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Results: 1 to 20 of 122

1.

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M.

Database (Oxford). 2014 Jul 22;2014. pii: bau075. doi: 10.1093/database/bau075. Print 2014.

PMID:
25052702
[PubMed - in process]
Free PMC Article
2.

OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain.

Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M.

PLoS One. 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014.

PMID:
25025130
[PubMed - in process]
Free PMC Article
3.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.

J Biomed Semantics. 2014 May 19;5:21. doi: 10.1186/2041-1480-5-21. eCollection 2014.

PMID:
25009735
[PubMed]
Free PMC Article
4.

Representing kidney development using the gene ontology.

Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP.

PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014.

PMID:
24941002
[PubMed - in process]
Free PMC Article
5.

A method for increasing expressivity of Gene Ontology annotations using a compositional approach.

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ.

BMC Bioinformatics. 2014 May 21;15:155. doi: 10.1186/1471-2105-15-155.

PMID:
24885854
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

DFLAT: functional annotation for human development.

Wick HC, Drabkin H, Ngu H, Sackman M, Fournier C, Haggett J, Blake JA, Bianchi DW, Slonim DK.

BMC Bioinformatics. 2014 Feb 7;15:45. doi: 10.1186/1471-2105-15-45.

PMID:
24507166
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Pax genes: regulators of lineage specification and progenitor cell maintenance.

Blake JA, Ziman MR.

Development. 2014 Feb;141(4):737-51. doi: 10.1242/dev.091785.

PMID:
24496612
[PubMed - indexed for MEDLINE]
Free Article
8.

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse.

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

Nucleic Acids Res. 2014 Jan;42(Database issue):D810-7. doi: 10.1093/nar/gkt1225. Epub 2013 Nov 26.

PMID:
24285300
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

PMID:
24270789
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Ten quick tips for using the gene ontology.

Blake JA.

PLoS Comput Biol. 2013;9(11):e1003343. doi: 10.1371/journal.pcbi.1003343. Epub 2013 Nov 14. No abstract available.

PMID:
24244145
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps.

Borda E, Kudenov JD, Chevaldonné P, Blake JA, Desbruyères D, Fabri MC, Hourdez S, Pleijel F, Shank TM, Wilson NG, Schulze A, Rouse GW.

Proc Biol Sci. 2013 Sep 11;280(1770):20131876. doi: 10.1098/rspb.2013.1876. Print 2013 Nov 7.

PMID:
24026823
[PubMed - indexed for MEDLINE]
12.

Ontology based molecular signatures for immune cell types via gene expression analysis.

Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD.

BMC Bioinformatics. 2013 Aug 30;14:263. doi: 10.1186/1471-2105-14-263.

PMID:
24004649
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.

Database (Oxford). 2013 Aug 27;2013:bat062. doi: 10.1093/database/bat062. Print 2013.

PMID:
23981286
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The characterisation of Pax3 expressant cells in adult peripheral nerve.

Blake JA, Ziman MR.

PLoS One. 2013;8(3):e59184. doi: 10.1371/journal.pone.0059184. Epub 2013 Mar 19.

PMID:
23527126
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The mouse genome database: genotypes, phenotypes, and models of human disease.

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

Nucleic Acids Res. 2013 Jan;41(Database issue):D885-91. doi: 10.1093/nar/gks1115. Epub 2012 Nov 21.

PMID:
23175610
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Gene Ontology annotations and resources.

Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-, Bonilla C, Bouguerleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz C, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5. doi: 10.1093/nar/gks1050. Epub 2012 Nov 17.

PMID:
23161678
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database.

Drabkin HJ, Blake JA; Mouse Genome Informatics Database.

Database (Oxford). 2012 Oct 29;2012:bas045. doi: 10.1093/database/bas045. Print 2012.

PMID:
23110975
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.

Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.

Database (Oxford). 2012 Oct 29;2012:bas036. doi: 10.1093/database/bas036. Print 2012.

PMID:
23110974
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Concept annotation in the CRAFT corpus.

Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA Jr, Cohen KB, Verspoor K, Blake JA, Hunter LE.

BMC Bioinformatics. 2012 Jul 9;13:161. doi: 10.1186/1471-2105-13-161.

PMID:
22776079
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Disease model curation improvements at Mouse Genome Informatics.

Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT.

Database (Oxford). 2012 Mar 20;2012:bar063. doi: 10.1093/database/bar063. Print 2012.

PMID:
22434831
[PubMed - indexed for MEDLINE]
Free PMC Article

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