Implications of compositionality in the gene ontology for its curation and usage

Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005

Volumn , Issue , 2005, Pages 174-185

  Ogren, Philip V ^a   Bretonnel Cohen, K ^b   Hunter, Lawrence ^b  

^a UCB 450   (United States)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC ANNOTATION; AUTOMATICALLY GENERATED; COMBINATORIAL PROPERTIES; COMPOSITIONAL STRUCTURE; COMPOSITIONAL VARIATION; COMPOSITIONALITY; CONCEPTUAL CHANGE; CURATION; DATABASE ANNOTATION; GENE ONTOLOGY; GO TERMS; NEW TERMS;

DNA;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; GENE; GENETICS; HUMAN; METHODOLOGY; NUCLEIC ACID DATABASE; PROTEIN DATABASE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; DNA; GENES; HUMANS; MODELS, GENETIC;

EID: 15944422180     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (14)

1. Gene Ontology Consortium, "Gene Ontology: tool for the unification of biology." Nature 25:25-29 (2000).
2. Gene Ontology Consortium, "Creating the Gene Ontology resource: design and implementation." Genome Research 11:1425-1433 (2001).
3. C.M. Verspoor, C. Joslyn and G.J. Papcun, "The Gene Ontology as a source of lexical semantic knowledge for a biological natural language processing application, " Participant notebook of the ACM SIGIR'03 workshop on text analysis and search for bioinformatics, pp. 51-56 (2003).
4. C.J. Wroe, R. Stevens, C.A. Goble and M. Ashburner, "A methodology to migrate the Gene Ontology to a description logic environment using DAML+OIL." Pacific Symposium on Biocomputing 2003.
5. I. Yeh, P.D. Karp, N.F. Noy and R.B. Altman, "Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)." Bioinformatics 19(2):241-248, 2003.
6. C.A. Joslyn, S.M. Mniszewski, A. Fulmer and G. Heaton, "The Gene Ontology categorizer." Bioinformatics, in press. C. Mungall, "Open Bio-Ontology Language." 7th Annual Bio-Ontologies Meeting (2004), http://bio-ontologies.man.ac.uk7obol-glasgow.ppt.
7. M. Bada, R. McEntire, C. Wroe and R. Stevens, "GOAT: The Gene Ontology Annotation Tool." Proceedings of the 2003 UK e-Science All Hands Meeting, 514-519 (2003).
8. K.M.Verspoor, J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L.M. Rocha and T.Simas, "Protein annotation as term categorization in the Gene Ontology using word proximity networks." BMC Bioinformatics in submission.
9. P.V. Ogren, K.B. Cohen, G.K. Acquaah-Mensah, J. Eberlein, and L. Hunter, "The compositional structure of Gene Ontology terms." Proceedings of the Pacific Symposium on Bio computing 2004, pp. 214-225.
10. D. Jurafsky and J.H. Martin, Speech and language processing. Prentice Hall (2000).
11. V.I. Levenshtein, "Binary codes capable of correcting deletions, insertions, and reversals." Cybernetics and control theory 10(8):707-710 (1966).
12. B.H. Partee, A. ter Meulen, and R.E. Wall, Mathematical methods in linguistics, corrected 1st edition. Kluwer Academic Publishers (1987).
13. A.L. Rector, "Clinical terminology: why is it so hard?" Methods of Information in Medicine. 38:239-52 (1999).
14. J. Bard and M. Ashburner, Cell Type Ontology, http://obo.sourceforge.net/ (2004).