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Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data.

Beck T, Morgan H, Blake A, Wells S, Hancock JM, Mallon AM.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S2.PMID: 19426459 [PubMed - indexed for MEDLINE]Related articlesFree article

PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.

Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier YA.

BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S8.PMID: 19208196 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2009 Nov 24.PMID: 19956802 [PubMed - in process]Related articlesFree article

The mouse genome database (MGD): new features facilitating a model system.

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group.

Nucleic Acids Res. 2007 Jan;35(Database issue):D630-7. Epub 2006 Nov 29.PMID: 17135206 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluation of BioCreAtIvE assessment of task 2.

Blaschke C, Leon EA, Krallinger M, Valencia A.

BMC Bioinformatics. 2005;6 Suppl 1:S16. Epub 2005 May 24.PMID: 15960828 [PubMed - indexed for MEDLINE]Related articlesFree article

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.

Smith CL, Goldsmith CA, Eppig JT.

Genome Biol. 2005;6(1):R7. Epub 2004 Dec 15.PMID: 15642099 [PubMed - indexed for MEDLINE]Related articlesFree article

Creating the gene ontology resource: design and implementation.

Gene Ontology Consortium.

Genome Res. 2001 Aug;11(8):1425-33.PMID: 11483584 [PubMed - indexed for MEDLINE]Related articlesFree article

PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.

Lussier Y, Borlawsky T, Rappaport D, Liu Y, Friedman C.

Pac Symp Biocomput. 2006:64-75.PMID: 17094228 [PubMed - indexed for MEDLINE]Related articlesFree article

EuroPhenome: a repository for high-throughput mouse phenotyping data.

Morgan H, Beck T, Blake A, Gates H, Adams N, Debouzy G, Leblanc S, Lengger C, Maier H, Melvin D, Meziane H, Richardson D, Wells S, White J, Wood J; The EUMODIC Consortium, de Angelis MH, Brown SD, Hancock JM, Mallon AM.

Nucleic Acids Res. 2009 Nov 23. [Epub ahead of print]PMID: 19933761 [PubMed - as supplied by publisher]Related articlesFree article

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.PMID: 14681408 [PubMed - indexed for MEDLINE]Related articlesFree article

TGF-beta signaling proteins and the Protein Ontology.

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S3.PMID: 19426460 [PubMed - indexed for MEDLINE]Related articlesFree article

Building mouse phenotype ontologies.

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

Pac Symp Biocomput. 2004:178-89.PMID: 14992502 [PubMed - indexed for MEDLINE]Related articlesFree article

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

Beauheim CC, Wymore F, Nitzberg M, Zachariah ZK, Jin H, Skene JH, Ball CA, Sherlock G.

BMC Bioinformatics. 2007 Sep 13;8:338.PMID: 17854506 [PubMed - indexed for MEDLINE]Related articlesFree article

Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology.

Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G.

BMC Genomics. 2008 Jul 24;9:347.PMID: 18652646 [PubMed - indexed for MEDLINE]Related articlesFree article

Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice.

Masuya H, Yoshikawa S, Heida N, Toyoda T, Wakana S, Shiroishi T.

J Bioinform Comput Biol. 2007 Dec;5(6):1173-91.PMID: 18172924 [PubMed - indexed for MEDLINE]Related articles

A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: the case of OBO disease ontologies.

Marquet G, Mosser J, Burgun A.

Int J Med Inform. 2007 Dec;76 Suppl 3:S353-61. Epub 2007 May 22.PMID: 17517532 [PubMed - indexed for MEDLINE]Related articles

Using an integrated ontology and information model for querying and reasoning about phenotypes: The case of autism.

Tu SW, Tennakoon L, O'Connor M, Shankar R, Das A.

AMIA Annu Symp Proc. 2008 Nov 6:727-31.PMID: 18999231 [PubMed - in process]Related articlesFree article

FlyBase : a database for the Drosophila research community.

Drysdale R; FlyBase Consortium.

Methods Mol Biol. 2008;420:45-59. Review.PMID: 18641940 [PubMed - indexed for MEDLINE]Related articles

A procedure for assessing GO annotation consistency.

Dolan ME, Ni L, Camon E, Blake JA.

Bioinformatics. 2005 Jun;21 Suppl 1:i136-43.PMID: 15961450 [PubMed - indexed for MEDLINE]Related articlesFree article

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies.

Hoehndorf R, Loebe F, Kelso J, Herre H.

BMC Bioinformatics. 2007 Oct 9;8:377.PMID: 17925014 [PubMed - indexed for MEDLINE]Related articlesFree article