References and Links

Many references have been used for Ontobee development or are related to Ontobee. Many web links also exist. This web page provides the paper reference you can use to cite Ontobee, references related to Ontobee, and many useful web links:

Please cite Ontobee with the following reference:

• Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: A Linked Data Server and Browser for Ontology Terms. Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), July 28-30, 2011, Buffalo, NY, USA. Pages 279-281. URL: http://ceur-ws.org/Vol-833/paper48.pdf.

OBO Foundry documents:

• The ontologies.txt: http://obo.cvs.sourceforge.net/viewvc/obo/obo/website/cgi-bin/ontologies.txt
• Configuration of the OBO PURL domain: https://code.google.com/p/obo-foundry-operations-committee/wiki/OBOPURLDomain
• HOWTO request a prefix and domain for a new resource: https://code.google.com/p/obo-foundry-operations-committee/wiki/Policy_for_OBO_namespace_and_associated_PURL_requests
• Setting up Protege to work with OBO ontologies: https://code.google.com/p/obo-foundry-operations-committee/wiki/SettingUpProtege
• OBO Foundry Operations Committee: http://code.google.com/p/obo-foundry-operations-committee/

W3C web references:

• W3C OWL 2: http://www.w3.org/TR/owl2-overview/
• W3C RDF: http://www.w3.org/RDF/
• W3C SPARQL: http://www.w3.org/TR/rdf-sparql-query/

Biomedical Ontologies:

• Ontologies in OBO Foundry: http://www.obofoundry.org
• OBI: Ontology for Biomedical Investigations: http://obi-ontology.org
• VO: Vaccine Ontology: http://www.violinet.org/vaccineontology
• Ontologies supported by Ontobee: http://www.ontobee.org/index.php.

Related Tools:

• Protege ontology editor: http://protege.stanford.edu/
• NCBO BioPortal: http://bioportal.bioontology.org/
• Linked Data Browsers: http://en.wikipedia.org/wiki/Linked_Data#Browsers

Other related paper references:

• Courtot M, Bug W, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. The OWL of Biomedical Investigations. OWLED 2008.
• Ruttenberg A, Rees JA, Samwald M, Marshall MS. Life sciences on the Semantic Web: the Neurocommons and beyond. Brief Bioinform. 2009 Mar;10(2):193-204. PMID: 19282504.
• Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25 (11): 1251-5. PMID 17989687.

Note: Please let us know if you want to recommend some other related information in this web page. Thanks.