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Please cite the following reference for your Ontodog use: 

Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu008. [PDF]

More Ontodog reference:

Zheng J, Xiang Z, Stoeckert C, He Y. Ontodog: A Web-based Ontology Community View Generator. International Conference on Biomedical Ontologies (ICBO 2012), University of Graz, Austria, July 2012. [One page abstract][Poster].


Related References:

Zheng J, Manduchi E, Stoeckert CJ Jr. Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations. International Conference on Biomedical Ontologies (ICBO 2013), Montreal, Canada, July 8-9, 2013.

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. [PMID: 20569493].

Courtot M, Gibson F, Lister AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. MIREOT: the Minimum Information to Reference an External Ontology Term. ICBO 2009.

MIREOT (Minimal information to reference external ontology terms): http://obi-ontology.org/page/MIREOT.

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.

Stuckenschmidt, Heiner; Parent, Christine; Spaccapietra, Stefano (Eds.). Modular Ontologies, Concepts, Theories and Techniques for Knowledge Modularization. In Lecture Notes in Computer Science (LNCS) Vol. 5445. 2009. Springer. ISBN 978-3-642-01906-7.