Schofield PN, Hoehndorf R, Gkoutos GV. Mouse genetic and phenotypic resources for human genetics. Hum Mutat. 2012; 33(5):826–36.
Article
Google Scholar
Hoehndorf R, Schofield PN, Gkoutos GV. The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform. 2011. doi:10.1093/bib/bbv011. http://bib.oxfordjournals.org/content/early/2015/04/10/bib.bbv011.full.pdf+html.
Hoehndorf R, Schofield PN, Gkoutos GV. Phenomenet: a whole-phenome approach to disease gene discovery. Nucleic Acids Res. 2011; 39(18):119.
Article
Google Scholar
Gkoutos GV, Green EC, Mallon A-MM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol. 2005; 6(1):5. doi:10.1186/gb-2004-6-1-r8.
Google Scholar
Hoehndorf R, Schofield PN, Gkoutos GV. An integrative, translational approach to understanding rare and orphan genetically based diseases. Interface Focus. 2013; 3(2):20120055. doi:10.1098/rsfs.2012.0055.
Article
Google Scholar
Hoehndorf R, Dumontier M, Gkoutos GV. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics. 2012; 28(16):2169–75. doi:10.1093/bioinformatics/bts350.
Article
Google Scholar
Hoehndorf R, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV. Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing. Pac Symp Biocomput (PSB). 2012; 2012:388–99.
Google Scholar
Hoehndorf R, Hiebert T, Hardy NW, Schofield PN, Gkoutos GV, Dumontier M. Mouse model phenotypes provide information about human drug targets. Bioinformatics. 2014; 30(5):719–25. doi:10.1093/bioinformatics/btt613.
Article
Google Scholar
Mungall C, Torniai C, Gkoutos G, Lewis S, Haendel M. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012; 13(1):5. doi:10.1186/gb-2012-13-1-r5.
Article
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry MJ, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Tarver LI, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000; 25(1):25–9. doi:10.1038/75556.
Article
Google Scholar
Gkoutos GV, Schofield PN, Hoehndorf R. The anatomy of phenotype ontologies: principles, properties and applications. Brief Bioinform. 2017. in press.
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, 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, Vooren SV, Wapner RJ, Wilkie AOM, Wright CF, Vulto-van Silfhout AT, Leeuw ND, de Vries BBA, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The human phenotype ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014; 42(D1):966–74.
Article
Google Scholar
Smith CL, Goldsmith C-AW, Eppig JT. The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2004; 6(1):7. doi:10.1186/gb-2004-6-1-r7.
Article
Google Scholar
Faria D, Pesquita C, Santos E, Palmonari M, Cruz IF, Couto FM. In: Meersman R, Panetto H, Dillon T, Eder J, Bellahsene Z, Ritter N, De Leenheer P, Dou D, (eds).The AgreementMakerLight Ontology Matching System. Berlin, Heidelberg: Springer; 2013, pp. 527–41.
Google Scholar
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM. Disease ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 2014; 43:1071–8. doi:10.1093/nar/gku1011.
Article
Google Scholar
Sarntivijai S, Vasant D, Jupp S, Saunders G, Bento AP, Gonzalez D, Betts J, Hasan S, Koscielny G, Dunham I, Parkinson H, Malone J. Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. J Biomed Semant. 2016; 7(1):1–11. doi:10.1186/s13326-016-0051-7.
Article
Google Scholar
Vasant D, Chanas L, Malone J, Hanauer M, Olry A, Jupp S, Robinson PN, Parkinson H, Rath A. Ordo: An ontology connecting rare disease, epidemiology and genetic data. In: Phenoday @ ISMB2014: 2014.
Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S. The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet. 2008; 83(5):610–5.
Article
Google Scholar
Smith CL, Eppig JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med. 2009; 1(3):390–9.
Article
Google Scholar
Schriml LM, Arze C, Nadendla S, Chang Y-WW, Mazaitis M, Felix V, Feng G, Kibbe WA. Disease ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2011; 40(D1):940–6.
Article
Google Scholar
Faria D, Martins C, Nanavaty A, Oliveira D, Sowkarthiga B, Taheri A, Pesquita C, Couto FM, Cruz IF. AML results for OAEI 2015 In: Shvaiko P, et al, editors. Proceedings of the 10th International Workshop on Ontology Matching. Aachen: CEUR-WS;2015. p. 116–23.
Google Scholar
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey M-AA, Chute CG, Musen MA. Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009; 37(Web Server issue):170–3. doi:10.1093/nar/gkp440.
Article
Google Scholar
Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT. Disease model curation improvements at mouse genome informatics. Database. 2012; 2012:063.
Article
Google Scholar
Resnik P. Semantic similarity in a taxonomy: An Information-Based measure and its application to problems of ambiguity in natural language. J Artif Intell Res. 1999; 11:95–130.
MATH
Google Scholar
Pesquita C, Faria D, Falcao AO, Lord P, Couto FM. Semantic similarity in biomedical ontologies. PLoS Comput Biol. 2009; 5(7):1000443.
Article
MathSciNet
Google Scholar
Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010; 11(1):2.
Article
Google Scholar
Hoehndorf R, Oellrich A, Rebholz-Schuhmann D. Interoperability between phenotype and anatomy ontologies. Bioinformatics. 2010; 26(24):3112–8.
Article
Google Scholar
Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R. Semantic prioritization of novel causative genomic variants. PLOS Comput Biol. 2017; 13(4):1–21. doi:10.1371/journal.pcbi.1005500.
Article
Google Scholar
Motik B, Grau BC, Horrocks I, Wu Z, Fokoue A, Lutz C. OWL 2 Web Ontology Language Profiles (Second Edition). World Wide Web Consortium. 2012. https://www.w3.org/TR/owl2-profiles/. Accessed 4 Dec 2017.
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV. A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics. 2011; 27(7):1001–8.
Article
Google Scholar
Kazakov Y, Krötzsch M, Simancik F. The incredible elk. J Autom Reason. 2014; 53(1):1–61. doi:10.1007/s10817-013-9296-3.
Article
MATH
Google Scholar
Degtyarenko K, Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M. Nucleic Acids Res. 2007; 36(Database issue):344–50.
Schofield PN, Sundberg JP, Sundberg BA, McKerlie C, Gkoutos GV. J Biomed Semant. 2013; 4(1):1–8. doi:10.1186/2041-1480-4-18.
Balhoff JP, Mikó I, Yoder MJ, Mullins PL, Deans AR. A semantic model for species description applied to the ensign wasps (hymenoptera: Evaniidae) of new caledonia. Syst Biol. 2013; 62(5):639–59. doi:10.1093/sysbio/syt028. http://sysbio.oxfordjournals.org/content/62/5/639.full.pdf+html.
Article
Google Scholar
Dahdul WM, Balhoff JP, Engeman J, Grande T, Hilton EJ, Kothari C, Lapp H, Lundberg JG, Midford PE, Vision TJ, Westerfield M, Mabee PM. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS ONE. 2010; 5(5):10708. doi:10.1371/journal.pone.0010708.
Article
Google Scholar
Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol. 2005;6(2). doi:10.1186/gb-2005-6-2-r21.
Hoehndorf R, Hancock JM, Hardy NW, Mallon AM, Schofield PN, Gkoutos GV. Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome. 2014; 25(1-2):32–40.
Article
Google Scholar
Hoehndorf R, Slater L, Schofield PN, Gkoutos GV. Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics. 2015; 16:26.
Article
Google Scholar
Jiménez-Ruiz E, Grau BC. Logmap: Logic-based and scalable ontology matching. In: International Semantic Web Conference. Heidelberg: Springer;2011. p. 273–88.
Google Scholar
Zhao M, Zhang S. FCA-Map results for OAEI 2016 In: Shvaiko P, et al, editors. Proceedings of the 11th International Workshop on Ontology Matching. Aachen: CEUR-WS;2016. p. 172–7.
Google Scholar
Harispe S, Ranwez S, Janaqi S, Montmain J. The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. Bioinformatics. 2014; 30(5):740–2. doi:10.1093/bioinformatics/btt581. http://bioinformatics.oxfordjournals.org/content/30/5/740.full.pdf+html.
Article
Google Scholar
Amberger J, Bocchini C, Hamosh A. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM). Hum Mutat. 2011; 32:564–7.
Article
Google Scholar
Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett. 2006; 27(8):861–74. doi:10.1016/j.patrec.2005.10.010.
Article
MathSciNet
Google Scholar
Lorena OC, Francisco JR-M, Alma GR. Ontology matching: A literature review. Expert Syst Appl. 2015; 42(2):949–71.
Article
Google Scholar
Djeddi WE, Khadir MT, Yahia SB. Xmap: results for oaei 2015 In: Shvaiko P, et al, editors. Proceedings of the 10th International Workshop on Ontology Matching. Aachen: CEUR-WS;2015. p. 216–21.
Google Scholar
Tigrine AN, Bellahsene Z, Todorov K. Lyam++ results for oaei 2015 In: Shvaiko P, et al., editors. Proceedings of the 10th International Workshop on Ontology Matching. Aachen: CEUR-WS;2015. p. 176–180.
Google Scholar
Wille R. In: Ganter B, Stumme G, Wille R, (eds).Formal Concept Analysis as Mathematical Theory of Concepts and Concept Hierarchies. Berlin, Heidelberg: Springer; 2005, pp. 1–33. doi:10.1007/11528784_1.
Google Scholar
Spiliopoulos V, Vouros GA, Karkaletsis V. Web Semant Sci Serv Agents World Wide Web. 2010; 8(1):69–88.
Spiliopoulos V, Valarakos AG, Vouros GA. In: Bechhofer S, Hauswirth M, Hoffmann J, Koubarakis M, (eds).CSR: Discovering Subsumption Relations for the Alignment of Ontologies. Berlin, Heidelberg: Springer; 2008, pp. 418–31.
Google Scholar
Gkoutos GV, Schofield PN, Hoehndorf R. Computational tools for comparative phenomics: the role and promise of ontologies. Mamm Genome. 2012; 23(9-10):669–79.
Article
Google Scholar
Sardana D, Vasa S, Vepachedu N, Chen J, Gudivada RC, Aronow BJ, Jegga AG. PhenoHM: human-mouse comparative phenome-genome server. Nucleic Acids Res. 2010; 38(Web Server issue):W165–74.
Article
Google Scholar
Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004; 32(Database issue):267–70.
Article
Google Scholar
Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Research. 2013;2. doi:10.12688/f1000research.2-30.v1.
Mungall CJ, McMurry JA, Koehler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JOB, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The monarch initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017; 45(D1):712–22.
Article
Google Scholar
McGary KL, Park TJ, Woods JO, Cha HJ, Wallingford JB, Marcotte EM. Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci. 2010; 107(14):6544–9. doi:10.1073/pnas.0910200107.
Article
Google Scholar
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. Systematic analysis of experimental phenotype data reveals gene functions. PLoS ONE. 2013; 8(4):60847. doi:10.1371/journal.pone.0060847.
Article
Google Scholar
Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Semantic integration of physiology phenotypes with an application to the cellular phenotype ontology. Bioinformatics. 2012; 28(13):1783–9. doi:10.1093/bioinformatics/bts250. http://bioinformatics.oxfordjournals.org/content/28/13/1783.full.pdf+html.
Article
Google Scholar
Jiménez-Ruiz E, Cuenca Grau B, Horrocks I, Berlanga R. In: Aroyo L, Traverso P, Ciravegna F, Cimiano P, Heath T, Hyvönen E, Mizoguchi R, Oren E, Sabou M, Simperl E, (eds).Ontology Integration Using Mappings: Towards Getting the Right Logical Consequences. Berlin, Heidelberg: Springer; 2009, pp. 173–87.
Google Scholar
Santos E, Faria D, Pesquita C, Couto FM. Ontology alignment repair through modularization and confidence-based heuristics. PLOS ONE. 2016; 10(12):1–19. doi:10.1371/journal.pone.0144807.
Google Scholar
Meilicke C, Stuckenschmidt H, Tamilin A. Repairing ontology mappings. In: Proceedings of the 22Nd National Conference on Artificial Intelligence - Volume 2, AAAI’07. AAAI Press;2007. p. 1408–13. http://dl.acm.org/citation.cfm?id=1619797.1619871.
Pesquita C, Faria D, Santos E, Couto FM. To repair or not to repair: Reconciling correctness and coherence in ontology reference alignments. In: Proceedings of the 8th International Conference on Ontology Matching - Volume 1111, OM’13. Aachen, Germany: CEUR-WS.org: 2013. p. 13–24. http://dl.acm.org/citation.cfm?id=2874493.2874495.
Google Scholar
Goldfain A, Smith B, Cowell L. Dispositions and the infectious disease ontology. In: Proceedings of Formal Ontologies in Information Systems (FOIS). Amsterdam: IOS Press: 2010. p. 400–13.
Google Scholar