strucontjcheminf.bib

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@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}
}

@TECHREPORT{magka2011,
  author = {Despoina Magka and Boris Motik and Ian Horrocks},
  title = {Modelling Structured Domains Using Description Graphs and Logic Programming},
  institution = {Department of Computer Science, University of Oxford},
  year = {2011}
}

@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 = {2011},
  note = {Last accessed September 2011},
  url = {http://www.w3.org/TR/owl-guide/}
}

@BOOK{sternberg2003,
  title = {Cognitive Psychology},
  publisher = {Thomson Wadsworth},
  year = {2003},
  author = {R J Sternberg},
  address = {Belmont, CA, USA},
  edition = {3rd},
  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} },
  title = {Gene ontology: tool for the unification of biology},
  journal = {Nature Genetics},
  year = {2000},
  volume = {25},
  pages = {25--9},
  issue = {1}
}

@BOOK{trinajstic1992,
  title = {Chemical graph theory},
  publisher = {CRC Press},
  year = {1992},
  author = {Nenad Trinajstic},
  address = {Florida, USA}
}

@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,
  author    = {Moshe Y. Vardi},
  title     = {Why is Modal Logic So Robustly Decidable?},
  booktitle = {Descriptive Complexity and Finite Models},
  year      = {1996},
  pages     = {149-184},
  crossref  = {DBLP:conf/dimacs/1996},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@proceedings{DBLP:conf/dimacs/1996,
  editor    = {Neil Immerman and
               Phokion G. Kolaitis},
  title     = {Descriptive Complexity and Finite Models, Proceedings of
               a DIMACS Workshop, January 14-17, 1996, Princeton University},
  booktitle = {Descriptive Complexity and Finite Models},
  publisher = {American Mathematical Society},
  series    = {DIMACS Series in Discrete Mathematics and Theoretical Computer
               Science},
  volume    = {31},
  year      = {1996},
  isbn      = {0-8218-0517-7},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{OWL2NextStep,
  author    = {Bernardo Cuenca Grau and Ian Horrocks and Boris Motik and Bijan Parsia and Peter F. Patel-Schneider and Ulrike Sattler},
  title     = {{OWL} 2: The next step for {OWL}},
  journal   = {J. Web Sem.},
  volume    = {6},
  number    = {4},
  year      = {2008},
  pages     = {309-322},
  ee        = {http://dx.doi.org/10.1016/j.websem.2008.05.001},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
	
@book{Todeschini2000,
author = {Todeschini, Roberto and Consonni, Viviana},
booktitle = {New York},
doi = {10.1002/9783527613106},
editor = {Todeschini, Roberto and Consonni, Viviana},
isbn = {3527299130},
issn = {35229913},
pages = {688},
publisher = {Wiley-VCH},
series = {Methods and Principles in Medicinal Chemistry},
title = {{Handbook of Molecular Descriptors}},
url = {http://surplus.cilea.it/bicocca-demo/oa/handle/10281/1964},
volume = {11},
year = {2000}
}

@misc{librarymcs,
  author = {Miklos Vargyas and Gabor Imre},
  title = {{ChemAxon Library MCS}},
  howpublished = "\url{http://www.chemaxon.com/shared/libMCS/}",
  year = {2008}, 
  note = "[Online]"
}

@article{Schuffenhauer2007,
author = {Schuffenhauer, Ansgar and Ertl, Peter and Roggo, Silvio and Wetzel, Stefan and Koch, Marcus a and Waldmann, Herbert},
doi = {10.1021/ci600338x},
issn = {1549-9596},
journal = {Journal of chemical information and modeling},
keywords = {Classification,Databases, Factual,Ligands,Molecular Structure,Organic Chemicals,Organic Chemicals: chemistry,Pesticides,Pyruvate Kinase},
number = {1},
pages = {47--58},
pmid = {17238248},
title = {{The scaffold tree--visualization of the scaffold universe by hierarchical scaffold classification.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17238248},
volume = {47},
year = {2007}
}

@article{Adamson1981,
author = {Adamson, G.W. and Bawden, D.},
journal = {Journal of Chemical Information and Computer Sciences},
number = {4},
pages = {204--209},
publisher = {ACS Publications},
title = {{Comparison of hierarchical cluster analysis techniques for automatic classification of chemical structures}},
url = {http://pubs.acs.org/doi/abs/10.1021/ci00032a005},
volume = {21},
year = {1981}
}

@inproceedings{Motik2008,
Author = {Boris Motik and Ian Horrocks},
Title = {OWL Datatypes: Design and Implementation},
Booktitle = {7th International Semantic Web Conference (ISWC2008)},
Year = {2008},
Month = {October},
}

 @Article{DLSafeBoris,
    author = "Boris Motik and Ulrike Sattler and Rudi Studer",
    title = "{Query Answering for OWL-DL with Rules}",
    journal = "Journal of Web Semantics: Science, Services and Agents on the World Wide Web",
    year = "2005",
    volume = "3",
    number = "1",
    pages = "41--60",
}

@Article{mghs09graphs-journal,
    author = "Boris Motik and Bernardo Cuenca Grau and Ian Horrocks and Ulrike Sattler",
    title = "{Representing Ontologies Using Description Logics, Description Graphs, and Rules}",
    journal = "Artificial Intelligence",
    year = "2009",
    volume = "173",
    number = "14",
    pages = "1275--1309",
}
	
	
@Misc{meshUrl,
	author = {NIH NCBI},
	title  = {Medical Subject Headings},
	note = {Last accessed September 2011},
	url = {http://www.ncbi.nlm.nih.gov/mesh}
}	


@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},
volume = {51},
number = {3},
pages = {739-753},
year = {2011},
doi = {10.1021/ci100384d},
URL = {http://pubs.acs.org/doi/abs/10.1021/ci100384d},
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}
}