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Results: 1 to 20 of 42

1.

Thematic series on biomedical ontologies in JBMS: challenges and new directions.

Hoehndorf R, Haendel M, Stevens R, Rebholz-Schuhmann D.

J Biomed Semantics. 2014 Mar 6;5:15. doi: 10.1186/2041-1480-5-15. eCollection 2014. Review.

PMID:
24602198
[PubMed]
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.

Analyzing gene expression data in mice with the Neuro Behavior Ontology.

Hoehndorf R, Hancock JM, Hardy NW, Mallon AM, Schofield PN, Gkoutos GV.

Mamm Genome. 2014 Feb;25(1-2):32-40. doi: 10.1007/s00335-013-9481-z. Epub 2013 Nov 1.

PMID:
24177753
[PubMed - in process]
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.

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).

Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I.

PLoS One. 2013 Oct 4;8(10):e75185. doi: 10.1371/journal.pone.0075185. eCollection 2013.

PMID:
24124474
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.

Rebholz-Schuhmann D, Kafkas S, Kim JH, Li C, Jimeno Yepes A, Hoehndorf R, Backofen R, Lewin I.

J Biomed Semantics. 2013 Oct 11;4(1):28. doi: 10.1186/2041-1480-4-28.

PMID:
24112383
[PubMed]
Free PMC Article
8.

An integrative, translational approach to understanding rare and orphan genetically based diseases.

Hoehndorf R, Schofield PN, Gkoutos GV.

Interface Focus. 2013 Apr 6;3(2):20120055. doi: 10.1098/rsfs.2012.0055.

PMID:
23853703
[PubMed]
Free PMC Article
9.

Representing physiological processes and their participants with PhysioMaps.

Cook DL, Neal ML, Hoehndorf R, Gkoutos GV, Gennari JH.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S2. doi: 10.1186/2041-1480-4-S1-S2. Epub 2013 Apr 15.

PMID:
23735231
[PubMed]
Free PMC Article
10.

Systematic analysis of experimental phenotype data reveals gene functions.

Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.

PLoS One. 2013 Apr 16;8(4):e60847. doi: 10.1371/journal.pone.0060847. Print 2013.

PMID:
23626672
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.

Gkoutos GV, Schofield PN, Hoehndorf R.

Int Rev Neurobiol. 2012;103:69-87. doi: 10.1016/B978-0-12-388408-4.00004-6. Review.

PMID:
23195121
[PubMed - indexed for MEDLINE]
12.

Text-mining solutions for biomedical research: enabling integrative biology.

Rebholz-Schuhmann D, Oellrich A, Hoehndorf R.

Nat Rev Genet. 2012 Dec;13(12):829-39. doi: 10.1038/nrg3337. Epub 2012 Nov 14. Review.

PMID:
23150036
[PubMed - indexed for MEDLINE]
13.

The Units Ontology: a tool for integrating units of measurement in science.

Gkoutos GV, Schofield PN, Hoehndorf R.

Database (Oxford). 2012 Oct 10;2012:bas033. doi: 10.1093/database/bas033. Print 2012.

PMID:
23060432
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes.

Gkoutos GV, Hoehndorf R.

J Biomed Semantics. 2012 Sep 21;3 Suppl 2:S6. doi: 10.1186/2041-1480-3-S2-S6. Epub 2012 Sep 21.

PMID:
23046642
[PubMed]
Free PMC Article
15.

Towards improving phenotype representation in OWL.

Loebe F, Stumpf F, Hoehndorf R, Herre H.

J Biomed Semantics. 2012 Sep 21;3 Suppl 2:S5. doi: 10.1186/2041-1480-3-S2-S5. Epub 2012 Sep 21.

PMID:
23046625
[PubMed]
Free PMC Article
16.

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.

Oellrich A, Gkoutos GV, Hoehndorf R, Rebholz-Schuhmann D.

J Biomed Semantics. 2012 Sep 21;3 Suppl 2:S1. doi: 10.1186/2041-1480-3-S2-S1. Epub 2012 Sep 21.

PMID:
23046555
[PubMed]
Free PMC Article
17.

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
18.

Computational tools for comparative phenomics: the role and promise of ontologies.

Gkoutos GV, Schofield PN, Hoehndorf R.

Mamm Genome. 2012 Oct;23(9-10):669-79. doi: 10.1007/s00335-012-9404-4. Epub 2012 Jul 20. Review.

PMID:
22814867
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases.

Oellrich A, Hoehndorf R, Gkoutos GV, Rebholz-Schuhmann D.

PLoS One. 2012;7(6):e38937. doi: 10.1371/journal.pone.0038937. Epub 2012 Jun 14.

PMID:
22719993
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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

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