BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology

BMC Bioinformatics

Volumn 10, Issue SUPPL. 5, 2009, Pages

  Hoehndorf, Robert ^a,b   Bacher, Joshua ^a,b   Backhaus, Michael ^a,b,d   Gregorio Jr , Sergio E ^c   Loebe, Frank ^a   Prüfer, Kay ^b   Uciteli, Alexandr ^a,b   Visagie, Johann ^b   Herre, Heinrich ^a   Kelso, Janet ^b  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^c INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^d UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACK-GROUND KNOWLEDGE; COLLABORATIVE PLATFORM; INTEGRATION OF KNOWLEDGE; LOGIC-BASED APPROACH; ONTOLOGY DEVELOPMENT; RESEARCH COMMUNITIES; SCIENTIFIC COMMUNITY; SEMANTIC WEB TECHNOLOGY;

KNOWLEDGE BASED SYSTEMS;

AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; CONFERENCE PAPER; INFORMATION PROCESSING; INTERNET; KNOWLEDGE BASE; PROCESS DEVELOPMENT; ARTICLE; BIOLOGY; COMPUTER INTERFACE; DATA BASE; INFORMATION RETRIEVAL; METHODOLOGY;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 65549095054     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S5-S5     Document Type: Conference Paper

References (34)

1. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25:25-29. 10.1038/75556 10802651
2. Wang K Gene-function wiki would let biologists pool worldwide resources Nature 2006, 439:7076-534. 10.1038/439534a 16452957
3. Hoehndorf R Prüfer K Backhaus M Herre H Kelso J Loebe F Visagie J A proposal for a gene functions wiki Proceedings of OTM 2006 Workshops, Montpellier, France, Oct 29 - Nov 3, Part I, Workshop Knowledge Systems in Bioinformatics, KSinBIT of Lecture Notes in Computer Science Berlin: Springer Meersman R, Tari Z, Herrero P 2006, 4277:669-678.
4. Giles J Key biology databases go wiki Nature 2007, 445:7129-691. 10.1038/ 445691a 17301755
5. Leuf B Cunningham W The Wiki Way: Collaboration and Sharing on the Internet Reading, Massachusetts: Addison-Wesley 2001.
6. Völkel M Schaffert S (Eds) SemWiki2006 - From Wiki to Semantics: Proceedings of the 1st Workshop on Semantic Wikis, Budva, Montenegro, Jun 12, of CEUR Workshop Proceedings Aachen, Germany: CEUR-WS.org 2006, 206.
7. Sirin E Parsia B Pellet: An OWL DL Reasoner Proceedings of the 2004 International Workshop on Description Logics, DL Whistler, British Columbia, Canada, Jun 6-8, of CEUR Workshop Proceedings Aachen, Germany: CEUR-WS.org Haarslev V, Möller R 2004, 104:212-213.
8. McGuinness DL van Harmelen F OWL Web Ontology Language Overview W3C Recommendation, World Wide Web Consortium (W3C) 2004.
9. Steup M The Analysis of Knowledge The Stanford Encyclopedia of Philosophy, Fall 2008 edition Stanford, California: Stanford University, Center for the Study of Language and Information (CSLI) Zalta EN 2008.
10. MediaWiki http://www.mediawiki.org
11. Krötzsch M Vrandečić D Völkel M Haller H Studer R Semantic Wikipedia Web Semantics: Science, Services and Agents on the World Wide Web 2007, 5(4)251-261. 10.1016/j.websem.2007.09.001
12. Backhaus M Kelso J Bacher J Herre H Hoehndorf R Loebe F Visagie J BOWiki - a collaborative annotation and ontology curation framework Proceedings of the Workshop on Social and Collaborative Construction of Structured Knowledge, CKC Banff, Canada, May 8, of CEUR Workshop Proceedings Aachen, Germany: CEUR-WS.org Noy N, Alani H, Stumme G, Mika P, Sure Y, Vrandecic D 2007, 273.
13. Valente A Breuker J Towards principled core ontologies Proceedings of the 10th Knowledge Acquisition Workshop, KAW'96, Banff, Alberta, Canada, Nov 9-14 Gaines BR, Musen MA 1996, 301-320.
14. Hoehndorf R Loebe F Kelso J Herre H Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies BMC Bioinformatics 2007, 8:377. 2180186 17925014 10.1186/1471-2105-8-377
15. Schulz S Beisswanger E Wermter J Hahn U Towards an Upper-Level Ontology for Molecular Biology AMIA Annu Symp Proc 2006 2006, 694-698.
16. Smith B Ashburner M Rosse C Bard J Bug W Ceusters W Goldberg LJ Eilbeck K Ireland A Mungall CJ Leontis N Rocca-Serra P Ruttenberg A Sansone SA Scheuermann RH Shah N Whetzel PL Lewis S The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration Nat Biotech 2007, 25(11):1251-1255. 10.1038/nbt1346
17. Horrocks I OBO Flat File Format Syntax and Semantics and Mapping to OWL Web Ontology Language http://www.cs.man.ac.uk/%7Ehorrocks/obo/
18. Loebe F Abstract vs. social roles - Towards a general theoretical account of roles Applied Ontology 2007, 2(2)127-158.
19. Hill DP Blake JA Richardson JE Ringwald M Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies Genome Res 2002, 12(12):1982-1991. 187579 12466303 10.1101/ gr.580102
20. Grenon P Smith B Goldberg L Biodynamic Ontology: Applying BFO in the Biomedial Domain Ontologies in Medicine, of Studies in Health Technology and Informatics Amsterdam: IOS Press Pisanelli DM 2004, 102:20-38.
21. Masolo C Borgo S Gangemi A Guarino N Oltramari A WonderWeb Deliverable D18: Ontology Library (final) Tech rep Laboratory for Applied Ontology, ISTC-CNR, Trento, Italy 2003.
22. Noy N Rector A Defining N-ary Relations on the Semantic Web W3C Working group note, World Wide Web Consortium (W3C) 2006.
23. Loebe F Herre H Formal Semantics and Ontologies: Towards an Ontological Account of Formal Semantics Formal Ontology in Information Systems: Proceedings of the 5th International Conference, FOIS Saarbrücken, Germany, Oct 31-Nov 3, of Frontiers in Artificial Intelligence Amsterdam: IOS Press Eschenbach C, Grüninger M 2008, 183:49-62.
24. Baader F Calvanese D McGuinness D Nardi D Patel-Schneider P (Eds) The Description Logic Handbook: Theory, Implementation and Applications Cambridge, UK: Cambridge University Press 2003.
25. Bechhofer S The DIG Description Logic Interface: DIG/1.1 Tech rep University of Manchester 2003.
26. Carroll JJ Dickinson I Dollin C Reynolds D Seaborne A Wilkinson K Jena: Implementing the Semantic Web Recommendations Tech Rep HPL-2003-146 Hewlett Packard, Bristol, UK 2003.
27. Sirin E Parsia B Cuenca Grau B Kalyanpur A Katz Y Pellet: A practical OWL-DL reasoner Web Semantics: Science, Services and Agents on the World Wide Web 2007, 5(2):51-53. 10.1016/j.websem.2007.03.004
28. Donini FM Nardi D Rosati R Autoepistemic Description Logics Proceedings of the Fifteenth International Joint Conference on Artificial Intelligence, IJCAI Nagoya, Japan, Aug 23-29 San Francisco: Morgan Kaufmann Pollack ME 1997, 1:136-141.
29. Reiter R A logic for default reasoning Artificial Intelligence 1980, 13(1-2):81-132. 10.1016/0004-3702(80)90014-4
30. Grimm S Motik B Closed World Reasoning in the Semantic Web through Epistemic Operators Proceedings of the Workshop on OWL: Experiences and Directions, OWLED Galway, Ireland, Nov 11-12, of CEUR Workshop Proceedings Aachen, Germany: CEUR-WS.org Cuenca Grau B, Horrocks I, Parsia B, Patel-Schneider P 2005, 188.
31. Motik B Cuenca Grau B Horrocks I Wu Z Fokoue A Lutz C OWL 2 Web Ontology Language: Profiles W3C Working draft, World Wide Web Consortium (W3C) 2008.
32. Boeckmann B Bairoch A Apweiler R Blatter MC Estreicher A Gasteiger E Martin MJ Michoud K O'Donovan C Phan I et al The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res 2003, 31:365-370. 165542 12520024 10.1093/nar/gkg095
33. Humphreys BL Lindberg DAB Schoolman HM Barnett GO The Unified Medical Language System: An informatics research collaboration J Am Med Inform Assoc 1998, 5(1):11. 61271 9452981
34. Schaffert S IkeWiki: A Semantic Wiki for Collaborative Knowledge Management Proceedings of the 1st International Workshop on Semantic Technologies in Collaborative Applications, STICA Manchester, UK, Jun 26-28 Los Alamitos, California: IEEE Computer Society 2006, 388:396.