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Results: 1 to 20 of 46

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 Article
2.

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
3.

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
4.

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 - in process]
Free PMC Article
5.

An atlas of active enhancers across human cell types and tissues.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.

Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787.

PMID:
24670763
[PubMed - indexed for MEDLINE]
6.

Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.

Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ.

Version 2. F1000Res. 2013 Feb 1 [revised 2014 Jan 21];2:30. doi: 10.12688/f1000research.2-30.v2. eCollection 2013.

PMID:
24358873
[PubMed]
Free PMC Article
7.

The environment ontology: contextualising biological and biomedical entities.

Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE; ENVO Consortium.

J Biomed Semantics. 2013 Dec 11;4(1):43. doi: 10.1186/2041-1480-4-43.

PMID:
24330602
[PubMed]
Free PMC Article
8.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN.

Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74. doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11.

PMID:
24217912
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Improved exome prioritization of disease genes through cross-species phenotype comparison.

Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D.

Genome Res. 2014 Feb;24(2):340-8. doi: 10.1101/gr.160325.113. Epub 2013 Oct 25.

PMID:
24162188
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall CJ, Lomax J.

J Biomed Semantics. 2013 Oct 7;4(1):20. doi: 10.1186/2041-1480-4-20.

PMID:
24093723
[PubMed]
Free PMC Article
11.

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
12.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.

PMID:
23895341
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A knowledge based approach to matching human neurodegenerative disease and animal models.

Maynard SM, Mungall CJ, Lewis SE, Imam FT, Martone ME.

Front Neuroinform. 2013 May 14;7:7. doi: 10.3389/fninf.2013.00007. eCollection 2013.

PMID:
23717278
[PubMed]
Free PMC Article
14.

A unified anatomy ontology of the vertebrate skeletal system.

Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM.

PLoS One. 2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10.

PMID:
23251424
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The plant ontology as a tool for comparative plant anatomy and genomic analyses.

Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P.

Plant Cell Physiol. 2013 Feb;54(2):e1. doi: 10.1093/pcp/pcs163. Epub 2012 Dec 5.

PMID:
23220694
[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.

Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish.

Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE.

Dis Model Mech. 2013 Mar;6(2):358-72. doi: 10.1242/dmm.010322. Epub 2012 Oct 25.

PMID:
23104991
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Ontologies as integrative tools for plant science.

Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW.

Am J Bot. 2012 Aug;99(8):1263-75. doi: 10.3732/ajb.1200222. Epub 2012 Jul 30.

PMID:
22847540
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A strategy for building neuroanatomy ontologies.

Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD.

Bioinformatics. 2012 May 1;28(9):1262-9. doi: 10.1093/bioinformatics/bts113. Epub 2012 Mar 7. Erratum in: Bioinformatics. 2012 Aug 1;28(15):2091.

PMID:
22402613
[PubMed - indexed for MEDLINE]
Free Article
20.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium.

PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16.

PMID:
22359495
[PubMed - indexed for MEDLINE]
Free PMC Article

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