Controlled vocabularies in bioinformatics: A case study in the gene ontology

Drug Discovery Today: BIOSILICO

Volumn 2, Issue 6, 2004, Pages 246-252

  Smith, Barry ^a   Kumar, Anand ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

Bioinformatics; Compositionality; Controlled Vocabulary; Gene Ontology; Gene Product Annotation; Genetics; Information Extraction; Ontology; Syntax; Terminology

Indexed keywords

BIOINFORMATICS; GENETICS; INFORMATION PROCESSING; LINGUISTICS; MEDICAL INFORMATION; MEDICAL LITERATURE; REVIEW;

EID: 7944230660     PISSN: 17418364     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1741-8364(04)02424-2     Document Type: Review

References (11)

1. Gene Ontology Consortium. Creating the Gene Ontology resource: Design and implementation. Genome Res. 11:2001;1425-1433
2. Grenon P., Smith B. SNAP and SPAN: Towards dynamic spatial ontology. Spatial Cognition and Computation. 4:2004;69-103
3. Bada M., et al. Using reasoning to guide annotation with Gene Ontology terms in GOAT. SIGMOD. Record. 33:2004;2
4. Kumar, A. et. at Dependence Relationships between Gene Ontology Terms based on TIGR Gene Product Annotations. CompuTerm 2004: 3rd International Workshop on Computational Terminology. (in press)
5. Kumar A., Smith B. The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. Günter R.,, et al. KI 2003: Advances in Artificial Intelligence. Lecture Notes in Artificial Intelligence 2821. 2003;135-145 Springer, Berlin
6. Smith B., et al. The Ontology of the Gene Ontology. Proc. Annual Symposium of the American Medical Informatics Association. 2003;609-613
7. Smith B., Rosse C. The Role of Foundational Relations in Biomedical Ontology Alignment. Fieschi M.,, et al. Proc MEDINFO. 2004;444-448 IOS Press, Amsterdam
8. Schulz S., Hahn U. Mereotopological reasoning about parts and (w)holes in bio-ontologies. Formal Ontology and Information Systems (FOIS 2001). 2001;210-221
9. Hahn U., et al. Mereological semantics for bio-Ontologies. 2004;257-262 AAAI
10. Smith B., et al. On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology. Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994). 2004;79-94 Springer, Berlin
11. Ogren P.V., et al. The Compositional Structure of Gene Ontology Terms. Pac. Symp. Biocomput. 9:2004;214-225