From aa6fa702ffd97a090e91d430054586b4c51012fb Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Thu, 20 Jun 2024 09:06:07 -0700 Subject: [PATCH 01/11] Updating java version --- src/main/bin/devreset-api.sh | 291 +++++++++++++++++++++++++++++++++++ src/main/bin/reindex.sh | 20 ++- 2 files changed, 304 insertions(+), 7 deletions(-) create mode 100755 src/main/bin/devreset-api.sh diff --git a/src/main/bin/devreset-api.sh b/src/main/bin/devreset-api.sh new file mode 100755 index 000000000..54a5ddfb7 --- /dev/null +++ b/src/main/bin/devreset-api.sh @@ -0,0 +1,291 @@ +#!/bin/bash -f +# +# PREREQUISITE: This script requires a download of the "UnitTestData" +# (https://drive.google.com/drive/u/0/folders/1kXIr9J3jgO-8fN01LJwhNkOuZbAfaQBh) +# to a directory called "UnitTestData" that must live under whatever +# directory is mounted as /data within the stardog container. Thus, while in +# the stardog container the path /data/UnitTestData must be available. +# +# It resets the stardog and elasticsearch data sets locally to update to +# the latest dev testing data set at that google drive URL. +# +help=0 +if [[ $db_type = "stardog" ]]; then + databases=("NCIT2" "CTRP") +elif [[ $db_type = "jena" ]]; then + databases=("NCIT2" "CTRP") +fi + +while [[ "$#" -gt 0 ]]; do case $1 in + --help) help=1;; + *) arr=( "${arr[@]}" "$1" );; +esac; shift; done + +if [ $help == 1 ] || [ ${#arr[@]} -ne 2 ]; then + echo "Usage: src/main/bin/devreset.sh \"c:/data/UnitTestData\" stardog" + echo " e.g. src/main/bin/devreset.sh ../data/UnitTestData stardog" + exit 1 +fi +dir=${arr[0]} +db_type=${arr[1]} +# Hardcode the history file +historyFile=$dir/cumulative_history_21.06e.txt + +# Set up ability to format json +jq --help >> /dev/null 2>&1 +if [[ $? -eq 0 ]]; then + jq="jq ." +else + jq="python -m json.tool" +fi + +echo "--------------------------------------------------" +echo "Starting ...`/bin/date`" +echo "--------------------------------------------------" +echo "dir = $dir" +echo "db_type = $db_type" +echo "" +#set -e + +# Check configuration +if [[ -z $STARDOG_HOST ]]; then + echo "ERROR: STARDOG_HOST is not set" + exit 1 +elif [[ -z $STARDOG_PORT ]]; then + echo "ERROR: STARDOG_PORT is not set" + exit 1 +elif [[ -z $STARDOG_USERNAME ]]; then + echo "ERROR: STARDOG_USERNAME is not set" + exit 1 +elif [[ -z $STARDOG_PASSWORD ]]; then + echo "ERROR: STARDOG_PASSWORD is not set" + exit 1 +elif [[ -z $ES_SCHEME ]]; then + echo "ERROR: ES_SCHEME is not set" + exit 1 +elif [[ -z $ES_HOST ]]; then + echo "ERROR: ES_HOST is not set" + exit 1 +elif [[ -z $ES_PORT ]]; then + echo "ERROR: ES_PORT is not set" + exit 1 +fi + +# Prerequisites - check the UnitTest +echo " Check prerequisites" + +# Check that reindex.sh is at src/main/bin +if [[ ! -e "src/main/bin/reindex.sh" ]]; then + echo "ERROR: src/main/bin/reindex.sh does not exist, run from top-level evsrestapi directory" + exit 1 +fi + +# Check NCIM +echo " check NCIM" +ct=`ls $dir/NCIM | grep RRF | wc -l` +if [[ $ct -le 20 ]]; then + echo "ERROR: unexpectedly small number of NCIM/*RRF files = $ct" + exit 1 +fi +# Check NCIt weekly +echo " check NCIt weekly" +if [[ ! -e "$dir/ThesaurusInferred_+1weekly.owl" ]]; then + echo "ERROR: unexpectedly ThesaurusInferred_+1weekly.owl file" + exit 1 +fi +# Check NCIt monthly +echo " check NCIt monthly" +if [[ ! -e "$dir/ThesaurusInferred_monthly.owl" ]]; then + echo "ERROR: unexpectedly ThesaurusInferred_monthly.owl file" + exit 1 +fi +# Check GO monthly +echo " check GO monthly" +if [[ ! -e "$dir/GO/go.2022-07-01.owl" ]]; then + echo "ERROR: unexpectedly missing GO/go.2022-07-01.owl file" + exit 1 +fi + +# Check HGNC monthly +echo " check HGNC monthly" +if [[ ! -e "$dir/HGNC/HGNC_202209.owl" ]]; then + echo "ERROR: unexpectedly missing HGNC/HGNC_202209.owl file" + exit 1 +fi + +# Check ChEBI monthly +echo " check ChEBI monthly" +if [[ ! -e "$dir/ChEBI/chebi_213.owl" ]]; then + echo "ERROR: unexpectedly missing ChEBI/chebi_213.owl file" + exit 1 +fi + +# Check DUO +echo " check DUO" +if [[ ! -e "$dir/DUO/duo_Feb21.owl" ]]; then + echo "ERROR: unexpectedly missing DUO/duo_Feb21.owl file" + exit 1 +fi + +# Check OBI +echo " check OBI" +if [[ ! -e "$dir/OBI/obi_2022_07.owl" ]]; then + echo "ERROR: unexpectedly missing OBI/obi_2022_07.owl file" + exit 1 +fi + +# Check OBIB +echo " check OBIB" +if [[ ! -e "$dir/OBIB/obib_2021-11.owl" ]]; then + echo "ERROR: unexpectedly missing OBI/obib_2021-11.owl file" + exit 1 +fi + +# Check NDFRT +echo " check NDFRT" +if [[ ! -e "$dir/NDFRT/NDFRT_Public_2018.02.05_Inferred.owl" ]]; then + echo "ERROR: unexpectedly missing NDFRT/NDFRT_Public_2018.02.05_Inferred.owl file" + exit 1 +fi + +# Verify docker stardog is running +echo " verify $db_type database is running" +if [[ $db_type = "stardog" ]]; then + curl -s -f "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/healthcheck" > /dev/null +elif [[ $db_type = "jena" ]]; then + curl -s -f "http://${STARDOG_HOST}:${STARDOG_PORT}/$/ping" > /dev/null +fi +if [[ $? -ne 0 ]]; then + echo "$db_type is not running" + exit 1 +fi + + +# Verify elasticsearch can be reached +echo " verify elasticsearch can be reached" +curl -s "$ES_SCHEME://$ES_HOST:$ES_PORT/_cat/indices" >> /dev/null +if [[ $? -ne 0 ]]; then + echo "ERROR: problem connecting to elasticsearch" + exit 1 +fi + +# Remove elasticsearch indexes +remove_elasticsearch_indexes(){ + echo " Remove elasticsearch indexes" + curl -s "$ES_SCHEME://$ES_HOST:$ES_PORT/_cat/indices" | cut -d\ -f 3 | egrep "metrics|concept|evs" | grep -v "snomed" | cat > /tmp/x.$$.txt + if [[ $? -ne 0 ]]; then + echo "ERROR: problem connecting to docker elasticsearch" + exit 1 + fi + for i in `cat /tmp/x.$$.txt`; do + echo " remove $i" + curl -s -X DELETE "$ES_SCHEME://$ES_HOST:$ES_PORT/$i" >> /dev/null + if [[ $? -ne 0 ]]; then + echo "ERROR: problem removing elasticsearch index $i" + exit 1 + fi + done +} +# Reindex ncim - individual terminologies +reindex_ncim(){ + for t in MDR ICD10CM ICD9CM LNC SNOMEDCT_US RADLEX PDQ ICD10 HL7V3.0; do + # Keep the NCIM folder around while we run + echo "Load $t (from downloaded data)" + src/main/bin/ncim-part.sh --noconfig $dir/NCIM --keep --terminology $t > /tmp/x.$$.txt 2>&1 + if [[ $? -ne 0 ]]; then + cat /tmp/x.$$.txt | sed 's/^/ /' + echo "ERROR: loading $t" + exit 1 + fi + done + # Reindex ncim - must run after the prior section so that maps can connect to loaded terminologies + echo " Reindex ncim" + src/main/bin/ncim-part.sh --noconfig $dir/NCIM > /tmp/x.$$.txt 2>&1 + if [[ $? -ne 0 ]]; then + cat /tmp/x.$$.txt | sed 's/^/ /' + echo "ERROR: problem running ncim-part.sh" + exit 1 + fi +} + +drop_databases(){ + for db in "${databases[@]}" + do + echo "Dropping $db" + if [[ $db_type = "stardog" ]]; then + curl -s -f -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases/${db}" > /dev/null + elif [[ $db_type = "jena" ]]; then + curl -s -f -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets/${db}" > /dev/null + fi + if [[ $? -ne 0 ]]; then + echo "Error occurred when dropping database ${db}. Response:$_" + exit 1 + fi + done +} + +create_databases(){ + for db in "${databases[@]}" + do + echo "Creating $db" + if [[ $db_type = "stardog" ]]; then + curl -s -f -X POST -F root="{\"dbname\":\"${db}\"}" "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases" > /dev/null + elif [[ $db_type = "jena" ]]; then + curl -s -f -X POST -F "dbName=${db}" -F "dbType=tdb2" "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets" > /dev/null + fi + if [[ $? -ne 0 ]]; then + echo "Error occurred when creating database ${db}. Response:$_" + exit 1 + fi + done +} + +load_data_in_transaction(){ + echo " Loading $3 into $1" + tx=$(curl -s -u "${STARDOG_USERNAME}":"${STARDOG_PASSWORD}" -X POST "http://localhost:5820/$1/transaction/begin") + curl -s -u "${STARDOG_USERNAME}":"${STARDOG_PASSWORD}" -X POST "http://localhost:5820/$1/${tx}/add?graph-uri=$2" -H "Content-Type: application/rdf+xml" -T - < "$dir/$3" + tx=$(curl -s -u "${STARDOG_USERNAME}":"${STARDOG_PASSWORD}" -X POST "http://localhost:5820/NCIT2/transaction/commit/${tx}") + if [[ $? -ne 0 ]]; then + echo "Error occurred when loading data into $1. Response:$_" + exit 1 + fi +} + +load_data(){ + echo " Loading data into stardog" + if [[ $db_type = "stardog" ]]; then + load_data_in_transaction NCIT2 http://DUO_monthly DUO/duo_Feb21.owl + load_data_in_transaction NCIT2 http://DUO_monthly DUO/iao_Dec20.owl + elif [[ $db_type = "jena" ]]; then + echo "" + fi +} + +reindex(){ +# Reindex stardog terminologies +echo " Reindex stardog terminologies" +# After this point, the log is stored in the tmp folder unless an error is hit +src/main/bin/reindex.sh --noconfig --history "$historyFile" > /tmp/x.$$.txt 2>&1 +if [[ $? -ne 0 ]]; then + cat /tmp/x.$$.txt | sed 's/^/ /' + echo "ERROR: problem running reindex.sh script" + exit 1 +fi +} + +# Clean and load stardog +echo " Remove stardog databases and load monthly/weekly" +drop_databases +create_databases +remove_elasticsearch_indexes +#reindex_ncim +#load_data +#reindex + +# Cleanup +/bin/rm -f /tmp/x.$$.txt $dir/x.{sh,txt} + +echo "" +echo "--------------------------------------------------" +echo "Finished ...`/bin/date`" +echo "--------------------------------------------------" \ No newline at end of file diff --git a/src/main/bin/reindex.sh b/src/main/bin/reindex.sh index b16dfebbb..bbc7e5c81 100755 --- a/src/main/bin/reindex.sh +++ b/src/main/bin/reindex.sh @@ -87,16 +87,22 @@ fi metadata_config_url=${CONFIG_BASE_URI:-"https://raw.githubusercontent.com/NCIEVS/evsrestapi-operations/main/config/metadata"} -curl -s -g -u "${STARDOG_USERNAME}:$STARDOG_PASSWORD" \ - "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases" |\ - $jq | perl -ne 's/\r//; $x=0 if /\]/; - if ($x) { s/.* "//; s/",?$//; print "$_"; }; - $x=1 if/\[/;' > /tmp/db.$$.txt +response=$(curl -f -s -g -u "${STARDOG_USERNAME}:$STARDOG_PASSWORD" \ + "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases") if [[ $? -ne 0 ]]; then - echo "ERROR: unexpected problem listing databases" - exit 1 + echo "ERROR: problem listing databases. Trying a different URL" + curl -s "http://${STARDOG_HOST}:${STARDOG_PORT}/$/server" | jq -r '.datasets|.[]|."ds.name" | gsub("^/";"")' > /tmp/db.$$.txt + if [[ $? -ne 0 ]]; then + echo "ERROR: unexpected problem listing databases. Exiting" + exit 1 + fi +else + echo "$response" | $jq | perl -ne 's/\r//; $x=0 if /\]/; + if ($x) { s/.* "//; s/",?$//; print "$_"; }; + $x=1 if/\[/;' > /tmp/db.$$.txt fi + echo " databases = " `cat /tmp/db.$$.txt` ct=`cat /tmp/db.$$.txt | wc -l` if [[ $ct -eq 0 ]]; then From c47f4a69a9746ecef639f3b7e30f882117f3308c Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Thu, 20 Jun 2024 09:24:48 -0700 Subject: [PATCH 02/11] Updating java version --- IDE_Integration.doc | Bin 1177600 -> 1177573 bytes src/main/resources/metadata/go.txt | 18 ++-- src/test/resources/samples/go-samples.txt | 126 +++++++++++----------- 3 files changed, 72 insertions(+), 72 deletions(-) diff --git a/IDE_Integration.doc b/IDE_Integration.doc index 9c8b88a07f43cf038f89678c9b221593a74dd184..26ecaaa1494e152c01bfbcd36db9f70aafbe0fe0 100644 GIT binary patch delta 194 zcmV;z06qVJ@JHqEN3c;Mvr;1X8?#G3eP6T5oncFZE9ti@=>a&Phh&KYw`7R}ed4#` zYXr@_x3DM$gcG+lJOxZJw}Na1ebcr;2K5cM_Du%QwYSCt2km*cw0#G*L$_#C5VoPWnwb%1UOGuxyZ`_I delta 249 zcmaF*-o4?2`-VUzM&8YVN Date: Mon, 5 Aug 2024 03:36:05 -0700 Subject: [PATCH 03/11] Updates due to running devreset on Jena --- src/main/bin/devreset-api.sh | 91 ++++++++++++++----- .../service/SparqlQueryManagerService.java | 3 + .../SparqlQueryManagerServiceImpl.java | 18 +++- src/main/resources/sparql-queries.properties | 39 +++++++- 4 files changed, 122 insertions(+), 29 deletions(-) diff --git a/src/main/bin/devreset-api.sh b/src/main/bin/devreset-api.sh index 54a5ddfb7..c02d7220b 100755 --- a/src/main/bin/devreset-api.sh +++ b/src/main/bin/devreset-api.sh @@ -10,12 +10,6 @@ # the latest dev testing data set at that google drive URL. # help=0 -if [[ $db_type = "stardog" ]]; then - databases=("NCIT2" "CTRP") -elif [[ $db_type = "jena" ]]; then - databases=("NCIT2" "CTRP") -fi - while [[ "$#" -gt 0 ]]; do case $1 in --help) help=1;; *) arr=( "${arr[@]}" "$1" );; @@ -31,6 +25,15 @@ db_type=${arr[1]} # Hardcode the history file historyFile=$dir/cumulative_history_21.06e.txt + +if [[ $db_type = "stardog" ]]; then + databases=("NCIT2" "CTRP") + curl_cmd="curl -s -f -u ${STARDOG_USERNAME}:${STARDOG_PASSWORD}" +elif [[ $db_type = "jena" ]]; then + databases=("NCIT2" "CTRP") + curl_cmd="curl -s -f" +fi + # Set up ability to format json jq --help >> /dev/null 2>&1 if [[ $? -eq 0 ]]; then @@ -151,9 +154,9 @@ fi # Verify docker stardog is running echo " verify $db_type database is running" if [[ $db_type = "stardog" ]]; then - curl -s -f "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/healthcheck" > /dev/null + $curl_cmd "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/healthcheck" > /dev/null elif [[ $db_type = "jena" ]]; then - curl -s -f "http://${STARDOG_HOST}:${STARDOG_PORT}/$/ping" > /dev/null + $curl_cmd -s -f "http://${STARDOG_HOST}:${STARDOG_PORT}/$/ping" > /dev/null fi if [[ $? -ne 0 ]]; then echo "$db_type is not running" @@ -211,11 +214,11 @@ reindex_ncim(){ drop_databases(){ for db in "${databases[@]}" do - echo "Dropping $db" + echo " Dropping $db" if [[ $db_type = "stardog" ]]; then - curl -s -f -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases/${db}" > /dev/null + $curl_cmd -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases/${db}" > /dev/null elif [[ $db_type = "jena" ]]; then - curl -s -f -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets/${db}" > /dev/null + $curl_cmd -X DELETE "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets/${db}" > /dev/null fi if [[ $? -ne 0 ]]; then echo "Error occurred when dropping database ${db}. Response:$_" @@ -227,11 +230,11 @@ drop_databases(){ create_databases(){ for db in "${databases[@]}" do - echo "Creating $db" + echo " Creating $db" if [[ $db_type = "stardog" ]]; then - curl -s -f -X POST -F root="{\"dbname\":\"${db}\"}" "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases" > /dev/null + $curl_cmd -X POST -F root="{\"dbname\":\"${db}\"}" "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases" > /dev/null elif [[ $db_type = "jena" ]]; then - curl -s -f -X POST -F "dbName=${db}" -F "dbType=tdb2" "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets" > /dev/null + $curl_cmd -X POST -d "dbName=${db}&dbType=tdb2" "http://${STARDOG_HOST}:${STARDOG_PORT}/$/datasets" > /dev/null fi if [[ $? -ne 0 ]]; then echo "Error occurred when creating database ${db}. Response:$_" @@ -240,7 +243,7 @@ create_databases(){ done } -load_data_in_transaction(){ +load_terminology_data_in_transaction(){ echo " Loading $3 into $1" tx=$(curl -s -u "${STARDOG_USERNAME}":"${STARDOG_PASSWORD}" -X POST "http://localhost:5820/$1/transaction/begin") curl -s -u "${STARDOG_USERNAME}":"${STARDOG_PASSWORD}" -X POST "http://localhost:5820/$1/${tx}/add?graph-uri=$2" -H "Content-Type: application/rdf+xml" -T - < "$dir/$3" @@ -251,16 +254,60 @@ load_data_in_transaction(){ fi } +load_terminology_data(){ + echo " Loading $3 into $1" + $curl_cmd -X POST -H "Content-Type: application/rdf+xml" -T "$dir/$3" "http://${STARDOG_HOST}:${STARDOG_PORT}/$1/data?graph=$2" > /dev/null + if [[ $? -ne 0 ]]; then + echo "Error occurred when loading data into $1. Response:$_" + exit 1 + fi +} + load_data(){ - echo " Loading data into stardog" if [[ $db_type = "stardog" ]]; then - load_data_in_transaction NCIT2 http://DUO_monthly DUO/duo_Feb21.owl - load_data_in_transaction NCIT2 http://DUO_monthly DUO/iao_Dec20.owl + load_terminology_data_in_transaction CTRP http://NCI_T_weekly ThesaurusInferred_+1weekly.owl + load_terminology_data_in_transaction CTRP http://NCI_T_monthly ThesaurusInferred_monthly.owl + load_terminology_data_in_transaction NCIT2 http://NCI_T_monthly ThesaurusInferred_monthly.owl + load_terminology_data_in_transaction NCIT2 http://GO_monthly GO/go.2022-07-01.owl + load_terminology_data_in_transaction NCIT2 http://HGNC_monthly HGNC/HGNC_202209.owl + load_terminology_data_in_transaction NCIT2 http://ChEBI_monthly ChEBI/chebi_213.owl + load_terminology_data_in_transaction NCIT2 http://UmlsSemNet UmlsSemNet/umlssemnet.owl + load_terminology_data_in_transaction NCIT2 http://MEDRT MED-RT/medrt.owl + load_terminology_data_in_transaction NCIT2 http://Canmed CanMed/canmed.owl + load_terminology_data_in_transaction NCIT2 http://CTCAE CTCAE/ctcae5.owl + load_terminology_data_in_transaction NCIT2 http://DUO_monthly DUO/duo_Feb21.owl + load_terminology_data_in_transaction NCIT2 http://DUO_monthly DUO/iao_Dec20.owl + load_terminology_data_in_transaction NCIT2 http://OBI_monthly OBI/obi_2022_07.owl + load_terminology_data_in_transaction NCIT2 http://OBIB OBIB/obib_2021-11.owl + load_terminology_data_in_transaction NCIT2 http://NDFRT2 NDFRT/NDFRT_Public_2018.02.05_Inferred.owl + load_terminology_data_in_transaction NCIT2 http://MGED MGED/MGEDOntology.owl + load_terminology_data_in_transaction NCIT2 http://NPO NPO/npo-2011-12-08_inferred.owl + load_terminology_data_in_transaction NCIT2 http://MA Mouse_Anatomy/ma_07_27_2016.owl + load_terminology_data_in_transaction NCIT2 http://Zebrafish Zebrafish/zfa_2019_08_02.owl elif [[ $db_type = "jena" ]]; then - echo "" + load_terminology_data CTRP http://NCI_T_weekly ThesaurusInferred_+1weekly.owl + load_terminology_data CTRP http://NCI_T_monthly ThesaurusInferred_monthly.owl + load_terminology_data NCIT2 http://NCI_T_monthly ThesaurusInferred_monthly.owl + load_terminology_data NCIT2 http://GO_monthly GO/go.2022-07-01.owl + load_terminology_data NCIT2 http://HGNC_monthly HGNC/HGNC_202209.owl + load_terminology_data NCIT2 http://ChEBI_monthly ChEBI/chebi_213.owl + load_terminology_data NCIT2 http://UmlsSemNet UmlsSemNet/umlssemnet.owl + load_terminology_data NCIT2 http://MEDRT MED-RT/medrt.owl + load_terminology_data NCIT2 http://Canmed CanMed/canmed.owl + load_terminology_data NCIT2 http://CTCAE CTCAE/ctcae5.owl + load_terminology_data NCIT2 http://DUO_monthly DUO/duo_Feb21.owl + load_terminology_data NCIT2 http://DUO_monthly DUO/iao_Dec20.owl + load_terminology_data NCIT2 http://OBI_monthly OBI/obi_2022_07.owl + load_terminology_data NCIT2 http://OBIB OBIB/obib_2021-11.owl + load_terminology_data NCIT2 http://NDFRT2 NDFRT/NDFRT_Public_2018.02.05_Inferred.owl + load_terminology_data NCIT2 http://MGED MGED/MGEDOntology.owl + load_terminology_data NCIT2 http://NPO NPO/npo-2011-12-08_inferred.owl + load_terminology_data NCIT2 http://MA Mouse_Anatomy/ma_07_27_2016.owl + load_terminology_data NCIT2 http://Zebrafish Zebrafish/zfa_2019_08_02.owl fi } + reindex(){ # Reindex stardog terminologies echo " Reindex stardog terminologies" @@ -278,9 +325,9 @@ echo " Remove stardog databases and load monthly/weekly" drop_databases create_databases remove_elasticsearch_indexes -#reindex_ncim -#load_data -#reindex +reindex_ncim +load_data +reindex # Cleanup /bin/rm -f /tmp/x.$$.txt $dir/x.{sh,txt} diff --git a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerService.java b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerService.java index 04902e487..0a01e4cd9 100644 --- a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerService.java +++ b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerService.java @@ -36,6 +36,9 @@ public interface SparqlQueryManagerService { public Concept getConcept(String conceptCode, Terminology terminology, IncludeParam ip) throws Exception; + public Concept getConceptFromElasticSearch( + String conceptCode, Terminology terminology, String include) throws Exception; + /** * Returns the all properties. * diff --git a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java index bed01da28..411b36e7a 100644 --- a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java +++ b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java @@ -8,6 +8,7 @@ import gov.nih.nci.evs.api.model.Axiom; import gov.nih.nci.evs.api.model.Concept; import gov.nih.nci.evs.api.model.ConceptMinimal; +import gov.nih.nci.evs.api.model.ConceptResultList; import gov.nih.nci.evs.api.model.DisjointWith; import gov.nih.nci.evs.api.model.HierarchyNode; import gov.nih.nci.evs.api.model.IncludeParam; @@ -16,6 +17,7 @@ import gov.nih.nci.evs.api.model.Property; import gov.nih.nci.evs.api.model.Qualifier; import gov.nih.nci.evs.api.model.Role; +import gov.nih.nci.evs.api.model.SearchCriteria; import gov.nih.nci.evs.api.model.Synonym; import gov.nih.nci.evs.api.model.Terminology; import gov.nih.nci.evs.api.model.TerminologyMetadata; @@ -252,6 +254,18 @@ public Concept getConcept( return getConceptByType("concept", conceptCode, terminology, ip); } + @Override + public Concept getConceptFromElasticSearch( + final String conceptCode, final Terminology terminology, final String include) + throws Exception { + SearchCriteria searchCriteria = new SearchCriteria(); + searchCriteria.setTerm(conceptCode); + searchCriteria.setInclude(include); + ConceptResultList result = + elasticSearchService.search(Collections.singletonList(terminology), searchCriteria); + return !result.getConcepts().isEmpty() ? result.getConcepts().get(0) : null; + } + /* see superclass */ @Override public List getMapsTo( @@ -2511,7 +2525,7 @@ public List getAllSubsets(final Terminology terminology) throws Excepti final List subsets = new ArrayList<>(); for (final String code : terminology.getMetadata().getSubset()) { final Concept concept = - getConcept(code, terminology, new IncludeParam("minimal,children,properties")); + getConceptFromElasticSearch(code, terminology, "minimal,children,properties"); getSubsetsHelper(concept, terminology, 0); subsets.add(concept); @@ -2533,7 +2547,7 @@ private void getSubsetsHelper( final List children = new ArrayList<>(); for (final Concept child : concept.getChildren()) { final Concept childFull = - getConcept(child.getCode(), terminology, new IncludeParam("minimal,children,properties")); + getConceptFromElasticSearch(child.getCode(), terminology, "minimal,children,properties"); boolean valInSubset = false; boolean found = false; for (final Property prop : childFull.getProperties()) { diff --git a/src/main/resources/sparql-queries.properties b/src/main/resources/sparql-queries.properties index 3a8af5cb9..cb5df5745 100644 --- a/src/main/resources/sparql-queries.properties +++ b/src/main/resources/sparql-queries.properties @@ -515,8 +515,7 @@ inverse.roles.batch=SELECT ?conceptCode ?relationship ?relationshipCode ?relatio { GRAPH <#{namedGraph}> \ { \ { \ - ?relatedConcept a owl:Class . \ - ?relatedConcept (owl:equivalentClass|rdfs:subClassOf) ?rs . \ + ?relatedConcept rdfs:subClassOf ?rs . \ ?rs a owl:Restriction . \ ?rs owl:onProperty ?relationship . \ ?rs owl:someValuesFrom ?x_concept . \ @@ -531,8 +530,38 @@ inverse.roles.batch=SELECT ?conceptCode ?relationship ?relationshipCode ?relatio } \ UNION \ { \ - ?relatedConcept a owl:Class . \ - ?relatedConcept (owl:equivalentClass|rdfs:subClassOf) ?rs . \ + ?relatedConcept owl:equivalentClass ?rs . \ + ?rs a owl:Restriction . \ + ?rs owl:onProperty ?relationship . \ + ?rs owl:someValuesFrom ?x_concept . \ + FILTER ( isIRI( ?x_concept ) ) . \ + ?x_concept a owl:Class . \ + ?x_concept #{codeCode} ?conceptCode . \ + FILTER (?conceptCode IN (#{inClause})) . \ + OPTIONAL { ?relatedConcept #{preferredNameCode} ?relatedConceptLabel } . \ + ?relatedConcept #{codeCode} ?relatedConceptCode . \ + OPTIONAL { ?relationship #{preferredNameCode} ?relationshipLabel } . \ + OPTIONAL { ?relationship #{codeCode} ?relationshipCode } . \ + } \ + UNION \ + { \ + ?relatedConcept rdfs:subClassOf ?rs . \ + ?rs a owl:Restriction . \ + ?rs owl:onProperty ?relationship . \ + ?rs owl:someValuesFrom ?x_concept . \ + FILTER ( isIRI( ?x_concept ) ) . \ + ?x_concept a owl:Class . \ + FILTER (?x_concept IN (#{aboutClause})) . \ + OPTIONAL { ?relatedConcept #{preferredNameCode} ?relatedConceptLabel } . \ + OPTIONAL { ?relatedConcept #{codeCode} ?relatedConceptCode } . \ + OPTIONAL { ?relationship #{preferredNameCode} ?relationshipLabel } . \ + OPTIONAL { ?relationship #{codeCode} ?relationshipCode } . \ + FILTER NOT EXISTS { ?x_concept #{codeCode} ?x_code } . \ + BIND(?x_concept AS ?conceptCode) \ + } \ + UNION \ + { \ + ?relatedConcept owl:equivalentClass ?rs . \ ?rs a owl:Restriction . \ ?rs owl:onProperty ?relationship . \ ?rs owl:someValuesFrom ?x_concept . \ @@ -870,10 +899,10 @@ disjoint.with.batch=SELECT ?conceptCode ?relatedConcept ?relatedConceptCode ?rel } \ UNION \ { \ - ?relatedConcept a owl:Class . \ ?x #{codeCode} ?conceptCode . \ FILTER (?conceptCode IN (#{inClause})) . \ ?relatedConcept owl:disjointWith ?x . \ + ?relatedConcept a owl:Class . \ FILTER (!isBlank(?x)) . \ OPTIONAL { ?relatedConcept #{preferredNameCode} ?relatedConceptLabel } . \ OPTIONAL { ?relatedConcept #{codeCode} ?relatedConceptCode } . \ From 53e1a35a855e2a496ed4f74082fe0edd9d6000f6 Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Mon, 5 Aug 2024 03:38:08 -0700 Subject: [PATCH 04/11] Updates due to running devreset on Jena --- .../evsrestapi-util/lib/xmlbeans-2.6.0.jar | Bin 2730866 -> 2730835 bytes software/evsrestapi-util/lib/xmlunit-1.3.jar | Bin 96751 -> 96750 bytes .../evsrestapi-util/lib/xstream-1.2.2.jar | Bin 373194 -> 373190 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/software/evsrestapi-util/lib/xmlbeans-2.6.0.jar b/software/evsrestapi-util/lib/xmlbeans-2.6.0.jar index d1b66271f5e379403207383db4ff6e4b9c4e24dd..62bd3668bb6cdcbb1d513986ba6600fd095dc985 100644 GIT binary patch delta 291 zcmex#Z5iWbAZ}=3Y+>5MoUmnk;uhwsvD?jsSdLY;|LbPi{;!+Wr*^wHC!4WFd%YtY z5VLQucjS1#WqbZNjyY=WJhGfX%(b0ImRq-FyVXMOH>bC&=kf%WZLfUHqjhupl0Cf7 z!rHrq`L=fp^J|~qzWovZu5Il_GX;QH5Qv4g7tIvzWonxvylsxiMY;A%yF`Fkbo-@U zVp81O-yRivcX|7rnc`Iy+rxz-4zoq1?8I@+wc;RgWobS3Rb<{K59K%ajV^w%fBR j`!85MoUnzFcYDGX=Bu$l+Ej?;SS2HG`|oa+?Z3NOeQJSX?woAK z7C^BoM>Zg4-(Ka&@gAfn^Bcz;HJ~`FEGH0iZD*C`)@=cb8!hC1a~ep?xKEY*9-G&p9hMqdc?nL8&E7|rT`EN0R zoGo%u4#+;VO9Y5Tw;$RiCdCcZcju_syURfO)J*ZJ3LxzwB*DP}ROcflvE4^XGSm#n zUKk*`ePMu9hBc7Q*&_wS(%U(EWPZ;Bs%O!bW!nU#x$er&QUKCR{>nN%2C94ZKyLf9 z2l6UUfo!g03fsAkDK38il;5~asW1*mE3qp3F9ymLu29}yxI(2X3CRA$T?&Z+ delta 20 acmaF&nf3i=)(yX`7U+e&QJ_?lp diff --git a/software/evsrestapi-util/lib/xstream-1.2.2.jar b/software/evsrestapi-util/lib/xstream-1.2.2.jar index 31721c5f38999f288420cf801b9f359361722fb8..2d813c229de641d1790cb361c076cab0da481b8d 100644 GIT binary patch delta 44 ycmX^0SnSwiu?;K-HnSdBxvPDB6(bNc0WtIT^;Im7UAIp@z@jU#{on-_&W8Z{p%rxi delta 52 zcmX^1SnSkeu?;K-7 Date: Sun, 11 Aug 2024 22:04:11 -0700 Subject: [PATCH 05/11] Changing the MGED owl file --- src/main/bin/devreset-api.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/bin/devreset-api.sh b/src/main/bin/devreset-api.sh index c02d7220b..4b2029cce 100755 --- a/src/main/bin/devreset-api.sh +++ b/src/main/bin/devreset-api.sh @@ -300,7 +300,7 @@ load_data(){ load_terminology_data NCIT2 http://OBI_monthly OBI/obi_2022_07.owl load_terminology_data NCIT2 http://OBIB OBIB/obib_2021-11.owl load_terminology_data NCIT2 http://NDFRT2 NDFRT/NDFRT_Public_2018.02.05_Inferred.owl - load_terminology_data NCIT2 http://MGED MGED/MGEDOntology.owl + load_terminology_data NCIT2 http://MGED MGED/MGEDOntology.fix.owl load_terminology_data NCIT2 http://NPO NPO/npo-2011-12-08_inferred.owl load_terminology_data NCIT2 http://MA Mouse_Anatomy/ma_07_27_2016.owl load_terminology_data NCIT2 http://Zebrafish Zebrafish/zfa_2019_08_02.owl From f0127281163905dbce0ca959debfff162c3a7cdb Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Wed, 13 Nov 2024 04:30:29 -0800 Subject: [PATCH 06/11] Fixing reindex.sh to work with stardog and jena --- src/main/bin/get_databases.py | 18 +++ src/main/bin/get_graphs.py | 14 +++ src/main/bin/reindex.sh | 225 +++++++++++++++++++++------------- 3 files changed, 175 insertions(+), 82 deletions(-) create mode 100644 src/main/bin/get_databases.py create mode 100644 src/main/bin/get_graphs.py diff --git a/src/main/bin/get_databases.py b/src/main/bin/get_databases.py new file mode 100644 index 000000000..0e0e6cff3 --- /dev/null +++ b/src/main/bin/get_databases.py @@ -0,0 +1,18 @@ +import json +import sys + +if len(sys.argv) > 1: + GRAPH_DB_TYPE = sys.argv[1] +else: + raise Exception("Expecting graph db type as a script argument") + +data = json.load(sys.stdin) + +if GRAPH_DB_TYPE.lower() == "stardog": + for db in data["databases"]: + print(db) +elif GRAPH_DB_TYPE.lower() == "jena": + for db in data["datasets"]: + print(db["ds.name"].replace("/", "")) +else: + raise Exception("Unknown graph DB") diff --git a/src/main/bin/get_graphs.py b/src/main/bin/get_graphs.py new file mode 100644 index 000000000..8353d4a66 --- /dev/null +++ b/src/main/bin/get_graphs.py @@ -0,0 +1,14 @@ +import json +import sys + +db = sys.argv[1] +data = json.load(sys.stdin) + +bindings = data["results"]["bindings"] + +for binding in bindings: + version = binding["version"]["value"] + graph_name = binding["graphName"]["value"] + source = binding["source"]["value"] + print("|".join((version, db, graph_name, source))) + diff --git a/src/main/bin/reindex.sh b/src/main/bin/reindex.sh index 09d6f7664..1ea752239 100755 --- a/src/main/bin/reindex.sh +++ b/src/main/bin/reindex.sh @@ -42,42 +42,106 @@ if [[ $historyFileOverride ]]; then fi echo "" -# Setup configuration -echo " Setup configuration" -if [[ $config -eq 1 ]]; then - APP_HOME=/local/content/evsrestapi - CONFIG_DIR=${APP_HOME}/${APP_NAME}/config +setup_configuration() { + if [[ $config -eq 1 ]]; then + APP_HOME="${APP_HOME:-/local/content/evsrestapi}" + CONFIG_DIR=${APP_HOME}/config CONFIG_ENV_FILE=${CONFIG_DIR}/setenv.sh - echo " config = $CONFIG_ENV_FILE" - . $CONFIG_ENV_FILE - if [[ $? -ne 0 ]]; then - echo "ERROR: $CONFIG_ENV_FILE does not exist or has a problem" - echo " consider using --noconfig (if working in dev environment)" - exit 1 + if [[ -e $CONFIG_ENV_FILE ]]; then + echo " config = $CONFIG_ENV_FILE" + . $CONFIG_ENV_FILE + else + echo " ERROR: $CONFIG_ENV_FILE does not exist, consider using --noconfig" + exit 1 fi -elif [[ -z $STARDOG_HOST ]]; then - echo "ERROR: STARDOG_HOST is not set" - exit 1 -elif [[ -z $STARDOG_PORT ]]; then - echo "ERROR: STARDOG_PORT is not set" - exit 1 -elif [[ -z $STARDOG_USERNAME ]]; then - echo "ERROR: STARDOG_USERNAME is not set" - exit 1 -elif [[ -z $STARDOG_PASSWORD ]]; then - echo "ERROR: STARDOG_PASSWORD is not set" - exit 1 -elif [[ -z $ES_SCHEME ]]; then - echo "ERROR: ES_SCHEME is not set" - exit 1 -elif [[ -z $ES_HOST ]]; then - echo "ERROR: ES_HOST is not set" - exit 1 -elif [[ -z $ES_PORT ]]; then - echo "ERROR: ES_PORT is not set" - exit 1 -fi + fi +} +# Setup configuration +setup_configuration() { + echo " Setup configuration" + if [[ $config -eq 1 ]]; then + APP_HOME=/local/content/evsrestapi + CONFIG_DIR=${APP_HOME}/${APP_NAME}/config + CONFIG_ENV_FILE=${CONFIG_DIR}/setenv.sh + echo " config = $CONFIG_ENV_FILE" + . $CONFIG_ENV_FILE + if [[ $? -ne 0 ]]; then + echo "ERROR: $CONFIG_ENV_FILE does not exist or has a problem" + echo " consider using --noconfig (if working in dev environment)" + exit 1 + fi + fi +} +setup_configuration +l_graph_db_type=${GRAPH_DB_TYPE:-"stardog"} +l_graph_db_port=${GRAPH_DB_PORT:-"5820"} +validate_setup() { + if [[ $l_graph_db_type == "stardog" ]]; then + if [[ -n "$GRAPH_DB_HOME" ]]; then + l_graph_db_home="$GRAPH_DB_HOME" + elif [[ -n "$STARDOG_HOME" ]]; then + l_graph_db_home="$STARDOG_HOME" + else + echo "Error: Both GRAPH_DB_HOME and STARDOG_HOME are not set." + exit 1 + fi + if [[ -n "$GRAPH_DB_HOST" ]]; then + l_graph_db_host="$GRAPH_DB_HOST" + elif [[ -n "$STARDOG_HOST" ]]; then + l_graph_db_host="$STARDOG_HOST" + else + echo "Error: Both GRAPH_DB_HOST and STARDOG_HOST are not set." + exit 1 + fi + if [[ -n "$GRAPH_DB_USERNAME" ]]; then + l_graph_db_username="$GRAPH_DB_USERNAME" + elif [[ -n "$STARDOG_USERNAME" ]]; then + l_graph_db_username="$STARDOG_USERNAME" + else + echo "Error: Both GRAPH_DB_USERNAME and STARDOG_USERNAME are not set." + exit 1 + fi + if [[ -n "$GRAPH_DB_PASSWORD" ]]; then + l_graph_db_password="$GRAPH_DB_PASSWORD" + elif [[ -n "$STARDOG_PASSWORD" ]]; then + l_graph_db_password="$STARDOG_PASSWORD" + else + echo "Error: Both GRAPH_DB_PASSWORD and STARDOG_PASSWORD are not set." + exit 1 + fi + elif [[ $l_graph_db_type == "jena" ]]; then + if [[ -n "$GRAPH_DB_HOST" ]]; then + l_graph_db_host="$GRAPH_DB_HOST" + elif [[ -n "$STARDOG_HOST" ]]; then + l_graph_db_host="$STARDOG_HOST" + else + echo "Error: Both GRAPH_DB_HOST and STARDOG_HOST are not set." + exit 1 + fi + if [[ -n "$GRAPH_DB_PORT" ]]; then + l_graph_db_port="$GRAPH_DB_PORT" + elif [[ -n "$STARDOG_PORT" ]]; then + l_graph_db_port="$STARDOG_PORT" + else + echo "Error: Both GRAPH_DB_PORT and STARDOG_PORT are not set." + exit 1 + fi + fi + if [[ -z $ES_SCHEME ]]; then + echo "ERROR: ES_SCHEME is not set" + exit 1 + elif [[ -z $ES_HOST ]]; then + echo "ERROR: ES_HOST is not set" + exit 1 + elif [[ -z $ES_PORT ]]; then + echo "ERROR: ES_PORT is not set" + exit 1 + fi +} +validate_setup +echo " GRAPH_DB_TYPE = $l_graph_db_type" +echo " GRAPH_DB_PORT = $l_graph_db_port" if [[ $force -eq 1 ]]; then echo " force = 1" elif [[ $ES_CLEAN == "true" ]]; then @@ -87,29 +151,29 @@ fi metadata_config_url=${CONFIG_BASE_URI:-"https://raw.githubusercontent.com/NCIEVS/evsrestapi-operations/main/config/metadata"} -response=$(curl -f -s -g -u "${STARDOG_USERNAME}:$STARDOG_PASSWORD" \ - "http://${STARDOG_HOST}:${STARDOG_PORT}/admin/databases") -if [[ $? -ne 0 ]]; then - echo "ERROR: problem listing databases. Trying a different URL" - curl -s "http://${STARDOG_HOST}:${STARDOG_PORT}/$/server" | jq -r '.datasets|.[]|."ds.name" | gsub("^/";"")' > /tmp/db.$$.txt - if [[ $? -ne 0 ]]; then - echo "ERROR: unexpected problem listing databases. Exiting" +get_databases(){ + if [[ $l_graph_db_type == "stardog" ]]; then + curl -s -g -u "${l_graph_db_username}:$l_graph_db_password" \ + "http://${l_graph_db_host}:${l_graph_db_port}/admin/databases" |\ + python3 "$DIR/get_databases.py" "$GRAPH_DB_TYPE" > /tmp/db.$$.txt + elif [[ $l_graph_db_type == "jena" ]]; then + curl -s -g "http://${l_graph_db_host}:${l_graph_db_port}/$/server" |\ + python3 "$DIR/get_databases.py" "$GRAPH_DB_TYPE" > /tmp/db.$$.txt + fi + if [[ $? -ne 0 ]]; then + echo "ERROR: unexpected problem listing databases" exit 1 - fi -else - echo "$response" | $jq | perl -ne 's/\r//; $x=0 if /\]/; - if ($x) { s/.* "//; s/",?$//; print "$_"; }; - $x=1 if/\[/;' > /tmp/db.$$.txt -fi - + fi -echo " databases = " `cat /tmp/db.$$.txt` -ct=`cat /tmp/db.$$.txt | wc -l` -if [[ $ct -eq 0 ]]; then - echo "ERROR: no stardog databases, this is unexpected" - exit 1 -fi + echo " databases = " `cat /tmp/db.$$.txt` + ct=`cat /tmp/db.$$.txt | wc -l` + if [[ $ct -eq 0 ]]; then + echo "ERROR: no graph databases, this is unexpected" + exit 1 + fi +} +get_databases # Open a new file descriptor that redirects to stdout: exec 3>&1 @@ -139,7 +203,8 @@ ignored_sources=$(get_ignored_sources) echo "Ignored source URLs:${ignored_sources}" # Prep query to read all version info -echo " Lookup terminology, version info in stardog" +echo " Lookup terminology, version info in graph db" +get_graph_query(){ if [ -n "$ignored_sources" ];then cat > /tmp/x.$$.txt << EOF query=PREFIX owl: @@ -189,35 +254,31 @@ select distinct ?source ?graphName ?version where { } EOF fi -query=`cat /tmp/x.$$.txt` - +query=$(cat /tmp/x.$$.txt) +} +get_graph_query # Run the query against each of the databases -/bin/rm -f /tmp/y.$$.txt -touch /tmp/y.$$.txt -for db in `cat /tmp/db.$$.txt`; do - curl -s -g -u "${STARDOG_USERNAME}:$STARDOG_PASSWORD" \ - http://${STARDOG_HOST}:${STARDOG_PORT}/$db/query \ - --data-urlencode "$query" -H "Accept: application/sparql-results+json" |\ - $jq | perl -ne ' - chop; $x="version" if /"version"/; - $x="source" if /"source"/; - $x=0 if /\}/; - if ($x && /"value"/) { - s/.* "//; s/".*//; - ${$x} = $_; - print "$version|'$db'|$source\n" if $x eq "version"; - } ' >> /tmp/y.$$.txt - if [[ $? -ne 0 ]]; then - echo "ERROR: unexpected problem obtaining $db versions from stardog" - exit 1 - fi -done -# Sort by version then reverse by DB (NCIT2 goes before CTRP) -# this is because we need "monthly" to be indexed from the "monthlyDb" -# defined in ncit.json -# NOTE: version isn't cleaned up here so from where versionIRI is still an IRI -sort -t\| -k 1,1 -k 2,2r -o /tmp/y.$$.txt /tmp/y.$$.txt -cat /tmp/y.$$.txt | sed 's/^/ version = /;' +get_graphs(){ + /bin/rm -f /tmp/y.$$.txt + touch /tmp/y.$$.txt + for db in `cat /tmp/db.$$.txt`; do + curl -s -g -u "${l_graph_db_username}:$l_graph_db_password" \ + http://${l_graph_db_host}:${l_graph_db_port}/$db/query \ + --data-urlencode "$query" -H "Accept: application/sparql-results+json" |\ + $jq | python3 "$DIR/get_graphs.py" "$db" >> /tmp/y.$$.txt + if [[ $? -ne 0 ]]; then + echo "ERROR: unexpected problem obtaining $db versions from stardog" + exit 1 + fi + done + # Sort by version then reverse by DB (NCIT2 goes before CTRP) + # this is because we need "monthly" to be indexed from the "monthlyDb" + # defined in ncit.json + # NOTE: version isn't cleaned up here so from where versionIRI is still an IRI + sort -t\| -k 1,1 -k 2,2r -o /tmp/y.$$.txt /tmp/y.$$.txt + cat /tmp/y.$$.txt | sed 's/^/ version = /;' +} +get_graphs if [[ $ES_CLEAN == "true" ]]; then echo " Remove and recreate evs_metadata index" From 2bd086e0ffc9911884126aa12bb4dd0758c94b0c Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Wed, 13 Nov 2024 04:31:22 -0800 Subject: [PATCH 07/11] Fixing reindex.sh to work with stardog and jena --- src/main/resources/metadata/chebi.txt | 4 +- src/main/resources/metadata/hgnc.txt | 8 +- src/main/resources/metadata/icd10cm.txt | 4 +- src/main/resources/metadata/ncim.txt | 4 +- src/main/resources/metadata/ncit.txt | 6 +- src/main/resources/metadata/snomedct.txt | 4 +- src/test/resources/samples/canmed-samples.txt | 54 +- src/test/resources/samples/chebi-samples.txt | 90 +- src/test/resources/samples/medrt-samples.txt | 46 +- src/test/resources/samples/ncit-samples.txt | 952 +++++++++--------- .../resources/samples/umlssemnet-samples.txt | 128 +-- 11 files changed, 650 insertions(+), 650 deletions(-) diff --git a/src/main/resources/metadata/chebi.txt b/src/main/resources/metadata/chebi.txt index e93a16ff1..cf70d36d0 100644 --- a/src/main/resources/metadata/chebi.txt +++ b/src/main/resources/metadata/chebi.txt @@ -1,3 +1,3 @@ -# Sample concepts to include in report -CHEBI:119915 +# Sample concepts to include in report +CHEBI:119915 CHEBI:13248 \ No newline at end of file diff --git a/src/main/resources/metadata/hgnc.txt b/src/main/resources/metadata/hgnc.txt index aa8ff2535..9355c9b15 100644 --- a/src/main/resources/metadata/hgnc.txt +++ b/src/main/resources/metadata/hgnc.txt @@ -1,4 +1,4 @@ -# Sample concepts to include in report -gene_with_protein_product -HGNC:10218 -HGCN:54003 +# Sample concepts to include in report +gene_with_protein_product +HGNC:10218 +HGCN:54003 diff --git a/src/main/resources/metadata/icd10cm.txt b/src/main/resources/metadata/icd10cm.txt index 8e7262792..ed3ec65b1 100644 --- a/src/main/resources/metadata/icd10cm.txt +++ b/src/main/resources/metadata/icd10cm.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (ORDER_NO) -I85 +# Sample concept for synonym qualifier (ORDER_NO) +I85 diff --git a/src/main/resources/metadata/ncim.txt b/src/main/resources/metadata/ncim.txt index cfdd5de6d..fd0853029 100644 --- a/src/main/resources/metadata/ncim.txt +++ b/src/main/resources/metadata/ncim.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) - +# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) + diff --git a/src/main/resources/metadata/ncit.txt b/src/main/resources/metadata/ncit.txt index bab98500b..9bd6ec28f 100644 --- a/src/main/resources/metadata/ncit.txt +++ b/src/main/resources/metadata/ncit.txt @@ -1,3 +1,3 @@ -# Sample concepts to include in report -C3224 -C100110 +# Sample concepts to include in report +C3224 +C100110 diff --git a/src/main/resources/metadata/snomedct.txt b/src/main/resources/metadata/snomedct.txt index 2831af55c..3f4776023 100644 --- a/src/main/resources/metadata/snomedct.txt +++ b/src/main/resources/metadata/snomedct.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) -130090009 +# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) +130090009 diff --git a/src/test/resources/samples/canmed-samples.txt b/src/test/resources/samples/canmed-samples.txt index 55ecf4aaf..632df957c 100644 --- a/src/test/resources/samples/canmed-samples.txt +++ b/src/test/resources/samples/canmed-samples.txt @@ -1,27 +1,27 @@ -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Preferred_Name Mercaptopurine 50.0 mg/1 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Status In Use -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Effective_Date 07/01/2005 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Description 250 TABLET in 1 BOTTLE, PLASTIC (0378-3547-25) -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Brand_Name Mercaptopurine -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Package_Code 00378-3547-25 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Administration_Route Oral -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Strength 50.0 mg/1 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Generic_Name Mercaptopurine -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Product_Code 00378-3547 -http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 Discontinue_Date 11/23/2021 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 owl:deprecated true -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 CMS_Effective_Date 01/01/2017 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 Oral No -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 FDA_Approval_Year 2008 -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 HCPCS_Code J9034 -http://seer.nci.nih.gov/CanMED.owl#C9235 C9235 CMS_Discontinuation_Date 12/31/2007 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#S0087 S0087 FDA_Discontinuation_Year 2012 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-style1 NDC_00378-3547 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547 child-style1 NDC_00378-3547-25 -http://seer.nci.nih.gov/CanMED.owl#NDC_PREDNISONE NDC_PREDNISONE max-children 487 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-count1 -http://seer.nci.nih.gov/CanMED.owl#HCPCS_BCMA HCPCS_BCMA parent-count2 -http://seer.nci.nih.gov/CanMED.owl#NDC_DRONABINOL NDC_DRONABINOL parent-count3 -http://seer.nci.nih.gov/CanMED.owl#HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR parent-count4 -http://seer.nci.nih.gov/CanMED.owl#HCPCS HCPCS root -http://seer.nci.nih.gov/CanMED.owl#NDC NDC root +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Preferred_Name Mercaptopurine 50.0 mg/1 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Status In Use +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Effective_Date 07/01/2005 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Description 250 TABLET in 1 BOTTLE, PLASTIC (0378-3547-25) +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Brand_Name Mercaptopurine +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Package_Code 00378-3547-25 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Administration_Route Oral +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Strength 50.0 mg/1 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Generic_Name Mercaptopurine +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Product_Code 00378-3547 +http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 Discontinue_Date 11/23/2021 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 owl:deprecated true +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 CMS_Effective_Date 01/01/2017 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 Oral No +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 FDA_Approval_Year 2008 +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 HCPCS_Code J9034 +http://seer.nci.nih.gov/CanMED.owl#C9235 C9235 CMS_Discontinuation_Date 12/31/2007 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#S0087 S0087 FDA_Discontinuation_Year 2012 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-style1 NDC_00378-3547 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547 child-style1 NDC_00378-3547-25 +http://seer.nci.nih.gov/CanMED.owl#NDC_PREDNISONE NDC_PREDNISONE max-children 487 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-count1 +http://seer.nci.nih.gov/CanMED.owl#HCPCS_BCMA HCPCS_BCMA parent-count2 +http://seer.nci.nih.gov/CanMED.owl#NDC_DRONABINOL NDC_DRONABINOL parent-count3 +http://seer.nci.nih.gov/CanMED.owl#HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR parent-count4 +http://seer.nci.nih.gov/CanMED.owl#HCPCS HCPCS root +http://seer.nci.nih.gov/CanMED.owl#NDC NDC root diff --git a/src/test/resources/samples/chebi-samples.txt b/src/test/resources/samples/chebi-samples.txt index cf7584b8f..6c0906575 100644 --- a/src/test/resources/samples/chebi-samples.txt +++ b/src/test/resources/samples/chebi-samples.txt @@ -1,46 +1,46 @@ -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:charge 0 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:formula C36H38N2O6 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchi InChI=1S/C36H38N2O6/c1-37-13-11-23-18-31(41-3)32-20-26(23)27(37)15-21-5-8-25(9-6-21)43-30-17-22(7-10-29(30)39)16-28-34-24(12-14-38(28)2)19-33(42-4)35(40)36(34)44-32/h5-10,17-20,27-28,39-40H,11-16H2,1-4H3/t27-,28-/m0/s1 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchikey XGEAUXVPBXUBKN-NSOVKSMOSA-N -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:mass 594.698 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:monoisotopicmass 594.27299 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:smiles COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5cc(C[C@@H]6N(C)CCc7cc(OC)c(O)c(Oc1cc23)c67)ccc5O)cc4 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasDbXref CAS:21008-67-3 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasExactSynonym (+)-Atherospermoline -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasOBONamespace chebi_ontology -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:inSubset 2_STAR -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 rdfs:label (+)-Atherospermoline -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~has_role CHEBI:76924 -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~is_enantiomer_of CHEBI:6714 -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 IAO_0000115 The (-)-enantiomer of medicarpin. -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 oboInOwl:hasRelatedSynonym medicarpin -http://purl.obolibrary.org/obo/CHEBI_10002 CHEBI:10002 rdfs:subClassOf/owl:Restriction~has_functional_parent CHEBI:173072 -http://purl.obolibrary.org/obo/CHEBI_10003 CHEBI:10003 rdfs:subClassOf/owl:Restriction~has_part CHEBI:65028 -http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 rdfs:subClassOf/owl:Restriction~is_conjugate_acid_of CHEBI:62070 -http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 oboInOwl:hasAlternativeId CHEBI:7456 -http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 rdfs:subClassOf/owl:Restriction~has_parent_hydride CHEBI:36372 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_conjugate_base_of CHEBI:192486 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_tautomer_of CHEBI:192484 -http://purl.obolibrary.org/obo/CHEBI_111516 CHEBI:111516 rdfs:subClassOf/owl:Restriction~is_substituent_group_from CHEBI:111513 -http://purl.obolibrary.org/obo/CHEBI_131515 CHEBI:131515 owl:deprecated true -http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasDbXref~oboInOwl:source CAS:35144-10-6~KEGG COMPOUND -http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasExactSynonym~oboInOwl:hasDbXref Viscidulin B~KEGG_COMPOUND -http://purl.obolibrary.org/obo/CHEBI_9997 CHEBI:9997 qualifier-oboInOwl:hasRelatedSynonym~oboInOwl:hasDbXref Virginiamycin factor M1~ChemIDplus -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-style1 CHEBI:133004 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:133004 child-style1 CHEBI:10 -http://purl.obolibrary.org/obo/CHEBI_24995 CHEBI:24995 max-children 7343 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-count1 -http://purl.obolibrary.org/obo/CHEBI_100002 CHEBI:100002 parent-count2 -http://purl.obolibrary.org/obo/CHEBI_100000 CHEBI:100000 parent-count3 -http://purl.obolibrary.org/obo/CHEBI_10018 CHEBI:10018 parent-count4 -http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 parent-count5 -http://purl.obolibrary.org/obo/CHEBI_10016 CHEBI:10016 parent-count6 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 parent-count7 -http://purl.obolibrary.org/obo/CHEBI_101257 CHEBI:101257 parent-count8 -http://purl.obolibrary.org/obo/CHEBI_10041 CHEBI:10041 parent-count9 -http://purl.obolibrary.org/obo/CHEBI_132640 CHEBI:132640 parent-count10 -http://purl.obolibrary.org/obo/CHEBI_167670 CHEBI:167670 parent-count11 -http://purl.obolibrary.org/obo/CHEBI_85616 CHEBI:85616 parent-count14 -http://purl.obolibrary.org/obo/CHEBI_24431 CHEBI:24431 root -http://purl.obolibrary.org/obo/CHEBI_36342 CHEBI:36342 root +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:charge 0 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:formula C36H38N2O6 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchi InChI=1S/C36H38N2O6/c1-37-13-11-23-18-31(41-3)32-20-26(23)27(37)15-21-5-8-25(9-6-21)43-30-17-22(7-10-29(30)39)16-28-34-24(12-14-38(28)2)19-33(42-4)35(40)36(34)44-32/h5-10,17-20,27-28,39-40H,11-16H2,1-4H3/t27-,28-/m0/s1 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchikey XGEAUXVPBXUBKN-NSOVKSMOSA-N +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:mass 594.698 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:monoisotopicmass 594.27299 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:smiles COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5cc(C[C@@H]6N(C)CCc7cc(OC)c(O)c(Oc1cc23)c67)ccc5O)cc4 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasDbXref CAS:21008-67-3 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasExactSynonym (+)-Atherospermoline +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasOBONamespace chebi_ontology +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:inSubset 2_STAR +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 rdfs:label (+)-Atherospermoline +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~has_role CHEBI:76924 +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~is_enantiomer_of CHEBI:6714 +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 IAO_0000115 The (-)-enantiomer of medicarpin. +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 oboInOwl:hasRelatedSynonym medicarpin +http://purl.obolibrary.org/obo/CHEBI_10002 CHEBI:10002 rdfs:subClassOf/owl:Restriction~has_functional_parent CHEBI:173072 +http://purl.obolibrary.org/obo/CHEBI_10003 CHEBI:10003 rdfs:subClassOf/owl:Restriction~has_part CHEBI:65028 +http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 rdfs:subClassOf/owl:Restriction~is_conjugate_acid_of CHEBI:62070 +http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 oboInOwl:hasAlternativeId CHEBI:7456 +http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 rdfs:subClassOf/owl:Restriction~has_parent_hydride CHEBI:36372 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_conjugate_base_of CHEBI:192486 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_tautomer_of CHEBI:192484 +http://purl.obolibrary.org/obo/CHEBI_111516 CHEBI:111516 rdfs:subClassOf/owl:Restriction~is_substituent_group_from CHEBI:111513 +http://purl.obolibrary.org/obo/CHEBI_131515 CHEBI:131515 owl:deprecated true +http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasDbXref~oboInOwl:source CAS:35144-10-6~KEGG COMPOUND +http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasExactSynonym~oboInOwl:hasDbXref Viscidulin B~KEGG_COMPOUND +http://purl.obolibrary.org/obo/CHEBI_9997 CHEBI:9997 qualifier-oboInOwl:hasRelatedSynonym~oboInOwl:hasDbXref Virginiamycin factor M1~ChemIDplus +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-style1 CHEBI:133004 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:133004 child-style1 CHEBI:10 +http://purl.obolibrary.org/obo/CHEBI_24995 CHEBI:24995 max-children 7343 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-count1 +http://purl.obolibrary.org/obo/CHEBI_100002 CHEBI:100002 parent-count2 +http://purl.obolibrary.org/obo/CHEBI_100000 CHEBI:100000 parent-count3 +http://purl.obolibrary.org/obo/CHEBI_10018 CHEBI:10018 parent-count4 +http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 parent-count5 +http://purl.obolibrary.org/obo/CHEBI_10016 CHEBI:10016 parent-count6 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 parent-count7 +http://purl.obolibrary.org/obo/CHEBI_101257 CHEBI:101257 parent-count8 +http://purl.obolibrary.org/obo/CHEBI_10041 CHEBI:10041 parent-count9 +http://purl.obolibrary.org/obo/CHEBI_132640 CHEBI:132640 parent-count10 +http://purl.obolibrary.org/obo/CHEBI_167670 CHEBI:167670 parent-count11 +http://purl.obolibrary.org/obo/CHEBI_85616 CHEBI:85616 parent-count14 +http://purl.obolibrary.org/obo/CHEBI_24431 CHEBI:24431 root +http://purl.obolibrary.org/obo/CHEBI_36342 CHEBI:36342 root http://purl.obolibrary.org/obo/CHEBI_50906 CHEBI:50906 root \ No newline at end of file diff --git a/src/test/resources/samples/medrt-samples.txt b/src/test/resources/samples/medrt-samples.txt index d474cf786..b86b05ec7 100644 --- a/src/test/resources/samples/medrt-samples.txt +++ b/src/test/resources/samples/medrt-samples.txt @@ -1,23 +1,23 @@ -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Preferred_Term 1-Compartment -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 CTY PK -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 NUI N0000000060 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Concept_Name 1-Compartment [PK] -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Status ACTIVE -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 Synonym Hydroxyphenylpyruvate Dioxygenase Inhibitor -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 rdfs:subClassOf/owl:Restriction~has_MoA N0000175808 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175771 N0000175771 rdfs:subClassOf/owl:Restriction~has_PE N0000008953 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193790 N0000193790 rdfs:subClassOf/owl:Restriction~has_SC N0000191722 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175874 N0000175874 rdfs:subClassOf/owl:Restriction~has_TC N0000178297 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-style1 N0000000059 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000059 child-style1 N0000000060 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193894 N0000193894 max-children 115 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-count1 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000215 N0000000215 parent-count2 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000177910 N0000177910 parent-count3 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175453 N0000175453 parent-count4 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000223 N0000000223 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000003 N0000000003 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000001 N0000000001 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000009802 N0000009802 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193784 N0000193784 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000178293 N0000178293 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Preferred_Term 1-Compartment +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 CTY PK +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 NUI N0000000060 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Concept_Name 1-Compartment [PK] +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Status ACTIVE +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 Synonym Hydroxyphenylpyruvate Dioxygenase Inhibitor +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 rdfs:subClassOf/owl:Restriction~has_MoA N0000175808 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175771 N0000175771 rdfs:subClassOf/owl:Restriction~has_PE N0000008953 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193790 N0000193790 rdfs:subClassOf/owl:Restriction~has_SC N0000191722 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175874 N0000175874 rdfs:subClassOf/owl:Restriction~has_TC N0000178297 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-style1 N0000000059 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000059 child-style1 N0000000060 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193894 N0000193894 max-children 115 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-count1 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000215 N0000000215 parent-count2 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000177910 N0000177910 parent-count3 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175453 N0000175453 parent-count4 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000223 N0000000223 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000003 N0000000003 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000001 N0000000001 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000009802 N0000009802 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193784 N0000193784 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000178293 N0000178293 root diff --git a/src/test/resources/samples/ncit-samples.txt b/src/test/resources/samples/ncit-samples.txt index 37adf6ffa..7989ec4af 100644 --- a/src/test/resources/samples/ncit-samples.txt +++ b/src/test/resources/samples/ncit-samples.txt @@ -1,476 +1,476 @@ -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P106 Amino Acid, Peptide, or Protein -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P108 Recombinant Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P207 C1514768 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P366 Recombinant_Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P90 AR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P97 A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04) -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 rdfs:label Recombinant Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 rdfs:subClassOf/owl:Restriction~R123 C405 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 rdfs:subClassOf/owl:Restriction~R163 C12686 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 A8 C101859 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P322 CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P325 A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms. -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100012 C100012 rdfs:subClassOf/owl:Restriction~R100 C12686 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P208 CL433438 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P329 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P330 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P399 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R126 C3270 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R101 C12415 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R103 C45714 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R104 C12578 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R105 C12917 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R108 C36115 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R115 C3090 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R139 C36760 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R142 C36122 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P107 Renal Cell Carcinoma Associated with Neuroblastoma -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P363 Malignant -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R101 C12341 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R103 C32365 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R104 C12591 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R108 C36027 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R115 C35841 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P171 12927386 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P210 77538-19-3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P319 R8WTH25YS2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R124 C45547 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R125 C16298 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R146 C37279 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100089 C100089 A32 C1909 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100089 C100089 P375 Interferon Gamma-1b -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R50 C14073 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R52 C16701 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R53 C16702 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R54 C21281 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 P100 153310 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 P93 Q05315 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R139 C36897 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 rdfs:subClassOf/owl:Restriction~R135 C12725 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100097 C100097 P317 SPL Flavor (C-DRG-0934) -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100098 C100098 P350 C15H22N6O5S -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100099 C100099 A7 C104498 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 P175 616524 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100103 C100103 A17 C45300 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100103 C100103 A18 C149570 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 A24 C173262 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P372 Yes -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P374 EVS/CDISC/SDTM/SDTM Terminology.xls|2:all -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P376 <p>The terminology subset that includes terms pertaining to the CDISC questionnaire terminology.</p> <p>The terminology can be downloaded at this location: <a href="https://evs.nci.nih.gov/ftp1/CDISC/SDTM/"> CDISC Questionnaire Terminology</a>.</p> -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P398 No -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100120 C100120 P361 No -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100132 C100132 A25 C100131 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 P368 CHEBI:22565 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P200 Coagulation_Study -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P98 Tue Jun 18 14:23:59 EDT 2013 - See 'Activated_PTT_Standard_Ratio_Measurement' -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 owl:deprecated true -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100428 C100428 A13 C84429 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R124 C40551 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R125 C17557 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R72 C13258 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 P302 Myelodysplastic syndrome; multiple myeloma; chronic myeloid leukemia; acute myelocytic leukemia -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100807 C100807 P364 A8|C100130 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100809 C100809 A35 C168870 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101043 C101043 rdfs:subClassOf/owl:Restriction~R116 C98898 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101046 C101046 rdfs:subClassOf/owl:Restriction~R175 C37193 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101048 C101048 rdfs:subClassOf/owl:Restriction~R37 C18497 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101056 C101056 rdfs:subClassOf/owl:Restriction~R133 C45208 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101063 C101063 P102 U41743 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101071 C101071 P204 Gene_Involved_In_Pathogenesis_Of_Disease some 'Acute Myeloid Leukemia with inv(3) (q21.3;q26.2) or t(3;3) (q21.3;q26.2); GATA2, MECOM' -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 P369 HGNC:18037 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101089 C101089 rdfs:subClassOf/owl:Restriction~R40 C24930 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101089 C101089 P321 196528 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R46 C13197 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R49 C12412 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R50 C13294 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R51 C156920 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R52 C16518 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R53 C19077 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R54 C101088 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-http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R107 C13271 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R89 C36712 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 P310 Obsolete_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P310 Retired_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C129445 C129445 P310 Provisional_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13037 C13037 P310 Header_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~AB AR~AB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P384~NCI AR~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~PT Recombinant Amphiregulin~PT -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P97~P378~NCI A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04)~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P325~P378~CDISC A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms.~CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P90~P384~CDISC PERCUTANEOUS CORONARY INTERVENTION (PCI) FOR ST ELEVATION MYOCARDIAL INFARCTION (STEMI) (STABLE, >12 HRS FROM SYMPTOM ONSET)~CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P384~SEER COPADRI-I~SEER -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P383~SY Cyclophosphamide-Vincristine-Melphalan-Doxorubicin~SY -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99996 C99996 qualifier-P90~P385 Number of Diseased Coronary Vessels~SDTM-CVTEST -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100022 C100022 qualifier-P90~P384~CPTAC Transcatheter Aortic Valve Implantation~CPTAC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 qualifier-P90~P383~FB Evozac~FB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P325~P378~CDISC-GLOSS A standard protocol for exchanging files between computers on the internet. See also TCP/IP.~CDISC-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P90~P384~CDISC-GLOSS File Transfer Protocol (FTP)~CDISC-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P383~DN Renal Cell Cancer Associated with Neuroblastoma~DN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P384~CTRP Renal Cell Cancer Associated with Neuroblastoma~CTRP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 qualifier-P90~P383~AQS Conjunctival Precancerous Melanosis~AQS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~BR Compritol 888 ATO~BR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~SN Docosanoic Acid, Diester with 1,2,3-propanetriol~SN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P384~FDA GLYCERYL DIBEHENATE~FDA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99905 C99905 qualifier-P90~P386 ROCILETINIB~UNII -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P325~P378~ACC/AHA Catheter ablation is an invasive procedure used to remove or terminate a faulty electrical pathway from sections of the hearts of those who are prone to developing cardiac arrhythmias such as atrial fibrillation, atrial flutter, SVT and Wolff-Parkinson-White syndrome.~ACC/AHA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P90~P384~ACC/AHA Catheter ablation~ACC/AHA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P393 Dependent relative needing care at home~Related To -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P394 Dependent relative needing care at home~PT -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P395 Dependent relative needing care at home~Z63.6 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P396 Dependent relative needing care at home~ICD10CM 2017 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 qualifier-P90~P384~CTEP Nongerminomatous GCT - CNS~CTEP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100096 C100096 qualifier-P90~P384~caDSR OMRS~caDSR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 qualifier-P90~P384~DTP Ampligen~DTP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100100 C100100 qualifier-P90~P383~CN AP611074~CN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~PCDC Clinical Signs or Symptoms~PCDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~NICHD Sign or Symptom~NICHD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P325~P378~NCI-GLOSS An anticancer drug that belongs to the family of drugs called antineoplastic antibiotics.~NCI-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P90~P384~NCI-GLOSS ansamycin~NCI-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1004 C1004 qualifier-P90~P384~DCP Antineoplaston A10~DCP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100805 C100805 qualifier-P90~P384~GDC Natural Grandchild~GDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100897 C100897 qualifier-P90~P384~UCUM 10*3.{copies}/mL~UCUM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101028 C101028 qualifier-P325~P378~NICHD Aspiration of amniotic fluid around the time of delivery resulting in severe respiratory distress.~NICHD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101029 C101029 qualifier-P90~P384~Cellosaurus Atrioventricular Septal Defect~Cellosaurus -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99537 C99537 qualifier-P375~P397 Venous thromboembolism~18.1 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99865 C99865 qualifier-P97~P381 A fusion gene that results from a complex chromosomal rearrangement where inversion of 22q12 is followed by a translocation t(1;22)(p34;q12) that disrupts intron 3 of the UQCRH gene. PCR analysis of tumor cDNA and genomic DNA detected a UQCRH/EWSR1 fusion transcript but it is out-of-frame and contains premature stop codons.~OMIM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 qualifier-P90~P384~HGNC ARID2~HGNC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101125 C101125 qualifier-P90~P383~AD Discordant~AD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P325~P378~CareLex A single activity that has occurred within a business process.~CareLex -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P90~P384~CareLex Task~CareLex -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101138 C101138 qualifier-P90~P384~BRIDG 5.3 ctdiVol~BRIDG 5.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P325~P378~INC The occipitofrontal circumference of a neonate's head at birth. Measurement to the nearest 0.1 cm should be taken at the broadest part of the forehead above the eyebrow and above the ears, most prominent part of the back of the head on the day of birth or the day after birth.~INC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P90~P384~INC Head Circumference at Birth~INC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CNU 535~CNU -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P384~GENC 535~GENC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA3 BES~CA3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA2 BQ~CA2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101250 C101250 qualifier-P325~P378~FDA Injury to the peripheral nervous system.~FDA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99286 C99286 qualifier-P325~P381 The catalog, reference, or product number found on the device label or accompanying packaging to identify a particular product.~CDRH-GUDID -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~ICDC WGS~ICDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~CTDC WGS (whole genome sequencing)~CTDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P325~P378~CRCH Carotenoid consisting of a cyclic structure on each end with additional double bonds at the number 5 and 5' carbon atoms of the cyclic structures.~CRCH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P90~P384~CRCH 3,7,12,16-tetramethyl-1,18-bis(2,6,6-trimethyl-1-cyclohexenyl)-octadeca-1,3,5,7,9,11,13,15,17-nonaene~CRCH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102405 C102405 qualifier-P90~P384~NCPDP Capful~NCPDP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102556 C102556 qualifier-P90~P384~BRIDG 3.0.3 IVL.LOW<TS.DATE>~BRIDG 3.0.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 5.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression OTHER NAME(S): Clinical Events Medical History NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 5.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 3.0.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression. NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 3.0.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102821 C102821 qualifier-P90~P384~CCPS SPRED1~CCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104030 C104030 qualifier-P90~P383~HD Adrenal Cortex Carcinoma by ENSAT Stage~HD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104438 C104438 qualifier-P325~P378~BRIDG Specifies whether this device bears a CE (Conformite Europeenne) mark. NOTE(S): CE is a mark for device products placed on the market in the European Economic Area (EEA). By placing the CE marking on a product, the manufacturer affirms that the product conforms with the requirements of the applicable European Community directives.~BRIDG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~CDC OTHER RACE~CDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~SeroNet Other~SeroNet -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P325~P378~CTCAE A disorder characterized by an acute inflammatory reaction resulting from the release of histamine and histamine-like substances from mast cells, causing a hypersensitivity immune response. Clinically, it presents with breathing difficulty, dizziness, hypotension, cyanosis and loss of consciousness and may lead to death.~CTCAE -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P90~P384~CTCAE Anaphylaxis~CTCAE -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P325~P378~EDQM-HC Exposure of a breast-feeding infant to a medicinal product administered to the lactating mother. Comment: This term is not intended to describe an authorised route of administration for use in marketing authorisations, and does not cover intentional administration of a medicinal product to a breastfeeding infant. It is intended for use in adverse event reporting for pharmacovigilance purposes.~EDQM-HC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P90~P384~EDQM-HC Transmammary~EDQM-HC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P325~P378~GAIA The death of a woman while pregnant or within 42 days of termination of pregnancy, irrespective of the duration and the site of the pregnancy (as defined by Maternal Death guidelines: http:www.brightoncollaboration.org).~GAIA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P90~P384~GAIA Maternal Death~GAIA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114560 C114560 qualifier-P90~P383~AQ Childhood L1 Acute Lymphoblastic Leukemia~AQ -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C118618 C118618 qualifier-P325~P378~CTEP Systemic chemotherapy with a regimen containing multiple agents.~CTEP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12241 C12241 qualifier-P90~P384~CTRM Branchial Cleft~CTRM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12261 C12261 qualifier-P325~P378~ICDO3 not classifiable to C16.1 to C16.4~ICDO3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12558 C12558 qualifier-P325~P378~NCI A cell that arises from stem cells and/or bone marrow-derived monocytes that function in different aspects of host defense and tissue repair; such as phagocytosis, cytotoxic activity, and regulation of the immune response (antigen presentation and T-cell activation).~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12599 C12599 qualifier-P325~P378~MSH2001 Female germ cells in stages between the prophase of the first maturation division and the completion of the second maturation division.~MSH2001 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12719 C12719 qualifier-P325~P378~UWDA142 is a macroscopic organ component of one or more nerves, which primarily consists of cell bodies of neurons located outside the central nervous system; together with nerve fibers, it constitutes a nerve or a nerve plexus. Example(s): spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion.~UWDA142 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12741 C12741 qualifier-P325~P378~CSP2000 type of cytotoxic leukocytes which attack and kill virus-infected or neoplastic cells independent of antibody coating or MHC restriction; may be derived from lymphocytes or monocytes.~CSP2000 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12842 C12842 qualifier-P325~P378~UMD2001 Grafts used in the treatment of skin loss, usually caused by burn injuries.~UMD2001 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C128574 C128574 qualifier-P90~P384~PI-RADS Apex L AS~PI-RADS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13061 C13061 qualifier-P325~P378~MeSH The cells of the body which stain with chromium salts. They occur along the sympathetic nerves, in the adrenal gland, and in various other organs.~MeSH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1396 C1396 qualifier-P325~P378~CSP2002 family of polypeptide growth factors produced by peripheral target tissues as well as the nervous system, which are critical to neuronal growth, regeneration, survival, and differentiation.~CSP2002 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142787 C142787 qualifier-P90~P384~CBDD Transduction~CBDD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14294 C14294 qualifier-P90~P384~JAX severe combined immune deficiency~JAX -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P325~P378~CTCAE 5.0 A disorder characterized by laboratory test results that indicate an increased number of eosinophils in the blood.~CTCAE 5.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P90~P384~CTCAE 5.0 Eosinophilia~CTCAE 5.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P325~P378~DICOM A drug that contains a radioactive substance and is used to diagnose or treat disease, including cancer.~DICOM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P90~P384~DICOM Radiopharmaceutical~DICOM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C153106 C153106 qualifier-P90~P384~BRIDG IntegratedStatisticalAnalysisPlan~BRIDG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15538 C15538 qualifier-P325~P378~PCDC Assigned Treatment Arm by Intention-To-Treat~PCDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C155838 C155838 qualifier-P90~P384~NDC ME~NDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15843 C15843 qualifier-P90~P384~HL7 PRYLX~HL7 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C168622 C168622 qualifier-P325~P378~PQCMC A mathematical symbol that denotes equality or inequality between two values Note: This is typically applicable to biologics.~PQCMC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16904 C16904 qualifier-P90~P383~CS NN~CS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17051 C17051 qualifier-P325~P378~MSH2002_06_01 The ability of some cells or tissues to withstand ionizing radiation without serious injury. Tolerance depends on the species, cell type, and physical and chemical variables, including RADIATION-PROTECTIVE AGENTS and RADIATION-SENSITIZING AGENTS.~MSH2002_06_01 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C179573 C179573 qualifier-P90~P384~WHO Alpha~WHO -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18063 C18063 qualifier-P90~P384~ICH Gy~ICH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18611 C18611 qualifier-P90~P384~KEGG Metabolism~KEGG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P387 extracellular~GO:0005576 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P389 extracellular~NAS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P390 extracellular~CGAP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P391 extracellular~29-SEP-2003 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C21639 C21639 qualifier-P325~P378~MMHCC Inflammation of the mammary gland~MMHCC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23247 C23247 qualifier-P325~P378~DCCPS The Corpus uteri, or body of uterus, is the part of the uterus above the isthmus, comprising about two thirds of the non-pregnant organ. 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.~DCCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23372 C23372 qualifier-P325~P378~DCTD-CD That portion of the nervous system consisting of the brain and spinal cord. (Dorland, 28th ed) (MSH98)~DCTD-CD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23373 C23373 qualifier-P325~P378~FMB-BUDGET That part of the central nervous system contained within the cranium, comprising the prosencephalon, mesencephalon, and rhombencephalon. It is derived from the anterior part of the embryonic neural tube. Functions include muscle control and coordination, sensory reception and integration, speech production, memory storage, and the elaboration of thought and emotions. (Dorland, 28th ed) (MSH98)~FMB-BUDGET -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23404 C23404 qualifier-P325~P378~OMS94 The natural covering of the body; the skin.~OMS94 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23415 C23415 qualifier-P325~P378~DCB-CB2 The layer of epithelial cells that lines the cavities of the heart and of the blood vessels (ENDOTHELIUM, VASCULAR) and lymph vessels (ENDOTHELIUM, LYMPHATIC), and the serous cavities of the body, originating from the MESODERM. (From Dorland, 28th ed) (MSH98)~DCB-CB2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23593 C23593 qualifier-P325~P378~MTH Primitive blood cells derived from embryonic mesenchyme capable of differentiating into any of the blood cell line progenitor cells (erythroblasts, young granulocytic series cells, megakaryocytes, etc.)~MTH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23887 C23887 qualifier-P325~P378~DEA-DEAIS exocrine gland. a gland from which secretions reach a free surface of the body by ducts.~DEA-DEAIS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25296 C25296 qualifier-P90~P384~CADSR BD~CADSR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26719 C26719 qualifier-P325~P378~MSH2003_2003_05_12 Presence of calcium salts, especially calcium pyrophosphate, in the cartilaginous structures of one or more joints. When accompanied by attacks of goutlike symptoms, it is called pseudogout. (Dorland, 27th ed)~MSH2003_2003_05_12 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26914 C26914 qualifier-P325~P378~CSP2003 abnormal development of secondary male sexual characteristics such as facial hair; in females, can be caused by androgen secretion by adrenal cortex.~CSP2003 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28245 C28245 qualifier-P90~P384~CTCAE 3.0 Aspiration~CTCAE 3.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28517 C28517 qualifier-P325~P378~MSH2002 Small containers or pellets of a solid drug implanted in the body to achieve sustained release of the drug.~MSH2002 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38778 C38778 qualifier-P325~P378~KEGG Alzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-beta (Abeta), a major component of senile plaques, has various pathological effects on cell and organelle function. The extracellular Abeta oligomers may activate caspases through activation of cell surface death receptors. Alternatively, intracellular Abeta may contribute to pathology by facilitating tau hyper-phosphorylation, disrupting mitochondria function, and triggering calcium dysfunction. To date genetic studies have revealed four genes that may be linked to autosomal dominant or familial early onset AD (FAD). These four genes include: amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2) and apolipoprotein E (ApoE). All mutations associated with APP and PS proteins can lead to an increase in the production of Abeta peptides, specifically the more amyloidogenic form, Abeta42. FAD-linked PS1 mutation downregulates the unfolded protein response and leads to vulnerability to ER stress.~KEGG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P325~P378~BIOCARTA Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. The major regulator of blood pressure homeostasis is the renin-angiotensin system. Angiotensinogen is digested by renin to produce angiotensin I (AGT I). AGT I is an inactive 10 amino-acid peptide that is further degraded to produce angiotensin II by the angiotensin-converting enzyme (ACE). Angiotensin II is the master regulator of blood pressure increase acting on the heart, kidneys and blood vessels. Angiotensin II causes direct constriction of the resistance vessels and stimulation of the adrenal thereby increasing blood volume and sodium absorption. In 2000, Tipnis et al. discovered ACE 2 a second carboxypeptidase that digests angiotensin. ACE is a di-peptidase, cleaving off 2 peptides from the c-terminal end of angiotensin. ACE 2 only cleaves 1 amino acid to produce angiotensin 1-9 (AGT 1-9) which has no identified function at this time. AGT 1-9 is not converted to angiotensin II but further degraded by ACE to AGT 1-7, a vasodilator. It would appear that ACE 2 inhibits the formation of angiotensin and reduces blood pressure increases. Crackower et al determined that ace2 -/- mice suffered significant heart defects at 6 months. Further deletion of ACE resulted in restored cardiac functions. (This definition may be outdated - see the DesignNote.)~BIOCARTA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P90~P384~BIOCARTA Angiotensin-converting enzyme 2 regulates heart function~BIOCARTA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42692 C42692 qualifier-P90~P384~NCICB latestVersionIndicator~NCICB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54742 C54742 qualifier-P325~P378~CTCAE 3.0 Transient flushing or rash; drug fever <38 degrees C (<100.4 degrees F)~CTCAE 3.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C60314 C60314 qualifier-P90~P384~RENI Tissue autolysed, diagnosis not possible (RENI)~RENI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C79954 C79954 qualifier-P90~P384~ZFin WIK~ZFin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8498 C8498 qualifier-P325~P378~CCPS A genetic predispostion to developing melanoma due to germline mutation in CDKN2A or CDK4. Subsets of patients are also at risk for pancreatic cancer or astrocytoma.~CCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C91532 C91532 qualifier-P90~P384~PID Signaling events mediated by the Hedgehog family~PID -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-style1 C1504 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1504 child-style1 C1000 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 parent-style2 C9385 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C9385 child-style2 C100051 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107687 C107687 max-children 3234 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-count1 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100063 C100063 parent-count2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101132 C101132 parent-count3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104006 C104006 parent-count4 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114836 C114836 parent-count5 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160034 C160034 parent-count6 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160054 C160054 parent-count7 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160053 C160053 parent-count8 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160005 C160005 parent-count9 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C159984 C159984 parent-count10 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160108 C160108 parent-count12 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160024 C160024 parent-count13 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160102 C160102 parent-count16 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12218 C12218 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12219 C12219 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12913 C12913 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14250 C14250 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16612 C16612 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17828 C17828 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1908 C1908 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20047 C20047 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20181 C20181 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20189 C20189 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20633 C20633 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22187 C22187 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22188 C22188 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26548 C26548 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28428 C28428 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3910 C3910 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43431 C43431 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057 C7057 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C97325 C97325 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P106 Amino Acid, Peptide, or Protein +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P108 Recombinant Amphiregulin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P207 C1514768 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P366 Recombinant_Amphiregulin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P90 AR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P97 A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. 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The presentation is past twelve hours since onset of symptoms. +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100012 C100012 rdfs:subClassOf/owl:Restriction~R100 C12686 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P208 CL433438 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P329 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P330 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P399 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R126 C3270 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R101 C12415 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R103 C45714 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R104 C12578 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+http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P376 <p>The terminology subset that includes terms pertaining to the CDISC questionnaire terminology.</p> <p>The terminology can be downloaded at this location: <a href="https://evs.nci.nih.gov/ftp1/CDISC/SDTM/"> CDISC Questionnaire Terminology</a>.</p> +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P398 No +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100120 C100120 P361 No +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100132 C100132 A25 C100131 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 P368 CHEBI:22565 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P200 Coagulation_Study +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P98 Tue Jun 18 14:23:59 EDT 2013 - See 'Activated_PTT_Standard_Ratio_Measurement' +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 owl:deprecated true 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+http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38112 C38112 rdfs:subClassOf/owl:Restriction~R165 C12389 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 P216 h_ace2Pathway +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42636 C42636 P320 2.16.840.1.113883.3.26.1.1.2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45454 C45454 A3 C43782 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45466 C45466 A4 C45465 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45598 C45598 rdfs:subClassOf/owl:Restriction~R159 C45424 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45600 C45600 rdfs:subClassOf/owl:Restriction~R158 C26533 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45600 C45600 P316 0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45616 C45616 rdfs:subClassOf/owl:Restriction~R160 C265 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45621 C45621 rdfs:subClassOf/owl:Restriction~R156 C13766 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C49349 C49349 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R145 C41648 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7024 C7024 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R114 C36421 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C71269 C71269 rdfs:subClassOf/owl:Class/owl:unionOf/owl:Restriction~R54 C28585 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7164 C7164 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:unionOf/owl:Class/owl:intersectionOf/owl:Restriction~R112 C38434 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7184 C7184 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R116 C26744 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7184 C7184 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R126 C2889 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7208 C7208 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R113 C39682 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7850 C7850 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R142 C3047 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C81756 C81756 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Restriction~R38 C3099 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82169 C82169 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R37 C19077 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82169 C82169 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R41 C14225 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C84455 C84455 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Restriction~R132 C45582 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R107 C13271 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R89 C36712 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 P310 Obsolete_Concept +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P310 Retired_Concept +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C129445 C129445 P310 Provisional_Concept +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13037 C13037 P310 Header_Concept +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~AB AR~AB +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P384~NCI AR~NCI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~PT Recombinant Amphiregulin~PT +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P97~P378~NCI A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04)~NCI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P325~P378~CDISC A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms.~CDISC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P90~P384~CDISC PERCUTANEOUS CORONARY INTERVENTION (PCI) FOR ST ELEVATION MYOCARDIAL INFARCTION (STEMI) (STABLE, >12 HRS FROM SYMPTOM ONSET)~CDISC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P384~SEER COPADRI-I~SEER +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P383~SY Cyclophosphamide-Vincristine-Melphalan-Doxorubicin~SY +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99996 C99996 qualifier-P90~P385 Number of Diseased Coronary Vessels~SDTM-CVTEST +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100022 C100022 qualifier-P90~P384~CPTAC Transcatheter Aortic Valve Implantation~CPTAC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 qualifier-P90~P383~FB Evozac~FB +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P325~P378~CDISC-GLOSS A standard protocol for exchanging files between computers on the internet. See also TCP/IP.~CDISC-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P90~P384~CDISC-GLOSS File Transfer Protocol (FTP)~CDISC-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P383~DN Renal Cell Cancer Associated with Neuroblastoma~DN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P384~CTRP Renal Cell Cancer Associated with Neuroblastoma~CTRP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 qualifier-P90~P383~AQS Conjunctival Precancerous Melanosis~AQS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~BR Compritol 888 ATO~BR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~SN Docosanoic Acid, Diester with 1,2,3-propanetriol~SN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P384~FDA GLYCERYL DIBEHENATE~FDA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99905 C99905 qualifier-P90~P386 ROCILETINIB~UNII +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P325~P378~ACC/AHA Catheter ablation is an invasive procedure used to remove or terminate a faulty electrical pathway from sections of the hearts of those who are prone to developing cardiac arrhythmias such as atrial fibrillation, atrial flutter, SVT and Wolff-Parkinson-White syndrome.~ACC/AHA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P90~P384~ACC/AHA Catheter ablation~ACC/AHA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P393 Dependent relative needing care at home~Related To +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P394 Dependent relative needing care at home~PT +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P395 Dependent relative needing care at home~Z63.6 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P396 Dependent relative needing care at home~ICD10CM 2017 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 qualifier-P90~P384~CTEP Nongerminomatous GCT - CNS~CTEP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100096 C100096 qualifier-P90~P384~caDSR OMRS~caDSR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 qualifier-P90~P384~DTP Ampligen~DTP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100100 C100100 qualifier-P90~P383~CN AP611074~CN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~PCDC Clinical Signs or Symptoms~PCDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~NICHD Sign or Symptom~NICHD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P325~P378~NCI-GLOSS An anticancer drug that belongs to the family of drugs called antineoplastic antibiotics.~NCI-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P90~P384~NCI-GLOSS ansamycin~NCI-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1004 C1004 qualifier-P90~P384~DCP Antineoplaston A10~DCP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100805 C100805 qualifier-P90~P384~GDC Natural Grandchild~GDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100897 C100897 qualifier-P90~P384~UCUM 10*3.{copies}/mL~UCUM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101028 C101028 qualifier-P325~P378~NICHD Aspiration of amniotic fluid around the time of delivery resulting in severe respiratory distress.~NICHD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101029 C101029 qualifier-P90~P384~Cellosaurus Atrioventricular Septal Defect~Cellosaurus +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99537 C99537 qualifier-P375~P397 Venous thromboembolism~18.1 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99865 C99865 qualifier-P97~P381 A fusion gene that results from a complex chromosomal rearrangement where inversion of 22q12 is followed by a translocation t(1;22)(p34;q12) that disrupts intron 3 of the UQCRH gene. PCR analysis of tumor cDNA and genomic DNA detected a UQCRH/EWSR1 fusion transcript but it is out-of-frame and contains premature stop codons.~OMIM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 qualifier-P90~P384~HGNC ARID2~HGNC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101125 C101125 qualifier-P90~P383~AD Discordant~AD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P325~P378~CareLex A single activity that has occurred within a business process.~CareLex +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P90~P384~CareLex Task~CareLex +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101138 C101138 qualifier-P90~P384~BRIDG 5.3 ctdiVol~BRIDG 5.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P325~P378~INC The occipitofrontal circumference of a neonate's head at birth. Measurement to the nearest 0.1 cm should be taken at the broadest part of the forehead above the eyebrow and above the ears, most prominent part of the back of the head on the day of birth or the day after birth.~INC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P90~P384~INC Head Circumference at Birth~INC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CNU 535~CNU +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P384~GENC 535~GENC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA3 BES~CA3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA2 BQ~CA2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101250 C101250 qualifier-P325~P378~FDA Injury to the peripheral nervous system.~FDA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99286 C99286 qualifier-P325~P381 The catalog, reference, or product number found on the device label or accompanying packaging to identify a particular product.~CDRH-GUDID +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~ICDC WGS~ICDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~CTDC WGS (whole genome sequencing)~CTDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P325~P378~CRCH Carotenoid consisting of a cyclic structure on each end with additional double bonds at the number 5 and 5' carbon atoms of the cyclic structures.~CRCH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P90~P384~CRCH 3,7,12,16-tetramethyl-1,18-bis(2,6,6-trimethyl-1-cyclohexenyl)-octadeca-1,3,5,7,9,11,13,15,17-nonaene~CRCH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102405 C102405 qualifier-P90~P384~NCPDP Capful~NCPDP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102556 C102556 qualifier-P90~P384~BRIDG 3.0.3 IVL.LOW<TS.DATE>~BRIDG 3.0.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 5.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression OTHER NAME(S): Clinical Events Medical History NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 5.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 3.0.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression. NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 3.0.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102821 C102821 qualifier-P90~P384~CCPS SPRED1~CCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104030 C104030 qualifier-P90~P383~HD Adrenal Cortex Carcinoma by ENSAT Stage~HD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104438 C104438 qualifier-P325~P378~BRIDG Specifies whether this device bears a CE (Conformite Europeenne) mark. NOTE(S): CE is a mark for device products placed on the market in the European Economic Area (EEA). By placing the CE marking on a product, the manufacturer affirms that the product conforms with the requirements of the applicable European Community directives.~BRIDG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~CDC OTHER RACE~CDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~SeroNet Other~SeroNet +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P325~P378~CTCAE A disorder characterized by an acute inflammatory reaction resulting from the release of histamine and histamine-like substances from mast cells, causing a hypersensitivity immune response. Clinically, it presents with breathing difficulty, dizziness, hypotension, cyanosis and loss of consciousness and may lead to death.~CTCAE +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P90~P384~CTCAE Anaphylaxis~CTCAE +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P325~P378~EDQM-HC Exposure of a breast-feeding infant to a medicinal product administered to the lactating mother. Comment: This term is not intended to describe an authorised route of administration for use in marketing authorisations, and does not cover intentional administration of a medicinal product to a breastfeeding infant. It is intended for use in adverse event reporting for pharmacovigilance purposes.~EDQM-HC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P90~P384~EDQM-HC Transmammary~EDQM-HC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P325~P378~GAIA The death of a woman while pregnant or within 42 days of termination of pregnancy, irrespective of the duration and the site of the pregnancy (as defined by Maternal Death guidelines: http:www.brightoncollaboration.org).~GAIA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P90~P384~GAIA Maternal Death~GAIA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114560 C114560 qualifier-P90~P383~AQ Childhood L1 Acute Lymphoblastic Leukemia~AQ +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C118618 C118618 qualifier-P325~P378~CTEP Systemic chemotherapy with a regimen containing multiple agents.~CTEP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12241 C12241 qualifier-P90~P384~CTRM Branchial Cleft~CTRM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12261 C12261 qualifier-P325~P378~ICDO3 not classifiable to C16.1 to C16.4~ICDO3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12558 C12558 qualifier-P325~P378~NCI A cell that arises from stem cells and/or bone marrow-derived monocytes that function in different aspects of host defense and tissue repair; such as phagocytosis, cytotoxic activity, and regulation of the immune response (antigen presentation and T-cell activation).~NCI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12599 C12599 qualifier-P325~P378~MSH2001 Female germ cells in stages between the prophase of the first maturation division and the completion of the second maturation division.~MSH2001 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12719 C12719 qualifier-P325~P378~UWDA142 is a macroscopic organ component of one or more nerves, which primarily consists of cell bodies of neurons located outside the central nervous system; together with nerve fibers, it constitutes a nerve or a nerve plexus. Example(s): spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion.~UWDA142 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12741 C12741 qualifier-P325~P378~CSP2000 type of cytotoxic leukocytes which attack and kill virus-infected or neoplastic cells independent of antibody coating or MHC restriction; may be derived from lymphocytes or monocytes.~CSP2000 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12842 C12842 qualifier-P325~P378~UMD2001 Grafts used in the treatment of skin loss, usually caused by burn injuries.~UMD2001 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C128574 C128574 qualifier-P90~P384~PI-RADS Apex L AS~PI-RADS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13061 C13061 qualifier-P325~P378~MeSH The cells of the body which stain with chromium salts. They occur along the sympathetic nerves, in the adrenal gland, and in various other organs.~MeSH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1396 C1396 qualifier-P325~P378~CSP2002 family of polypeptide growth factors produced by peripheral target tissues as well as the nervous system, which are critical to neuronal growth, regeneration, survival, and differentiation.~CSP2002 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142787 C142787 qualifier-P90~P384~CBDD Transduction~CBDD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14294 C14294 qualifier-P90~P384~JAX severe combined immune deficiency~JAX +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P325~P378~CTCAE 5.0 A disorder characterized by laboratory test results that indicate an increased number of eosinophils in the blood.~CTCAE 5.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P90~P384~CTCAE 5.0 Eosinophilia~CTCAE 5.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P325~P378~DICOM A drug that contains a radioactive substance and is used to diagnose or treat disease, including cancer.~DICOM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P90~P384~DICOM Radiopharmaceutical~DICOM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C153106 C153106 qualifier-P90~P384~BRIDG IntegratedStatisticalAnalysisPlan~BRIDG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15538 C15538 qualifier-P325~P378~PCDC Assigned Treatment Arm by Intention-To-Treat~PCDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C155838 C155838 qualifier-P90~P384~NDC ME~NDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15843 C15843 qualifier-P90~P384~HL7 PRYLX~HL7 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C168622 C168622 qualifier-P325~P378~PQCMC A mathematical symbol that denotes equality or inequality between two values Note: This is typically applicable to biologics.~PQCMC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16904 C16904 qualifier-P90~P383~CS NN~CS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17051 C17051 qualifier-P325~P378~MSH2002_06_01 The ability of some cells or tissues to withstand ionizing radiation without serious injury. Tolerance depends on the species, cell type, and physical and chemical variables, including RADIATION-PROTECTIVE AGENTS and RADIATION-SENSITIZING AGENTS.~MSH2002_06_01 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C179573 C179573 qualifier-P90~P384~WHO Alpha~WHO +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18063 C18063 qualifier-P90~P384~ICH Gy~ICH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18611 C18611 qualifier-P90~P384~KEGG Metabolism~KEGG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P387 extracellular~GO:0005576 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P389 extracellular~NAS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P390 extracellular~CGAP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P391 extracellular~29-SEP-2003 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C21639 C21639 qualifier-P325~P378~MMHCC Inflammation of the mammary gland~MMHCC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23247 C23247 qualifier-P325~P378~DCCPS The Corpus uteri, or body of uterus, is the part of the uterus above the isthmus, comprising about two thirds of the non-pregnant organ. 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.~DCCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23372 C23372 qualifier-P325~P378~DCTD-CD That portion of the nervous system consisting of the brain and spinal cord. (Dorland, 28th ed) (MSH98)~DCTD-CD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23373 C23373 qualifier-P325~P378~FMB-BUDGET That part of the central nervous system contained within the cranium, comprising the prosencephalon, mesencephalon, and rhombencephalon. It is derived from the anterior part of the embryonic neural tube. Functions include muscle control and coordination, sensory reception and integration, speech production, memory storage, and the elaboration of thought and emotions. (Dorland, 28th ed) (MSH98)~FMB-BUDGET +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23404 C23404 qualifier-P325~P378~OMS94 The natural covering of the body; the skin.~OMS94 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23415 C23415 qualifier-P325~P378~DCB-CB2 The layer of epithelial cells that lines the cavities of the heart and of the blood vessels (ENDOTHELIUM, VASCULAR) and lymph vessels (ENDOTHELIUM, LYMPHATIC), and the serous cavities of the body, originating from the MESODERM. (From Dorland, 28th ed) (MSH98)~DCB-CB2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23593 C23593 qualifier-P325~P378~MTH Primitive blood cells derived from embryonic mesenchyme capable of differentiating into any of the blood cell line progenitor cells (erythroblasts, young granulocytic series cells, megakaryocytes, etc.)~MTH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23887 C23887 qualifier-P325~P378~DEA-DEAIS exocrine gland. a gland from which secretions reach a free surface of the body by ducts.~DEA-DEAIS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25296 C25296 qualifier-P90~P384~CADSR BD~CADSR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26719 C26719 qualifier-P325~P378~MSH2003_2003_05_12 Presence of calcium salts, especially calcium pyrophosphate, in the cartilaginous structures of one or more joints. When accompanied by attacks of goutlike symptoms, it is called pseudogout. (Dorland, 27th ed)~MSH2003_2003_05_12 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26914 C26914 qualifier-P325~P378~CSP2003 abnormal development of secondary male sexual characteristics such as facial hair; in females, can be caused by androgen secretion by adrenal cortex.~CSP2003 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28245 C28245 qualifier-P90~P384~CTCAE 3.0 Aspiration~CTCAE 3.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28517 C28517 qualifier-P325~P378~MSH2002 Small containers or pellets of a solid drug implanted in the body to achieve sustained release of the drug.~MSH2002 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38778 C38778 qualifier-P325~P378~KEGG Alzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-beta (Abeta), a major component of senile plaques, has various pathological effects on cell and organelle function. The extracellular Abeta oligomers may activate caspases through activation of cell surface death receptors. Alternatively, intracellular Abeta may contribute to pathology by facilitating tau hyper-phosphorylation, disrupting mitochondria function, and triggering calcium dysfunction. To date genetic studies have revealed four genes that may be linked to autosomal dominant or familial early onset AD (FAD). These four genes include: amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2) and apolipoprotein E (ApoE). All mutations associated with APP and PS proteins can lead to an increase in the production of Abeta peptides, specifically the more amyloidogenic form, Abeta42. FAD-linked PS1 mutation downregulates the unfolded protein response and leads to vulnerability to ER stress.~KEGG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P325~P378~BIOCARTA Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. The major regulator of blood pressure homeostasis is the renin-angiotensin system. Angiotensinogen is digested by renin to produce angiotensin I (AGT I). AGT I is an inactive 10 amino-acid peptide that is further degraded to produce angiotensin II by the angiotensin-converting enzyme (ACE). Angiotensin II is the master regulator of blood pressure increase acting on the heart, kidneys and blood vessels. Angiotensin II causes direct constriction of the resistance vessels and stimulation of the adrenal thereby increasing blood volume and sodium absorption. In 2000, Tipnis et al. discovered ACE 2 a second carboxypeptidase that digests angiotensin. ACE is a di-peptidase, cleaving off 2 peptides from the c-terminal end of angiotensin. ACE 2 only cleaves 1 amino acid to produce angiotensin 1-9 (AGT 1-9) which has no identified function at this time. AGT 1-9 is not converted to angiotensin II but further degraded by ACE to AGT 1-7, a vasodilator. It would appear that ACE 2 inhibits the formation of angiotensin and reduces blood pressure increases. Crackower et al determined that ace2 -/- mice suffered significant heart defects at 6 months. Further deletion of ACE resulted in restored cardiac functions. (This definition may be outdated - see the DesignNote.)~BIOCARTA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P90~P384~BIOCARTA Angiotensin-converting enzyme 2 regulates heart function~BIOCARTA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42692 C42692 qualifier-P90~P384~NCICB latestVersionIndicator~NCICB +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54742 C54742 qualifier-P325~P378~CTCAE 3.0 Transient flushing or rash; drug fever <38 degrees C (<100.4 degrees F)~CTCAE 3.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C60314 C60314 qualifier-P90~P384~RENI Tissue autolysed, diagnosis not possible (RENI)~RENI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C79954 C79954 qualifier-P90~P384~ZFin WIK~ZFin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8498 C8498 qualifier-P325~P378~CCPS A genetic predispostion to developing melanoma due to germline mutation in CDKN2A or CDK4. Subsets of patients are also at risk for pancreatic cancer or astrocytoma.~CCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C91532 C91532 qualifier-P90~P384~PID Signaling events mediated by the Hedgehog family~PID +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-style1 C1504 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1504 child-style1 C1000 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 parent-style2 C9385 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C9385 child-style2 C100051 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107687 C107687 max-children 3234 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-count1 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100063 C100063 parent-count2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101132 C101132 parent-count3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104006 C104006 parent-count4 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114836 C114836 parent-count5 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160034 C160034 parent-count6 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160054 C160054 parent-count7 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160053 C160053 parent-count8 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160005 C160005 parent-count9 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C159984 C159984 parent-count10 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160108 C160108 parent-count12 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160024 C160024 parent-count13 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160102 C160102 parent-count16 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12218 C12218 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12219 C12219 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12913 C12913 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14250 C14250 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16612 C16612 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17828 C17828 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1908 C1908 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20047 C20047 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20181 C20181 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20189 C20189 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20633 C20633 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22187 C22187 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22188 C22188 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26548 C26548 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28428 C28428 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3910 C3910 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43431 C43431 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057 C7057 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C97325 C97325 root diff --git a/src/test/resources/samples/umlssemnet-samples.txt b/src/test/resources/samples/umlssemnet-samples.txt index e0578eaa6..e0a9513f9 100644 --- a/src/test/resources/samples/umlssemnet-samples.txt +++ b/src/test/resources/samples/umlssemnet-samples.txt @@ -1,64 +1,64 @@ -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Semantic_Type STY -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Preferred_Name Organism -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Synonym orgm -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 STN A1.1 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 DEF Generally, a living individual, including all plants and animals. -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T142 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T165 T090 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T002 T002 rdfs:subClassOf/owl:Restriction~T135 T123 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T004 T004 rdfs:subClassOf/owl:Restriction~T147 T046 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T005 T005 rdfs:subClassOf/owl:Restriction~T166 T123 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T008 T008 rdfs:subClassOf/owl:Restriction~T145 T053 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T010 T010 UN Few concepts will be assigned to this broad type. -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 NH Y -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 rdfs:subClassOf/owl:Restriction~T133 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T134 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T175 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T176 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T179 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T137 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T149 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T150 T038 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T151 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T152 T096 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T157 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T021 T021 rdfs:subClassOf/owl:Restriction~T144 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T022 T022 rdfs:subClassOf/owl:Restriction~T160 T021 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T172 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T173 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T174 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T177 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T198 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T199 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T028 T028 rdfs:subClassOf/owl:Restriction~T141 T044 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T031 T031 rdfs:subClassOf/owl:Restriction~T178 T024 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+http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T164 T038 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T193 T031 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T060 T060 rdfs:subClassOf/owl:Restriction~T155 T073 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T148 T046 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T154 T019 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T093 T093 rdfs:subClassOf/owl:Restriction~T153 T101 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T096 T096 rdfs:subClassOf/owl:Restriction~T188 T052 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T097 T097 rdfs:subClassOf/owl:Restriction~T143 T090 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RTN R1 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RI physically_related_to +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-style1 T072 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T072 child-style1 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T158 T158 max-children 12 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-count1 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T051 T051 root +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T071 T071 root +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T186 T186 root From 9122c01f29ad69c06b6d88ace9c80a0183616ed3 Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Wed, 13 Nov 2024 04:32:12 -0800 Subject: [PATCH 08/11] Fixing reindex.sh to work with stardog and jena --- src/main/resources/metadata/chebi.txt | 4 +- src/main/resources/metadata/hgnc.txt | 8 +- src/main/resources/metadata/icd10cm.txt | 4 +- src/main/resources/metadata/ncim.txt | 4 +- src/main/resources/metadata/ncit.txt | 6 +- src/main/resources/metadata/snomedct.txt | 4 +- src/test/resources/samples/canmed-samples.txt | 54 +- src/test/resources/samples/chebi-samples.txt | 90 +- src/test/resources/samples/medrt-samples.txt | 46 +- src/test/resources/samples/ncit-samples.txt | 952 +++++++++--------- .../resources/samples/umlssemnet-samples.txt | 128 +-- 11 files changed, 650 insertions(+), 650 deletions(-) diff --git a/src/main/resources/metadata/chebi.txt b/src/main/resources/metadata/chebi.txt index e93a16ff1..cf70d36d0 100644 --- a/src/main/resources/metadata/chebi.txt +++ b/src/main/resources/metadata/chebi.txt @@ -1,3 +1,3 @@ -# Sample concepts to include in report -CHEBI:119915 +# Sample concepts to include in report +CHEBI:119915 CHEBI:13248 \ No newline at end of file diff --git a/src/main/resources/metadata/hgnc.txt b/src/main/resources/metadata/hgnc.txt index aa8ff2535..9355c9b15 100644 --- a/src/main/resources/metadata/hgnc.txt +++ b/src/main/resources/metadata/hgnc.txt @@ -1,4 +1,4 @@ -# Sample concepts to include in report -gene_with_protein_product -HGNC:10218 -HGCN:54003 +# Sample concepts to include in report +gene_with_protein_product +HGNC:10218 +HGCN:54003 diff --git a/src/main/resources/metadata/icd10cm.txt b/src/main/resources/metadata/icd10cm.txt index 8e7262792..ed3ec65b1 100644 --- a/src/main/resources/metadata/icd10cm.txt +++ b/src/main/resources/metadata/icd10cm.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (ORDER_NO) -I85 +# Sample concept for synonym qualifier (ORDER_NO) +I85 diff --git a/src/main/resources/metadata/ncim.txt b/src/main/resources/metadata/ncim.txt index cfdd5de6d..fd0853029 100644 --- a/src/main/resources/metadata/ncim.txt +++ b/src/main/resources/metadata/ncim.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) - +# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) + diff --git a/src/main/resources/metadata/ncit.txt b/src/main/resources/metadata/ncit.txt index bab98500b..9bd6ec28f 100644 --- a/src/main/resources/metadata/ncit.txt +++ b/src/main/resources/metadata/ncit.txt @@ -1,3 +1,3 @@ -# Sample concepts to include in report -C3224 -C100110 +# Sample concepts to include in report +C3224 +C100110 diff --git a/src/main/resources/metadata/snomedct.txt b/src/main/resources/metadata/snomedct.txt index 2831af55c..3f4776023 100644 --- a/src/main/resources/metadata/snomedct.txt +++ b/src/main/resources/metadata/snomedct.txt @@ -1,2 +1,2 @@ -# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) -130090009 +# Sample concept for synonym qualifier (CASE_SIGNIFICANCE_ID, TYPE_ID) +130090009 diff --git a/src/test/resources/samples/canmed-samples.txt b/src/test/resources/samples/canmed-samples.txt index 55ecf4aaf..632df957c 100644 --- a/src/test/resources/samples/canmed-samples.txt +++ b/src/test/resources/samples/canmed-samples.txt @@ -1,27 +1,27 @@ -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Preferred_Name Mercaptopurine 50.0 mg/1 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Discontinue_Date 11/23/2021 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 owl:deprecated true -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 CMS_Effective_Date 01/01/2017 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 Oral No -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 FDA_Approval_Year 2008 -http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 HCPCS_Code J9034 -http://seer.nci.nih.gov/CanMED.owl#C9235 C9235 CMS_Discontinuation_Date 12/31/2007 00:00:00 -http://seer.nci.nih.gov/CanMED.owl#S0087 S0087 FDA_Discontinuation_Year 2012 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-style1 NDC_00378-3547 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547 child-style1 NDC_00378-3547-25 -http://seer.nci.nih.gov/CanMED.owl#NDC_PREDNISONE NDC_PREDNISONE max-children 487 -http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-count1 -http://seer.nci.nih.gov/CanMED.owl#HCPCS_BCMA HCPCS_BCMA parent-count2 -http://seer.nci.nih.gov/CanMED.owl#NDC_DRONABINOL NDC_DRONABINOL parent-count3 -http://seer.nci.nih.gov/CanMED.owl#HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR parent-count4 -http://seer.nci.nih.gov/CanMED.owl#HCPCS HCPCS root -http://seer.nci.nih.gov/CanMED.owl#NDC NDC root +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Preferred_Name Mercaptopurine 50.0 mg/1 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Status In Use +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Effective_Date 07/01/2005 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Description 250 TABLET in 1 BOTTLE, PLASTIC (0378-3547-25) +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Brand_Name Mercaptopurine +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Package_Code 00378-3547-25 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Administration_Route Oral +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Strength 50.0 mg/1 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 Generic_Name Mercaptopurine +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 NDC_Product_Code 00378-3547 +http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 Discontinue_Date 11/23/2021 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#NDC_55289-0603-07 NDC_55289-0603-07 owl:deprecated true +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 CMS_Effective_Date 01/01/2017 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 Oral No +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 FDA_Approval_Year 2008 +http://seer.nci.nih.gov/CanMED.owl#J9034 J9034 HCPCS_Code J9034 +http://seer.nci.nih.gov/CanMED.owl#C9235 C9235 CMS_Discontinuation_Date 12/31/2007 00:00:00 +http://seer.nci.nih.gov/CanMED.owl#S0087 S0087 FDA_Discontinuation_Year 2012 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-style1 NDC_00378-3547 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547 child-style1 NDC_00378-3547-25 +http://seer.nci.nih.gov/CanMED.owl#NDC_PREDNISONE NDC_PREDNISONE max-children 487 +http://seer.nci.nih.gov/CanMED.owl#NDC_00378-3547-25 NDC_00378-3547-25 parent-count1 +http://seer.nci.nih.gov/CanMED.owl#HCPCS_BCMA HCPCS_BCMA parent-count2 +http://seer.nci.nih.gov/CanMED.owl#NDC_DRONABINOL NDC_DRONABINOL parent-count3 +http://seer.nci.nih.gov/CanMED.owl#HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR HCPCS_GRANULOCYTE_COLONY_STIMULATING_FACTOR parent-count4 +http://seer.nci.nih.gov/CanMED.owl#HCPCS HCPCS root +http://seer.nci.nih.gov/CanMED.owl#NDC NDC root diff --git a/src/test/resources/samples/chebi-samples.txt b/src/test/resources/samples/chebi-samples.txt index cf7584b8f..6c0906575 100644 --- a/src/test/resources/samples/chebi-samples.txt +++ b/src/test/resources/samples/chebi-samples.txt @@ -1,46 +1,46 @@ -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:charge 0 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:formula C36H38N2O6 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchi InChI=1S/C36H38N2O6/c1-37-13-11-23-18-31(41-3)32-20-26(23)27(37)15-21-5-8-25(9-6-21)43-30-17-22(7-10-29(30)39)16-28-34-24(12-14-38(28)2)19-33(42-4)35(40)36(34)44-32/h5-10,17-20,27-28,39-40H,11-16H2,1-4H3/t27-,28-/m0/s1 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchikey XGEAUXVPBXUBKN-NSOVKSMOSA-N -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:mass 594.698 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:monoisotopicmass 594.27299 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:smiles COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5cc(C[C@@H]6N(C)CCc7cc(OC)c(O)c(Oc1cc23)c67)ccc5O)cc4 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasDbXref CAS:21008-67-3 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasExactSynonym (+)-Atherospermoline -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasOBONamespace chebi_ontology -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:inSubset 2_STAR -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 rdfs:label (+)-Atherospermoline -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~has_role CHEBI:76924 -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~is_enantiomer_of CHEBI:6714 -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 IAO_0000115 The (-)-enantiomer of medicarpin. -http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 oboInOwl:hasRelatedSynonym medicarpin -http://purl.obolibrary.org/obo/CHEBI_10002 CHEBI:10002 rdfs:subClassOf/owl:Restriction~has_functional_parent CHEBI:173072 -http://purl.obolibrary.org/obo/CHEBI_10003 CHEBI:10003 rdfs:subClassOf/owl:Restriction~has_part CHEBI:65028 -http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 rdfs:subClassOf/owl:Restriction~is_conjugate_acid_of CHEBI:62070 -http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 oboInOwl:hasAlternativeId CHEBI:7456 -http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 rdfs:subClassOf/owl:Restriction~has_parent_hydride CHEBI:36372 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_conjugate_base_of CHEBI:192486 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_tautomer_of CHEBI:192484 -http://purl.obolibrary.org/obo/CHEBI_111516 CHEBI:111516 rdfs:subClassOf/owl:Restriction~is_substituent_group_from CHEBI:111513 -http://purl.obolibrary.org/obo/CHEBI_131515 CHEBI:131515 owl:deprecated true -http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasDbXref~oboInOwl:source CAS:35144-10-6~KEGG COMPOUND -http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasExactSynonym~oboInOwl:hasDbXref Viscidulin B~KEGG_COMPOUND -http://purl.obolibrary.org/obo/CHEBI_9997 CHEBI:9997 qualifier-oboInOwl:hasRelatedSynonym~oboInOwl:hasDbXref Virginiamycin factor M1~ChemIDplus -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-style1 CHEBI:133004 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:133004 child-style1 CHEBI:10 -http://purl.obolibrary.org/obo/CHEBI_24995 CHEBI:24995 max-children 7343 -http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-count1 -http://purl.obolibrary.org/obo/CHEBI_100002 CHEBI:100002 parent-count2 -http://purl.obolibrary.org/obo/CHEBI_100000 CHEBI:100000 parent-count3 -http://purl.obolibrary.org/obo/CHEBI_10018 CHEBI:10018 parent-count4 -http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 parent-count5 -http://purl.obolibrary.org/obo/CHEBI_10016 CHEBI:10016 parent-count6 -http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 parent-count7 -http://purl.obolibrary.org/obo/CHEBI_101257 CHEBI:101257 parent-count8 -http://purl.obolibrary.org/obo/CHEBI_10041 CHEBI:10041 parent-count9 -http://purl.obolibrary.org/obo/CHEBI_132640 CHEBI:132640 parent-count10 -http://purl.obolibrary.org/obo/CHEBI_167670 CHEBI:167670 parent-count11 -http://purl.obolibrary.org/obo/CHEBI_85616 CHEBI:85616 parent-count14 -http://purl.obolibrary.org/obo/CHEBI_24431 CHEBI:24431 root -http://purl.obolibrary.org/obo/CHEBI_36342 CHEBI:36342 root +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:charge 0 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:formula C36H38N2O6 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchi InChI=1S/C36H38N2O6/c1-37-13-11-23-18-31(41-3)32-20-26(23)27(37)15-21-5-8-25(9-6-21)43-30-17-22(7-10-29(30)39)16-28-34-24(12-14-38(28)2)19-33(42-4)35(40)36(34)44-32/h5-10,17-20,27-28,39-40H,11-16H2,1-4H3/t27-,28-/m0/s1 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:inchikey XGEAUXVPBXUBKN-NSOVKSMOSA-N +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:mass 594.698 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:monoisotopicmass 594.27299 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 chebi:smiles COc1cc2CCN(C)[C@H]3Cc4ccc(Oc5cc(C[C@@H]6N(C)CCc7cc(OC)c(O)c(Oc1cc23)c67)ccc5O)cc4 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasDbXref CAS:21008-67-3 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasExactSynonym (+)-Atherospermoline +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:hasOBONamespace chebi_ontology +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 oboInOwl:inSubset 2_STAR +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 rdfs:label (+)-Atherospermoline +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~has_role CHEBI:76924 +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 rdfs:subClassOf/owl:Restriction~is_enantiomer_of CHEBI:6714 +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 IAO_0000115 The (-)-enantiomer of medicarpin. +http://purl.obolibrary.org/obo/CHEBI_100 CHEBI:100 oboInOwl:hasRelatedSynonym medicarpin +http://purl.obolibrary.org/obo/CHEBI_10002 CHEBI:10002 rdfs:subClassOf/owl:Restriction~has_functional_parent CHEBI:173072 +http://purl.obolibrary.org/obo/CHEBI_10003 CHEBI:10003 rdfs:subClassOf/owl:Restriction~has_part CHEBI:65028 +http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 rdfs:subClassOf/owl:Restriction~is_conjugate_acid_of CHEBI:62070 +http://purl.obolibrary.org/obo/CHEBI_100147 CHEBI:100147 oboInOwl:hasAlternativeId CHEBI:7456 +http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 rdfs:subClassOf/owl:Restriction~has_parent_hydride CHEBI:36372 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_conjugate_base_of CHEBI:192486 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 rdfs:subClassOf/owl:Restriction~is_tautomer_of CHEBI:192484 +http://purl.obolibrary.org/obo/CHEBI_111516 CHEBI:111516 rdfs:subClassOf/owl:Restriction~is_substituent_group_from CHEBI:111513 +http://purl.obolibrary.org/obo/CHEBI_131515 CHEBI:131515 owl:deprecated true +http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasDbXref~oboInOwl:source CAS:35144-10-6~KEGG COMPOUND +http://purl.obolibrary.org/obo/CHEBI_9999 CHEBI:9999 qualifier-oboInOwl:hasExactSynonym~oboInOwl:hasDbXref Viscidulin B~KEGG_COMPOUND +http://purl.obolibrary.org/obo/CHEBI_9997 CHEBI:9997 qualifier-oboInOwl:hasRelatedSynonym~oboInOwl:hasDbXref Virginiamycin factor M1~ChemIDplus +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-style1 CHEBI:133004 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:133004 child-style1 CHEBI:10 +http://purl.obolibrary.org/obo/CHEBI_24995 CHEBI:24995 max-children 7343 +http://purl.obolibrary.org/obo/CHEBI_10 CHEBI:10 parent-count1 +http://purl.obolibrary.org/obo/CHEBI_100002 CHEBI:100002 parent-count2 +http://purl.obolibrary.org/obo/CHEBI_100000 CHEBI:100000 parent-count3 +http://purl.obolibrary.org/obo/CHEBI_10018 CHEBI:10018 parent-count4 +http://purl.obolibrary.org/obo/CHEBI_10015 CHEBI:10015 parent-count5 +http://purl.obolibrary.org/obo/CHEBI_10016 CHEBI:10016 parent-count6 +http://purl.obolibrary.org/obo/CHEBI_100241 CHEBI:100241 parent-count7 +http://purl.obolibrary.org/obo/CHEBI_101257 CHEBI:101257 parent-count8 +http://purl.obolibrary.org/obo/CHEBI_10041 CHEBI:10041 parent-count9 +http://purl.obolibrary.org/obo/CHEBI_132640 CHEBI:132640 parent-count10 +http://purl.obolibrary.org/obo/CHEBI_167670 CHEBI:167670 parent-count11 +http://purl.obolibrary.org/obo/CHEBI_85616 CHEBI:85616 parent-count14 +http://purl.obolibrary.org/obo/CHEBI_24431 CHEBI:24431 root +http://purl.obolibrary.org/obo/CHEBI_36342 CHEBI:36342 root http://purl.obolibrary.org/obo/CHEBI_50906 CHEBI:50906 root \ No newline at end of file diff --git a/src/test/resources/samples/medrt-samples.txt b/src/test/resources/samples/medrt-samples.txt index d474cf786..b86b05ec7 100644 --- a/src/test/resources/samples/medrt-samples.txt +++ b/src/test/resources/samples/medrt-samples.txt @@ -1,23 +1,23 @@ -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Preferred_Term 1-Compartment -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 CTY PK -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 NUI N0000000060 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Concept_Name 1-Compartment [PK] -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Status ACTIVE -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 Synonym Hydroxyphenylpyruvate Dioxygenase Inhibitor -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 rdfs:subClassOf/owl:Restriction~has_MoA N0000175808 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175771 N0000175771 rdfs:subClassOf/owl:Restriction~has_PE N0000008953 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193790 N0000193790 rdfs:subClassOf/owl:Restriction~has_SC N0000191722 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175874 N0000175874 rdfs:subClassOf/owl:Restriction~has_TC N0000178297 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-style1 N0000000059 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000059 child-style1 N0000000060 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193894 N0000193894 max-children 115 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-count1 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000215 N0000000215 parent-count2 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000177910 N0000177910 parent-count3 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000175453 N0000175453 parent-count4 -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000223 N0000000223 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000003 N0000000003 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000000001 N0000000001 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000009802 N0000009802 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000193784 N0000193784 root -http://ncicb.nci.nih.gov/MEDRT.owl#N0000178293 N0000178293 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Preferred_Term 1-Compartment +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 CTY PK +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 NUI N0000000060 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Concept_Name 1-Compartment [PK] +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 Status ACTIVE +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 Synonym Hydroxyphenylpyruvate Dioxygenase Inhibitor +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175809 N0000175809 rdfs:subClassOf/owl:Restriction~has_MoA N0000175808 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175771 N0000175771 rdfs:subClassOf/owl:Restriction~has_PE N0000008953 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193790 N0000193790 rdfs:subClassOf/owl:Restriction~has_SC N0000191722 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175874 N0000175874 rdfs:subClassOf/owl:Restriction~has_TC N0000178297 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-style1 N0000000059 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000059 child-style1 N0000000060 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193894 N0000193894 max-children 115 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000060 N0000000060 parent-count1 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000215 N0000000215 parent-count2 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000177910 N0000177910 parent-count3 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000175453 N0000175453 parent-count4 +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000223 N0000000223 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000003 N0000000003 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000000001 N0000000001 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000009802 N0000009802 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000193784 N0000193784 root +http://ncicb.nci.nih.gov/MEDRT.owl#N0000178293 N0000178293 root diff --git a/src/test/resources/samples/ncit-samples.txt b/src/test/resources/samples/ncit-samples.txt index 37adf6ffa..7989ec4af 100644 --- a/src/test/resources/samples/ncit-samples.txt +++ b/src/test/resources/samples/ncit-samples.txt @@ -1,476 +1,476 @@ -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P106 Amino Acid, Peptide, or Protein -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P108 Recombinant Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P207 C1514768 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P366 Recombinant_Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P90 AR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P97 A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04) -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 rdfs:label Recombinant Amphiregulin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 rdfs:subClassOf/owl:Restriction~R123 C405 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 rdfs:subClassOf/owl:Restriction~R163 C12686 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 A8 C101859 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P322 CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P325 A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms. -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100012 C100012 rdfs:subClassOf/owl:Restriction~R100 C12686 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P208 CL433438 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P329 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P330 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P399 725443 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R126 C3270 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R101 C12415 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R103 C45714 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R104 C12578 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R105 C12917 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R108 C36115 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R115 C3090 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R139 C36760 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R142 C36122 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P107 Renal Cell Carcinoma Associated with Neuroblastoma -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P363 Malignant -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R101 C12341 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R103 C32365 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R104 C12591 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R108 C36027 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R115 C35841 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P171 12927386 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P210 77538-19-3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P319 R8WTH25YS2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R124 C45547 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R125 C16298 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R146 C37279 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100089 C100089 A32 C1909 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100089 C100089 P375 Interferon Gamma-1b -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R50 C14073 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R52 C16701 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R53 C16702 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 rdfs:subClassOf/owl:Restriction~R54 C21281 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 P100 153310 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100091 C100091 P93 Q05315 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R139 C36897 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 rdfs:subClassOf/owl:Restriction~R135 C12725 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100097 C100097 P317 SPL Flavor (C-DRG-0934) -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100098 C100098 P350 C15H22N6O5S -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100099 C100099 A7 C104498 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 P175 616524 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100103 C100103 A17 C45300 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100103 C100103 A18 C149570 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 A24 C173262 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P372 Yes -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P374 EVS/CDISC/SDTM/SDTM Terminology.xls|2:all -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P376 <p>The terminology subset that includes terms pertaining to the CDISC questionnaire terminology.</p> <p>The terminology can be downloaded at this location: <a href="https://evs.nci.nih.gov/ftp1/CDISC/SDTM/"> CDISC Questionnaire Terminology</a>.</p> -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100110 C100110 P398 No -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100120 C100120 P361 No -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100132 C100132 A25 C100131 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 P368 CHEBI:22565 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P200 Coagulation_Study -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P98 Tue Jun 18 14:23:59 EDT 2013 - See 'Activated_PTT_Standard_Ratio_Measurement' -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 owl:deprecated true -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100428 C100428 A13 C84429 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R124 C40551 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R125 C17557 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R72 C13258 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1005 C1005 P302 Myelodysplastic syndrome; multiple myeloma; chronic myeloid leukemia; acute myelocytic leukemia -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100807 C100807 P364 A8|C100130 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100809 C100809 A35 C168870 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101043 C101043 rdfs:subClassOf/owl:Restriction~R116 C98898 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101046 C101046 rdfs:subClassOf/owl:Restriction~R175 C37193 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101048 C101048 rdfs:subClassOf/owl:Restriction~R37 C18497 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101056 C101056 rdfs:subClassOf/owl:Restriction~R133 C45208 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101063 C101063 P102 U41743 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101071 C101071 P204 Gene_Involved_In_Pathogenesis_Of_Disease some 'Acute Myeloid Leukemia with inv(3) (q21.3;q26.2) or t(3;3) (q21.3;q26.2); GATA2, MECOM' -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 P369 HGNC:18037 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101089 C101089 rdfs:subClassOf/owl:Restriction~R40 C24930 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101089 C101089 P321 196528 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101090 C101090 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-http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101092 C101092 rdfs:subClassOf/owl:Restriction~R130 C91675 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101093 C101093 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R131 C91675 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101097 C101097 rdfs:subClassOf/owl:Restriction~R46 C13197 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101110 C101110 rdfs:subClassOf/owl:Restriction~R41 C14225 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101111 C101111 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R130 C39233 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101111 C101111 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R40 C24979 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101118 C101118 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R44 C21256 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101138 C101138 A23 C25337 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C101735 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 rdfs:subClassOf/owl:Restriction~R27 C26320 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101250 C101250 oboInOwl:hasDbXref IMDRF:E0128 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101262 C101262 rdfs:subClassOf/owl:Restriction~R72 C12543 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101266 C101266 rdfs:subClassOf/owl:Restriction~R167 C13018 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101266 C101266 rdfs:subClassOf/owl:Restriction~R169 C13018 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101293 C101293 A28 C158954 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101403 C101403 rdfs:subClassOf/owl:Restriction~R131 C39187 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101461 C101461 A1 C43431 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101461 C101461 A2 C7057 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101527 C101527 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rdfs:subClassOf/owl:Restriction~R32 C1909 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102819 C102819 rdfs:subClassOf/owl:Restriction~R51 C26065 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102845 C102845 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R105 C37145 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102845 C102845 rdfs:subClassOf/owl:Restriction~R114 C36484 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102845 C102845 rdfs:subClassOf/owl:Restriction~R89 C36673 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102884 C102884 rdfs:subClassOf/owl:Restriction~R126 C26726 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102897 C102897 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R110 C14158 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102897 C102897 rdfs:subClassOf/owl:Restriction~R110 C14158 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10303 C10303 rdfs:subClassOf/owl:Restriction~R172 C3224 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C103239 C103239 rdfs:subClassOf/owl:Restriction~R171 C12382 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104080 C104080 rdfs:subClassOf/owl:Restriction~R30 C12439 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104109 C104109 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R45 C14225 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104457 C104457 rdfs:subClassOf/owl:Restriction~R81 C13226 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105104 C105104 P201 Lamina-Associated_Polypeptide_2_Isoform_Alpha -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105362 C105362 P315 rs429358 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105364 C105364 rdfs:subClassOf/owl:Restriction~R48 C2866 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105555 C105555 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R106 C118396 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C105555 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C2889 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7208 C7208 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R113 C39682 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7850 C7850 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R142 C3047 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C81756 C81756 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Restriction~R38 C3099 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82169 C82169 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R37 C19077 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C82169 C82169 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R41 C14225 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C84455 C84455 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Restriction~R132 C45582 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R107 C13271 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C9128 C9128 rdfs:subClassOf/owl:Class/owl:intersectionOf/owl:Class/owl:intersectionOf/owl:Restriction~R89 C36712 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 P310 Obsolete_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100421 C100421 P310 Retired_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C129445 C129445 P310 Provisional_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13037 C13037 P310 Header_Concept -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~AB AR~AB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P384~NCI AR~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P90~P383~PT Recombinant Amphiregulin~PT -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P97~P378~NCI A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04)~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P325~P378~CDISC A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms.~CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P90~P384~CDISC PERCUTANEOUS CORONARY INTERVENTION (PCI) FOR ST ELEVATION MYOCARDIAL INFARCTION (STEMI) (STABLE, >12 HRS FROM SYMPTOM ONSET)~CDISC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P384~SEER COPADRI-I~SEER -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P383~SY Cyclophosphamide-Vincristine-Melphalan-Doxorubicin~SY -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99996 C99996 qualifier-P90~P385 Number of Diseased Coronary Vessels~SDTM-CVTEST -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100022 C100022 qualifier-P90~P384~CPTAC Transcatheter Aortic Valve Implantation~CPTAC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 qualifier-P90~P383~FB Evozac~FB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P325~P378~CDISC-GLOSS A standard protocol for exchanging files between computers on the internet. See also TCP/IP.~CDISC-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P90~P384~CDISC-GLOSS File Transfer Protocol (FTP)~CDISC-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P383~DN Renal Cell Cancer Associated with Neuroblastoma~DN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P384~CTRP Renal Cell Cancer Associated with Neuroblastoma~CTRP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 qualifier-P90~P383~AQS Conjunctival Precancerous Melanosis~AQS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~BR Compritol 888 ATO~BR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~SN Docosanoic Acid, Diester with 1,2,3-propanetriol~SN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P384~FDA GLYCERYL DIBEHENATE~FDA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99905 C99905 qualifier-P90~P386 ROCILETINIB~UNII -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P325~P378~ACC/AHA Catheter ablation is an invasive procedure used to remove or terminate a faulty electrical pathway from sections of the hearts of those who are prone to developing cardiac arrhythmias such as atrial fibrillation, atrial flutter, SVT and Wolff-Parkinson-White syndrome.~ACC/AHA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P90~P384~ACC/AHA Catheter ablation~ACC/AHA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P393 Dependent relative needing care at home~Related To -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P394 Dependent relative needing care at home~PT -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P395 Dependent relative needing care at home~Z63.6 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P396 Dependent relative needing care at home~ICD10CM 2017 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 qualifier-P90~P384~CTEP Nongerminomatous GCT - CNS~CTEP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100096 C100096 qualifier-P90~P384~caDSR OMRS~caDSR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 qualifier-P90~P384~DTP Ampligen~DTP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100100 C100100 qualifier-P90~P383~CN AP611074~CN -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~PCDC Clinical Signs or Symptoms~PCDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~NICHD Sign or Symptom~NICHD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P325~P378~NCI-GLOSS An anticancer drug that belongs to the family of drugs called antineoplastic antibiotics.~NCI-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P90~P384~NCI-GLOSS ansamycin~NCI-GLOSS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1004 C1004 qualifier-P90~P384~DCP Antineoplaston A10~DCP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100805 C100805 qualifier-P90~P384~GDC Natural Grandchild~GDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100897 C100897 qualifier-P90~P384~UCUM 10*3.{copies}/mL~UCUM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101028 C101028 qualifier-P325~P378~NICHD Aspiration of amniotic fluid around the time of delivery resulting in severe respiratory distress.~NICHD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101029 C101029 qualifier-P90~P384~Cellosaurus Atrioventricular Septal Defect~Cellosaurus -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99537 C99537 qualifier-P375~P397 Venous thromboembolism~18.1 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99865 C99865 qualifier-P97~P381 A fusion gene that results from a complex chromosomal rearrangement where inversion of 22q12 is followed by a translocation t(1;22)(p34;q12) that disrupts intron 3 of the UQCRH gene. PCR analysis of tumor cDNA and genomic DNA detected a UQCRH/EWSR1 fusion transcript but it is out-of-frame and contains premature stop codons.~OMIM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 qualifier-P90~P384~HGNC ARID2~HGNC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101125 C101125 qualifier-P90~P383~AD Discordant~AD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P325~P378~CareLex A single activity that has occurred within a business process.~CareLex -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P90~P384~CareLex Task~CareLex -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101138 C101138 qualifier-P90~P384~BRIDG 5.3 ctdiVol~BRIDG 5.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P325~P378~INC The occipitofrontal circumference of a neonate's head at birth. Measurement to the nearest 0.1 cm should be taken at the broadest part of the forehead above the eyebrow and above the ears, most prominent part of the back of the head on the day of birth or the day after birth.~INC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P90~P384~INC Head Circumference at Birth~INC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CNU 535~CNU -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P384~GENC 535~GENC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA3 BES~CA3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA2 BQ~CA2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101250 C101250 qualifier-P325~P378~FDA Injury to the peripheral nervous system.~FDA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99286 C99286 qualifier-P325~P381 The catalog, reference, or product number found on the device label or accompanying packaging to identify a particular product.~CDRH-GUDID -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~ICDC WGS~ICDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~CTDC WGS (whole genome sequencing)~CTDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P325~P378~CRCH Carotenoid consisting of a cyclic structure on each end with additional double bonds at the number 5 and 5' carbon atoms of the cyclic structures.~CRCH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P90~P384~CRCH 3,7,12,16-tetramethyl-1,18-bis(2,6,6-trimethyl-1-cyclohexenyl)-octadeca-1,3,5,7,9,11,13,15,17-nonaene~CRCH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102405 C102405 qualifier-P90~P384~NCPDP Capful~NCPDP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102556 C102556 qualifier-P90~P384~BRIDG 3.0.3 IVL.LOW<TS.DATE>~BRIDG 3.0.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 5.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression OTHER NAME(S): Clinical Events Medical History NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 5.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 3.0.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression. NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 3.0.3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102821 C102821 qualifier-P90~P384~CCPS SPRED1~CCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104030 C104030 qualifier-P90~P383~HD Adrenal Cortex Carcinoma by ENSAT Stage~HD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104438 C104438 qualifier-P325~P378~BRIDG Specifies whether this device bears a CE (Conformite Europeenne) mark. NOTE(S): CE is a mark for device products placed on the market in the European Economic Area (EEA). By placing the CE marking on a product, the manufacturer affirms that the product conforms with the requirements of the applicable European Community directives.~BRIDG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~CDC OTHER RACE~CDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~SeroNet Other~SeroNet -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P325~P378~CTCAE A disorder characterized by an acute inflammatory reaction resulting from the release of histamine and histamine-like substances from mast cells, causing a hypersensitivity immune response. Clinically, it presents with breathing difficulty, dizziness, hypotension, cyanosis and loss of consciousness and may lead to death.~CTCAE -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P90~P384~CTCAE Anaphylaxis~CTCAE -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P325~P378~EDQM-HC Exposure of a breast-feeding infant to a medicinal product administered to the lactating mother. Comment: This term is not intended to describe an authorised route of administration for use in marketing authorisations, and does not cover intentional administration of a medicinal product to a breastfeeding infant. It is intended for use in adverse event reporting for pharmacovigilance purposes.~EDQM-HC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P90~P384~EDQM-HC Transmammary~EDQM-HC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P325~P378~GAIA The death of a woman while pregnant or within 42 days of termination of pregnancy, irrespective of the duration and the site of the pregnancy (as defined by Maternal Death guidelines: http:www.brightoncollaboration.org).~GAIA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P90~P384~GAIA Maternal Death~GAIA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114560 C114560 qualifier-P90~P383~AQ Childhood L1 Acute Lymphoblastic Leukemia~AQ -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C118618 C118618 qualifier-P325~P378~CTEP Systemic chemotherapy with a regimen containing multiple agents.~CTEP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12241 C12241 qualifier-P90~P384~CTRM Branchial Cleft~CTRM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12261 C12261 qualifier-P325~P378~ICDO3 not classifiable to C16.1 to C16.4~ICDO3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12558 C12558 qualifier-P325~P378~NCI A cell that arises from stem cells and/or bone marrow-derived monocytes that function in different aspects of host defense and tissue repair; such as phagocytosis, cytotoxic activity, and regulation of the immune response (antigen presentation and T-cell activation).~NCI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12599 C12599 qualifier-P325~P378~MSH2001 Female germ cells in stages between the prophase of the first maturation division and the completion of the second maturation division.~MSH2001 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12719 C12719 qualifier-P325~P378~UWDA142 is a macroscopic organ component of one or more nerves, which primarily consists of cell bodies of neurons located outside the central nervous system; together with nerve fibers, it constitutes a nerve or a nerve plexus. Example(s): spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion.~UWDA142 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12741 C12741 qualifier-P325~P378~CSP2000 type of cytotoxic leukocytes which attack and kill virus-infected or neoplastic cells independent of antibody coating or MHC restriction; may be derived from lymphocytes or monocytes.~CSP2000 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12842 C12842 qualifier-P325~P378~UMD2001 Grafts used in the treatment of skin loss, usually caused by burn injuries.~UMD2001 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C128574 C128574 qualifier-P90~P384~PI-RADS Apex L AS~PI-RADS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13061 C13061 qualifier-P325~P378~MeSH The cells of the body which stain with chromium salts. They occur along the sympathetic nerves, in the adrenal gland, and in various other organs.~MeSH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1396 C1396 qualifier-P325~P378~CSP2002 family of polypeptide growth factors produced by peripheral target tissues as well as the nervous system, which are critical to neuronal growth, regeneration, survival, and differentiation.~CSP2002 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142787 C142787 qualifier-P90~P384~CBDD Transduction~CBDD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14294 C14294 qualifier-P90~P384~JAX severe combined immune deficiency~JAX -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P325~P378~CTCAE 5.0 A disorder characterized by laboratory test results that indicate an increased number of eosinophils in the blood.~CTCAE 5.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P90~P384~CTCAE 5.0 Eosinophilia~CTCAE 5.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P325~P378~DICOM A drug that contains a radioactive substance and is used to diagnose or treat disease, including cancer.~DICOM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P90~P384~DICOM Radiopharmaceutical~DICOM -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C153106 C153106 qualifier-P90~P384~BRIDG IntegratedStatisticalAnalysisPlan~BRIDG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15538 C15538 qualifier-P325~P378~PCDC Assigned Treatment Arm by Intention-To-Treat~PCDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C155838 C155838 qualifier-P90~P384~NDC ME~NDC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15843 C15843 qualifier-P90~P384~HL7 PRYLX~HL7 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C168622 C168622 qualifier-P325~P378~PQCMC A mathematical symbol that denotes equality or inequality between two values Note: This is typically applicable to biologics.~PQCMC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16904 C16904 qualifier-P90~P383~CS NN~CS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17051 C17051 qualifier-P325~P378~MSH2002_06_01 The ability of some cells or tissues to withstand ionizing radiation without serious injury. Tolerance depends on the species, cell type, and physical and chemical variables, including RADIATION-PROTECTIVE AGENTS and RADIATION-SENSITIZING AGENTS.~MSH2002_06_01 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C179573 C179573 qualifier-P90~P384~WHO Alpha~WHO -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18063 C18063 qualifier-P90~P384~ICH Gy~ICH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18611 C18611 qualifier-P90~P384~KEGG Metabolism~KEGG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P387 extracellular~GO:0005576 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P389 extracellular~NAS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P390 extracellular~CGAP -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P391 extracellular~29-SEP-2003 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C21639 C21639 qualifier-P325~P378~MMHCC Inflammation of the mammary gland~MMHCC -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23247 C23247 qualifier-P325~P378~DCCPS The Corpus uteri, or body of uterus, is the part of the uterus above the isthmus, comprising about two thirds of the non-pregnant organ. 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.~DCCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23372 C23372 qualifier-P325~P378~DCTD-CD That portion of the nervous system consisting of the brain and spinal cord. (Dorland, 28th ed) (MSH98)~DCTD-CD -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23373 C23373 qualifier-P325~P378~FMB-BUDGET That part of the central nervous system contained within the cranium, comprising the prosencephalon, mesencephalon, and rhombencephalon. It is derived from the anterior part of the embryonic neural tube. Functions include muscle control and coordination, sensory reception and integration, speech production, memory storage, and the elaboration of thought and emotions. (Dorland, 28th ed) (MSH98)~FMB-BUDGET -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23404 C23404 qualifier-P325~P378~OMS94 The natural covering of the body; the skin.~OMS94 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23415 C23415 qualifier-P325~P378~DCB-CB2 The layer of epithelial cells that lines the cavities of the heart and of the blood vessels (ENDOTHELIUM, VASCULAR) and lymph vessels (ENDOTHELIUM, LYMPHATIC), and the serous cavities of the body, originating from the MESODERM. (From Dorland, 28th ed) (MSH98)~DCB-CB2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23593 C23593 qualifier-P325~P378~MTH Primitive blood cells derived from embryonic mesenchyme capable of differentiating into any of the blood cell line progenitor cells (erythroblasts, young granulocytic series cells, megakaryocytes, etc.)~MTH -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23887 C23887 qualifier-P325~P378~DEA-DEAIS exocrine gland. a gland from which secretions reach a free surface of the body by ducts.~DEA-DEAIS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25296 C25296 qualifier-P90~P384~CADSR BD~CADSR -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26719 C26719 qualifier-P325~P378~MSH2003_2003_05_12 Presence of calcium salts, especially calcium pyrophosphate, in the cartilaginous structures of one or more joints. When accompanied by attacks of goutlike symptoms, it is called pseudogout. (Dorland, 27th ed)~MSH2003_2003_05_12 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26914 C26914 qualifier-P325~P378~CSP2003 abnormal development of secondary male sexual characteristics such as facial hair; in females, can be caused by androgen secretion by adrenal cortex.~CSP2003 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28245 C28245 qualifier-P90~P384~CTCAE 3.0 Aspiration~CTCAE 3.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28517 C28517 qualifier-P325~P378~MSH2002 Small containers or pellets of a solid drug implanted in the body to achieve sustained release of the drug.~MSH2002 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38778 C38778 qualifier-P325~P378~KEGG Alzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-beta (Abeta), a major component of senile plaques, has various pathological effects on cell and organelle function. The extracellular Abeta oligomers may activate caspases through activation of cell surface death receptors. Alternatively, intracellular Abeta may contribute to pathology by facilitating tau hyper-phosphorylation, disrupting mitochondria function, and triggering calcium dysfunction. To date genetic studies have revealed four genes that may be linked to autosomal dominant or familial early onset AD (FAD). These four genes include: amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2) and apolipoprotein E (ApoE). All mutations associated with APP and PS proteins can lead to an increase in the production of Abeta peptides, specifically the more amyloidogenic form, Abeta42. FAD-linked PS1 mutation downregulates the unfolded protein response and leads to vulnerability to ER stress.~KEGG -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P325~P378~BIOCARTA Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. The major regulator of blood pressure homeostasis is the renin-angiotensin system. Angiotensinogen is digested by renin to produce angiotensin I (AGT I). AGT I is an inactive 10 amino-acid peptide that is further degraded to produce angiotensin II by the angiotensin-converting enzyme (ACE). Angiotensin II is the master regulator of blood pressure increase acting on the heart, kidneys and blood vessels. Angiotensin II causes direct constriction of the resistance vessels and stimulation of the adrenal thereby increasing blood volume and sodium absorption. In 2000, Tipnis et al. discovered ACE 2 a second carboxypeptidase that digests angiotensin. ACE is a di-peptidase, cleaving off 2 peptides from the c-terminal end of angiotensin. ACE 2 only cleaves 1 amino acid to produce angiotensin 1-9 (AGT 1-9) which has no identified function at this time. AGT 1-9 is not converted to angiotensin II but further degraded by ACE to AGT 1-7, a vasodilator. It would appear that ACE 2 inhibits the formation of angiotensin and reduces blood pressure increases. Crackower et al determined that ace2 -/- mice suffered significant heart defects at 6 months. Further deletion of ACE resulted in restored cardiac functions. (This definition may be outdated - see the DesignNote.)~BIOCARTA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P90~P384~BIOCARTA Angiotensin-converting enzyme 2 regulates heart function~BIOCARTA -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42692 C42692 qualifier-P90~P384~NCICB latestVersionIndicator~NCICB -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54742 C54742 qualifier-P325~P378~CTCAE 3.0 Transient flushing or rash; drug fever <38 degrees C (<100.4 degrees F)~CTCAE 3.0 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C60314 C60314 qualifier-P90~P384~RENI Tissue autolysed, diagnosis not possible (RENI)~RENI -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C79954 C79954 qualifier-P90~P384~ZFin WIK~ZFin -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8498 C8498 qualifier-P325~P378~CCPS A genetic predispostion to developing melanoma due to germline mutation in CDKN2A or CDK4. Subsets of patients are also at risk for pancreatic cancer or astrocytoma.~CCPS -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C91532 C91532 qualifier-P90~P384~PID Signaling events mediated by the Hedgehog family~PID -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-style1 C1504 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1504 child-style1 C1000 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 parent-style2 C9385 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C9385 child-style2 C100051 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107687 C107687 max-children 3234 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-count1 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100063 C100063 parent-count2 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101132 C101132 parent-count3 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104006 C104006 parent-count4 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114836 C114836 parent-count5 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160034 C160034 parent-count6 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160054 C160054 parent-count7 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160053 C160053 parent-count8 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160005 C160005 parent-count9 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C159984 C159984 parent-count10 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160108 C160108 parent-count12 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160024 C160024 parent-count13 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160102 C160102 parent-count16 -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12218 C12218 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12219 C12219 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12913 C12913 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14250 C14250 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16612 C16612 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17828 C17828 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1908 C1908 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20047 C20047 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20181 C20181 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20189 C20189 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20633 C20633 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22187 C22187 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22188 C22188 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26548 C26548 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28428 C28428 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3910 C3910 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43431 C43431 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057 C7057 root -http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C97325 C97325 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P106 Amino Acid, Peptide, or Protein +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P108 Recombinant Amphiregulin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P207 C1514768 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P366 Recombinant_Amphiregulin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P90 AR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 P97 A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04) +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 rdfs:label Recombinant Amphiregulin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10000 C10000 rdfs:subClassOf/owl:Restriction~R123 C405 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 rdfs:subClassOf/owl:Restriction~R163 C12686 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 A8 C101859 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P322 CDISC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 P325 A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms. +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100012 C100012 rdfs:subClassOf/owl:Restriction~R100 C12686 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P208 CL433438 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P329 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P330 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 P399 725443 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R126 C3270 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R101 C12415 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R103 C45714 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R104 C12578 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R105 C12917 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R108 C36115 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R115 C3090 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R139 C36760 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 rdfs:subClassOf/owl:Restriction~R142 C36122 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P107 Renal Cell Carcinoma Associated with Neuroblastoma +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 P363 Malignant +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R101 C12341 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R103 C32365 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R104 C12591 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R108 C36027 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 owl:equivalentClass/owl:Class/owl:intersectionOf/owl:Restriction~R115 C35841 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P171 12927386 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P210 77538-19-3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 P319 R8WTH25YS2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R124 C45547 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100088 C100088 rdfs:subClassOf/owl:Restriction~R125 C16298 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+http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 qualifier-P97~P378~NCI A recombinant form of amphiregulin, a member of the heparin-binding epidermal growth factor (EGF) family. Endogenous amphiregulin is an autocrine growth factor, and binds to the EGF receptor. Overexpressed in several cancer cell types, endogenous amphiregulin may contribute to tumor cell proliferation and metastasis. (NCI04)~NCI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P325~P378~CDISC A percutaneous coronary intervention is necessary for a myocardial infarction that presents with ST segment elevation and the subject does not have recurrent or persistent symptoms, symptoms of heart failure or ventricular arrhythmia. The presentation is past twelve hours since onset of symptoms.~CDISC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100000 C100000 qualifier-P90~P384~CDISC PERCUTANEOUS CORONARY INTERVENTION (PCI) FOR ST ELEVATION MYOCARDIAL INFARCTION (STEMI) (STABLE, >12 HRS FROM SYMPTOM ONSET)~CDISC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P384~SEER COPADRI-I~SEER +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C10001 C10001 qualifier-P90~P383~SY Cyclophosphamide-Vincristine-Melphalan-Doxorubicin~SY +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99996 C99996 qualifier-P90~P385 Number of Diseased Coronary Vessels~SDTM-CVTEST +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100022 C100022 qualifier-P90~P384~CPTAC Transcatheter Aortic Valve Implantation~CPTAC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100046 C100046 qualifier-P90~P383~FB Evozac~FB +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P325~P378~CDISC-GLOSS A standard protocol for exchanging files between computers on the internet. See also TCP/IP.~CDISC-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100047 C100047 qualifier-P90~P384~CDISC-GLOSS File Transfer Protocol (FTP)~CDISC-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P383~DN Renal Cell Cancer Associated with Neuroblastoma~DN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 qualifier-P90~P384~CTRP Renal Cell Cancer Associated with Neuroblastoma~CTRP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100054 C100054 qualifier-P90~P383~AQS Conjunctival Precancerous Melanosis~AQS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~BR Compritol 888 ATO~BR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P383~SN Docosanoic Acid, Diester with 1,2,3-propanetriol~SN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100065 C100065 qualifier-P90~P384~FDA GLYCERYL DIBEHENATE~FDA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99905 C99905 qualifier-P90~P386 ROCILETINIB~UNII +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P325~P378~ACC/AHA Catheter ablation is an invasive procedure used to remove or terminate a faulty electrical pathway from sections of the hearts of those who are prone to developing cardiac arrhythmias such as atrial fibrillation, atrial flutter, SVT and Wolff-Parkinson-White syndrome.~ACC/AHA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100068 C100068 qualifier-P90~P384~ACC/AHA Catheter ablation~ACC/AHA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P393 Dependent relative needing care at home~Related To +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P394 Dependent relative needing care at home~PT +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P395 Dependent relative needing care at home~Z63.6 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99957 C99957 qualifier-P375~P396 Dependent relative needing care at home~ICD10CM 2017 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100093 C100093 qualifier-P90~P384~CTEP Nongerminomatous GCT - CNS~CTEP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100096 C100096 qualifier-P90~P384~caDSR OMRS~caDSR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1001 C1001 qualifier-P90~P384~DTP Ampligen~DTP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100100 C100100 qualifier-P90~P383~CN AP611074~CN +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~PCDC Clinical Signs or Symptoms~PCDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100104 C100104 qualifier-P90~P384~NICHD Sign or Symptom~NICHD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P325~P378~NCI-GLOSS An anticancer drug that belongs to the family of drugs called antineoplastic antibiotics.~NCI-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1003 C1003 qualifier-P90~P384~NCI-GLOSS ansamycin~NCI-GLOSS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1004 C1004 qualifier-P90~P384~DCP Antineoplaston A10~DCP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100805 C100805 qualifier-P90~P384~GDC Natural Grandchild~GDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100897 C100897 qualifier-P90~P384~UCUM 10*3.{copies}/mL~UCUM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101028 C101028 qualifier-P325~P378~NICHD Aspiration of amniotic fluid around the time of delivery resulting in severe respiratory distress.~NICHD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101029 C101029 qualifier-P90~P384~Cellosaurus Atrioventricular Septal Defect~Cellosaurus +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99537 C99537 qualifier-P375~P397 Venous thromboembolism~18.1 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99865 C99865 qualifier-P97~P381 A fusion gene that results from a complex chromosomal rearrangement where inversion of 22q12 is followed by a translocation t(1;22)(p34;q12) that disrupts intron 3 of the UQCRH gene. PCR analysis of tumor cDNA and genomic DNA detected a UQCRH/EWSR1 fusion transcript but it is out-of-frame and contains premature stop codons.~OMIM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101088 C101088 qualifier-P90~P384~HGNC ARID2~HGNC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101125 C101125 qualifier-P90~P383~AD Discordant~AD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P325~P378~CareLex A single activity that has occurred within a business process.~CareLex +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101129 C101129 qualifier-P90~P384~CareLex Task~CareLex +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101138 C101138 qualifier-P90~P384~BRIDG 5.3 ctdiVol~BRIDG 5.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P325~P378~INC The occipitofrontal circumference of a neonate's head at birth. Measurement to the nearest 0.1 cm should be taken at the broadest part of the forehead above the eyebrow and above the ears, most prominent part of the back of the head on the day of birth or the day after birth.~INC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101221 C101221 qualifier-P90~P384~INC Head Circumference at Birth~INC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CNU 535~CNU +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P384~GENC 535~GENC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA3 BES~CA3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101224 C101224 qualifier-P90~P383~CA2 BQ~CA2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101250 C101250 qualifier-P325~P378~FDA Injury to the peripheral nervous system.~FDA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99286 C99286 qualifier-P325~P381 The catalog, reference, or product number found on the device label or accompanying packaging to identify a particular product.~CDRH-GUDID +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~ICDC WGS~ICDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101294 C101294 qualifier-P90~P384~CTDC WGS (whole genome sequencing)~CTDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P325~P378~CRCH Carotenoid consisting of a cyclic structure on each end with additional double bonds at the number 5 and 5' carbon atoms of the cyclic structures.~CRCH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1016 C1016 qualifier-P90~P384~CRCH 3,7,12,16-tetramethyl-1,18-bis(2,6,6-trimethyl-1-cyclohexenyl)-octadeca-1,3,5,7,9,11,13,15,17-nonaene~CRCH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102405 C102405 qualifier-P90~P384~NCPDP Capful~NCPDP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102556 C102556 qualifier-P90~P384~BRIDG 3.0.3 IVL.LOW<TS.DATE>~BRIDG 3.0.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 5.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression OTHER NAME(S): Clinical Events Medical History NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 5.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102559 C102559 qualifier-P325~P378~BRIDG 3.0.3 Any sign, symptom, disease, or other medical occurrence. EXAMPLE(S): death, back pain, headache, pulmonary embolism, heart attack, pregnancy, flu, broken bone, menstrual period, depression. NOTE(S): This condition may have been recalled by the subject or a caregiver or provided in their medical record.~BRIDG 3.0.3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C102821 C102821 qualifier-P90~P384~CCPS SPRED1~CCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104030 C104030 qualifier-P90~P383~HD Adrenal Cortex Carcinoma by ENSAT Stage~HD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104438 C104438 qualifier-P325~P378~BRIDG Specifies whether this device bears a CE (Conformite Europeenne) mark. NOTE(S): CE is a mark for device products placed on the market in the European Economic Area (EEA). By placing the CE marking on a product, the manufacturer affirms that the product conforms with the requirements of the applicable European Community directives.~BRIDG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~CDC OTHER RACE~CDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104495 C104495 qualifier-P90~P384~SeroNet Other~SeroNet +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P325~P378~CTCAE A disorder characterized by an acute inflammatory reaction resulting from the release of histamine and histamine-like substances from mast cells, causing a hypersensitivity immune response. Clinically, it presents with breathing difficulty, dizziness, hypotension, cyanosis and loss of consciousness and may lead to death.~CTCAE +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107101 C107101 qualifier-P90~P384~CTCAE Anaphylaxis~CTCAE +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P325~P378~EDQM-HC Exposure of a breast-feeding infant to a medicinal product administered to the lactating mother. Comment: This term is not intended to describe an authorised route of administration for use in marketing authorisations, and does not cover intentional administration of a medicinal product to a breastfeeding infant. It is intended for use in adverse event reporting for pharmacovigilance purposes.~EDQM-HC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111326 C111326 qualifier-P90~P384~EDQM-HC Transmammary~EDQM-HC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P325~P378~GAIA The death of a woman while pregnant or within 42 days of termination of pregnancy, irrespective of the duration and the site of the pregnancy (as defined by Maternal Death guidelines: http:www.brightoncollaboration.org).~GAIA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C111860 C111860 qualifier-P90~P384~GAIA Maternal Death~GAIA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114560 C114560 qualifier-P90~P383~AQ Childhood L1 Acute Lymphoblastic Leukemia~AQ +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C118618 C118618 qualifier-P325~P378~CTEP Systemic chemotherapy with a regimen containing multiple agents.~CTEP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12241 C12241 qualifier-P90~P384~CTRM Branchial Cleft~CTRM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12261 C12261 qualifier-P325~P378~ICDO3 not classifiable to C16.1 to C16.4~ICDO3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12558 C12558 qualifier-P325~P378~NCI A cell that arises from stem cells and/or bone marrow-derived monocytes that function in different aspects of host defense and tissue repair; such as phagocytosis, cytotoxic activity, and regulation of the immune response (antigen presentation and T-cell activation).~NCI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12599 C12599 qualifier-P325~P378~MSH2001 Female germ cells in stages between the prophase of the first maturation division and the completion of the second maturation division.~MSH2001 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12719 C12719 qualifier-P325~P378~UWDA142 is a macroscopic organ component of one or more nerves, which primarily consists of cell bodies of neurons located outside the central nervous system; together with nerve fibers, it constitutes a nerve or a nerve plexus. Example(s): spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion.~UWDA142 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12741 C12741 qualifier-P325~P378~CSP2000 type of cytotoxic leukocytes which attack and kill virus-infected or neoplastic cells independent of antibody coating or MHC restriction; may be derived from lymphocytes or monocytes.~CSP2000 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12842 C12842 qualifier-P325~P378~UMD2001 Grafts used in the treatment of skin loss, usually caused by burn injuries.~UMD2001 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C128574 C128574 qualifier-P90~P384~PI-RADS Apex L AS~PI-RADS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13061 C13061 qualifier-P325~P378~MeSH The cells of the body which stain with chromium salts. They occur along the sympathetic nerves, in the adrenal gland, and in various other organs.~MeSH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1396 C1396 qualifier-P325~P378~CSP2002 family of polypeptide growth factors produced by peripheral target tissues as well as the nervous system, which are critical to neuronal growth, regeneration, survival, and differentiation.~CSP2002 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C142787 C142787 qualifier-P90~P384~CBDD Transduction~CBDD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14294 C14294 qualifier-P90~P384~JAX severe combined immune deficiency~JAX +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P325~P378~CTCAE 5.0 A disorder characterized by laboratory test results that indicate an increased number of eosinophils in the blood.~CTCAE 5.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C143190 C143190 qualifier-P90~P384~CTCAE 5.0 Eosinophilia~CTCAE 5.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P325~P378~DICOM A drug that contains a radioactive substance and is used to diagnose or treat disease, including cancer.~DICOM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1446 C1446 qualifier-P90~P384~DICOM Radiopharmaceutical~DICOM +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C153106 C153106 qualifier-P90~P384~BRIDG IntegratedStatisticalAnalysisPlan~BRIDG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15538 C15538 qualifier-P325~P378~PCDC Assigned Treatment Arm by Intention-To-Treat~PCDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C155838 C155838 qualifier-P90~P384~NDC ME~NDC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C15843 C15843 qualifier-P90~P384~HL7 PRYLX~HL7 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C168622 C168622 qualifier-P325~P378~PQCMC A mathematical symbol that denotes equality or inequality between two values Note: This is typically applicable to biologics.~PQCMC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16904 C16904 qualifier-P90~P383~CS NN~CS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17051 C17051 qualifier-P325~P378~MSH2002_06_01 The ability of some cells or tissues to withstand ionizing radiation without serious injury. Tolerance depends on the species, cell type, and physical and chemical variables, including RADIATION-PROTECTIVE AGENTS and RADIATION-SENSITIZING AGENTS.~MSH2002_06_01 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C179573 C179573 qualifier-P90~P384~WHO Alpha~WHO +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18063 C18063 qualifier-P90~P384~ICH Gy~ICH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C18611 C18611 qualifier-P90~P384~KEGG Metabolism~KEGG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P387 extracellular~GO:0005576 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P389 extracellular~NAS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P390 extracellular~CGAP +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C99760 C99760 qualifier-P211~P391 extracellular~29-SEP-2003 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C21639 C21639 qualifier-P325~P378~MMHCC Inflammation of the mammary gland~MMHCC +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23247 C23247 qualifier-P325~P378~DCCPS The Corpus uteri, or body of uterus, is the part of the uterus above the isthmus, comprising about two thirds of the non-pregnant organ. 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.~DCCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23372 C23372 qualifier-P325~P378~DCTD-CD That portion of the nervous system consisting of the brain and spinal cord. (Dorland, 28th ed) (MSH98)~DCTD-CD +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23373 C23373 qualifier-P325~P378~FMB-BUDGET That part of the central nervous system contained within the cranium, comprising the prosencephalon, mesencephalon, and rhombencephalon. It is derived from the anterior part of the embryonic neural tube. Functions include muscle control and coordination, sensory reception and integration, speech production, memory storage, and the elaboration of thought and emotions. (Dorland, 28th ed) (MSH98)~FMB-BUDGET +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23404 C23404 qualifier-P325~P378~OMS94 The natural covering of the body; the skin.~OMS94 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23415 C23415 qualifier-P325~P378~DCB-CB2 The layer of epithelial cells that lines the cavities of the heart and of the blood vessels (ENDOTHELIUM, VASCULAR) and lymph vessels (ENDOTHELIUM, LYMPHATIC), and the serous cavities of the body, originating from the MESODERM. (From Dorland, 28th ed) (MSH98)~DCB-CB2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23593 C23593 qualifier-P325~P378~MTH Primitive blood cells derived from embryonic mesenchyme capable of differentiating into any of the blood cell line progenitor cells (erythroblasts, young granulocytic series cells, megakaryocytes, etc.)~MTH +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C23887 C23887 qualifier-P325~P378~DEA-DEAIS exocrine gland. a gland from which secretions reach a free surface of the body by ducts.~DEA-DEAIS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25296 C25296 qualifier-P90~P384~CADSR BD~CADSR +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26719 C26719 qualifier-P325~P378~MSH2003_2003_05_12 Presence of calcium salts, especially calcium pyrophosphate, in the cartilaginous structures of one or more joints. When accompanied by attacks of goutlike symptoms, it is called pseudogout. (Dorland, 27th ed)~MSH2003_2003_05_12 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26914 C26914 qualifier-P325~P378~CSP2003 abnormal development of secondary male sexual characteristics such as facial hair; in females, can be caused by androgen secretion by adrenal cortex.~CSP2003 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28245 C28245 qualifier-P90~P384~CTCAE 3.0 Aspiration~CTCAE 3.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28517 C28517 qualifier-P325~P378~MSH2002 Small containers or pellets of a solid drug implanted in the body to achieve sustained release of the drug.~MSH2002 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38778 C38778 qualifier-P325~P378~KEGG Alzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-beta (Abeta), a major component of senile plaques, has various pathological effects on cell and organelle function. The extracellular Abeta oligomers may activate caspases through activation of cell surface death receptors. Alternatively, intracellular Abeta may contribute to pathology by facilitating tau hyper-phosphorylation, disrupting mitochondria function, and triggering calcium dysfunction. To date genetic studies have revealed four genes that may be linked to autosomal dominant or familial early onset AD (FAD). These four genes include: amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2) and apolipoprotein E (ApoE). All mutations associated with APP and PS proteins can lead to an increase in the production of Abeta peptides, specifically the more amyloidogenic form, Abeta42. FAD-linked PS1 mutation downregulates the unfolded protein response and leads to vulnerability to ER stress.~KEGG +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P325~P378~BIOCARTA Cardiovascular diseases are predicted to be the most common cause of death worldwide by 2020. The major regulator of blood pressure homeostasis is the renin-angiotensin system. Angiotensinogen is digested by renin to produce angiotensin I (AGT I). AGT I is an inactive 10 amino-acid peptide that is further degraded to produce angiotensin II by the angiotensin-converting enzyme (ACE). Angiotensin II is the master regulator of blood pressure increase acting on the heart, kidneys and blood vessels. Angiotensin II causes direct constriction of the resistance vessels and stimulation of the adrenal thereby increasing blood volume and sodium absorption. In 2000, Tipnis et al. discovered ACE 2 a second carboxypeptidase that digests angiotensin. ACE is a di-peptidase, cleaving off 2 peptides from the c-terminal end of angiotensin. ACE 2 only cleaves 1 amino acid to produce angiotensin 1-9 (AGT 1-9) which has no identified function at this time. AGT 1-9 is not converted to angiotensin II but further degraded by ACE to AGT 1-7, a vasodilator. It would appear that ACE 2 inhibits the formation of angiotensin and reduces blood pressure increases. Crackower et al determined that ace2 -/- mice suffered significant heart defects at 6 months. Further deletion of ACE resulted in restored cardiac functions. (This definition may be outdated - see the DesignNote.)~BIOCARTA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C38969 C38969 qualifier-P90~P384~BIOCARTA Angiotensin-converting enzyme 2 regulates heart function~BIOCARTA +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C42692 C42692 qualifier-P90~P384~NCICB latestVersionIndicator~NCICB +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C54742 C54742 qualifier-P325~P378~CTCAE 3.0 Transient flushing or rash; drug fever <38 degrees C (<100.4 degrees F)~CTCAE 3.0 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C60314 C60314 qualifier-P90~P384~RENI Tissue autolysed, diagnosis not possible (RENI)~RENI +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C79954 C79954 qualifier-P90~P384~ZFin WIK~ZFin +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C8498 C8498 qualifier-P325~P378~CCPS A genetic predispostion to developing melanoma due to germline mutation in CDKN2A or CDK4. Subsets of patients are also at risk for pancreatic cancer or astrocytoma.~CCPS +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C91532 C91532 qualifier-P90~P384~PID Signaling events mediated by the Hedgehog family~PID +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-style1 C1504 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1504 child-style1 C1000 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C100051 parent-style2 C9385 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100051 C9385 child-style2 C100051 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C107687 C107687 max-children 3234 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1000 C1000 parent-count1 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C100063 C100063 parent-count2 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C101132 C101132 parent-count3 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C104006 C104006 parent-count4 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C114836 C114836 parent-count5 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160034 C160034 parent-count6 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160054 C160054 parent-count7 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160053 C160053 parent-count8 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160005 C160005 parent-count9 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C159984 C159984 parent-count10 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160108 C160108 parent-count12 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160024 C160024 parent-count13 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C160102 C160102 parent-count16 +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12218 C12218 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12219 C12219 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12913 C12913 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C14250 C14250 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C16612 C16612 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C17828 C17828 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C1908 C1908 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20047 C20047 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20181 C20181 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20189 C20189 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C20633 C20633 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22187 C22187 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22188 C22188 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C26548 C26548 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C28428 C28428 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C3910 C3910 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C43431 C43431 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057 C7057 root +http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C97325 C97325 root diff --git a/src/test/resources/samples/umlssemnet-samples.txt b/src/test/resources/samples/umlssemnet-samples.txt index e0578eaa6..e0a9513f9 100644 --- a/src/test/resources/samples/umlssemnet-samples.txt +++ b/src/test/resources/samples/umlssemnet-samples.txt @@ -1,64 +1,64 @@ -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Semantic_Type STY -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Preferred_Name Organism -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Synonym orgm -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 STN A1.1 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 DEF Generally, a living individual, including all plants and animals. -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T142 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T165 T090 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T002 T002 rdfs:subClassOf/owl:Restriction~T135 T123 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T004 T004 rdfs:subClassOf/owl:Restriction~T147 T046 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T005 T005 rdfs:subClassOf/owl:Restriction~T166 T123 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T008 T008 rdfs:subClassOf/owl:Restriction~T145 T053 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T010 T010 UN Few concepts will be assigned to this broad type. -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 NH Y -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 rdfs:subClassOf/owl:Restriction~T133 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T134 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T175 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T176 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T179 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T137 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T149 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T150 T038 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T151 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T152 T096 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T157 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T021 T021 rdfs:subClassOf/owl:Restriction~T144 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T022 T022 rdfs:subClassOf/owl:Restriction~T160 T021 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T172 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T173 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T174 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T177 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T198 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T199 T023 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T028 T028 rdfs:subClassOf/owl:Restriction~T141 T044 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T031 T031 rdfs:subClassOf/owl:Restriction~T178 T024 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T031 T031 rdfs:subClassOf/owl:Restriction~T202 T200 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T159 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T180 T032 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T182 T039 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T033 T033 rdfs:subClassOf/owl:Restriction~T161 T032 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T034 T034 rdfs:subClassOf/owl:Restriction~T156 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T037 T037 rdfs:subClassOf/owl:Restriction~T146 T018 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T038 T038 rdfs:subClassOf/owl:Restriction~T140 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T039 T039 rdfs:subClassOf/owl:Restriction~T138 T039 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T047 T047 rdfs:subClassOf/owl:Restriction~T158 T050 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T057 T057 rdfs:subClassOf/owl:Restriction~T183 T090 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T162 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T163 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T164 T038 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T193 T031 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T060 T060 rdfs:subClassOf/owl:Restriction~T155 T073 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T148 T046 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T154 T019 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T093 T093 rdfs:subClassOf/owl:Restriction~T153 T101 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T096 T096 rdfs:subClassOf/owl:Restriction~T188 T052 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T097 T097 rdfs:subClassOf/owl:Restriction~T143 T090 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RTN R1 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RI physically_related_to -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-style1 T072 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T072 child-style1 T001 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T158 T158 max-children 12 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-count1 -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T051 T051 root -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T071 T071 root -http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T186 T186 root +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Semantic_Type STY +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Preferred_Name Organism +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 Synonym orgm +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 STN A1.1 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 DEF Generally, a living individual, including all plants and animals. +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T142 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 rdfs:subClassOf/owl:Restriction~T165 T090 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T002 T002 rdfs:subClassOf/owl:Restriction~T135 T123 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T004 T004 rdfs:subClassOf/owl:Restriction~T147 T046 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T005 T005 rdfs:subClassOf/owl:Restriction~T166 T123 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T008 T008 rdfs:subClassOf/owl:Restriction~T145 T053 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T010 T010 UN Few concepts will be assigned to this broad type. +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 NH Y +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T017 T017 rdfs:subClassOf/owl:Restriction~T133 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T134 T031 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T175 T018 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T176 T018 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T018 T018 rdfs:subClassOf/owl:Restriction~T179 T018 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T137 T019 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T149 T019 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T150 T038 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T151 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T152 T096 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T019 T019 rdfs:subClassOf/owl:Restriction~T157 T019 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T021 T021 rdfs:subClassOf/owl:Restriction~T144 T031 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T022 T022 rdfs:subClassOf/owl:Restriction~T160 T021 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T172 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T173 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T174 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T177 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T198 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T023 T023 rdfs:subClassOf/owl:Restriction~T199 T023 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T028 T028 rdfs:subClassOf/owl:Restriction~T141 T044 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T031 T031 rdfs:subClassOf/owl:Restriction~T178 T024 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T031 T031 rdfs:subClassOf/owl:Restriction~T202 T200 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T159 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T180 T032 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T032 T032 rdfs:subClassOf/owl:Restriction~T182 T039 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+http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T164 T038 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T059 T059 rdfs:subClassOf/owl:Restriction~T193 T031 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T060 T060 rdfs:subClassOf/owl:Restriction~T155 T073 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T148 T046 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T061 T061 rdfs:subClassOf/owl:Restriction~T154 T019 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T093 T093 rdfs:subClassOf/owl:Restriction~T153 T101 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T096 T096 rdfs:subClassOf/owl:Restriction~T188 T052 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T097 T097 rdfs:subClassOf/owl:Restriction~T143 T090 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RTN R1 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T132 T132 RI physically_related_to +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-style1 T072 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T072 child-style1 T001 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T158 T158 max-children 12 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T001 T001 parent-count1 +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T051 T051 root +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T071 T071 root +http://www.nlm.nih.gov/research/umls/umlssemnet.owl#T186 T186 root From fc63b562c2054e29859767452c5350730963c1c8 Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Fri, 22 Nov 2024 16:32:17 -0800 Subject: [PATCH 09/11] Fix CRLF --- .gitattributes | 8 +- gradlew.bat | 168 ++-- .../nci/evs/restapi/bean/AltDefinition2.java | 242 ++--- .../nci/evs/restapi/bean/ComplexProperty.java | 168 ++-- .../nci/evs/restapi/bean/ConceptDetails.java | 622 ++++++------- .../nih/nci/evs/restapi/bean/Definition2.java | 242 ++--- .../nci/evs/restapi/bean/GoAnnotation2.java | 278 +++--- .../nci/evs/restapi/bean/MatchedConcept.java | 280 +++--- .../evs/restapi/bean/MetaRelationship.java | 254 +++--- .../nci/evs/restapi/bean/MetaTreeNode.java | 274 +++--- .../src/gov/nih/nci/evs/restapi/bean/Row.java | 124 +-- .../nih/nci/evs/restapi/bean/Synonym2.java | 296 +++--- .../evs/restapi/util/SPARQLUtilsClient.java | 856 +++++++++--------- src/main/resources/META-INF/MANIFEST.MF | 22 +- src/test/resources/samples/ctcae5-samples.txt | 32 +- .../resources/samples/icd10cm-samples.txt | 90 +- src/test/resources/samples/icd9cm-samples.txt | 70 +- src/test/resources/samples/lnc-samples.txt | 210 ++--- src/test/resources/samples/mdr-samples.txt | 266 +++--- src/test/resources/samples/ncim-samples.txt | 132 +-- .../resources/samples/snomedct_us-samples.txt | 274 +++--- 21 files changed, 2457 insertions(+), 2451 deletions(-) diff --git a/.gitattributes b/.gitattributes index a42d8128e..dc6b24f27 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,9 +1,15 @@ ## Settings for ensuring windows and mac settings are aligned for this project # Declare java files will have LF line ending on checkout, even on Windows -*.java eol=lf # Set the default behavior for text to use LF line ending * text eol=lf +*.java text +*.txt text # Denote all files that are truly binary and should not be modified. *.png binary *.jpg binary *.jar binary +*.gif binary +*.bmp binary +*.db binary +*.gz binary +*.exe binary diff --git a/gradlew.bat b/gradlew.bat index e95643d6a..f9553162f 100644 --- a/gradlew.bat +++ b/gradlew.bat @@ -1,84 +1,84 @@ -@if "%DEBUG%" == "" @echo off -@rem ########################################################################## -@rem -@rem Gradle startup script for Windows -@rem -@rem ########################################################################## - -@rem Set local scope for the variables with windows NT shell -if "%OS%"=="Windows_NT" setlocal - -set DIRNAME=%~dp0 -if "%DIRNAME%" == "" set DIRNAME=. -set APP_BASE_NAME=%~n0 -set APP_HOME=%DIRNAME% - -@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. -set DEFAULT_JVM_OPTS= - -@rem Find java.exe -if defined JAVA_HOME goto findJavaFromJavaHome - -set JAVA_EXE=java.exe -%JAVA_EXE% -version >NUL 2>&1 -if "%ERRORLEVEL%" == "0" goto init - -echo. -echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. - -goto fail - -:findJavaFromJavaHome -set JAVA_HOME=%JAVA_HOME:"=% -set JAVA_EXE=%JAVA_HOME%/bin/java.exe - -if exist "%JAVA_EXE%" goto init - -echo. -echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% -echo. -echo Please set the JAVA_HOME variable in your environment to match the -echo location of your Java installation. - -goto fail - -:init -@rem Get command-line arguments, handling Windows variants - -if not "%OS%" == "Windows_NT" goto win9xME_args - -:win9xME_args -@rem Slurp the command line arguments. -set CMD_LINE_ARGS= -set _SKIP=2 - -:win9xME_args_slurp -if "x%~1" == "x" goto execute - -set CMD_LINE_ARGS=%* - -:execute -@rem Setup the command line - -set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar - -@rem Execute Gradle -"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% - -:end -@rem End local scope for the variables with windows NT shell -if "%ERRORLEVEL%"=="0" goto mainEnd - -:fail -rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of -rem the _cmd.exe /c_ return code! -if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 -exit /b 1 - -:mainEnd -if "%OS%"=="Windows_NT" endlocal - -:omega +@if "%DEBUG%" == "" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%" == "" set DIRNAME=. +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS= + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if "%ERRORLEVEL%" == "0" goto init + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto init + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:init +@rem Get command-line arguments, handling Windows variants + +if not "%OS%" == "Windows_NT" goto win9xME_args + +:win9xME_args +@rem Slurp the command line arguments. +set CMD_LINE_ARGS= +set _SKIP=2 + +:win9xME_args_slurp +if "x%~1" == "x" goto execute + +set CMD_LINE_ARGS=%* + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% + +:end +@rem End local scope for the variables with windows NT shell +if "%ERRORLEVEL%"=="0" goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 +exit /b 1 + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition2.java b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition2.java index af865ceb7..5a6d57a56 100644 --- a/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition2.java +++ b/software/evsrestapi-util/src/gov/nih/nci/evs/restapi/bean/AltDefinition2.java @@ -1,138 +1,138 @@ -package gov.nih.nci.evs.restapi.bean; - -import java.io.*; -import java.util.*; -import java.net.*; - -import com.google.gson.*; -import com.google.gson.GsonBuilder; -import com.google.gson.reflect.TypeToken; -import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver; -import com.thoughtworks.xstream.io.xml.DomDriver; -import com.thoughtworks.xstream.XStream; - -public class AltDefinition2 -{ - -// Variable declaration - private String code; - private String label; - private String propertyCode; - private String propertyLabel; - private String description; - private String attribution; - private String source; - -// Default constructor - public AltDefinition2() { - } - -// Constructor - public AltDefinition2( - String code, - String label, - String propertyCode, - String propertyLabel, - String description, - String attribution, +package gov.nih.nci.evs.restapi.bean; + +import java.io.*; +import java.util.*; +import java.net.*; + +import com.google.gson.*; +import com.google.gson.GsonBuilder; +import com.google.gson.reflect.TypeToken; +import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver; +import com.thoughtworks.xstream.io.xml.DomDriver; +import com.thoughtworks.xstream.XStream; + +public class AltDefinition2 +{ + +// Variable declaration + private String code; + private String label; + private String propertyCode; + private String propertyLabel; + private String description; + private String attribution; + private String source; + +// Default constructor + public AltDefinition2() { + } + +// Constructor + public AltDefinition2( + String code, + String label, + String propertyCode, + String propertyLabel, + String description, + String attribution, String source) { - - this.code = code; - this.label = label; - this.propertyCode = propertyCode; - this.propertyLabel = propertyLabel; - this.description = description; - this.attribution = attribution; - this.source = source; - } - -// Set methods - public void setCode(String code) { - this.code = code; + + this.code = code; + this.label = label; + this.propertyCode = propertyCode; + this.propertyLabel = propertyLabel; + this.description = description; + this.attribution = attribution; + this.source = source; } - - public void setLabel(String label) { - this.label = label; + +// Set methods + public void setCode(String code) { + this.code = code; } - - public void setPropertyCode(String propertyCode) { - this.propertyCode = propertyCode; + + public void setLabel(String label) { + this.label = label; } - - public void setPropertyLabel(String propertyLabel) { - this.propertyLabel = propertyLabel; + + public void setPropertyCode(String propertyCode) { + this.propertyCode = propertyCode; } - - public void setDescription(String description) { - this.description = description; + + public void setPropertyLabel(String propertyLabel) { + this.propertyLabel = propertyLabel; } - - public void setAttribution(String attribution) { - this.attribution = attribution; + + public void setDescription(String description) { + this.description = description; } - - public void setSource(String source) { - this.source = source; + + public void setAttribution(String attribution) { + this.attribution = attribution; } - -// Get methods - public String getCode() { - return this.code; + public void setSource(String source) { + this.source = source; } - - public String getLabel() { - return this.label; + + +// Get methods + public String getCode() { + return this.code; } - - public String getPropertyCode() { - return this.propertyCode; + + public String getLabel() { + return this.label; } - - public String getPropertyLabel() { - return this.propertyLabel; + + public String getPropertyCode() { + return this.propertyCode; } - - public String getDescription() { - return this.description; + + public String getPropertyLabel() { + return this.propertyLabel; } - - public String getAttribution() { - return this.attribution; + + public String getDescription() { + return this.description; } - - public String getSource() { - return this.source; - } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i qualifiers; - -// Default constructor - public ComplexProperty() { - } - -// Constructor - public ComplexProperty( - String name, - String value, +package gov.nih.nci.evs.restapi.bean; + +import java.io.*; +import java.util.*; +import java.net.*; + +import com.google.gson.*; +import com.google.gson.GsonBuilder; +import com.google.gson.reflect.TypeToken; +import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver; +import com.thoughtworks.xstream.io.xml.DomDriver; +import com.thoughtworks.xstream.XStream; + +public class ComplexProperty extends Property +{ + +// Variable declaration + private String name; + private String value; + private List qualifiers; + +// Default constructor + public ComplexProperty() { + } + +// Constructor + public ComplexProperty( + String name, + String value, List qualifiers) { - this.name = name; - this.value = value; - this.qualifiers = qualifiers; - } - -// Set methods - public void setName(String name) { - this.name = name; + this.name = name; + this.value = value; + this.qualifiers = qualifiers; + } + +// Set methods + public void setName(String name) { + this.name = name; + } + + public void setValue(String value) { + this.value = value; + } + + public void setQualifiers(List qualifiers) { + this.qualifiers = qualifiers; + } + + +// Get methods + public String getName() { + return this.name; } - - public void setValue(String value) { - this.value = value; + + public String getValue() { + return this.value; } - - public void setQualifiers(List qualifiers) { - this.qualifiers = qualifiers; + + public List getQualifiers() { + return this.qualifiers; } - -// Get methods - public String getName() { - return this.name; + public String toXML() { + XStream xstream_xml = new XStream(new DomDriver()); + String xml = xstream_xml.toXML(this); + xml = escapeDoubleQuotes(xml); + StringBuffer buf = new StringBuffer(); + String XML_DECLARATION = ""; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; } - - public String getValue() { - return this.value; + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); } - - public List getQualifiers() { - return this.qualifiers; + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i 0) { + for (int j=0; j 0) { - for (int j=0; j"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; } - - public String toXML() { - XStream xstream_xml = new XStream(new DomDriver()); - String xml = xstream_xml.toXML(this); - xml = escapeDoubleQuotes(xml); - StringBuffer buf = new StringBuffer(); - String XML_DECLARATION = ""; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i row; +import java.io.*; +import java.util.*; +import java.net.*; -// Default constructor - public Row() { - } +import com.google.gson.*; +import com.google.gson.GsonBuilder; +import com.google.gson.reflect.TypeToken; +import com.thoughtworks.xstream.io.json.JettisonMappedXmlDriver; +import com.thoughtworks.xstream.io.xml.DomDriver; +import com.thoughtworks.xstream.XStream; -// Constructor - public Row( +public class Row +{ + +// Variable declaration + private List row; + +// Default constructor + public Row() { + } + +// Constructor + public Row( List row) { - this.row = row; - } + this.row = row; + } + +// Set methods + public void setrow(List row) { + this.row = row; + } + + +// Get methods + public List getrow() { + return this.row; + } + + public String toXML() { + XStream xstream_xml = new XStream(new DomDriver()); + String xml = xstream_xml.toXML(this); + xml = escapeDoubleQuotes(xml); + StringBuffer buf = new StringBuffer(); + String XML_DECLARATION = ""; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } -// Set methods - public void setrow(List row) { - this.row = row; + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); } - -// Get methods - public List getrow() { - return this.row; + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; - buf.append(XML_DECLARATION).append("\n").append(xml); - xml = buf.toString(); - return xml; - } - - public String toJson() { - JsonParser parser = new JsonParser(); - Gson gson = new GsonBuilder().setPrettyPrinting().create(); - return gson.toJson(this); - } - - public String escapeDoubleQuotes(String inputStr) { - char doubleQ = '"'; - StringBuffer buf = new StringBuffer(); - for (int i=0; i"; + buf.append(XML_DECLARATION).append("\n").append(xml); + xml = buf.toString(); + return xml; + } + + public String toJson() { + JsonParser parser = new JsonParser(); + Gson gson = new GsonBuilder().setPrettyPrinting().create(); + return gson.toJson(this); + } + + public String escapeDoubleQuotes(String inputStr) { + char doubleQ = '"'; + StringBuffer buf = new StringBuffer(); + for (int i=0; i - * Copyright 2008-2017 NGIS. This software was developed in conjunction - * with the National Cancer Institute, and so to the extent government - * employees are co-authors, any rights in such works shall be subject - * to Title 17 of the United States Code, section 105. - * Redistribution and use in source and binary forms, with or without - * modification, are permitted provided that the following conditions - * are met: - * 1. Redistributions of source code must retain the above copyright - * notice, this list of conditions and the disclaimer of Article 3, - * below. Redistributions in binary form must reproduce the above - * copyright notice, this list of conditions and the following - * disclaimer in the documentation and/or other materials provided - * with the distribution. - * 2. The end-user documentation included with the redistribution, - * if any, must include the following acknowledgment: - * "This product includes software developed by NGIS and the National - * Cancer Institute." If no such end-user documentation is to be - * included, this acknowledgment shall appear in the software itself, - * wherever such third-party acknowledgments normally appear. - * 3. The names "The National Cancer Institute", "NCI" and "NGIS" must - * not be used to endorse or promote products derived from this software. - * 4. This license does not authorize the incorporation of this software - * into any third party proprietary programs. This license does not - * authorize the recipient to use any trademarks owned by either NCI - * or NGIS - * 5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED - * WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES - * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE - * DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE, - * NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, - * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, - * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER - * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT - * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN - * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE - * POSSIBILITY OF SUCH DAMAGE. - * - */ - -/** - * @author EVS Team - * @version 1.0 - * - * Modification history: - * Initial implementation kim.ong@ngc.com - * - */ - -public class SPARQLUtilsClient { - String serviceUrl = null; - String sparql_endpoint = null; - HashMap OWLSPARQLUtilsMap = null; - HashMap codingSchemeNameAndVersion2NamedGraphMap = null; - HashMap namedGraph2codingSchemeNameAndVersionMap = null; - - public SPARQLUtilsClient() { - - } - - public SPARQLUtilsClient(String serviceUrl) { - this.serviceUrl = serviceUrl; - initialize(); - } - - public void initialize() { - String[] sparql_endpoints = new String[1]; - sparql_endpoint = serviceUrl + "?query="; - sparql_endpoints[0] = sparql_endpoint; - OWLSPARQLUtilsMap = OWLSPARQLUtilsExt.getCodingSchemeNameVersion2OWLSPARQLUtilsMap(sparql_endpoints); - Vector v = OWLSPARQLUtilsExt.getSupportedCodingSchemesAndVersions(OWLSPARQLUtilsMap); - //Utils.dumpVector("Supported coding schemes", v); - codingSchemeNameAndVersion2NamedGraphMap = new HashMap(); - namedGraph2codingSchemeNameAndVersionMap = new HashMap(); - for (int k=0; k " + key); - //System.out.println(key + " --> " + owlSPARQLUtils.get_named_graph()); - Vector w = owlSPARQLUtils.getTripleCount(owlSPARQLUtils.get_named_graph()); - String count = new ParserUtils().getValue((String) w.elementAt(0)); - System.out.println(key + " triple count: " + count); - Vector named_graphs = owlSPARQLUtils.getNamedGraphs(); - Utils.dumpVector("named_graphs", named_graphs); - */ - } - } - } - - public Vector execute(String named_graph, String query_file) { - String key = (String) codingSchemeNameAndVersion2NamedGraphMap.get(named_graph); - gov.nih.nci.evs.restapi.util.OWLSPARQLUtils owlSPARQLUtils = (gov.nih.nci.evs.restapi.util.OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - HTTPUtils httpUtils = new HTTPUtils(sparql_endpoint, null, null); - String query = httpUtils.loadQuery(query_file, false); - //System.out.println(query); - return owlSPARQLUtils.execute(query_file); - } - - public String getNamedGraphByCodingSchemeAndVersion(String codingScheme, String version) { - return (String) codingSchemeNameAndVersion2NamedGraphMap.get(codingScheme + "|" + version); - } - - public String getCodingSchemeAndVersionByNamedGraph(String namedGraph) { - return (String) namedGraph2codingSchemeNameAndVersionMap.get(namedGraph); - } - - public Vector getOntologyInfo(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.get_ontology_info(named_graph); - } - - - public Vector getNamedGraph() { - OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); - return owlSPARQLUtils.getNamedGraph(); - } - - - public Vector getOntologyInfo() { - OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); - return owlSPARQLUtils.get_ontology_info(); - } - - - public Vector getLabelByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getLabelByCode(named_graph, code); - } - - - public Vector getInverseRolesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getInverseRolesByCode(named_graph, code); - } - - - public Vector getCodeAndLabel(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getCodeAndLabel(named_graph); - } - - - public Vector getClassCounts() { - OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); - return owlSPARQLUtils.getClassCounts(); - } - - - public Vector getClassCount(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getClassCount(named_graph); - } - - - public Vector getTripleCount(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getTripleCount(named_graph); - } - - - public Vector getSuperclassesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSuperclassesByCode(named_graph, code); - } - - - public Vector getSubclassesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSubclassesByCode(named_graph, code); - } - - - public Vector getRolesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getRolesByCode(named_graph, code); - } - - - public Vector getPropertiesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - Vector v = owlSPARQLUtils.getPropertiesByCode(named_graph, code, false); - v = ParserUtils.formatOutput(v); - return ParserUtils.excludePropertyType(v, "#A|#R"); - } - - - public Vector getOntologyVersionInfo(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getOntologyVersionInfo(named_graph); - } - - - public Vector getSynonyms(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSynonyms(named_graph, code); - } - - - public Vector getAnnotationProperties(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getAnnotationProperties(named_graph); - } - - - public Vector getObjectProperties(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getObjectProperties(named_graph); - } - - - public Vector getPropertyQualifiersByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getPropertyQualifiersByCode(named_graph, code); - } - - - public Vector getInboundRolesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getInboundRolesByCode(named_graph, code); - } - - - public Vector getOutboundRolesByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getOutboundRolesByCode(named_graph, code); - } - - - public Vector getRoleRelationships(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getRoleRelationships(named_graph); - } - - - public Vector getInverseAssociationsByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getInverseAssociationsByCode(named_graph, code); - } - - - public Vector getAssociationsByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getAssociationsByCode(named_graph, code); - } - - - public Vector getDiseaseIsStageSourceCodes(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getDiseaseIsStageSourceCodes(named_graph); - } - - - public Vector getDiseaseIsGradeSourceCodes(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getDiseaseIsGradeSourceCodes(named_graph); - } - - - public Vector getAssociationSourceCodes(String named_graph, String associationName) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getAssociationSourceCodes(named_graph, associationName); - } - - - public Vector getDisjointWithByCode(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getDisjointWithByCode(named_graph, code); - } - - - public Vector getObjectPropertiesDomainRange(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getObjectPropertiesDomainRange(named_graph); - } - - - public Vector getObjectValuedAnnotationProperties(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getObjectValuedAnnotationProperties(named_graph); - } - - - public Vector getStringValuedAnnotationProperties(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getStringValuedAnnotationProperties(named_graph); - } - - - public Vector getSupportedProperties(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSupportedProperties(named_graph); - } - - - public Vector getSupportedAssociations(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSupportedAssociations(named_graph); - } - - - public Vector getSupportedRoles(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getSupportedRoles(named_graph); - } - - - public Vector getHierarchicalRelationships(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getHierarchicalRelationships(named_graph); - } - - - public Vector getConceptsInSubset(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getConceptsInSubset(named_graph, code); - } - - - public Vector getAvailableOntologies() { - OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); - return owlSPARQLUtils.getAvailableOntologies(); - } - - - public Vector getOntologyVersion(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getOntologyVersion(named_graph); - } - - - public Vector getOntology(String named_graph) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getOntology(named_graph); - } - - - public Vector getNamedGraphs() { - OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); - return owlSPARQLUtils.getNamedGraphs(); - } - - public Vector getTree(String named_graph, String code) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getTree(named_graph, code); - } - - - public Vector getTree(String named_graph, String code, int maxLevel) { - String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); - OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); - return owlSPARQLUtils.getTree(named_graph, code, maxLevel); - } - - - public static void main(String[] args) { - String serviceUrl = args[0]; - SPARQLUtilsClient testCodeGen = new SPARQLUtilsClient(serviceUrl); - String codingScheme = "NCI_Thesaurus"; - String version = "17.07d"; - String namedGraph = testCodeGen.getNamedGraphByCodingSchemeAndVersion(codingScheme, version); - String header_concept_code = "C54456"; - Vector codes = testCodeGen.getConceptsInSubset(namedGraph, header_concept_code); - for (int i=0; i + * Copyright 2008-2017 NGIS. This software was developed in conjunction + * with the National Cancer Institute, and so to the extent government + * employees are co-authors, any rights in such works shall be subject + * to Title 17 of the United States Code, section 105. + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the disclaimer of Article 3, + * below. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * 2. The end-user documentation included with the redistribution, + * if any, must include the following acknowledgment: + * "This product includes software developed by NGIS and the National + * Cancer Institute." If no such end-user documentation is to be + * included, this acknowledgment shall appear in the software itself, + * wherever such third-party acknowledgments normally appear. + * 3. The names "The National Cancer Institute", "NCI" and "NGIS" must + * not be used to endorse or promote products derived from this software. + * 4. This license does not authorize the incorporation of this software + * into any third party proprietary programs. This license does not + * authorize the recipient to use any trademarks owned by either NCI + * or NGIS + * 5. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED + * WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE + * DISCLAIMED. IN NO EVENT SHALL THE NATIONAL CANCER INSTITUTE, + * NGIS, OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, + * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + * ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + * POSSIBILITY OF SUCH DAMAGE. + * + */ + +/** + * @author EVS Team + * @version 1.0 + * + * Modification history: + * Initial implementation kim.ong@ngc.com + * + */ + +public class SPARQLUtilsClient { + String serviceUrl = null; + String sparql_endpoint = null; + HashMap OWLSPARQLUtilsMap = null; + HashMap codingSchemeNameAndVersion2NamedGraphMap = null; + HashMap namedGraph2codingSchemeNameAndVersionMap = null; + + public SPARQLUtilsClient() { + + } + + public SPARQLUtilsClient(String serviceUrl) { + this.serviceUrl = serviceUrl; + initialize(); + } + + public void initialize() { + String[] sparql_endpoints = new String[1]; + sparql_endpoint = serviceUrl + "?query="; + sparql_endpoints[0] = sparql_endpoint; + OWLSPARQLUtilsMap = OWLSPARQLUtilsExt.getCodingSchemeNameVersion2OWLSPARQLUtilsMap(sparql_endpoints); + Vector v = OWLSPARQLUtilsExt.getSupportedCodingSchemesAndVersions(OWLSPARQLUtilsMap); + //Utils.dumpVector("Supported coding schemes", v); + codingSchemeNameAndVersion2NamedGraphMap = new HashMap(); + namedGraph2codingSchemeNameAndVersionMap = new HashMap(); + for (int k=0; k " + key); + //System.out.println(key + " --> " + owlSPARQLUtils.get_named_graph()); + Vector w = owlSPARQLUtils.getTripleCount(owlSPARQLUtils.get_named_graph()); + String count = new ParserUtils().getValue((String) w.elementAt(0)); + System.out.println(key + " triple count: " + count); + Vector named_graphs = owlSPARQLUtils.getNamedGraphs(); + Utils.dumpVector("named_graphs", named_graphs); + */ + } + } + } + + public Vector execute(String named_graph, String query_file) { + String key = (String) codingSchemeNameAndVersion2NamedGraphMap.get(named_graph); + gov.nih.nci.evs.restapi.util.OWLSPARQLUtils owlSPARQLUtils = (gov.nih.nci.evs.restapi.util.OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + HTTPUtils httpUtils = new HTTPUtils(sparql_endpoint, null, null); + String query = httpUtils.loadQuery(query_file, false); + //System.out.println(query); + return owlSPARQLUtils.execute(query_file); + } + + public String getNamedGraphByCodingSchemeAndVersion(String codingScheme, String version) { + return (String) codingSchemeNameAndVersion2NamedGraphMap.get(codingScheme + "|" + version); + } + + public String getCodingSchemeAndVersionByNamedGraph(String namedGraph) { + return (String) namedGraph2codingSchemeNameAndVersionMap.get(namedGraph); + } + + public Vector getOntologyInfo(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.get_ontology_info(named_graph); + } + + + public Vector getNamedGraph() { + OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); + return owlSPARQLUtils.getNamedGraph(); + } + + + public Vector getOntologyInfo() { + OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); + return owlSPARQLUtils.get_ontology_info(); + } + + + public Vector getLabelByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getLabelByCode(named_graph, code); + } + + + public Vector getInverseRolesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getInverseRolesByCode(named_graph, code); + } + + + public Vector getCodeAndLabel(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getCodeAndLabel(named_graph); + } + + + public Vector getClassCounts() { + OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); + return owlSPARQLUtils.getClassCounts(); + } + + + public Vector getClassCount(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getClassCount(named_graph); + } + + + public Vector getTripleCount(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getTripleCount(named_graph); + } + + + public Vector getSuperclassesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSuperclassesByCode(named_graph, code); + } + + + public Vector getSubclassesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSubclassesByCode(named_graph, code); + } + + + public Vector getRolesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getRolesByCode(named_graph, code); + } + + + public Vector getPropertiesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + Vector v = owlSPARQLUtils.getPropertiesByCode(named_graph, code, false); + v = ParserUtils.formatOutput(v); + return ParserUtils.excludePropertyType(v, "#A|#R"); + } + + + public Vector getOntologyVersionInfo(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getOntologyVersionInfo(named_graph); + } + + + public Vector getSynonyms(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSynonyms(named_graph, code); + } + + + public Vector getAnnotationProperties(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getAnnotationProperties(named_graph); + } + + + public Vector getObjectProperties(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getObjectProperties(named_graph); + } + + + public Vector getPropertyQualifiersByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getPropertyQualifiersByCode(named_graph, code); + } + + + public Vector getInboundRolesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getInboundRolesByCode(named_graph, code); + } + + + public Vector getOutboundRolesByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getOutboundRolesByCode(named_graph, code); + } + + + public Vector getRoleRelationships(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getRoleRelationships(named_graph); + } + + + public Vector getInverseAssociationsByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getInverseAssociationsByCode(named_graph, code); + } + + + public Vector getAssociationsByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getAssociationsByCode(named_graph, code); + } + + + public Vector getDiseaseIsStageSourceCodes(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getDiseaseIsStageSourceCodes(named_graph); + } + + + public Vector getDiseaseIsGradeSourceCodes(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getDiseaseIsGradeSourceCodes(named_graph); + } + + + public Vector getAssociationSourceCodes(String named_graph, String associationName) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getAssociationSourceCodes(named_graph, associationName); + } + + + public Vector getDisjointWithByCode(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getDisjointWithByCode(named_graph, code); + } + + + public Vector getObjectPropertiesDomainRange(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getObjectPropertiesDomainRange(named_graph); + } + + + public Vector getObjectValuedAnnotationProperties(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getObjectValuedAnnotationProperties(named_graph); + } + + + public Vector getStringValuedAnnotationProperties(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getStringValuedAnnotationProperties(named_graph); + } + + + public Vector getSupportedProperties(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSupportedProperties(named_graph); + } + + + public Vector getSupportedAssociations(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSupportedAssociations(named_graph); + } + + + public Vector getSupportedRoles(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getSupportedRoles(named_graph); + } + + + public Vector getHierarchicalRelationships(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getHierarchicalRelationships(named_graph); + } + + + public Vector getConceptsInSubset(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getConceptsInSubset(named_graph, code); + } + + + public Vector getAvailableOntologies() { + OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); + return owlSPARQLUtils.getAvailableOntologies(); + } + + + public Vector getOntologyVersion(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getOntologyVersion(named_graph); + } + + + public Vector getOntology(String named_graph) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getOntology(named_graph); + } + + + public Vector getNamedGraphs() { + OWLSPARQLUtils owlSPARQLUtils = new OWLSPARQLUtils(sparql_endpoint, null, null); + return owlSPARQLUtils.getNamedGraphs(); + } + + public Vector getTree(String named_graph, String code) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getTree(named_graph, code); + } + + + public Vector getTree(String named_graph, String code, int maxLevel) { + String key = (String) namedGraph2codingSchemeNameAndVersionMap.get(named_graph); + OWLSPARQLUtils owlSPARQLUtils = (OWLSPARQLUtils) OWLSPARQLUtilsMap.get(key); + return owlSPARQLUtils.getTree(named_graph, code, maxLevel); + } + + + public static void main(String[] args) { + String serviceUrl = args[0]; + SPARQLUtilsClient testCodeGen = new SPARQLUtilsClient(serviceUrl); + String codingScheme = "NCI_Thesaurus"; + String version = "17.07d"; + String namedGraph = testCodeGen.getNamedGraphByCodingSchemeAndVersion(codingScheme, version); + String header_concept_code = "C54456"; + Vector codes = testCodeGen.getConceptsInSubset(namedGraph, header_concept_code); + for (int i=0; iFDA UNII ftp -C0000294 C0000294 Semantic_Type Organic Chemical -C0000294 C0000294 Semantic_Type Pharmacologic Substance -C0000734 C0000734 Semantic_Type Finding -C0000739 C0000739 Semantic_Type Body Part, Organ, or Organ Component -C0000744 C0000744 Semantic_Type Disease or Syndrome -C0000768 C0000768 Semantic_Type Congenital Abnormality -C0000850 C0000850 Semantic_Type Fungus -C0005898 C0005898 Semantic_Type Body Location or Region -C0008902 C0008902 Semantic_Type Classification -C0012238 C0012238 Semantic_Type Organism Function -C0012240 C0012240 Semantic_Type Body System -C0013221 C0013221 Semantic_Type Injury or Poisoning -C0013395 C0013395 Semantic_Type Sign or Symptom -C0013557 C0013557 Semantic_Type Functional Concept -C0018943 C0018943 Semantic_Type Biomedical Occupation or Discipline -C0019080 C0019080 Semantic_Type Pathologic Function -C0019270 C0019270 Semantic_Type Anatomical Abnormality -C0021423 C0021423 Semantic_Type Occupation or Discipline -C0027672 C0027672 Semantic_Type Neoplastic Process -C0031150 C0031150 Semantic_Type Diagnostic Procedure -C0033613 C0033613 Semantic_Type Chemical Viewed Functionally -C0035359 C0035359 Semantic_Type Body Space or Junction -C0052796 C0052796 Semantic_Type Antibiotic -C0065541 C0065541 Semantic_Type Therapeutic or Preventive Procedure -C0220965 C0220965 Semantic_Type Intellectual Product -C0242481 C0242481 Semantic_Type Research Activity -C0444868 C0444868 Semantic_Type Quantitative Concept -C0494710 C0494710 Semantic_Type Acquired Abnormality -C0718043 C0718043 Semantic_Type Amino Acid, Peptide, or Protein -C0718043 C0718043 Semantic_Type Enzyme -C0993159 C0993159 Semantic_Type Biomedical or Dental Material -C1511989 C1511989 Semantic_Type Conceptual Entity -C1512910 C1512910 Semantic_Type Spatial Concept -C1619351 C1619351 Semantic_Type Qualitative Concept -C1710021 C1710021 Semantic_Type Regulation or Law -CL343444 CL343444 Semantic_Type Professional or Occupational Group -CL555329 CL555329 Semantic_Type Manufactured Object -C0000294 C0000294 DEFINITION A sulfhydryl compound that is used to reduce the incidence of hemorrhagic cystitis associated with certain chemotherapeutic agents. Mesna is converted to a free thiol compound in the kidney, where it binds to and inactivates acrolein and other urotoxic metabolites of ifosfamide and cyclophosphamide, thereby reducing their toxic effects on the urinary tract during urinary excretion. (NCI04) +C0000294 C0000294 synonym Mesna +C0000294 C0000294 term-type PT +C0000294 C0000294 term-type SY +C0000294 C0000294 term-type CSN +C0000294 C0000294 term-type CCN +C0000294 C0000294 term-type FBD +C0000294 C0000294 term-type BN +C0000477 C0000477 term-type AB +C0012238 C0012238 term-type AD +C1333305 C1333305 term-type HD +C0000294 C0000294 PDQ_Closed_Trial_Search_ID 39759 +C0000294 C0000294 Contributing_Source CTRP +C0000294 C0000294 Chemical_Formula C2H5O3S2.Na +C0000294 C0000294 PDQ_Open_Trial_Search_ID 39759 +C0000294 C0000294 CAS_Registry 19767-45-4 +C0000294 C0000294 Accepted_Therapeutic_Use_For Ifosfamide-induced hemorrhagic cystitis, prophylaxis +C0000294 C0000294 FDA_UNII_Code NR7O1405Q9 +C0000294 C0000294 NSC_Number 113891 +C0000477 C0000477 CHEBI_ID CHEBI:34385 +C0000768 C0000768 NICHD_Hierarchy_Term Congenital Malformation +C0000768 C0000768 FDA_Table Patient Code (Appendix B) +C0000850 C0000850 NCBI_Taxon_ID 4828 +C0013227 C0013227 Design_Note This category represents drug products, not their individual ingredients. +C0019080 C0019080 Use_For Blood pooling +C0206646 C0206646 Neoplastic_Status Undetermined +C0206646 C0206646 ICD-O-3_Code 8822/1 +C1880653 C1880653 Publish_Value_Set Yes +C1880653 C1880653 Term_Browser_Value_Set_Description The terminology that includes terms pertaining to FDA/USP Substance Registration System (SRS), which is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices The text and Microsoft Excel versions of this subset can be downloaded from here: FDA UNII ftp +C0000294 C0000294 Semantic_Type Organic Chemical +C0000294 C0000294 Semantic_Type Pharmacologic Substance +C0000734 C0000734 Semantic_Type Finding +C0000739 C0000739 Semantic_Type Body Part, Organ, or Organ Component +C0000744 C0000744 Semantic_Type Disease or Syndrome +C0000768 C0000768 Semantic_Type Congenital Abnormality +C0000850 C0000850 Semantic_Type Fungus +C0005898 C0005898 Semantic_Type Body Location or Region +C0008902 C0008902 Semantic_Type Classification +C0012238 C0012238 Semantic_Type Organism Function +C0012240 C0012240 Semantic_Type Body System +C0013221 C0013221 Semantic_Type Injury or Poisoning +C0013395 C0013395 Semantic_Type Sign or Symptom +C0013557 C0013557 Semantic_Type Functional Concept +C0018943 C0018943 Semantic_Type Biomedical Occupation or Discipline +C0019080 C0019080 Semantic_Type Pathologic Function +C0019270 C0019270 Semantic_Type Anatomical Abnormality +C0021423 C0021423 Semantic_Type Occupation or Discipline +C0027672 C0027672 Semantic_Type Neoplastic Process +C0031150 C0031150 Semantic_Type Diagnostic Procedure +C0033613 C0033613 Semantic_Type Chemical Viewed Functionally +C0035359 C0035359 Semantic_Type Body Space or Junction +C0052796 C0052796 Semantic_Type Antibiotic +C0065541 C0065541 Semantic_Type Therapeutic or Preventive Procedure +C0220965 C0220965 Semantic_Type Intellectual Product +C0242481 C0242481 Semantic_Type Research Activity +C0444868 C0444868 Semantic_Type Quantitative Concept +C0494710 C0494710 Semantic_Type Acquired Abnormality +C0718043 C0718043 Semantic_Type Amino Acid, Peptide, or Protein +C0718043 C0718043 Semantic_Type Enzyme +C0993159 C0993159 Semantic_Type Biomedical or Dental Material +C1511989 C1511989 Semantic_Type Conceptual Entity +C1512910 C1512910 Semantic_Type Spatial Concept +C1619351 C1619351 Semantic_Type Qualitative Concept +C1710021 C1710021 Semantic_Type Regulation or Law +CL343444 CL343444 Semantic_Type Professional or Occupational Group +CL555329 CL555329 Semantic_Type Manufactured Object +C0000294 C0000294 DEFINITION A sulfhydryl compound that is used to reduce the incidence of hemorrhagic cystitis associated with certain chemotherapeutic agents. Mesna is converted to a free thiol compound in the kidney, where it binds to and inactivates acrolein and other urotoxic metabolites of ifosfamide and cyclophosphamide, thereby reducing their toxic effects on the urinary tract during urinary excretion. (NCI04) diff --git a/src/test/resources/samples/snomedct_us-samples.txt b/src/test/resources/samples/snomedct_us-samples.txt index a1a4fcc89..73e079a98 100644 --- a/src/test/resources/samples/snomedct_us-samples.txt +++ b/src/test/resources/samples/snomedct_us-samples.txt @@ -1,137 +1,137 @@ -58488005 58488005 synonym 1,4-alpha-Glucan branching enzyme -58488005 58488005 term-type PT -58488005 58488005 term-type SY -58488005 58488005 term-type FN -128050000 128050000 term-type SYGB -190787008 190787008 term-type PTGB -900000000000538005 900000000000538005 term-type SB -447562003 447562003 term-type XM -58488005 58488005 qualifier-synonym~TYPE_ID 1,4-alpha-Glucan branching enzyme~900000000000013009 -58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID 1,4-alpha-Glucan branching enzyme~900000000000020002 -58488005 58488005 DEFINITION_STATUS_ID 900000000000074008 -58488005 58488005 ACTIVE 1 -58488005 58488005 CTV3ID XUH01 -58488005 58488005 EFFECTIVE_TIME 20170131 -58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID Branching enzyme~900000000000448009 -58488005 58488005 qualifier-synonym~TYPE_ID Branching enzyme~900000000000013009 -58488005 58488005 qualifier-synonym~TYPE_ID 1,4-alpha-Glucan branching enzyme (substance)~900000000000003001 -58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID 1,4-alpha-Glucan branching enzyme (substance)~900000000000020002 -128050000 128050000 qualifier-synonym~TYPE_ID Tumour of abdomen~900000000000013009 -128050000 128050000 qualifier-synonym~CASE_SIGNIFICANCE_ID Tumour of abdomen~900000000000448009 -195879000 195879000 ICD-O-3_CODE C76.2 -190787008 190787008 qualifier-synonym~TYPE_ID Abetalipoproteinaemia~900000000000013009 -190787008 190787008 qualifier-synonym~CASE_SIGNIFICANCE_ID Abetalipoproteinaemia~900000000000448009 -278201002 278201002 qualifier-synonym~MODULE_ID Classification (attribute)~900000000000012004 -278201002 278201002 qualifier-synonym~MODULE_NAME Classification (attribute)~SNOMED CT model component module -278201002 278201002 qualifier-synonym~MODULE_ID Classification~900000000000012004 -278201002 278201002 qualifier-synonym~MODULE_NAME Classification~SNOMED CT model component module -278201002 278201002 MODULE_ID 900000000000012004 -278201002 278201002 MODULE_NAME SNOMED CT model component module -416093006 416093006 qualifier-synonym~MODULE_NAME Allergic reaction to medication~US National Library of Medicine maintained module -416093006 416093006 qualifier-synonym~MODULE_ID Allergic reaction to medication~731000124108 -260878002 260878002 qualifier-synonym~MODULE_ID T - Tumour stage~900000000000012004 -260878002 260878002 qualifier-synonym~MODULE_NAME T - Tumour stage~SNOMED CT model component module -138875005 138875005 DEFAULT_MODULE_ID 900000000000207008 -138875005 138875005 DEFAULT_LANGUAGECODE en -900000000000538005 900000000000538005 REFSET_PATTERN Description format type -900000000000531004 900000000000531004 UMLSRELA refers_to -900000000000531004 900000000000531004 UMLSREL RN -447562003 447562003 qualifier-synonym~MAPSETSID SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~447562003 -447562003 447562003 qualifier-synonym~MAPSETNAME SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD-10 complex map reference set -447562003 447562003 qualifier-synonym~MAPSETVERSION SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~20200901 -447562003 447562003 qualifier-synonym~MAPSETXRTARGETID SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~100051 -447562003 447562003 qualifier-synonym~MAPSETRSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US -447562003 447562003 qualifier-synonym~MAPSETVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US_2020_09_01 -447562003 447562003 qualifier-synonym~FROMRSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US -447562003 447562003 qualifier-synonym~FROMVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US_2020_09_01 -447562003 447562003 qualifier-synonym~TORSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD10 -447562003 447562003 qualifier-synonym~TOVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD10_2016 -447562003 447562003 qualifier-synonym~SOS SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~This set maps SNOMEDCT_US concept identifiers to ICD-10 codes; a single SNOMEDCT_US concept id may be mapped to one or more ICD-10 codes -447562003 447562003 qualifier-synonym~MTH_MAPSETCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N_TO_N -447562003 447562003 qualifier-synonym~MTH_MAPFROMCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SINGLE SCUI -447562003 447562003 qualifier-synonym~MTH_MAPTOCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SINGLE SDUI, MULTIPLE SDUI -447562003 447562003 qualifier-synonym~MTH_MAPFROMEXHAUSTIVE SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N -447562003 447562003 qualifier-synonym~MTH_MAPTOEXHAUSTIVE SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N -58488005 58488005 Semantic_Type Amino Acid, Peptide, or Protein -58488005 58488005 Semantic_Type Enzyme -285407008 285407008 Semantic_Type Organic Chemical -285407008 285407008 Semantic_Type Hazardous or Poisonous Substance -386922000 386922000 Semantic_Type Pharmacologic Substance -818983003 818983003 Semantic_Type Body Location or Region -9209005 9209005 Semantic_Type Sign or Symptom -271860004 271860004 Semantic_Type Finding -128050000 128050000 Semantic_Type Neoplastic Process -195879000 195879000 Semantic_Type Body Part, Organ, or Organ Component -190787008 190787008 Semantic_Type Disease or Syndrome -276654001 276654001 Semantic_Type Congenital Abnormality -57145009 57145009 Semantic_Type Fungus -278201002 278201002 Semantic_Type Classification -106079008 106079008 Semantic_Type Organism Function -86762007 86762007 Semantic_Type Body System -416098002 416098002 Semantic_Type Pathologic Function -7895008 7895008 Semantic_Type Injury or Poisoning -414403008 414403008 Semantic_Type Anatomical Abnormality -72888009 72888009 Semantic_Type Acquired Abnormality -64908006 64908006 Semantic_Type Diagnostic Procedure -65823007 65823007 Semantic_Type Chemical Viewed Functionally -82849001 82849001 Semantic_Type Body Space or Junction -387531004 387531004 Semantic_Type Antibiotic -15905001 15905001 Semantic_Type Therapeutic or Preventive Procedure -106234000 106234000 Semantic_Type Qualitative Concept -818997006 818997006 Semantic_Type Tissue -38456008 38456008 Semantic_Type Embryonic Structure -159558008 159558008 Semantic_Type Professional or Occupational Group -259381005 259381005 Semantic_Type Biologically Active Substance -261188006 261188006 Semantic_Type Anatomical Structure -246231009 246231009 Semantic_Type Intellectual Product -104436003 104436003 Semantic_Type Laboratory Procedure -327053003 327053003 Semantic_Type Clinical Drug -421026006 421026006 Semantic_Type Biomedical or Dental Material -391277002 391277002 Semantic_Type Health Care Activity -118234003 118234003 Semantic_Type Functional Concept -472904006 472904006 Semantic_Type Body Substance -767407009 767407009 Semantic_Type Inorganic Chemical -818983003 818983003 DEFINITION This is considered the most commonly used clinical variant of 'abdomen' and relates to the space and content within the abdominopelvic cavity plus the anterior and lateral abdominal wall. The volume is bounded by, but excludes: superiorly the thoracic diaphragm; inferiorly the pelvic diaphragm; and posteriorly the posterior wall of the abdomen proper: The pelvic component consists of the cavity of the true pelvis, which is bounded by, but excludes, the pelvic wall. Anteriorly this volume is bounded and includes the anterior abdominal (including the lateral abdominal wall). -21390004 21390004 qualifier-RO~MODULE_ID 731000124108 -21390004 21390004 qualifier-RO~RELA associated_morphology_of -21390004 21390004 qualifier-RO~MODULE_NAME US National Library of Medicine maintained module -21390004 21390004 RO 32201000119107 -34707002 34707002 root -416098002 416098002 root -410942007 410942007 root -130090009 130090009 root -52612000 52612000 root -237130006 237130006 root -60654006 60654006 root -426965005 426965005 root -90290004 90290004 root -21371007 21371007 root -84668001 84668001 root -68526006 68526006 root -45036003 45036003 root -106234000 106234000 root -87770006 87770006 root -9846003 9846003 root -18639004 18639004 root -63337009 63337009 root -83137009 83137009 root -73063007 73063007 root -24908005 24908005 root -259381005 259381005 root -229144001 229144001 root -277046005 277046005 root -178025000 178025000 root -225162003 225162003 root -303790000 303790000 root -91723000 91723000 root -138875005 138875005 root -49120005 49120005 root -609624008 609624008 root -71922006 71922006 root -818982008 818982008 root -277112006 277112006 root -768610006 768610006 root -58488005 58488005 parent-count2 -108821000 108821000 parent-count1 -41788008 41788008 parent-count4 -399269003 399269003 parent-count3 +58488005 58488005 synonym 1,4-alpha-Glucan branching enzyme +58488005 58488005 term-type PT +58488005 58488005 term-type SY +58488005 58488005 term-type FN +128050000 128050000 term-type SYGB +190787008 190787008 term-type PTGB +900000000000538005 900000000000538005 term-type SB +447562003 447562003 term-type XM +58488005 58488005 qualifier-synonym~TYPE_ID 1,4-alpha-Glucan branching enzyme~900000000000013009 +58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID 1,4-alpha-Glucan branching enzyme~900000000000020002 +58488005 58488005 DEFINITION_STATUS_ID 900000000000074008 +58488005 58488005 ACTIVE 1 +58488005 58488005 CTV3ID XUH01 +58488005 58488005 EFFECTIVE_TIME 20170131 +58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID Branching enzyme~900000000000448009 +58488005 58488005 qualifier-synonym~TYPE_ID Branching enzyme~900000000000013009 +58488005 58488005 qualifier-synonym~TYPE_ID 1,4-alpha-Glucan branching enzyme (substance)~900000000000003001 +58488005 58488005 qualifier-synonym~CASE_SIGNIFICANCE_ID 1,4-alpha-Glucan branching enzyme (substance)~900000000000020002 +128050000 128050000 qualifier-synonym~TYPE_ID Tumour of abdomen~900000000000013009 +128050000 128050000 qualifier-synonym~CASE_SIGNIFICANCE_ID Tumour of abdomen~900000000000448009 +195879000 195879000 ICD-O-3_CODE C76.2 +190787008 190787008 qualifier-synonym~TYPE_ID Abetalipoproteinaemia~900000000000013009 +190787008 190787008 qualifier-synonym~CASE_SIGNIFICANCE_ID Abetalipoproteinaemia~900000000000448009 +278201002 278201002 qualifier-synonym~MODULE_ID Classification (attribute)~900000000000012004 +278201002 278201002 qualifier-synonym~MODULE_NAME Classification (attribute)~SNOMED CT model component module +278201002 278201002 qualifier-synonym~MODULE_ID Classification~900000000000012004 +278201002 278201002 qualifier-synonym~MODULE_NAME Classification~SNOMED CT model component module +278201002 278201002 MODULE_ID 900000000000012004 +278201002 278201002 MODULE_NAME SNOMED CT model component module +416093006 416093006 qualifier-synonym~MODULE_NAME Allergic reaction to medication~US National Library of Medicine maintained module +416093006 416093006 qualifier-synonym~MODULE_ID Allergic reaction to medication~731000124108 +260878002 260878002 qualifier-synonym~MODULE_ID T - Tumour stage~900000000000012004 +260878002 260878002 qualifier-synonym~MODULE_NAME T - Tumour stage~SNOMED CT model component module +138875005 138875005 DEFAULT_MODULE_ID 900000000000207008 +138875005 138875005 DEFAULT_LANGUAGECODE en +900000000000538005 900000000000538005 REFSET_PATTERN Description format type +900000000000531004 900000000000531004 UMLSRELA refers_to +900000000000531004 900000000000531004 UMLSREL RN +447562003 447562003 qualifier-synonym~MAPSETSID SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~447562003 +447562003 447562003 qualifier-synonym~MAPSETNAME SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD-10 complex map reference set +447562003 447562003 qualifier-synonym~MAPSETVERSION SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~20200901 +447562003 447562003 qualifier-synonym~MAPSETXRTARGETID SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~100051 +447562003 447562003 qualifier-synonym~MAPSETRSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US +447562003 447562003 qualifier-synonym~MAPSETVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US_2020_09_01 +447562003 447562003 qualifier-synonym~FROMRSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US +447562003 447562003 qualifier-synonym~FROMVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SNOMEDCT_US_2020_09_01 +447562003 447562003 qualifier-synonym~TORSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD10 +447562003 447562003 qualifier-synonym~TOVSAB SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~ICD10_2016 +447562003 447562003 qualifier-synonym~SOS SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~This set maps SNOMEDCT_US concept identifiers to ICD-10 codes; a single SNOMEDCT_US concept id may be mapped to one or more ICD-10 codes +447562003 447562003 qualifier-synonym~MTH_MAPSETCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N_TO_N +447562003 447562003 qualifier-synonym~MTH_MAPFROMCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SINGLE SCUI +447562003 447562003 qualifier-synonym~MTH_MAPTOCOMPLEXITY SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~SINGLE SDUI, MULTIPLE SDUI +447562003 447562003 qualifier-synonym~MTH_MAPFROMEXHAUSTIVE SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N +447562003 447562003 qualifier-synonym~MTH_MAPTOEXHAUSTIVE SNOMEDCT_US_2020_09_01 to ICD10_2016 Mappings~N +58488005 58488005 Semantic_Type Amino Acid, Peptide, or Protein +58488005 58488005 Semantic_Type Enzyme +285407008 285407008 Semantic_Type Organic Chemical +285407008 285407008 Semantic_Type Hazardous or Poisonous Substance +386922000 386922000 Semantic_Type Pharmacologic Substance +818983003 818983003 Semantic_Type Body Location or Region +9209005 9209005 Semantic_Type Sign or Symptom +271860004 271860004 Semantic_Type Finding +128050000 128050000 Semantic_Type Neoplastic Process +195879000 195879000 Semantic_Type Body Part, Organ, or Organ Component +190787008 190787008 Semantic_Type Disease or Syndrome +276654001 276654001 Semantic_Type Congenital Abnormality +57145009 57145009 Semantic_Type Fungus +278201002 278201002 Semantic_Type Classification +106079008 106079008 Semantic_Type Organism Function +86762007 86762007 Semantic_Type Body System +416098002 416098002 Semantic_Type Pathologic Function +7895008 7895008 Semantic_Type Injury or Poisoning +414403008 414403008 Semantic_Type Anatomical Abnormality +72888009 72888009 Semantic_Type Acquired Abnormality +64908006 64908006 Semantic_Type Diagnostic Procedure +65823007 65823007 Semantic_Type Chemical Viewed Functionally +82849001 82849001 Semantic_Type Body Space or Junction +387531004 387531004 Semantic_Type Antibiotic +15905001 15905001 Semantic_Type Therapeutic or Preventive Procedure +106234000 106234000 Semantic_Type Qualitative Concept +818997006 818997006 Semantic_Type Tissue +38456008 38456008 Semantic_Type Embryonic Structure +159558008 159558008 Semantic_Type Professional or Occupational Group +259381005 259381005 Semantic_Type Biologically Active Substance +261188006 261188006 Semantic_Type Anatomical Structure +246231009 246231009 Semantic_Type Intellectual Product +104436003 104436003 Semantic_Type Laboratory Procedure +327053003 327053003 Semantic_Type Clinical Drug +421026006 421026006 Semantic_Type Biomedical or Dental Material +391277002 391277002 Semantic_Type Health Care Activity +118234003 118234003 Semantic_Type Functional Concept +472904006 472904006 Semantic_Type Body Substance +767407009 767407009 Semantic_Type Inorganic Chemical +818983003 818983003 DEFINITION This is considered the most commonly used clinical variant of 'abdomen' and relates to the space and content within the abdominopelvic cavity plus the anterior and lateral abdominal wall. The volume is bounded by, but excludes: superiorly the thoracic diaphragm; inferiorly the pelvic diaphragm; and posteriorly the posterior wall of the abdomen proper: The pelvic component consists of the cavity of the true pelvis, which is bounded by, but excludes, the pelvic wall. Anteriorly this volume is bounded and includes the anterior abdominal (including the lateral abdominal wall). +21390004 21390004 qualifier-RO~MODULE_ID 731000124108 +21390004 21390004 qualifier-RO~RELA associated_morphology_of +21390004 21390004 qualifier-RO~MODULE_NAME US National Library of Medicine maintained module +21390004 21390004 RO 32201000119107 +34707002 34707002 root +416098002 416098002 root +410942007 410942007 root +130090009 130090009 root +52612000 52612000 root +237130006 237130006 root +60654006 60654006 root +426965005 426965005 root +90290004 90290004 root +21371007 21371007 root +84668001 84668001 root +68526006 68526006 root +45036003 45036003 root +106234000 106234000 root +87770006 87770006 root +9846003 9846003 root +18639004 18639004 root +63337009 63337009 root +83137009 83137009 root +73063007 73063007 root +24908005 24908005 root +259381005 259381005 root +229144001 229144001 root +277046005 277046005 root +178025000 178025000 root +225162003 225162003 root +303790000 303790000 root +91723000 91723000 root +138875005 138875005 root +49120005 49120005 root +609624008 609624008 root +71922006 71922006 root +818982008 818982008 root +277112006 277112006 root +768610006 768610006 root +58488005 58488005 parent-count2 +108821000 108821000 parent-count1 +41788008 41788008 parent-count4 +399269003 399269003 parent-count3 From 65bc867e814d16d2f7746d711e45da21c6e36ee9 Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Wed, 5 Feb 2025 17:39:18 -0800 Subject: [PATCH 10/11] Merge develop --- .../evs/api/controller/SearchController.java | 220 +++++++++++++++++- .../SparqlQueryManagerServiceImpl.java | 2 +- 2 files changed, 219 insertions(+), 3 deletions(-) diff --git a/src/main/java/gov/nih/nci/evs/api/controller/SearchController.java b/src/main/java/gov/nih/nci/evs/api/controller/SearchController.java index 89b535e5f..b6414c0c5 100644 --- a/src/main/java/gov/nih/nci/evs/api/controller/SearchController.java +++ b/src/main/java/gov/nih/nci/evs/api/controller/SearchController.java @@ -338,8 +338,224 @@ public void postInit() throws Exception { return search(new SearchCriteria(searchCriteria, terminology), bindingResult, license); } - // generate openapi documentation for this endpoint. generate parameters from SearchCriteria. - + /** + * Search. + * + * @param searchCriteria the filter criteria elastic fields + * @param bindingResult the binding result + * @param license the license + * @return the string + * @throws Exception the exception + */ + @Operation( + summary = "Get concept search results", + description = + "Use cases for search range from very simple term searches, use of paging " + + "parameters, additional filters, searches properties, roles, and associations," + + " and so on. To further explore the range of search options, take a look " + + "at the " + + "Github client SDK library created for the NCI EVS Rest API.") + @ApiResponses({ + @ApiResponse( + responseCode = "200", + description = "Successfully retrieved the requested information"), + @ApiResponse( + responseCode = "400", + description = "Bad request", + content = + @Content( + mediaType = "application/json", + schema = @Schema(implementation = RestException.class))), + @ApiResponse( + responseCode = "404", + description = "Resource not found", + content = + @Content( + mediaType = "application/json", + schema = @Schema(implementation = RestException.class))), + @ApiResponse( + responseCode = "417", + description = "Expectation failed", + content = + @Content( + mediaType = "application/json", + schema = @Schema(implementation = RestException.class))) + }) + @Parameters({ + @Parameter(name = "searchCriteria", hidden = true), + @Parameter( + name = "terminology", + description = + "Comma-separated list of terminologies to search, e.g. 'ncit' or 'ncim' (See" + + " here for complete list)", + required = false, + schema = @Schema(implementation = String.class), + example = "ncit"), + @Parameter( + name = "term", + description = "The term, phrase, or code to be searched, e.g. 'melanoma'", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "type", + description = + "The match type, one of: contains, match, startsWith, phrase, AND, OR, fuzzy.", + required = false, + schema = @Schema(implementation = String.class), + example = "contains"), + @Parameter( + name = "sort", + description = "The search parameter to sort results by", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "ascending", + description = "Sort ascending (if true) or descending (if false)", + required = false, + schema = @Schema(implementation = Boolean.class)), + @Parameter( + name = "include", + description = + "Indicator of how much data to return. Comma-separated list of any of the following" + + " values: minimal, summary, full, associations, children, definitions," + + " disjointWith, history, inverseAssociations, inverseRoles, maps, parents," + + " properties, roles, synonyms. See here for detailed information.", + required = false, + schema = @Schema(implementation = String.class), + example = "minimal"), + @Parameter( + name = "fromRecord", + description = "Start index of the search results", + required = false, + schema = @Schema(implementation = Integer.class), + example = "0"), + @Parameter( + name = "pageSize", + description = "Max number of results to return", + required = false, + schema = @Schema(implementation = Integer.class), + example = "10"), + @Parameter( + name = "conceptStatus", + description = + "Comma-separated list of concept status values to restrict search results by.

Click here for a" + + " list of NCI Thesaurus values. This parameter is only meaningful for" + + " terminology=ncit.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "property", + description = + "Comma-separated list of properties to restrict search results by (see also" + + " value). e.g.
  • 'P106,P322' for" + + " terminology=ncit
  • 'COLOR,SHAPE' for" + + " terminology=ncim

Click here for a list of NCI Thesaurus properties.

Click here for a list" + + " of NCI Metathesaurus properties.

The properties can be specified as" + + " code or name. NOTE: This feature works with value to find concepts" + + " having one of the specified properties with an exact value matching the" + + " value parameter. Using a term will further restrict results to" + + " those also matching the term.", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "value", + description = + "A property value to restrict search results by. NOTE: This feature works with" + + " property to find concepts having one of the specified properties with an" + + " exact value matching this parameter. Using a term will further restrict" + + " results to those also matching the term.", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "definitionSource", + description = + "Comma-separated list of definition sources to restrict search results by.

Click here for a" + + " list of NCI Thesaurus values.

Click here for a" + + " list of NCI Metathesaurus values.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "definitionType", + description = + "Comma-separated list of definition types to restrict search results by, e.g." + + " 'DEFINITION,ALT_DEFINITION' for terminology=ncit.

Click here for a" + + " list of NCI Thesaurus values. This parameter is only meaningful for" + + " terminology=ncit.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "synonymSource", + description = + "Comma-separated list of synonym sources to restrict search results by.

Click here for a" + + " list of NCI Thesaurus values.

Click here for a" + + " list of NCI Metathesaurus values.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "synonymType", + description = + "Comma-separated list of synonym types to restrict search results by, e.g. " + + "'FULL_SYN'.

" + + "Click here for a list of NCI Thesaurus values. This parameter is only " + + "meaningful for terminology=ncit.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "synonymTermType", + description = + "Comma-separated list of synonym term type values to restrict search results by. " + + "

Click here for a " + + "list of NCI Thesaurus values.

" + + "

Click here for a " + + "list of NCI Metathesaurus values.

", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "subset", + description = + "Comma-separated list of subsets to restrict search results by, e.g. 'C157225'. The" + + " value '*' can also be used to return results that participate in at least one" + + " subset. This parameter is only meaningful for terminology=ncit", + required = false, + schema = @Schema(implementation = String.class)), + @Parameter( + name = "X-EVSRESTAPI-License-Key", + description = + "Required license information for restricted terminologies. See here for detailed information.", + required = false, + schema = @Schema(implementation = String.class)) + // These are commented out because they are currently not supported + // @Parameter(name = "inverse", value = "Used with \"associations\" + // or \"roles\" when true to indicate that inverse associations or roles + // should be searched", required = false, schema = @Schema(implementation = String.class), + // paramType = + // "query", example = "false"), + // @Parameter(name = "association", value = "Comma-separated list + // of associations to search. e.g A10,A215. Click here for + // a list of NCI Thesaurus associations. The associations can be + // specified as code or name", required = false, schema = @Schema(implementation = + // String.class), + // paramType = "query"), + // @Parameter(name = "role", value = "Comma-separated list of roles + // to search. e.g R15,R193. Click here for a list of NCI Thesaurus roles. The + // roles can be specified as code or name", required = false, dataTypeClass = + // String.class) + }) @RecordMetric @RequestMapping( method = RequestMethod.GET, diff --git a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java index be34d249c..a4d3d899e 100644 --- a/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java +++ b/src/main/java/gov/nih/nci/evs/api/service/SparqlQueryManagerServiceImpl.java @@ -260,7 +260,7 @@ public Concept getConceptFromElasticSearch( searchCriteria.setTerm(conceptCode); searchCriteria.setInclude(include); ConceptResultList result = - elasticSearchService.search(Collections.singletonList(terminology), searchCriteria); + elasticSearchService.findConcepts(Collections.singletonList(terminology), searchCriteria); return !result.getConcepts().isEmpty() ? result.getConcepts().get(0) : null; } From 90ab5f64aa36e7ec51792d565c2fe70d4ec5c800 Mon Sep 17 00:00:00 2001 From: akuppusamy-wci Date: Wed, 5 Feb 2025 17:46:37 -0800 Subject: [PATCH 11/11] Reverting some code --- src/main/bin/devreset.sh | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/src/main/bin/devreset.sh b/src/main/bin/devreset.sh index cbd39e0b6..43985d381 100755 --- a/src/main/bin/devreset.sh +++ b/src/main/bin/devreset.sh @@ -251,26 +251,26 @@ echo " create databases" /opt/stardog/bin/stardog-admin db create -n CTRP | sed 's/^/ /' /opt/stardog/bin/stardog-admin db create -n NCIT2 | sed 's/^/ /' echo " load data" -/opt/stardog/bin/stardog data add --named-graph http://NCI_T_weekly CTRP /Users/squareroot/temp/UnitTestData/ThesaurusInferred_+1weekly.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://NCI_T_monthly CTRP /Users/squareroot/temp/UnitTestData/ThesaurusInferred_monthly.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://NCI_T_monthly NCIT2 /Users/squareroot/temp/UnitTestData/ThesaurusInferred_monthly.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://GO_monthly NCIT2 /Users/squareroot/temp/UnitTestData/GO/go.2022-07-01.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://HGNC_monthly NCIT2 /Users/squareroot/temp/UnitTestData/HGNC/HGNC_202209.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://ChEBI_monthly NCIT2 /Users/squareroot/temp/UnitTestData/ChEBI/chebi_213.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://UmlsSemNet NCIT2 /Users/squareroot/temp/UnitTestData/UmlsSemNet/umlssemnet.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://MEDRT NCIT2 /Users/squareroot/temp/UnitTestData/MED-RT/medrt.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://Canmed NCIT2 /Users/squareroot/temp/UnitTestData/Canmed/canmed.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://CTCAE NCIT2 /Users/squareroot/temp/UnitTestData/CTCAE/ctcae5.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://DUO_monthly NCIT2 /Users/squareroot/temp/UnitTestData/DUO/duo_Feb21.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://DUO_monthly NCIT2 /Users/squareroot/temp/UnitTestData/DUO/iao_Dec20.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://OBI_monthly NCIT2 /Users/squareroot/temp/UnitTestData/OBI/obi_2022_07.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://OBIB NCIT2 /Users/squareroot/temp/UnitTestData/OBIB/obib_2021-11.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://NDFRT2 NCIT2 /Users/squareroot/temp/UnitTestData/NDFRT/NDFRT_Public_2018.02.05_Inferred.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://NCI_T_weekly CTRP /data/UnitTestData/ThesaurusInferred_+1weekly.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://NCI_T_monthly CTRP /data/UnitTestData/ThesaurusInferred_monthly.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://NCI_T_monthly NCIT2 /data/UnitTestData/ThesaurusInferred_monthly.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://GO_monthly NCIT2 /data/UnitTestData/GO/go.2022-07-01.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://HGNC_monthly NCIT2 /data/UnitTestData/HGNC/HGNC_202209.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://ChEBI_monthly NCIT2 /data/UnitTestData/ChEBI/chebi_213.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://UmlsSemNet NCIT2 /data/UnitTestData/UmlsSemNet/umlssemnet.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://MEDRT NCIT2 /data/UnitTestData/MED-RT/medrt.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://Canmed NCIT2 /data/UnitTestData/Canmed/canmed.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://CTCAE NCIT2 /data/UnitTestData/CTCAE/ctcae5.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://DUO_monthly NCIT2 /data/UnitTestData/DUO/duo_Feb21.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://DUO_monthly NCIT2 /data/UnitTestData/DUO/iao_Dec20.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://OBI_monthly NCIT2 /data/UnitTestData/OBI/obi_2022_07.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://OBIB NCIT2 /data/UnitTestData/OBIB/obib_2021-11.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://NDFRT2 NCIT2 /data/UnitTestData/NDFRT/NDFRT_Public_2018.02.05_Inferred.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://MGED NCIT2 /Users/squareroot/temp/UnitTestData/MGED/MGEDOntology.fix.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://NPO NCIT2 /Users/squareroot/temp/UnitTestData/NPO/npo-2011-12-08_inferred.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://MA NCIT2 /Users/squareroot/temp/UnitTestData/Mouse_Anatomy/ma_07_27_2016.owl | sed 's/^/ /' -/opt/stardog/bin/stardog data add --named-graph http://Zebrafish NCIT2 /Users/squareroot/temp/UnitTestData/Zebrafish/zfa_2019_08_02.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://MGED NCIT2 /data/UnitTestData/MGED/MGEDOntology.fix.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://NPO NCIT2 /data/UnitTestData/NPO/npo-2011-12-08_inferred.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://MA NCIT2 /data/UnitTestData/Mouse_Anatomy/ma_07_27_2016.owl | sed 's/^/ /' +/opt/stardog/bin/stardog data add --named-graph http://Zebrafish NCIT2 /data/UnitTestData/Zebrafish/zfa_2019_08_02.owl | sed 's/^/ /' echo " optimize databases" # The -n parameter removed before DB name as per updated stardog (may need to re-pull latest) /opt/stardog/bin/stardog-admin db optimize CTRP | sed 's/^/ /'