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Items: 20

1.

Uberon, an integrative multi-species anatomy ontology.

Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA.

Genome Biol. 2012 Jan 31;13(1):R5. doi: 10.1186/gb-2012-13-1-r5.

2.

Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community.

Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW.

BMC Bioinformatics. 2011 Jan 24;12:32. doi: 10.1186/1471-2105-12-32.

3.

The human phenotype ontology.

Robinson PN, Mundlos S.

Clin Genet. 2010 Jun;77(6):525-34. doi: 10.1111/j.1399-0004.2010.01436.x. Review.

PMID:
20412080
4.

Cross-product extensions of the Gene Ontology.

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J.

J Biomed Inform. 2011 Feb;44(1):80-6. doi: 10.1016/j.jbi.2010.02.002.

5.

Integrating phenotype ontologies across multiple species.

Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M.

Genome Biol. 2010 Jan 8;11(1):R2. doi: 10.1186/gb-2010-11-1-r2.

6.

Linking human diseases to animal models using ontology-based phenotype annotation.

Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE.

PLoS Biol. 2009 Nov;7(11):e1000247. doi: 10.1371/journal.pbio.1000247.

7.

Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease.

Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN.

Mamm Genome. 2009 Aug;20(8):457-61. doi: 10.1007/s00335-009-9208-3.

8.

Ontology quality assurance through analysis of term transformations.

Verspoor K, Dvorkin D, Cohen KB, Hunter L.

Bioinformatics. 2009 Jun 15;25(12):i77-84. doi: 10.1093/bioinformatics/btp195.

9.

The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.

Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S.

Am J Hum Genet. 2008 Nov;83(5):610-5. doi: 10.1016/j.ajhg.2008.09.017.

10.

Identification of OBO nonalignments and its implications for OBO enrichment.

Bada M, Hunter L.

Bioinformatics. 2008 Jun 15;24(12):1448-55. doi: 10.1093/bioinformatics/btn194.

11.

The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D768-72.

12.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

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.

Nat Biotechnol. 2007 Nov;25(11):1251-5.

13.

ChEBI: a database and ontology for chemical entities of biological interest.

Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D344-50.

14.

Mistakes in medical ontologies: where do they come from and how can they be detected?

Ceusters W, Smith B, Kumar A, Dhaen C.

Stud Health Technol Inform. 2004;102:145-63.

PMID:
15853269
15.

Using ontologies to describe mouse phenotypes.

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D.

Genome Biol. 2005;6(1):R8.

16.
17.

Building mouse phenotype ontologies.

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D.

Pac Symp Biocomput. 2004:178-89.

18.

A reference ontology for biomedical informatics: the Foundational Model of Anatomy.

Rosse C, Mejino JL Jr.

J Biomed Inform. 2003 Dec;36(6):478-500.

19.

Protégé-2000: an open-source ontology-development and knowledge-acquisition environment.

Noy NF, Crubezy M, Fergerson RW, Knublauch H, Tu SW, Vendetti J, Musen MA.

AMIA Annu Symp Proc. 2003:953.

20.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

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