OntoFox: web-based support for ontology reuse
Tóm tắt
Từ khóa
Tài liệu tham khảo
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038/75556.
Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in biomedical ontologies. Genome Biol. 2005, 6 (5): R46-10.1186/gb-2005-6-5-r46.
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25 (11): 1251-1255. 10.1038/nbt1346.
The PubMed database. [ http://www.ncbi.nlm.nih.gov/pubmed/ ]
Spasic I, Ananiadou S, McNaught J, Kumar A: Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform. 2005, 6 (3): 239-251. 10.1093/bib/6.3.239.
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. 10.1093/bib/bbp004.
Pathak J, Johnson TM, Chute CG: Survey of modular ontology techniques and their applications in the biomedical domain. Integrated Computer-Aided Engineering. 2009, 16 (3): 225-242.
Grau BC, Horrocks I, Kazakov Y, Sattler U: Modular Reuse of Ontologies: Theory and Practice. Journal of Artificial Intelligence Research. 2008, 31: 273-318.
He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C: VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO 2009) Nature Precedings. 2009, Buffalo, NY, USA, July 24-26, 2009 2009, [ http://precedings.nature.com/documents/3553/version/1 ]
OWL 2 Web Ontology Language document overview. [ http://www.w3.org/TR/2009/REC-owl2-overview-20091027/ ]
The protege ontology editor. [ http://protege.stanford.edu/ ]
Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y: Pellet: A practical OWL-DL reasoner. Web Semant. 2007, 5: 51-53.
Tsarkov D, Horrocks I: FaCT++ Description Logic Reasoner: System Description. Proc of the Int Joint Conf on Automated Reasoning (IJCAR 2006). 2006, 292-297. 4130 of Lecture Notes in Artificial Intelligence
Courtot M, Gibson F, Lister A, Malone J, Schober D, Brinkman R, Ruttenberg A: MIREOT: the Minimum Information to Reference an External Ontology Term. The 1st International Conference on Biomedical Ontology (ICBO 2009). 2009, Buffalo, NY, USA
Grau BC, Horrocks I, Kazakov Y, Sattler U: Just the right amount: extracting modules from ontologies. Proceedings of the 16th international conference on World Wide Web. 2007, 717-726. full_text.
Jiménez-Ruiz E, Grau BC, Sattler U, Schneider T, Llavori RB: Safe and Economic Re-Use of Ontologies: A Logic-Based Methodology and Tool Support. Proceedings of the European Semantic Web Conference. 2008, 5021: 185-199.
Seidenberg J, Rector A: Web ontology segmentation: analysis, classification and use. Proceedings of the 15th international conference on World Wide Web. 2006, 13-22. full_text.
Crau BC, Horrocks I, Kazakov Y, Sattler U: Extracting modules from ontologies: a logic-based approach. Modular Ontologies LNCS 5445. 2009, Edited by Stuckenschmidt H: Springer-Verlag Berlin Heidelberg, 159-186.
Doran P, Tamma V, Iannone L: Ontology Module Extraction for Ontology Reuse: An Ontology Engineering Perspective. CIKM'07, November 6-8: 2007. 2007, Lisboa, Portugal
Kontchakov R, Pulina L, Sattler U, Schneider T, Selmer P, Wolter F, Zakharyaschev M: Minimal Module Extraction from DL-Lite Ontologies using QBF Solvers. Proceedings of IJCAI-09 2009; Pasadena. 2009, 836-841.
Noy NF, Musen MA: Specifying ontology views by traversal. Third International Conference on the Semantic Web (ISWC-2004): 2004. 2004, Hisroshima, Japan
Grau BC, Horrocks I, Kazakov Y, Sattler U: Extracting modules from ontologies: a logic-based approach. Modular Ontologies LNCS 5445. 2009, Editedd by Stuckenschmidt H: Springer-Verlag Berlin Heidelberg, 159-186. full_text.
Courtot M, Gibson F, Lister A, Malone J, Schober D, Brinkman R, Ruttenberg A: MIREOT: the Minimum Information to Reference an External Ontology Term. Submitted. 2010
SPARQL queries template file. Retrieved December 2, 2009, [ http://obi.svn.sourceforge.net/svnroot/obi/trunk/src/tools/build/external-templates.txt ]
RDF/XML syntax specification. [ http://www.w3.org/TR/rdf-syntax-grammar/ ]
SPARQL query language for RDF. [ http://www.w3.org/TR/rdf-sparql-query/ ]
Pressman RS: Software Engineering a Practitioner's Approach. 2001, McGraw-Hill Higher Education, Princeton, New Jersey, 5
Information Artifact Ontology. [ http://code.google.com/p/information-artifact-ontology/ ]
CBD - Concise Bounded Description. [ http://www.w3.org/Submission/CBD/ ]
PATO - Phenotypic Quality Ontology. [ http://obofoundry.org/wiki/index.php/PATO:Main_Page ]
Smith CL, Goldsmith CA, Eppig JT: The Mammalian Phenotype Ontology as a tool for annotating analyzing and comparing phenotypic information. Genome Biol. 2005, 6 (1): R7-10.1186/gb-2004-6-1-r7.