The use of web ontology languages and other semantic web tools in drug discovery

Bibliography

• Goble C, Stevens R. State of the nation in data integration for bioinformatics. J Biomed Inform 2008;41:687-93
   PubMed Web of Science ®Google Scholar
• Stein LD. Integrating biological databases. Nat Rev Genet 2003;4:337-45
   PubMed Web of Science ®Google Scholar
• Hey T, Trefethen AE. Cyberinfrastructure for e-Science. Science 2005;308:817-21
   PubMed Web of Science ®Google Scholar
• Stevens RD, Robinson AJ, Goble CA. Goble myGrid: personalised bioinformatics on the information grid. Bioinformatics 2003;19(Suppl 1):i302-4
   PubMedGoogle Scholar
• Berners-Lee T, Handler J, Lassila O. The semantic web. Scientific American; 2001
   Google Scholar
• Lee Feigenbaum, Ivan Herman, Tonya Hongsermeier, The semantic web in action. Scientific American Magazine; December 2007
   Google Scholar
• N Shadbolt, W Hall, T Berners-Lee. The semantic web revisited. IEEE intelligent systems; 2006
   Google Scholar
• RDF: Resource Description Framework. Available from: http://www.w3.org/RDF/
   Google Scholar
• OWL: Web Ontology Language. Available from: http://www.w3.org/TR/owl-features/
   Google Scholar
• Neumann EK. A life science semantic web: are we there yet? Sci STKE 2005;283:22-5
   Google Scholar
• Neumann EK, Miller E, Wilbanks J. What the semantic web could do for the life sciences. Drug Discov Today: BIOSILICO 2006;2:228-34
   Google Scholar
• Ruttenberg A, Clark T, Bug W, Advancing translational research with the semantic web. BMC Bioinformatics 2007;8(Suppl 3):S2
   PubMedGoogle Scholar
• Wang X, Gorlitsky R, Almeida JS. From XML to RDF: how semantic web technologies will change the design of omic standards. Nat Biotechnol 2005;23:1099-103
   PubMed Web of Science ®Google Scholar
• Golbreich C. OBO and OWL: leveraging semantic web technologies for the life sciences. In: Proceedings of the International Semantic Web Conference; 2007
   Google Scholar
• World Wide Web Consortium. Available from: http://www.w3.org
   Google Scholar
• W3C Health Care and Life Sciences Interest Group. Available from: http://www.w3.org/2001/sw/HCLS
   Google Scholar
• Jentzsch A, Zhao J, Hassanzadeh O, Linking Open Drug Data. Triplification Challenge; 2009
   Google Scholar
• Denney C, Batchelor C, Bodenreider O, Creating a Translational Medicine Ontology. International Conference on Biomedical Ontology, 24 July 2009
   Google Scholar
• Adida B, Birbeck M. RDFa primer 1.0: Embedding rdf in XHTML
   Google Scholar
• Connolly D. Gleaning resource descriptions from dialects of languages (GRDDL). W3C Candidate Recommendation; 2007
   Google Scholar
• Horrocks I, Patel-Schneider PF, van Harmelen F. From SHIQ and RDF to OWL: the making of a web ontology language. J Web Semant 2003;1:7-26
   Google Scholar
• SKOS: Simple Knowledge Organization for the Web. Available from: http://www.w3.org/2004/02/skos/intro
   Google Scholar
• Bodenreider O, Stevens R. Bio-ontologies: current trends and future directions. Brief Bioinform 2006;7(3):256-74
   PubMed Web of Science ®Google Scholar
• Stevens R, Goble CA, Bechhofer S. Ontology-based knowledge representation for bioinformatics. Brief Bioinform 2000;1(4):398-416
   PubMedGoogle Scholar
• Daniel LR, Nigam HS, Natalya F. Biomedical ontologies: a functional perspective. Brief Bioinform 9(1):75-90
   PubMed Web of Science ®Google Scholar
• Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res 2006;34(Database issue):D322-6
   PubMedGoogle Scholar
• Whetzel PL, Parkinson H, Causton HC, The MGED ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 2006;22(7):866-73
   PubMed Web of Science ®Google Scholar
• Huq SZ, Karras BT. A proposed ontology for online healthcare surveys. AMIA Annu Symp Proc 2003;304-9
   PubMedGoogle Scholar
• Ma J. Building an ontology-driven database for clinical immune research. AMIA Annu Symp Proc 2006;1018
   PubMedGoogle Scholar
• National Center for Biomedical Ontology. Available from: http://bioontology.org/
   Google Scholar
• Pierre G, Barry S, Louis G. Biodynamic ontology: applying BFO in the biomedical domain. Ontologies in Medicine, Amsterdam; 2004. p.20-38
   Google Scholar
• Beißwanger E, Schulz S, Stenzhorn H, Hahn U. BioTop: an upper domain ontology for the life sciences – A description of its current structure, contents, and interfaces to OBO ontologies in applied ontology, Amsterdam, The Netherlands. IOS Press 2008;3(4):205-12
   Google Scholar
• Disease ontology. Available from: http://do-wiki.nubic.northwestern.edu/index.php/Main_Page
   Google Scholar
• de Matos P, Alcántara R, Dekker A, Chemical entities of biological interest: an update. Nucleic Acids Res 2009. In press
   Google Scholar
• Luciano JS, Stevens RD. e-Science and biological pathway semantics. BMC Bioinformatics 2007;8(Suppl 3):S3
   PubMedGoogle Scholar
• Coulet A, Smaïl-Tabbone M, Napoli A, Devignes M-D. Suggested Ontology for Pharmacogenomics (SO-Pharm): modular construction and preliminary testing. Lect Notes Comput Sci 2006;4277:648-57
   Google Scholar
• Eilbeck K, Lewis SE, Mungall CJ, The sequence ontology: a tool for the unification of genome annotations. Genome Biol 2005;6(5):R44
   PubMedGoogle Scholar
• Grenon P, Smith B, Goldberg L. Biodynamic ontology: applying BFO in the biomedical domain. Ontologies in Medicine, Amsterdam 2004, 20-38
   Google Scholar
• Shankar RD, Martins SB, O'Connor MJ, Epoch: an ontological framework to support clinical trials management. In HIKM '06: Proceedings of the international workshop on Healthcare information and knowledge management, New York, NY, USA; ACM Press; 2006. p. 25-32
   Google Scholar
• Courtot M, Bug W, Gibson F, OWL of Biomedical Investigations, OWLED; 2008
   Google Scholar
• Ontology for Drug Discovery Investigations (DDI). Available from: http://users.aber.ac.uk/ddq/ddi/wiki/index.php
   Google Scholar
• Clark T, Ocana M, Systems B. Semantic Web Applications in Neuromedicine (SWAN) ontology. W3C working note. Available from: http://www.w3.org/TR/hcls-swan/
   Google Scholar
• Rosse C, Mejino JLV. The Foundational Model of Anatomy Ontology. In: Burger A, Davidson D, Baldock R, editors, Anatomy Ontologies for bioinformatics: principles and practice. Volume 6. Springer, London; 2007. p. 59-117
   Google Scholar
• Infectious Disease Ontology (IDO). Available from: http://www.infectiousdiseaseontology.org/Home.html
   Google Scholar
• Vaccine Ontology. Available from: http://www.violinet.org/vaccineontology/
   Google Scholar
• Cheung KH, Yip KY, Townsend JP, Scotch M. HCLS 2.0/3.0: health care and life sciences data mashup using web 2.0/3.0. J Biomed Inform 2008;41(5):694-705
   PubMed Web of Science ®Google Scholar
• Mirhaji P, Zhu M, Vagnoni M, Ontology driven integration platform for clinical and translational research. BMC Bioinformatics 2009;10(Suppl 2):S2
   PubMedGoogle Scholar
• Ruttenberg A, Rees JA, Samwald M, Marshall MS. Life sciences on the semantic web: the neurocommons and beyond. Brief Bioinform 2009;10(2):193-204
   PubMed Web of Science ®Google Scholar
• Linked data project. Available from: http://linkeddata.org/
   Google Scholar
• Jentzsch A, Andersson B, Hassanzadeh O, Enabling tailored therapeutics with linked data. Proceedings of the WWW2009 workshop on Linked Data on the Web (LDOW2009)
   Google Scholar
• Fang Y-C, Huang H-C, Chen H-H, Juan H-F. TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. BMC Complemeny Altern Med 2008;8(1):58
   PubMedGoogle Scholar
• Diseasome. Available from: http://www4.wiwiss.fu-berlin.de/diseasome/
   Google Scholar
• Bizer C, Cyganiak R. D2R server – publishing relational databases on the semantic web. Poster at the 5th International Semantic Web Conference; 2006
   Google Scholar
• Belleau F, Nolin M-A, Tourigny N, Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008;41:706-16
   PubMed Web of Science ®Google Scholar
• Volz J, Bizer C, Gaedke M, Kobilarov G. Silk – a link discovery framework for the web of data. In: Linked Data on the Web workshop at WWW2009; 2009
   Google Scholar
• Hassanzadeh O, Xin R, Miller RJ, Linkage query writer. To appear in Proceedings of the 35th International Conference on Very Large Data Bases (VLDB 2009) – Demonstrations Track; 2009
   Google Scholar
• Lam HY, Marenco L, Clark T, AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 2007;8(Suppl 3):S4
   PubMedGoogle Scholar
• Neumann EK, Quan D. BioDash: a semantic web dashboard for drug development. Pac Symp Biocomput 2006:176-87
   PubMedGoogle Scholar
• RDFa. Available from: http://www.w3.org/TR/xhtml-rdfa-primer/
   Google Scholar
• Holford ME, Rajeevan H, Zhao H, Semantic web-based integration of cancer pathways and allele frequency data. Cancer Inform 2009;8:19-30
   PubMedGoogle Scholar
• Stephens S, Morales A, Quinlan M. Applying semantic web technologies to drug safety determination. IEEE Intell Syst 2006;21:82-6
   Web of Science ®Google Scholar
• Antezana E, Blondé W, Egaña M, BioGateway: a semantic systems biology tool for the life sciences. BMC Bioinformatics 2009;10(Suppl 10):S11
   PubMedGoogle Scholar
• LarKC. Available from: http://www.larkc.eu/
   Google Scholar
• Cheung KH, Yip KY, Smith A, YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics 2005;21(Suppl 1):i85-96
   PubMedGoogle Scholar
• Samwald M, Lim E, Masiar P, Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research. Stud Health Technol Inform 2009;150:317-21
   PubMedGoogle Scholar
• Stollberg M, Haller A. Semantic web services tutorial. In Proceedings of ICWS'2005
   Google Scholar
• Qu C, Zimmermann F, Kumpf K, Semantics-enabled service discovery framework in the SIMDAT pharma grid. IEEE Trans Inf Technol Biomed 2008;12(2):182-90
   PubMed Web of Science ®Google Scholar
• Wolstencroft K, Alper P, Hull D, The myGrid ontology: bioinformatics service discovery. Int J Bioinform Res Appl 2007;3(3):303-25
   PubMedGoogle Scholar
• Yip KY, Qi P, Schultz M, SemBiosphere: a semantic web approach to recommending microarray clustering services. Pac Symp Biocomput 2006:188-99
   PubMedGoogle Scholar
• DiBernardo M, Pottinger R, Wilkinson M. Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. J Biomed Inform 2008;41(5):837-47
   PubMed Web of Science ®Google Scholar
• Wilkinson M, Schoof H, Ernst R, Haase D. BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case. Plant Physiol 2005;138(1):5-17
   PubMedGoogle Scholar
• Lamprecht AL, Margaria T, Steffen B. Bio-jETI: a framework for semantics-based service composition. BMC Bioinformatics 2009;10(Suppl 10):S8
   PubMedGoogle Scholar
• Tsiknakis M, Brochhausen M, Nabrzyski J, A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of postgenomic clinical trials on cancer. IEEE Trans Inf Technol Biomed 2008;12(2):205-17
   PubMed Web of Science ®Google Scholar
• Hoehndorf R, Bacher J, Backhaus M, BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics 2009;10(Suppl 5):S5
   PubMedGoogle Scholar
• Chen H, Ding L, Wu Z, Semantic web for integrated network analysis in biomedicine. Brief Bioinform 10(2):177-192 (2009)
   PubMed Web of Science ®Google Scholar
• Ding L, Pan R, Finin T, Finding and ranking knowledge on the semantic web. In: Proceedings of the International SemanticWeb Conference; 2005. p. 156-170
   Google Scholar
• Mukherjea S. Information retrieval and knowledge discovery utilising a biomedical semantic web. Brief Bioinform 2005;6:252-62
   PubMed Web of Science ®Google Scholar
• Gudivada RC, Qu XA, Jegga AG, A genome-phenome integrated approach for mining disease-causal genes using semantic web. In: Proceedings of the WWW2007 Workshop on Health Care and Life Science Data Integration for the Semantic Web; 2007
   Google Scholar
• Robinson PN, Köhler S, Bauer S, The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet 2008; 83(5):610-5
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Hattori M, From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006;34:354-7
   PubMed Web of Science ®Google Scholar
• Karp PD, Ouzounis CA, Moore-Kochlacs C, Expansion of the Bio-Cyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005;33:6083-9
   PubMed Web of Science ®Google Scholar
• Hamosh A, Scott AF, Amberger JS, Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:514-7
   PubMed Web of Science ®Google Scholar
• Lauren Eric Kriege. Jablonski's dictionary of syndromes and eponymic diseases. 2nd edition. Yale J Biol Med 1991;64(5):544
   Google Scholar
• Bhuvan B, Sougata M. Utilizing resource importance for ranking semantic web query results. In: Proceedings of the International Workshop on Semantic Web and Database; 2005
   Google Scholar
• Kleinberg JM. Authoritative sources in a hyperlinked environment. JACM 1999;46:604-32
   Web of Science ®Google Scholar
• Anyanwu K, Maduko A, Sheth A. Semrank: ranking complex relationship search results on the semantic web. In: Proceedings of the World Wide Web Conference; 2005. p. 117-27
   Google Scholar
• Dhanapalan L, Chen JY. A case study of integrating protein interaction data using semantic web technology. J Bioinform Res Appl 2007;3(3):286-302
   PubMedGoogle Scholar
• Chen JY, Zhong Y, Changyu S, A systems biology approach to the study of cisplatin drug resistance in ovarian cancers. J Bioinform Comput Biol 2007;5:383-405
   PubMedGoogle Scholar
• Tong Y, Chen H. Semantic graph mining for biomedical network analysis. In: Proceedings of the WWW Workshop on Semantic Web for Health Care and life Science; 2008
   Google Scholar
• Dietze H, Schroeder M. GoWeb: a semantic search engine for the life science web. BMC Bioinformatics 2009;10(Suppl 10):S7
   PubMedGoogle Scholar
• Qu XA, Gudivada RC, Jegga AG, Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. BMC Bioinformatics 2009;10(Suppl 5):S4
   PubMedGoogle Scholar
• Good BM, Wilkinson MD. The life sciences semantic web is full of creeps! Brief Bioinform 2006;7(3):275-86
   PubMed Web of Science ®Google Scholar
• SPARQL query language for RDF. Available from: http://www.w3.org/TR/rdf-sparql-query/
   Google Scholar
• Rajeevan H, Osier MV, Cheung KH, ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Res 2003;31(1):270-1
   PubMed Web of Science ®Google Scholar
• Joshi-Tope G, Gillespie M, Vastrik I, Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 30 2005;33:428-32
   PubMed Web of Science ®Google Scholar