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Items: 1 to 50 of 62

1.

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.

Boudellioua I, Kulmanov M, Schofield PN, Gkoutos GV, Hoehndorf R.

Sci Rep. 2018 Oct 2;8(1):14681. doi: 10.1038/s41598-018-32876-3.

2.

Integrating phenotype ontologies with PhenomeNET.

Rodríguez-García MÁ, Gkoutos GV, Schofield PN, Hoehndorf R.

J Biomed Semantics. 2017 Dec 19;8(1):58. doi: 10.1186/s13326-017-0167-4.

3.

Semantic prioritization of novel causative genomic variants.

Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R.

PLoS Comput Biol. 2017 Apr 17;13(4):e1005500. doi: 10.1371/journal.pcbi.1005500. eCollection 2017 Apr.

4.

The anatomy of phenotype ontologies: principles, properties and applications.

Gkoutos GV, Schofield PN, Hoehndorf R.

Brief Bioinform. 2018 Sep 28;19(5):1008-1021. doi: 10.1093/bib/bbx035.

5.

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.

Hoehndorf R, Alshahrani M, Gkoutos GV, Gosline G, Groom Q, Hamann T, Kattge J, de Oliveira SM, Schmidt M, Sierra S, Smets E, Vos RA, Weiland C.

J Biomed Semantics. 2016 Nov 14;7(1):65.

6.

Duplication of the mitochondrial control region is associated with increased longevity in birds.

Skujina I, McMahon R, Lenis VP, Gkoutos GV, Hegarty M.

Aging (Albany NY). 2016 Aug;8(8):1781-9. doi: 10.18632/aging.101012.

7.

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

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

J Biomed Semantics. 2016 Aug 8;7(1):49. doi: 10.1186/s13326-016-0090-0.

8.

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.

9.

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
10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

17.

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.

18.

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
19.

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.

20.

The Drosophila phenotype ontology.

Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.

J Biomed Semantics. 2013 Oct 18;4(1):30. doi: 10.1186/2041-1480-4-30.

21.

The mouse pathology ontology, MPATH; structure and applications.

Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV.

J Biomed Semantics. 2013 Sep 13;4(1):18. doi: 10.1186/2041-1480-4-18.

22.

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.

23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.

Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV.

Bioinformatics. 2012 Jul 1;28(13):1783-9. doi: 10.1093/bioinformatics/bts250. Epub 2012 Apr 26.

35.

Mouse genetic and phenotypic resources for human genetics.

Schofield PN, Hoehndorf R, Gkoutos GV.

Hum Mutat. 2012 May;33(5):826-36. doi: 10.1002/humu.22077. Review.

36.

MouseFinder: Candidate disease genes from mouse phenotype data.

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

Hum Mutat. 2012 May;33(5):858-66. doi: 10.1002/humu.22051. Epub 2012 Mar 16.

37.

Uberon, an integrative multi-species anatomy ontology.

Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA.

Genome Biol. 2012 Jan 31;13(1):R5. doi: 10.1186/gb-2012-13-1-r5.

38.

Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing.

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

Pac Symp Biocomput. 2012:388-99.

39.

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

Wimalaratne SM, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.

Bioinformatics. 2012 Feb 1;28(3):448-50. doi: 10.1093/bioinformatics/btr662. Epub 2011 Nov 29.

PMID:
22130590
40.

Improving ontologies by automatic reasoning and evaluation of logical definitions.

Köhler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN.

BMC Bioinformatics. 2011 Oct 27;12:418. doi: 10.1186/1471-2105-12-418.

41.

Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice.

Schofield PN, Vogel P, Gkoutos GV, Sundberg JP.

Dis Model Mech. 2012 Jan;5(1):19-25. doi: 10.1242/dmm.008334. Epub 2011 Oct 25. Review.

42.

New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models.

Schofield PN, Sundberg JP, Hoehndorf R, Gkoutos GV.

Brief Funct Genomics. 2011 Sep;10(5):258-65. doi: 10.1093/bfgp/elr031. Review.

43.

PIDO: the primary immunodeficiency disease ontology.

Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hennig C.

Bioinformatics. 2011 Nov 15;27(22):3193-9. doi: 10.1093/bioinformatics/btr531. Epub 2011 Sep 22.

PMID:
21949270
44.

Integrating systems biology models and biomedical ontologies.

Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.

BMC Syst Biol. 2011 Aug 11;5:124. doi: 10.1186/1752-0509-5-124.

45.

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning.

Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV.

PLoS One. 2011;6(7):e22006. doi: 10.1371/journal.pone.0022006. Epub 2011 Jul 18.

46.

PhenomeNET: a whole-phenome approach to disease gene discovery.

Hoehndorf R, Schofield PN, Gkoutos GV.

Nucleic Acids Res. 2011 Oct;39(18):e119. doi: 10.1093/nar/gkr538. Epub 2011 Jul 6.

47.

A common layer of interoperability for biomedical ontologies based on OWL EL.

Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.

Bioinformatics. 2011 Apr 1;27(7):1001-8. doi: 10.1093/bioinformatics/btr058. Epub 2011 Feb 21.

48.

Phenotype ontologies for mouse and man: bridging the semantic gap.

Schofield PN, Gkoutos GV, Gruenberger M, Sundberg JP, Hancock JM.

Dis Model Mech. 2010 May-Jun;3(5-6):281-9. doi: 10.1242/dmm.002790. Review.

49.

Integrating phenotype ontologies across multiple species.

Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M.

Genome Biol. 2010 Jan 8;11(1):R2. doi: 10.1186/gb-2010-11-1-r2.

50.

Entity/quality-based logical definitions for the human skeletal phenome using PATO.

Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:7069-72. doi: 10.1109/IEMBS.2009.5333362.

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