical squamous cell carcinoma' == d: - report_labels[rid]['cancer_scc_inv'] = 1 + report_labels[rid]['labels']['cancer_scc_inv'] = 1 if 'squamous carcinoma in situ' == d or 'squamous intraepithelial neoplasia' == d: - report_labels[rid]['cancer_scc_insitu'] = 1 + report_labels[rid]['labels']['cancer_scc_insitu'] = 1 if 'cervical adenocarcinoma' in d: if 'cervical adenocarcinoma in situ' == d: - report_labels[rid]['cancer_adeno_insitu'] = 1 + report_labels[rid]['labels']['cancer_adeno_insitu'] = 1 else: - report_labels[rid]['cancer_adeno_inv'] = 1 + report_labels[rid]['labels']['cancer_adeno_inv'] = 1 if 'low grade cervical squamous intraepithelial neoplasia' == d: - report_labels[rid]['lgd'] = 1 + report_labels[rid]['labels']['lgd'] = 1 if 'squamous carcinoma in situ' == d or \ 'squamous intraepithelial neoplasia' == d or \ 'cervical squamous intraepithelial neoplasia 2' == d or \ 'cervical intraepithelial neoplasia grade 2/3' == d: - report_labels[rid]['hgd'] = 1 + report_labels[rid]['labels']['hgd'] = 1 if 'human papilloma virus infection' == d: - report_labels[rid]['hpv'] = 1 + report_labels[rid]['labels']['hpv'] = 1 if 'koilocytotic squamous cell' == d: - report_labels[rid]['koilocytes'] = 1 + report_labels[rid]['labels']['koilocytes'] = 1 # update when no label has been set to 1 - if sum(report_labels[rid].values()) == 0: - report_labels[rid]['glands_norm'] = 1 - report_labels[rid]['squamous_norm'] = 1 + if sum(report_labels[rid]['labels'].values()) == 0: + report_labels[rid]['labels']['glands_norm'] = 1 + report_labels[rid]['labels']['squamous_norm'] = 1 if 'slide_ids' in rconcepts: report_labels[rid]['slide_ids'] = rconcepts['slide_ids'] @@ -651,30 +732,68 @@ def radboud_cervix_labels2aggregates(report_labels): fine_labels = dict() # loop over reports for rid, rlabels in report_labels.items(): + coarse_labels[rid] = dict() + fine_labels[rid] = dict() # assign aggregated labels to current report - coarse_labels[rid] = {'cancer': 0, 'dysplasia': 0, 'normal': 0} - fine_labels[rid] = {'cancer_adeno': 0, 'cancer_scc': 0, 'dysplasia': 0, 'glands_norm': 0, 'squamous_norm': 0} + coarse_labels[rid]['labels'] = {'cancer': 0, 'dysplasia': 0, 'normal': 0} + fine_labels[rid]['labels'] = {'cancer_adeno': 0, 'cancer_scc': 0, 'dysplasia': 0, 'glands_norm': 0, 'squamous_norm': 0} # update aggregated labels w/ 1 in case of label presence if rlabels['cancer_adeno_inv'] == 1 or rlabels['cancer_adeno_insitu'] == 1: - coarse_labels[rid]['cancer'] = 1 - fine_labels[rid]['cancer_adeno'] = 1 + coarse_labels[rid]['labels']['cancer'] = 1 + fine_labels[rid]['labels']['cancer_adeno'] = 1 if rlabels['cancer_scc_inv'] == 1 or rlabels['cancer_scc_insitu'] == 1: - coarse_labels[rid]['cancer'] = 1 - fine_labels[rid]['cancer_scc'] = 1 + coarse_labels[rid]['labels']['cancer'] = 1 + fine_labels[rid]['labels']['cancer_scc'] = 1 if rlabels['lgd'] == 1 or rlabels['hgd'] == 1: - coarse_labels[rid]['dysplasia'] = 1 - fine_labels[rid]['dysplasia'] = 1 + coarse_labels[rid]['labels']['dysplasia'] = 1 + fine_labels[rid]['labels']['dysplasia'] = 1 if rlabels['glands_norm'] == 1: - coarse_labels[rid]['normal'] = 1 - fine_labels[rid]['glands_norm'] = 1 + coarse_labels[rid]['labels']['normal'] = 1 + fine_labels[rid]['labels']['glands_norm'] = 1 if rlabels['squamous_norm'] == 1: - coarse_labels[rid]['normal'] = 1 - fine_labels[rid]['squamous_norm'] = 1 + coarse_labels[rid]['labels']['normal'] = 1 + fine_labels[rid]['labels']['squamous_norm'] = 1 if 'slide_ids' in rlabels: coarse_labels[rid]['slide_ids'] = rlabels['slide_ids'] fine_labels[rid]['slide_ids'] = rlabels['slide_ids'] return coarse_labels, fine_labels +def radboud_celiac_concepts2labels(report_concepts): + """ + Convert the concepts extracted from celiac reports to the set of pre-defined labels used for classification + + Params: + report_concepts (dict(list)): the dict containing for each celiac report the extracted concepts + + Returns: a dict containing for each celiac report the set of pre-defined labels where 0 = absence and 1 = presence + """ + + report_labels = dict() + # loop over reports + for rid, rconcepts in report_concepts.items(): + report_labels[rid] = dict() + # assign pre-defined set of labels to current report + report_labels[rid]['labels'] = { + 'celiac_disease': 0, 'duodenitis': 0, 'inconclusive': 0, 'normal': 0} + # make diagnosis section a set + diagnosis = set([concept[1].lower() for concept in rconcepts['Diagnosis']]) + # update pre-defined labels w/ 1 in case of label presence + for d in diagnosis: + if 'positive to celiac disease' == d: + report_labels[rid]['labels']['celiac_disease'] = 1 + if 'duodenitis' == d: + report_labels[rid]['labels']['duodenitis'] = 1 + if 'inconclusive outcome' == d: + report_labels[rid]['inconclusive'] = 1 + if 'negative result' == d: + report_labels[rid]['labels']['normal'] = 1 + # update when no label has been set to 1 + if sum(report_labels[rid]['labels'].values()) == 0: + report_labels[rid]['labels']['normal'] = 1 + if 'slide_ids' in rconcepts: + report_labels[rid]['slide_ids'] = rconcepts['slide_ids'] + return report_labels + # GENERAL-PURPOSE FUNCTIONS @@ -691,6 +810,7 @@ def colon_concepts2labels(report_concepts): report_labels = dict() # loop over reports for rid, rconcepts in report_concepts.items(): + report_labels[rid] = dict() # assign pre-defined set of labels to current report report_labels[rid] = {'cancer': 0, 'hgd': 0, 'lgd': 0, 'hyperplastic': 0, 'ni': 0} # textify diagnosis section @@ -852,3 +972,37 @@ def lung_concepts2labels(report_concepts): if sum(report_labels[rid].values()) == 0: report_labels[rid]['no_cancer'] = 1 return report_labels + + +def celiac_concepts2labels(report_concepts): + """ + Convert the concepts extracted from celiac reports to the set of pre-defined labels used for classification + + Params: + report_concepts (dict(list)): the dict containing for each celiac report the extracted concepts + + Returns: a dict containing for each celiac report the set of pre-defined labels where 0 = absence and 1 = presence + """ + + report_labels = dict() + # loop over reports + for rid, rconcepts in report_concepts.items(): + # assign pre-defined set of labels to current report + report_labels[rid] = { + 'celiac_disease': 0, 'duodenitis': 0, 'inconclusive': 0, 'normal': 0} + # make diagnosis section a set + diagnosis = set([concept[1].lower() for concept in rconcepts['Diagnosis']]) + # update pre-defined labels w/ 1 in case of label presence + for d in diagnosis: + if 'positive to celiac disease' == d: + report_labels[rid]['celiac_disease'] = 1 + if 'duodenitis' == d: + report_labels[rid]['duodenitis'] = 1 + if 'inconclusive outcome' == d: + report_labels[rid]['inconclusive'] = 1 + if 'negative result' == d: + report_labels[rid]['normal'] = 1 + # update when no label has been set to 1 + if sum(report_labels[rid].values()) == 0: + report_labels[rid]['normal'] = 1 + return report_labels