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Results: 1 to 20 of 68

1.

Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest.

Boyce RD, Ryan PB, Norén GN, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifirò G, Harpaz R, Overhage JM, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, Dumontier M.

Drug Saf. 2014 Aug;37(8):557-67. doi: 10.1007/s40264-014-0189-0.

PMID:
24985530
[PubMed - in process]
Free PMC Article
2.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.

J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14.

PMID:
24602174
[PubMed]
Free PMC Article
3.

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
4.

Sub-NOAEL amounts of vinclozolin and xenoestrogens target rat chondrogenesis in vivo.

Auxietre TA, Dumontier MF, Balguy I, Frapart Y, Canivenc-Lavier MC, Berges R, Boudalia S, Auger J, Corvol MT, Savouret JF.

Biochimie. 2014 Apr;99:169-77. doi: 10.1016/j.biochi.2013.12.001. Epub 2013 Dec 12.

PMID:
24333988
[PubMed - indexed for MEDLINE]
5.

Mouse model phenotypes provide information about human drug targets.

Hoehndorf R, Hiebert T, Hardy NW, Schofield PN, Gkoutos GV, Dumontier M.

Bioinformatics. 2014 Mar 1;30(5):719-25. doi: 10.1093/bioinformatics/btt613. Epub 2013 Oct 24.

PMID:
24158600
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics.

Samwald M, Freimuth R, Luciano JS, Lin S, Powers RL, Marshall MS, Adlassnig KP, Dumontier M, Boyce RD.

Stud Health Technol Inform. 2013;192:539-42.

PMID:
23920613
[PubMed - in process]
Free PMC Article
7.

Ontology-Based Querying with Bio2RDF's Linked Open Data.

Callahan A, Cruz-Toledo J, Dumontier M.

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

PMID:
23735196
[PubMed]
Free PMC Article
8.

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

Soldatova LN, Sansone SA, Dumontier M, Shah NH.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:I1. doi: 10.1186/2041-1480-4-S1-I1. Epub 2013 Apr 15.

PMID:
23735191
[PubMed]
Free PMC Article
9.

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

Vandervalk B, McCarthy EL, Cruz-Toledo J, Klein A, Baker CJ, Dumontier M, Wilkinson MD.

JMIR Res Protoc. 2013 Apr 5;2(1):e14. doi: 10.2196/resprot.2315.

PMID:
23612187
[PubMed]
Free PMC Article
10.

State of the art and open challenges in community-driven knowledge curation.

Groza T, Tudorache T, Dumontier M.

J Biomed Inform. 2013 Feb;46(1):1-4. doi: 10.1016/j.jbi.2012.11.007. Epub 2012 Dec 3. No abstract available.

PMID:
23219718
[PubMed - indexed for MEDLINE]
Free Article
11.

Evaluation of research in biomedical ontologies.

Hoehndorf R, Dumontier M, Gkoutos GV.

Brief Bioinform. 2013 Nov;14(6):696-712. doi: 10.1093/bib/bbs053. Epub 2012 Sep 8.

PMID:
22962340
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.

Hoehndorf R, Dumontier M, Gkoutos GV.

Bioinformatics. 2012 Aug 15;28(16):2169-75. doi: 10.1093/bioinformatics/bts350. Epub 2012 Jun 17.

PMID:
22711793
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

Soldatova LN, Sansone SA, Dumontier M, Shah NH.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:I1. doi: 10.1186/2041-1480-3-S1-I1.

PMID:
22541591
[PubMed]
Free PMC Article
14.

Aptamer Base: a collaborative knowledge base to describe aptamers and SELEX experiments.

Cruz-Toledo J, McKeague M, Zhang X, Giamberardino A, McConnell E, Francis T, DeRosa MC, Dumontier M.

Database (Oxford). 2012 Mar 20;2012:bas006. doi: 10.1093/database/bas006. Print 2012.

PMID:
22434840
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Semantically enabling pharmacogenomic data for the realization of personalized medicine.

Samwald M, Coulet A, Huerga I, Powers RL, Luciano JS, Freimuth RR, Whipple F, Pichler E, Prud'hommeaux E, Dumontier M, Marshall MS.

Pharmacogenomics. 2012 Jan;13(2):201-12. doi: 10.2217/pgs.11.179. Review. Erratum in: Pharmacogenomics. 2012 Apr;13(5):628.

PMID:
22256869
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Building an HIV data mashup using Bio2RDF.

Nolin MA, Dumontier M, Belleau F, Corbeil J.

Brief Bioinform. 2012 Jan;13(1):98-106. doi: 10.1093/bib/bbr003. Epub 2011 Mar 24.

PMID:
22223742
[PubMed - indexed for MEDLINE]
Free Article
17.

Self-organizing ontology of biochemically relevant small molecules.

Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M.

BMC Bioinformatics. 2012 Jan 6;13:3. doi: 10.1186/1471-2105-13-3.

PMID:
22221313
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

PMID:
22027554
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.

PLoS One. 2011;6(10):e25513. doi: 10.1371/journal.pone.0025513. Epub 2011 Oct 3.

PMID:
21991315
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Towards an interoperable information infrastructure providing decision support for genomic medicine.

Samwald M, Stenzhorn H, Dumontier M, Marshall MS, Luciano J, Adlassnig KP.

Stud Health Technol Inform. 2011;169:165-9.

PMID:
21893735
[PubMed - indexed for MEDLINE]
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