Datamining with ontologies

Methods in Molecular Biology

Volumn 1415, Issue , 2016, Pages 385-397

  Hoehndorf, Robert ^a   Gkoutos, Georgios V ^a   Schofield, Paul N ^a  

^a NONE

Author keywords

Automated reasoning; Data integration; Enrichment; Graph algorithms; Ontology; Semantic similarity; Semantic Web; Web Ontology Language (OWL)

Indexed keywords

BIOMEDICINE; DATA MINING; HUMAN; MEDICAL ONTOLOGY; NONHUMAN; ALGORITHM; BIOLOGICAL ONTOLOGY; BIOLOGY; FACTUAL DATABASE; PROCEDURES; SEMANTIC WEB;

ALGORITHMS; BIOLOGICAL ONTOLOGIES; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, FACTUAL; SEMANTIC WEB;

EID: 84984979145     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3572-7_19     Document Type: Chapter

References (55)

1. Herre H, Heller B, Burek P, Hoehndorf R, Loebe F, Michalek H (2006) General Formal Ontology (GFO)–a foundational ontology integrating objects and processes [Version 1.0]. Onto-Med Report, IMISE, University of Leipzig, Leipzig, Germany
2. Gruber TR (1995) Toward principles for the design of ontologies used for knowledge sharing. Int J Hum Comput Stud 43: 907–928
3. Salvadores M, Alexander PR, Musen MA, Noy NF (2013) Bioportal as a dataset of linked biomedical ontologies and terminologies in RDF. Semant Web 4: 277–284
4. Cote R, Jones P, Apweiler R, Hermjakob H (2006) The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7: 97
5. Xiang Z, Mungall CJ, Ruttenberg A, He Y (2011) Ontobee: a linked data server and browser for ontology terms. In: Proceedings of international conference on biomedical ontology, pp 279–281
6. Hoehndorf R, Slater L, Schofield PN, Gkoutos GV (2015) Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics 16: 26
7. Berners-Lee T, Hendler J, Lassila O, et al. (2001) The semantic web. Sci Am 284: 28–37
8. Grau B, Horrocks I, Motik B, Parsia B, Patelschneider P, Sattler U (2008) OWL 2: the next step for OWL. Web Semant 6: 309–322
9. Horrocks I (2007) OBO flat file format syntax and semantics and mapping to OWL Web Ontology Language. Tech. rep. http://www.cs.man.ac.uk/~horrocks/obo/, University of Manchester
10. Baader F (2003) The description logic handbook: theory implementation and applications. Cambridge University Press, Cambridge
11. Barwise J (1989) The situation in logic. CSLI, Stanford, CA
12. Noy NF, Sintek M, Decker S, Crubezy M, Fergerson RW, Musen MA (2001) Creating semantic web contents with protege-2000. IEEE Intell Syst 16: 60–71
13. Horridge M, Bechhofer S, Noppens O (2007) Igniting the OWL 1.1 touch paper: the OWL API. In: Proceedings of OWLED 2007: third international workshop on OWL experiences and directions
14. Carroll JJ, Dickinson I, Dollin C, Reynolds D, Seaborne A, Wilkinson K (2003) Jena: implementing the semantic web recommendations. Technical Report, Hewlett Packard, Bristol, UK
15. Hoehndorf R, Schofield PN, Gkoutos GV (2015) The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform 16: 1069–1080
16. Gkoutos GV, Green EC, Mallon AMM, Hancock JM, Davidson D (2005) Using ontologies to describe mouse phenotypes. Genome Biol 6: R5
17. Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, Ashburner M (2010) Integrating phenotype ontologies across multiple species. Genome Biol 11: R2+
18. Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Howe DG, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Bauer Schaper H, Schaper K, Shao X, Singer A, Sprague J, Sprunger B, Van Slyke C, Westerfield M (2011) ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res 39 (Suppl 1): D822–D829
19. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545–15550
20. Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C (2012) Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform 13: 281–291
21. Wittkop T, TerAvest E, Evani U, Fleisch K, Berman A, Powell C, Shah N, Mooney S (2013) STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. BMC Bioinformatics 14: 53
22. Hoehndorf R, Hancock JM, Hardy NW, Mallon AM, Schofield PN, Gkoutos GV (2014) Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome 25: 32–40
23. Prfer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Paabo S, Lachmann M, Enard W (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41+
24. Guzzi PH, Mina M, Guerra C, Cannataro M (2011) Semantic similarity analysis of protein data: assessment with biological features and issues. Brief Bioinform 13: 569–585
25. Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD (2010) IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics 11: 588
26. Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res 39: e119
27. Hoehndorf R, Hiebert T, Hardy NW, Schofield PN, Gkoutos GV, Dumontier M (2014) Mouse model phenotypes provide information about human drug targets. Bioinformatics 30: 719–725
28. Zemojtel T, Khler S, Mackenroth L, Jger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, ien NC, Schweiger MR, Krger U, Frommer G, Fischer B, Kornak U, Flttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN (2014) Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med 6: 252ra123
29. Ferreira JD, Couto FM (2010) Semantic similarity for automatic classification of chemical compounds. PLoS Comput Biol 6: e1000937
30. Pesquita C, Faria D, Falcao AO, Lord P, Couto FM (2009) Semantic similarity in biomedical ontologies. PLoS Comput Biol 5: e1000443
31. Resnik P (1999) Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. J Artif Intell Res 11: 95–130
32. Harispe S, Ranwez S, Janaqi S, Montmain J (2014) The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. Bioinformatics 30: 740–742
33. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 7: e1000247
34. Khler S, Schulz MH, Krawitz P, Bauer S, Doelken S, Ott CE, Mundlos C, Horn D, Mundlos S, Robinson PN (2009) Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am J Hum Genet 85: 457–464
35. Yu G, Wang LG, Yan GR, He QY (2015) DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics 31: 608–609
36. Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976–978
37. Deng Y, Gao L, Wang B, Guo X (2015) HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PLoS ONE 10: e0115692
38. Zhu S, Zeng J, Mamitsuka H (2009) Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinformatics 25: 1944–1951
39. Oellrich A, Jacobsen J, Papatheodorou I, Project TSMG, Smedley D (2014) Using association rule mining to determine promising secondary phenotyping hypotheses. Bioinformatics 30: i52–i59
40. Zhou X, Menche J, Barabsi AL, Sharma A (2014) Human symptoms–disease network. Nat Commun 5: 4212
41. Hoehndorf R, Schofield PN, Gkoutos GV (2015b) Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. Sci Rep 5: 10888
42. Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJF, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z (2014) Overview of the gene ontology task at BioCreative IV. Database 2014: bau086
43. Funk C, Baumgartner W, Garcia B, Roeder C, Bada M, Cohen K, Hunter L, Verspoor K (2014) Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics 15: 59
44. Rebholz-Schuhmann D, Oellrich A, Hoehndorf R (2012) Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet 13: 829–839
45. Wolstencroft K, Lord P, Tabernero L, Brass A, Stevens R (2006) Protein classification using ontology classification. Bioinformatics 22: e530–e538
46. Croset S, Overington JP, Rebholz-Schuhmann D (2013) Brain: biomedical knowledge manipulation. Bioinformatics 29: 1238–1239
47. Huntley R, Harris M, Alam-Faruque Y, Blake J, Carbon S, Dietze H, Dimmer E, Foulger R, Hill D, Khodiyar V, Lock A, Lomax J, Lovering R, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall C (2014) A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics 15: 155
48. Kazakov Y (2008) RIQ and SROIQ are harder than SHOIQ. In: Proceeding of KR. AAAI Press, Menlo Park, pp 274–284
49. Stuckenschmidt H, Parent C, Spaccapietra S (2009) Modular ontologies: concepts, theories and techniques for knowledge modularization, 1st edn. Springer, Berlin
50. Motik B, Grau BC, Horrocks I, Wu Z, Fokoue A, Lutz C (2009) OWL 2 Web Ontology Language: profiles. Recommendation, World Wide Web Consortium (W3C)
51. Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV (2011) A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics 27: 1001–1008
52. Kazakov Y, Krtzsch M, Simank F (2011) Unchain my EL reasoner. In: Proceedings of the 23rd international workshop on description logics (DL’10). CEUR workshop proceedings. CEUR-WS.org
53. Bail S, Glimm B, Jimnez-Ruiz E, Matentzoglu N, Parsia B, Steigmiller A (eds) (2014) ORE 2014: OWL reasoner evaluation workshop. CEUR workshop proceedings. CEUR-WS. org, Aachen, Germany
54. McInnes BT, Pedersen T (2013) Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. J Biomed Inform 46: 1116–1124 (Spec Sect Soc Media Environ)
55. Lord PW, Stevens RD, Brass A, Goble CA (2003) Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275–1283