strucontjcheminf.bib

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% Encoding: Cp1252

@ARTICLE{chebi2010,
  author = {P {de Matos} and R Alc\'{a}ntara and A Dekker and M Ennis and J Hastings
	and K Haug and I Spiteri and S Turner and C Steinbeck},
  title = {{Chemical Entities of Biological Interest}: an update},
  journal = {Nucleic Acids Research},
  year = {2010},
  volume = {38},
  pages = {D249--D254}
}

@ARTICLE{alterovitz2010,
  author = {Alterovitz, Gil and Xiang, Michael and Hill, David P. and Lomax,
	Jane and Liu, Jonathan and Cherkassky, Michael and Dreyfuss, Jonathan
	and Mungall, Chris and Harris, Midori A. and Dolan, Mary E. and Blake,
	Judith A. and Ramoni, Marco F.},
  title = {{Ontology engineering}},
  journal = {Nature Biotechnology},
  year = {2010},
  volume = {28},
  pages = {128--130},
  number = {2},
  month = {February},
  abstract = {Gene Ontology (GO)1 and similar biomedical ontologies are critical
	tools of today's genetic research. These ontologies are crafted through
	a painstaking process of manual editing, and their organization relies
	on the intuition of human curators.},
  citeulike-article-id = {6634567},
  citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt0210-128},
  citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt0210-128},
  day = {01},
  doi = {10.1038/nbt0210-128},
  issn = {1087-0156},
  keywords = {content, go, ic, information, mine, ontology},
  posted-at = {2010-02-10 18:02:50},
  priority = {0},
  publisher = {Nature Publishing Group},
  url = {http://dx.doi.org/10.1038/nbt0210-128}
}

@ARTICLE{barnard1992,
  author = {Barnard, J. M. and Downs, G. M.},
  title = {Clustering of chemical structures on the basis of two-dimensional
	similarity measures},
  journal = {Journal of Chemical Information and Computer Sciences},
  year = {1992},
  volume = {32},
  pages = {644-649},
  number = {6},
  doi = {10.1021/ci00010a010},
  eprint = {http://pubs.acs.org/doi/pdf/10.1021/ci00010a010},
  url = {http://pubs.acs.org/doi/abs/10.1021/ci00010a010}
}

@ARTICLE{chepelevlipids2011,
  author = {Chepelev, Leonid and Riazanov, Alexandre and Kouznetsov, Alexandre
	and Low, Hong S. and Dumontier, Michel and Baker, Christopher},
  title = {{Prototype Semantic Infrastructure for Automated Small Molecule Classification
	and Annotation in Lipidomics}},
  journal = {BMC Bioinformatics},
  year = {2011},
  volume = {12},
  pages = {303},
  number = {1},
  abstract = {{BACKGROUND:The development of high-throughput experimentation has
	led to astronomical growth in biologically relevant lipids and lipid
	derivatives identified, screened, and deposited in numerous online
	databases. Unfortunately, efforts to annotate, classify, and analyze
	these chemical entities have largely remained in the hands of human
	curators using manual or semi-automated protocols, leaving many novel
	entities unclassified. Since chemical function is often closely linked
	to structure, accurate structure-based classification and annotation
	of chemical entities is imperative to understanding their functionality.RESULTS:As
	part of an exploratory study, we have investigated the utility of
	semantic web technologies in automated chemical classification and
	annotation of lipids. Our prototype framework consists of two components:
	an ontology and a set of federated web services that operate upon
	it. The formal lipid ontology we use here extends a part of the LiPrO
	ontology and draws on the lipid hierarchy in the LIPID MAPS database,
	as well as literature-derived knowledge. The federated semantic web
	services that operate upon this ontology are deployed within the
	Semantic Annotation, Discovery, and Integration (SADI) framework.
	Structure-based lipid classification is enacted by two core services.
	Firstly, a structural annotation service detects and enumerates relevant
	functional groups for a specified chemical structure. A second service
	reasons over lipid ontology class descriptions using the attributes
	obtained from the annotation service and identifies the appropriate
	lipid classification. We extend the utility of these core services
	by combining them with additional SADI services that retrieve associations
	between lipids and proteins and identify publications related to
	specified lipid types. We analyze the performance of SADI-enabled
	eicosanoid classification relative to the LIPID MAPS classification
	and reflect on the contribution of our integrative methodology in
	the context of high-throughput lipidomics. CONCLUSIONS:Our prototype
	framework is capable of accurate automated classification of lipids
	and facile integration of lipid class information with additional
	data obtained with SADI web services. The potential of programming-free
	integration of external web services through the SADI framework offers
	an opportunity for development of powerful novel applications in
	lipidomics. We conclude that semantic web technologies can provide
	an accurate and versatile means of classification and annotation
	of lipids.}},
  issn = {1471-2105},
  keywords = {cdk--usespackage--smiles, cdk--usespackage--smiles\_smarts, cito--usesmethodin--423382},
  pmid = {21791100},
  posted-at = {2011-07-31 08:38:49},
  priority = {2},
  url = {http://dx.doi.org/10.1186/1471-2105-12-303}
}

@INPROCEEDINGS{corbett2006,
  author = {Peter Corbett and Peter {Murray-Rust}},
  title = {High-Throughput Identification of Chemistry in Life Science Texts},
  booktitle = {Computational Life Sciences II},
  year = {2006},
  editor = {MR Berthold and R Glen and I Fischer},
  pages = {107-118},
  publisher = {Springer Berlin/Heidelberg}
}

@ARTICLE{deshpande2005,
  author = {Mukund Deshpande and Michihiro Kuramochi and Nikil Wale and George
	Karypis},
  title = {Frequent Substructure-Based Approaches for Classifying Chemical Compounds},
  journal = {IEEE Transactions on Knowledge and Data Engineering},
  year = {2005},
  volume = {17},
  pages = {1036-1050},
  address = {Los Alamitos, CA, USA},
  doi = {http://doi.ieeecomputersociety.org/10.1109/TKDE.2005.127},
  issn = {1041-4347},
  publisher = {IEEE Computer Society}
}

@INPROCEEDINGS{hastings2011,
  author = {Janna Hastings and Oliver Kutz and Till Mossakowski},
  title = {How to model the shapes of molecules? Combining topology and ontology
	using heterogeneous specifications},
  booktitle = {Proceedings of the DKR Challenge Workshop, Banff, Alberta, Canada,
	June 2011.},
  year = {2011}
}

@ARTICLE{kerrien2007,
  author = {S. Kerrien and Y. {Alam-Faruque} and B. Aranda and I. Bancarz and
	A. Bridge and C. Derow and E. Dimmer and M. Feuermann and A. Friedrichsen
	and R. Huntley and C. Kohler and J. Khadake and C. Leroy and A. Liban
	and C. Lieftink and L. {Montecchi-Palazzi} and S. Orchard and J.
	Risse and K. Robbe and B. Roechert and D. Thorneycroft and Y. Zhang
	and R. Apweiler and H. Hermjakob},
  title = {IntAct -- open source resource for molecular interaction data},
  journal = {Nucleic Acids Res.},
  year = {2007},
  volume = {35},
  pages = {D561--D565},
  issue = {(Database issue)}
}

@incollection{lambrix2004,
  author = {Patrick Lambrix},
  title = {Ontologies in Bioinformatics and Systems Biology},
  booktitle = {Artificial Intelligence Methods And Tools For Systems Biology},
  publisher = {Springer Netherlands},
  year = {2004},
  editor = {Dubitzky, Werner and Azuaje, Francisco and Dress, Andreas and Vingron,
	Martin and Myers, Gene and Giegerich, Robert and Fitch, Walter and
	Pevzner, Pavel A.},
  volume = {5},
  series = {Computational Biology},
  pages = {129-145},
  isbn = {978-1-4020-5811-0},
  keyword = {Computer Science}
}

@inproceedings{magka2011,
  author    = {Despoina Magka and Boris Motik and Ian Horrocks},
  title     = {Modelling Structured Domains Using Description Graphs and Logic Programming},
  year = {2012},
  booktitle = {Proceedings of the 9th  Extended Semantic Web Conference (ESWC 2012)},
  location = {Heraklion, Greece},
  note = {Accepted for Publication},

}

@ARTICLE{matthews2009,
  author = {L Matthews and G Gopinath and M Gillespie and M Caudy and D Croft
	and B {de Bono} and P Garapati and J Hemish and H Hermjakob and B
	Jassal and A Kanapin and S Lewis and S Mahajan and B May and E Schmidt
	and I Vastrik and G Wu and E Birney and L Stein and E D'Eustachio},
  title = {Reactome knowledgebase of human biological pathways and processes},
  journal = {Nucleic Acids Res.},
  year = {2009},
  volume = {37},
  pages = {D619--622},
  issue = {(Database issue)}
}

@ARTICLE{mungall2010,
  author = {Christopher J. Mungall and Michael Bada and Tanya Z. Berardini and
	Jennifer Deegan and Amelia Ireland and Midori A. Harris and David
	P. Hill and Jane Lomax},
  title = {Cross-product extensions of the {Gene Ontology}},
  journal = {Journal of Biomedical Informatics},
  doi = {10.1016/j.jbi.2010.02.002},
  issn = {1532-0464}
}

@MISC{owlformat,
  author = {Michael K. Smith and Chris Welty and Deborah L. McGuinness },
  title = {{The Web Ontology Language}},
  year = {2012},
  note = {Last accessed January 2012},
  url = {http://www.w3.org/TR/owl-guide/}
}

@BOOK{sternberg2003,
  title = {Cognitive Psychology},
  publisher = {Thomson Wadsworth},
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  author = {R J Sternberg},
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  booktitle = {Cognitive Psychology}
}

@INPROCEEDINGS{swainston2010,
  author = {Swainston, Neil and Jameson, Daniel and Li, Peter and Spasic, Irena
	and Mendes, Pedro and Paton, Norman W.},
  title = {Integrative information management for systems biology},
  booktitle = {Proceedings of the 7th international conference on Data integration
	in the life sciences},
  year = {2010},
  series = {DILS'10},
  pages = {164--178},
  address = {Berlin, Heidelberg},
  publisher = {Springer-Verlag},
  acmid = {1884495},
  isbn = {3-642-15119-1, 978-3-642-15119-4},
  keywords = {computational systems biology, workflow},
  location = {Gothenburg, Sweden},
  numpages = {15},
  url = {http://dl.acm.org/citation.cfm?id=1884477.1884495}
}

@ARTICLE{go2000,
  author = { {The Gene Ontology Consortium} },
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  issue = {1}
}

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  title = {Chemical graph theory},
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@INPROCEEDINGS{dumontier2007,
  author = {N Villanueva-Rosales and M Dumontier},
  title = {Describing chemical functional groups in {OWL-DL} for the classification
	of chemical compounds},
  booktitle = {Proc. of OWL: Experiences and Directions {(OWLED 2007)}},
  year = {2007}
}

@article{couto2010,
    author = {Ferreira, Jo\~{a}o D. AND Couto, Francisco M.},
    journal = {PLoS Computational Biology},
    publisher = {Public Library of Science},
    title = {Semantic Similarity for Automatic Classification of Chemical Compounds},
    year = {2010},
    month = {09},
    volume = {6},
    pages = {e1000937},
    abstract = {<title>Author Summary</title>
<p>Among the existing systems capable of computationally comparing chemical compounds, the majority use only structural and physicochemical properties. However, with the emergence of ChEBI and other chemical compound databases, it has become feasible to create a system that can use the relevance of compounds in a biological context as well. This setting enables the distinction of molecules with different roles in nature but similar structures, or similar roles and different structures. ChEBI is organized as an ontology that classifies chemical compounds, which we use to derive a semantic similarity measure that reflects the biological relevance of molecules. In an effort to use as much information as possible, we introduce Chym, a system that integrates structural and semantic information in a single hybrid metric, and we show the accuracy of the system in three distinct classification problems, which consist in deciding whether a compound crosses the blood brain barrier, is a P-glycoprotein substrate or an estrogen receptor ligand. Chym outperforms the previous attempts to solve these three problems, with a maximum accuracy of 90.0%.</p>
},
    number = {9},
    doi = {10.1371/journal.pcbi.1000937}
}        

@Article{libiomodels2010,
	author = {C Li and M Donizelli and N Rodriguez and H Dharuri and L Endler and V Chelliah and L Li and E He and A Henry and MI Stefan and JL Snoep and M Hucka and N {Le Nov$\grave{e}$re} and C Laibe},
	title = {BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models},
	year  ={2010},
	journal = {BMC Syst Biol.},
	volume={ 4},
	issue={92}
} 


@inproceedings{horridgeentail09,
	Author = {Matthew Horridge and Bijan Parsia and Ulrike Sattler},
	Booktitle = {16th Automated Reasoning Workshop (ARW 2009)},
	Title = {Computing Explanations for Entailments in Description Logic Based Ontologies},
	Year = {2009}}
	
@inproceedings{batchelor2010,
	  author={Colin Batchelor and Janna Hastings and Christoph Steinbeck},
	  year= 2010,
	  title={Ontological dependence, dispositions and institutional reality in chemistry},
	  booktitle={Proceedings of the 6th Formal Ontology in Information Systems conference},
	  address={Toronto, Canada},
	  editor={Antony Galton and Riichiro Mizoguchi}
}

@inproceedings{VardiModalLogic,
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@misc{librarymcs,
  author = {Miklos Vargyas and Gabor Imre},
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Author = {Boris Motik and Ian Horrocks},
Title = {OWL Datatypes: Design and Implementation},
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Month = {October},
}

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    author = "Boris Motik and Ulrike Sattler and Rudi Studer",
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@Misc{meshUrl,
	author = {NIH NCBI},
	title  = {Medical Subject Headings},
	note = {Last accessed January 2012},
	url = {http://www.ncbi.nlm.nih.gov/mesh}
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@article{lowe2011,
author = {Lowe, Daniel M. and Corbett, Peter T. and Murray-Rust, Peter and Glen, Robert C.},
title = {Chemical Name to Structure: OPSIN, an Open Source Solution},
journal = {Journal of Chemical Information and Modeling},
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eprint = {http://pubs.acs.org/doi/pdf/10.1021/ci100384d}
}

@inproceedings{corbett2008,
	author={Peter Corbett and Colin Batchelor and Anne Copestake}, 
	title={Pyridines, pyridine and pyridine rings: disambiguating chemical name entities}, 
	booktitle={BERBMTM-08 at LREC-2008, Marrakech, Morocco}, 
	year={2008}
} 

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	year  ={2009},
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	and Janna Hastings and Noel {O'Boyle} and 
John Overington and Herman {Van Vlijmen} and Egon Willighagen},
	title = {Cheminformatics: The Computer Science of Chemical Discovery},
	year  = {2012, to appear},
	journal = {Communications of the ACM}
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@Article{chepelevmol2011,
	author = {Leonid L Chepelev and Janna Hastings and Marcus Ennis and Christoph Steinbeck and Michel Dumontier},
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	year  ={2012},
	volume = {13},
	issue = {3},
	journal = {BMC Bioinformatics}
}

@Article{courtotsysbio2011,
	author = {M\'{e}lanie Courtot and Nick Juty and Christian Kn\"{u}pfer and Dagmar Waltemath and Anna Zhukova and Andreas Dr\"{a}ger and Michel Dumontier and Andrew Finney and Martin Golebiewski and Janna Hastings and Stefan Hoops and Sarah Keating and Douglas B Kell and Samuel Kerrien and James Lawson and Allyson Lister and James Lu and Rainer Machne and Pedro Mendes and Matthew Pocock and Nicolas Rodriguez and Alice Villeger and Darren J Wilkinson and Sarala Wimalaratne and Camille Laibe and Michael Hucka and Nicolas Le Nov\`{e}re},
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	year  ={2011},
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title = {Klymollins A--H, Bioactive Eunicellin-Based Diterpenoids from the Formosan Soft Coral Klyxum molle},
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year = {2011},
doi={doi:10.1021/np200589n}
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@book{Frege1884-FREGDA-3,
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    pages={2111--2120}
}

@misc{horridgems2009,
title = {{OWL} 2 Web Ontology Language Manchester Syntax},
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author = {Matthew Horridge and Peter F. {Patel-Schneider}},
year = {2009},
note={Last accessed January 2012}
}

@Misc{smarts2011,
	author = {David Weininger and {Daylight Inc}},
	title  = {The {SM}iles {AR}bitrary {T}arget {S}pecification {(SMARTS)} manual},
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	url = {http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html} 
}

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	author = {K. Schomburg and H.-C. Ehrlich and K. Stierand and M. Rarey},
	title = {From Structure Diagrams to Visual Chemical Patterns},
	year  ={2010},
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	issue = {9},
	pages = {1529--1535}
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@Misc{stevens2011,
	author = {Robert Stevens},
	title  ={An Ontology of the Periodic Table Using electronic structure of the atom},
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@inproceedings{hastingsowled2010,
    author={Janna Hastings and Michel Dumontier and Duncan Hull and Matthew Horridge and Christoph Steinbeck and Ulrike Sattler and Robert Stevens and Tertia H\"{o}rne and Katarina Britz},
    year={2010},
    title={Representing chemicals using {OWL}, description graphs and rules},
    booktitle={Proc. of OWL: Experiences and Directions {(OWLED 2010)}}
} 

@Inproceedings{hastingswomo2011,
	author = {Janna Hastings and Colin Batchelor and Stefan Schulz and Christoph Steinbeck},
	title  = {Modularization requirements in bio-ontologies: A case study of ChEBI},
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@article{simmons2003,
    abstract = {{The indexing and retrieval of Markush structures has always been among the most problematic aspects of patent information and the most expensive. Indexing advanced from the simple classification systems of the 1950s to proprietary fragmentation systems, which were followed in the 1980s by topological systems. The cost of access to the latest indexing systems has varied widely over the years. In spite of improvements in indexing and less restrictive access conditions, comprehensive Markush structure searches remain the sole province of well financed organizations.}},
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@Article{ihlenfeldt2009,
AUTHOR = {Ihlenfeldt, Wolf and Bolton, Evan and Bryant, Stephen},
TITLE = {The PubChem chemical structure sketcher},
JOURNAL = {Journal of Cheminformatics},
VOLUME = {1},
YEAR = {2009},
NUMBER = {1},
PAGES = {20},
URL = {http://www.jcheminf.com/content/1/1/20},
DOI = {10.1186/1758-2946-1-20},
PubMedID = {20298522},
ISSN = {1758-2946},
ABSTRACT = {PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.}
}