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

Robert Hoehndorf; Joshua Bacher; Michael Backhaus; Sergio E. Gregorio; Frank Loebe; Kay Prüfer; Alexandr Uciteli; Johann Visagie; Heinrich Herre; Janet Kelso

doi:10.1186/1471-2105-10-S5-S5

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

Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio, Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

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Abstract

MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns.

RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively.

AVAILABILITY: The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

Original language	English
Article number	S5
Journal	BMC Bioinformatics
Volume	10
Issue number	Supplement 5
DOIs	https://doi.org/10.1186/1471-2105-10-S5-S5
Publication status	Published - 06 May 2009
Event	Proceedings of the Bio-Ontologies Special Interest Group Workshop 2008: Knowledge in Biology - Toronto, Canada Duration: 20 Jul 2008 → 20 Jul 2008

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title = "BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.",

abstract = "MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.",

author = "Robert Hoehndorf and Joshua Bacher and Michael Backhaus and Gregorio, {Sergio E.} and Frank Loebe and Kay Pr{\"u}fer and Alexandr Uciteli and Johann Visagie and Heinrich Herre and Janet Kelso",

note = "Paper presented at: Proceedings of the Bio-Ontologies Special Interest Group Workshop 2008: Knowledge in Biology, Toronto, Canada, 20 July 2008. Editors: Phillip Lord; Nigam Shah; Susanna-Assunta Sansone; Matthew Cockerill; Proceedings of the Bio-Ontologies Special Interest Group Workshop 2008: Knowledge in Biology ; Conference date: 20-07-2008 Through 20-07-2008",

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AU - Hoehndorf, Robert

AU - Bacher, Joshua

AU - Backhaus, Michael

AU - Gregorio, Sergio E.

AU - Loebe, Frank

AU - Prüfer, Kay

AU - Uciteli, Alexandr

AU - Visagie, Johann

AU - Herre, Heinrich

AU - Kelso, Janet

N1 - Paper presented at: Proceedings of the Bio-Ontologies Special Interest Group Workshop 2008: Knowledge in Biology, Toronto, Canada, 20 July 2008. Editors: Phillip Lord; Nigam Shah; Susanna-Assunta Sansone; Matthew Cockerill

PY - 2009/5/6

Y1 - 2009/5/6

N2 - MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

AB - MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

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

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