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Results: 1 to 20 of 21

1.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

PMID:
24495517
[PubMed]
Free PMC Article
2.

NCBO Technology: Powering semantically aware applications.

Whetzel PL; NCBO Team.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S8. doi: 10.1186/2041-1480-4-S1-S8. Epub 2013 Apr 15.

PMID:
23734708
[PubMed]
Free PMC Article
3.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

Maguire E, González-Beltrán A, Whetzel PL, Sansone SA, Rocca-Serra P.

Bioinformatics. 2013 Feb 15;29(4):525-7. doi: 10.1093/bioinformatics/bts718. Epub 2012 Dec 24.

PMID:
23267176
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The National Center for Biomedical Ontology.

Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. doi: 10.1136/amiajnl-2011-000523. Epub 2011 Nov 10.

PMID:
22081220
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. doi: 10.1093/nar/gkr469. Epub 2011 Jun 14.

PMID:
21672956
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.

J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.

PMID:
21624155
[PubMed]
Free PMC Article
7.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.

Stand Genomic Sci. 2010 Dec 25;3(3):259-66. doi: 10.4056/sigs.147362.

PMID:
21304730
[PubMed]
Free PMC Article
8.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Database (Oxford). 2011 Jan 4;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

PMID:
21205783
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C; BioDBCore Working Group.

Nucleic Acids Res. 2011 Jan;39(Database issue):D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

PMID:
21097465
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P.

J Biomed Inform. 2011 Feb;44(1):137-45. doi: 10.1016/j.jbi.2010.10.003. Epub 2010 Oct 16.

PMID:
20955817
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

BioPortal: ontologies and integrated data resources at the click of a mouse.

Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. doi: 10.1093/nar/gkp440. Epub 2009 May 29.

PMID:
19483092
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
17989687
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.

Nat Biotechnol. 2007 Oct;25(10):1127-33.

PMID:
17921998
[PubMed - indexed for MEDLINE]
14.

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.

BMC Bioinformatics. 2006 Nov 6;7:489.

PMID:
17087822
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Using ontologies to annotate microarray experiments.

Whetzel PL, Parkinson H, Stoeckert CJ Jr.

Methods Enzymol. 2006;411:325-39. Review.

PMID:
16939798
[PubMed - indexed for MEDLINE]
16.

Development of FuGO: an ontology for functional genomics investigations.

Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A; FuGO Working Group.

OMICS. 2006 Summer;10(2):199-204. Review.

PMID:
16901226
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The MGED Ontology: a resource for semantics-based description of microarray experiments.

Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.

Bioinformatics. 2006 Apr 1;22(7):866-73. Epub 2006 Jan 21.

PMID:
16428806
[PubMed - indexed for MEDLINE]
Free Article
18.

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

Manduchi E, Grant GR, He H, Liu J, Mailman MD, Pizarro AD, Whetzel PL, Stoeckert CJ Jr.

Bioinformatics. 2004 Mar 1;20(4):452-9. Epub 2004 Jan 22.

PMID:
14990441
[PubMed - indexed for MEDLINE]
Free Article
19.

Transposon mutagenesis of Mycoplasma gallisepticum.

Whetzel PL, Hnatow LL, Keeler CL Jr, Dohms JE.

Plasmid. 2003 Jan;49(1):34-43.

PMID:
12583999
[PubMed - indexed for MEDLINE]
20.

Cloning and characterization of a putative cytadhesin gene (mgc1) from Mycoplasma gallisepticum.

Keeler CL Jr, Hnatow LL, Whetzel PL, Dohms JE.

Infect Immun. 1996 May;64(5):1541-7.

PMID:
8613358
[PubMed - indexed for MEDLINE]
Free PMC Article

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