Bioinformatics pp 123-135 | Cite as

Working with Ontologies

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1525)

Abstract

Ontologies are powerful and popular tools to encode data in a structured format and manage knowledge. A large variety of existing ontologies offer users access to biomedical knowledge. This chapter contains a short theoretical background of ontologies and introduces two notable examples: The Gene Ontology and the ontology for Biological Pathways Exchange. For both ontologies a short overview and working bioinformatic applications, i.e., Gene Ontology enrichment analyses and pathway data visualization, are provided.

Key words

Data management Knowledge management Ontologies BioPAX rBiopaxParser Gene ontology topGO GOstat 

References

  1. 1.
    Gruber TR (1995) Toward principles for the design of ontologies used for knowledge sharing? Int J Hum Comput Stud 43:907–928CrossRefGoogle Scholar
  2. 2.
    Berners-Lee T, Hendler J, Lassila O et al (2001) The semantic web. Sci Am 284:28–37CrossRefGoogle Scholar
  3. 3.
    Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Demir E, Cary MP, Paley S et al (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28:935–942CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Burkhardt H, Smith B (1991) Handbook of metaphysics and ontology. Philosophia Verlag, MuenchenGoogle Scholar
  6. 6.
    Gruber TR (1993) A translation approach to portable ontology specifications. Knowl Acquis 5(2):199–220CrossRefGoogle Scholar
  7. 7.
    Noy NF, McGuinness DL et al (2001) Ontology development 101: a guide to creating your first ontology. Stanford knowledge systems laboratory technical report KSL-01-05 and Stanford medical informatics technical report SMI-2001-0880Google Scholar
  8. 8.
    Hitzler P, Krotzsch M, Rudolph S (2011) Foundations of semantic web technologies. CRC Press, Boca Raton, FLGoogle Scholar
  9. 9.
    du Plessis L, Škunca N, Dessimoz C (2011) The what, where, how and why of gene ontology—a primer for bioinformaticians. Brief Bioinform 12:723–735CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Beißbarth T, Speed TP (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20:1464–1465CrossRefPubMedGoogle Scholar
  11. 11.
    Beißbarth T (2006) Interpreting experimental results using gene ontologies. In: Kimmel A, Oliver B (eds) Methods Enzymol. Academic, Waltham, pp 340–352Google Scholar
  12. 12.
    Guo X, Liu R, Shriver CD et al (2006) Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 22:967–973CrossRefPubMedGoogle Scholar
  13. 13.
    Fröhlich H, Speer N, Poustka A, Beißbarth T (2007) GOSim—an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 8:166CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Cheng L, Li J, Ju P et al (2014) SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PLoS One 9:e99415CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Hoehndorf R, Hancock JM, Hardy NW et al (2014) Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome Off J Int Mamm Genome Soc 25:32–40CrossRefGoogle Scholar
  16. 16.
    Xu Q, Shi Y, Lu Q et al (2008) GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics 9(Suppl 1):S6CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Chi Y-L, Chen T-Y, Tsai W-T (2015) A chronic disease dietary consultation system using OWL-based ontologies and semantic rules. J Biomed Inform 53:208–219CrossRefPubMedGoogle Scholar
  18. 18.
    Nadkarni PM, Marenco LA (2010) Implementing description-logic rules for SNOMED-CT attributes through a table-driven approach. J Am Med Inform Assoc 17:182–184CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Rector AL, Brandt S (2008) Why do it the hard way? The case for an expressive description logic for SNOMED. J Am Med Inform Assoc 15:744–751CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Degtyarenko K, de Matos P, Ennis M et al (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36:D344–D350CrossRefPubMedGoogle Scholar
  21. 21.
    Smith B, Ashburner M, Rosse C et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251–1255CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Noy NF, Shah NH, Whetzel PL et al (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37:W170–W173CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Rubin DL, Shah NH, Noy NF (2008) Biomedical ontologies: a functional perspective. Brief Bioinform 9:75–90CrossRefPubMedGoogle Scholar
  24. 24.
    Côté R, Reisinger F, Martens L et al (2010) The Ontology Lookup Service: bigger and better. Nucleic Acids Res 38:W155–W160CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    McGuinness DL, Van Harmelen F et al (2004) OWL web ontology language overview. W3C Recomm 10Google Scholar
  26. 26.
    Beckett D, McBride B (2004) RDF/XML syntax specification (revised). W3C Recomm 10Google Scholar
  27. 27.
    Bray T, Paoli J, Sperberg-McQueen CM et al (1997) Extensible markup language (XML). World Wide Web J 2:27–66Google Scholar
  28. 28.
    Klyne G, Carroll JJ, McBride B (2004) Resource description framework (RDF): concepts and abstract syntax. W3C Recomm 10Google Scholar
  29. 29.
    Gennari JH, Musen MA, Fergerson RW et al (2003) The evolution of Protégé: an environment for knowledge-based systems development. Int J Hum Comput Stud 58:89–123CrossRefGoogle Scholar
  30. 30.
    Horridge M, Tudorache T, Nuylas C et al (2014) WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. Bioinformatics 30:2384–2385CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Demir E, Babur Ö, Rodchenkov I et al (2013) Using biological pathway data with Paxtools. PLoS Comput Biol 9:e1003194CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    The Geno Ontology Consortium (2014) Gene Ontology Consortium: going forward. Nucleic Acids Res 43(Database issue):D1049–D1056Google Scholar
  33. 33.
    Bindea G, Mlecnik B, Hackl H et al (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091–1093CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Kramer F, Bayerlová M, Klemm F et al (2013) rBiopaxParser—an R package to parse, modify and visualize BioPAX data. Bioinformatics 29:520–522CrossRefPubMedGoogle Scholar
  35. 35.
    The Geno Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36:D440–D444CrossRefGoogle Scholar
  36. 36.
    Shannon P, Markiel A, Ozier O et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    R Core Team (2013) R: a language and environment for statistical computing, Vienna, AustriaGoogle Scholar
  38. 38.
    Schröder MS, Gusenleitner D, Quackenbush J et al (2013) RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. Bioinformatics 29:666–668CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Pesquita C, Faria D, Bastos H et al (2008) Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics 9:S4CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Jiang R, Gan M, He P (2011) Constructing a gene semantic similarity network for the inference of disease genes. BMC Syst Biol 5:S2CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Andronis C, Sharma A, Virvilis V et al (2011) Literature mining, ontologies and information visualization for drug repurposing. Brief Bioinform 12:357–368CrossRefPubMedGoogle Scholar
  42. 42.
    Kramer M, Dutkowski J, Yu M et al (2014) Inferring gene ontologies from pairwise similarity data. Bioinformatics 30:i34–i42CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Dutkowski J, Ono K, Kramer M et al (2014) NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res 42:D1269–D1274CrossRefPubMedGoogle Scholar
  44. 44.
    Dutkowski J, Kramer M, Surma MA et al (2013) A gene ontology inferred from molecular networks. Nat Biotechnol 31:38–45CrossRefPubMedGoogle Scholar
  45. 45.
    Zheng Q, Wang X-J (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36:W358–W363CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Huang DW, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1–13CrossRefGoogle Scholar
  47. 47.
    Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0—a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24:1650–1651CrossRefPubMedGoogle Scholar
  48. 48.
    Eden E, Navon R, Steinfeld I et al (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Huang DW, Sherman BT, Tan Q et al (2007) DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res 35:W169–W175CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21:3448–3449CrossRefPubMedGoogle Scholar
  51. 51.
    Hucka M, Finney A, Sauro HM et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531CrossRefPubMedGoogle Scholar
  52. 52.
    Hermjakob H, Montecchi-Palazzi L, Bader G et al (2004) The HUPO PSI’s Molecular Interaction format—a community standard for the representation of protein interaction data. Nat Biotechnol 22:177–183CrossRefPubMedGoogle Scholar
  53. 53.
    Strömbäck L, Lambrix P (2005) Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics 21:4401–4407CrossRefPubMedGoogle Scholar
  54. 54.
    Cary MP, Bader GD, Sander C (2005) Pathway information for systems biology. FEBS Lett 579:1815–1820CrossRefPubMedGoogle Scholar
  55. 55.
    Kramer F (2014) Integration of pathway data as prior knowledge into methods for network reconstruction. Georg-August-Universitat Göttingen, GöttingenGoogle Scholar
  56. 56.
    Bader GD, Cary MP, Sander C (2006) Pathguide: a pathway resource list. Nucleic Acids Res 34:D504–D506CrossRefPubMedGoogle Scholar
  57. 57.
    Ogata H, Goto S, Sato K et al (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–34CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Joshi-Tope G, Gillespie M, Vastrik I et al (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 33:D428–D432CrossRefPubMedGoogle Scholar
  59. 59.
    Kelder T, van Iersel MP, Hanspers K et al (2011) WikiPathways: building research communities on biological pathways. Nucleic Acids Res 40:D1301–D1307CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Pico AR, Kelder T, van Iersel MP et al (2008) WikiPathways: pathway editing for the people. PLoS Biol 6:e184CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Vastrik I, D’Eustachio P, Schmidt E et al (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8:R39CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Schaefer CF, Anthony K, Krupa S et al (2009) PID: the pathway interaction database. Nucleic Acids Res 37:D674–D679CrossRefPubMedGoogle Scholar
  63. 63.
    Bauer-Mehren A, Furlong LI, Sanz F (2009) Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol Syst Biol 5:290CrossRefPubMedPubMedCentralGoogle Scholar
  64. 64.
    Cerami EG, Gross BE, Demir E et al (2011) Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 39:D685–D690CrossRefPubMedGoogle Scholar
  65. 65.
    Gentleman RC, Carey VJ, Bates DM et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80CrossRefPubMedPubMedCentralGoogle Scholar
  66. 66.
    Kramer F, Bayerlová M, Beißbarth T (2014) R-based software for the integration of pathway data into bioinformatic algorithms. Biology 3:85–100CrossRefPubMedPubMedCentralGoogle Scholar
  67. 67.
    Shannon PT, Grimes M, Kutlu B et al (2013) RCytoscape: tools for exploratory network analysis. BMC Bioinformatics 14:217CrossRefPubMedPubMedCentralGoogle Scholar
  68. 68.
    Csardi G, Nepusz T (2006) The igraph software package for complex network research. Int J Complex Syst 1695Google Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Medical StatisticsUniversity Medical Center GöttingenGöttingenGermany

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