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

Bioinformatics

Volumn 28, Issue 3, 2012, Pages 448-450

  Wimalaratne, Sarala M ^a   Grenon, Pierre ^a   Hoehndorf, Robert ^b   Gkoutos, Georgios V ^b   de Bono, Bernard ^a,c  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER LANGUAGE; FACTUAL DATABASE; HEART; HUMAN; INFORMATION RETRIEVAL; KNOWLEDGE BASE; PHYSIOLOGY; SEMANTICS;

DATABASES, FACTUAL; HEART; HUMANS; INFORMATION STORAGE AND RETRIEVAL; KNOWLEDGE BASES; PROGRAMMING LANGUAGES; SEMANTICS;

EID: 84856569589     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr662     Document Type: Article

References (18)

1. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
2. Bard, J. et al. (2005) An ontology for cell types. Genome Biol., 6, R21.
3. de Bono, B. et al. (2011) The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res. Notes, 4, 313.
4. Côté, R.G. et al. (2008) The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res., 36, W372-W376.
5. Erling, O. and Mikhailov, I. (2007) RDF support in the virtuoso DBMS. Network. Know. Network. Media, 221, 59-68.
6. Fielding, R.T. (2000) Architectural Styles and the Design of Network-based Software Architectures. PhD Thesis. Avaliable at http://www.ics.uci.edu/~fielding/pubs/dissertation/top.htm.
7. Gkoutos, G.V. et al. (2005) Using ontologies to describe mouse phenotypes. Genome Biol., 6, R8.
8. Gkoutos, G.V. et al. (2009) Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf. Proc. IEEE Eng. Med. Biol. Soc., 2009, 7069-7072.
9. Hoehndorf, R. et al. (2011)Acommon layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics, 27, 1001-8.
10. Horridge, M. et al. (2006) The Manchester OWL Syntax. Syntax, 216, 10-11.
11. Hucka, M. et al. (2004) Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Syst. Biol., 1, 41-53.
12. Laibe, C. and Le Novère, N. (2007) MIRIAM resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Syst. Biol., 1, 58.
13. Lloyd, C.M. et al. (2004) CellML: its future, present and past. Progr. Biophys. Mol. Biol., 85, 433-450.
14. De Matos, P. et al. (2010) ChEBI: a chemistry ontology and database. J. Cheminformat., 2, P6.
15. Le Novère, N. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
16. Robinson, P. N. and Mundlos, S. (2010) The human phenotype ontology. Clin. Genet., 77, 525-534.
17. Rosse, C. and Mejino, J.L.V. (2007) The foundational model of anatomy ontology. Esophagus, 2007, 59-117.
18. Smith, B. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251-1255.