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Items: 1 to 20 of 57

1.

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.

Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V.

PLoS One. 2016 Jul 8;11(7):e0158896. doi: 10.1371/journal.pone.0158896. eCollection 2016.

2.

DermO; an ontology for the description of dermatologic disease.

Fisher HM, Hoehndorf R, Bazelato BS, Dadras SS, King LE Jr, Gkoutos GV, Sundberg JP, Schofield PN.

J Biomed Semantics. 2016 Jun 13;7:38. doi: 10.1186/s13326-016-0085-x.

3.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ.

J Biomed Semantics. 2016 Jun 13;7:39. doi: 10.1186/s13326-016-0067-z.

4.

Datamining with Ontologies.

Hoehndorf R, Gkoutos GV, Schofield PN.

Methods Mol Biol. 2016;1415:385-97. doi: 10.1007/978-1-4939-3572-7_19.

PMID:
27115643
5.

DESM: portal for microbial knowledge exploration systems.

Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simoes MF, Lafi FF, Motwalli OA, Bokhari A, Malas T, Amoudi SA, Othum G, Allam I, Mineta K, Gao X, Hoehndorf R, C Archer JA, Gojobori T, Bajic VB.

Nucleic Acids Res. 2016 Jan 4;44(D1):D624-33. doi: 10.1093/nar/gkv1147. Epub 2015 Nov 5.

6.

Best behaviour? Ontologies and the formal description of animal behaviour.

Gkoutos GV, Hoehndorf R, Tsaprouni L, Schofield PN.

Mamm Genome. 2015 Oct;26(9-10):540-7. doi: 10.1007/s00335-015-9590-y. Epub 2015 Jul 28. Review.

PMID:
26215546
7.

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

Hrabě de Angelis M, Nicholson G, Selloum M, White JK, Morgan H, Ramirez-Solis R, Sorg T, Wells S, Fuchs H, Fray M, Adams DJ, Adams NC, Adler T, Aguilar-Pimentel A, Ali-Hadji D, Amann G, André P, Atkins S, Auburtin A, Ayadi A, Becker J, Becker L, Bedu E, Bekeredjian R, Birling MC, Blake A, Bottomley J, Bowl MR, Brault V, Busch DH, Bussell JN, Calzada-Wack J, Cater H, Champy MF, Charles P, Chevalier C, Chiani F, Codner GF, Combe R, Cox R, Dalloneau E, Dierich A, Di Fenza A, Doe B, Duchon A, Eickelberg O, Esapa CT, Fertak LE, Feigel T, Emelyanova I, Estabel J, Favor J, Flenniken A, Gambadoro A, Garrett L, Gates H, Gerdin AK, Gkoutos G, Greenaway S, Glasl L, Goetz P, Da Cruz IG, Götz A, Graw J, Guimond A, Hans W, Hicks G, Hölter SM, Höfler H, Hancock JM, Hoehndorf R, Hough T, Houghton R, Hurt A, Ivandic B, Jacobs H, Jacquot S, Jones N, Karp NA, Katus HA, Kitchen S, Klein-Rodewald T, Klingenspor M, Klopstock T, Lalanne V, Leblanc S, Lengger C, le Marchand E, Ludwig T, Lux A, McKerlie C, Maier H, Mandel JL, Marschall S, Mark M, Melvin DG, Meziane H, Micklich K, Mittelhauser C, Monassier L, Moulaert D, Muller S, Naton B, Neff F, Nolan PM, Nutter LM, Ollert M, Pavlovic G, Pellegata NS, Peter E, Petit-Demoulière B, Pickard A, Podrini C, Potter P, Pouilly L, Puk O, Richardson D, Rousseau S, Quintanilla-Fend L, Quwailid MM, Racz I, Rathkolb B, Riet F, Rossant J, Roux M, Rozman J, Ryder E, Salisbury J, Santos L, Schäble KH, Schiller E, Schrewe A, Schulz H, Steinkamp R, Simon M, Stewart M, Stöger C, Stöger T, Sun M, Sunter D, Teboul L, Tilly I, Tocchini-Valentini GP, Tost M, Treise I, Vasseur L, Velot E, Vogt-Weisenhorn D, Wagner C, Walling A, Wattenhofer-Donze M, Weber B, Wendling O, Westerberg H, Willershäuser M, Wolf E, Wolter A, Wood J, Wurst W, Yildirim AÖ, Zeh R, Zimmer A, Zimprich A; EUMODIC Consortium, Holmes C, Steel KP, Herault Y, Gailus-Durner V, Mallon AM, Brown SD.

Nat Genet. 2015 Sep;47(9):969-78. doi: 10.1038/ng.3360. Epub 2015 Jul 27.

8.

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases.

Hoehndorf R, Schofield PN, Gkoutos GV.

Sci Rep. 2015 Jun 8;5:10888. doi: 10.1038/srep10888.

9.

GFVO: the Genomic Feature and Variation Ontology.

Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M.

PeerJ. 2015 May 5;3:e933. doi: 10.7717/peerj.933. eCollection 2015.

10.

The role of ontologies in biological and biomedical research: a functional perspective.

Hoehndorf R, Schofield PN, Gkoutos GV.

Brief Bioinform. 2015 Nov;16(6):1069-80. doi: 10.1093/bib/bbv011. Epub 2015 Apr 10.

11.

Ranking adverse drug reactions with crowdsourcing.

Gottlieb A, Hoehndorf R, Dumontier M, Altman RB.

J Med Internet Res. 2015 Mar 23;17(3):e80. doi: 10.2196/jmir.3962.

12.

An ontology approach to comparative phenomics in plants.

Oellrich A, Walls RL, Cannon EK, Cannon SB, Cooper L, Gardiner J, Gkoutos GV, Harper L, He M, Hoehndorf R, Jaiswal P, Kalberer SR, Lloyd JP, Meinke D, Menda N, Moore L, Nelson RT, Pujar A, Lawrence CJ, Huala E.

Plant Methods. 2015 Feb 25;11:10. doi: 10.1186/s13007-015-0053-y. eCollection 2015.

13.

Similarity-based search of model organism, disease and drug effect phenotypes.

Hoehndorf R, Gruenberger M, Gkoutos GV, Schofield PN.

J Biomed Semantics. 2015 Feb 19;6:6. doi: 10.1186/s13326-015-0001-9. eCollection 2015.

PMID:
25763178
Free PMC Article
14.

Aber-OWL: a framework for ontology-based data access in biology.

Hoehndorf R, Slater L, Schofield PN, Gkoutos GV.

BMC Bioinformatics. 2015 Jan 28;16:26. doi: 10.1186/s12859-015-0456-9.

15.

Enriched biodiversity data as a resource and service.

Vos RA, Biserkov JV, Balech B, Beard N, Blissett M, Brenninkmeijer C, van Dooren T, Eades D, Gosline G, Groom QJ, Hamann TD, Hettling H, Hoehndorf R, Holleman A, Hovenkamp P, Kelbert P, King D, Kirkup D, Lammers Y, DeMeulemeester T, Mietchen D, Miller JA, Mounce R, Nicolson N, Page R, Pawlik A, Pereira S, Penev L, Richards K, Sautter G, Shorthouse DP, Tähtinen M, Weiland C, Williams AR, Sierra S.

Biodivers Data J. 2014 Jun 16;(2):e1125. doi: 10.3897/BDJ.2.e1125. eCollection 2014.

16.

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.

17.

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.

18.

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.

19.

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
20.

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.

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