Towards a proteomics meta-classification

Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Volumn , Issue , 2004, Pages 419-426

  Kumar, Anand ^a,b   Smith, Barry ^a,c  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF PAVIA   (Italy)

^c UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESSES; MOLECULAR FUNCTIONS; PROTEIN DATA BANK (PDB); STRUCTURAL CLASSIFICATION OF PROTEINS (SCOP);

CELL MEMBRANES; DATA ACQUISITION; DATABASE SYSTEMS; GENES; PATHOLOGY; PHYSIOLOGY; POLYPEPTIDES; RNA;

PROTEINS;

EID: 4544299739     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2004.1317373     Document Type: Conference Paper

References (27)

1. Ouzounis CA, Coulson RM, Enright AJ, Kunin V, Pereira-Leal JB. Classification schemes for protein structure and function. Nat Rev Genet. 2003 Jul; 4(7):508-19.
2. Liu J, Rost B. Comparing function and structure between entire proteomes. Prote Sci. Oct;10(10):1970-9, 2001.
3. Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acid Res. 30(1), 264-267.
4. http://scop.mrc-lmb.cam.ac.uk/scop/
5. Bourne PE, Weissig H. The Protein Data Bank. Structural Bioinformatics. Hoboken NJ, John Wiley. 2003; 181-198.
6. http://www.rcsb.org/pdb/
7. Gasteiger E, Jung E, Bairoch A. Swiss-Prot: connecting biomolecular knowledge via a protein database. Curr Issues Mol Biol. 2001 Jul;3(3):47-55.
8. http://us.expasy.org/sprot/
9. Gene Ontology Consortium. Creating the Gene Ontology Genome Res. 2001. 11: 1425-1433.
10. http://www.geneontology.org/
11. Smith B, Williams J and Schulze-Kremer S. The Ontology of the Gene Ontology. Proc AMIA Symp. 2003.
12. http://www.geneontology.org/doc/GO.doc.html
13. http://www.ncbi.nlm.nih.gov/LocusLink/
14. http://www.uni-leipzig.de/~akumar/colon_cancer.zip
15. http://www.uni-leipzig.de/~akumar/colorectal_cancer.-zip
16. Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L. The compositional structure of Gene Ontology terms. Pacific Symp Biocomputing 2004. http://www-smi.stanford.edu/projects/helix/psb04/ogren.pdf
17. Achour LS, Dojat M, Rieux C, Bierling P, Lepage E. A UMLS-based Knowledge Acquisition Tool for Rule-based Clinical Decision Support System Development. J Am Med Inform Assoc 2001;8(4):351-360.
18. http://www.uni-leipzig.de/~akumar/terms_GO.htm
19. Smith B, Rosse C. The role of foundational relations in the alignment of biomedical ontologies. Medinfo 2004.
20. Smith B and Mulligan K, Framework for formal ontology, Topoi, 1983; 3: 73-85.
21. http://www.geneontology.org/GO.usage.html#partof.
22. Mejino JLV, Agoncillo AV, Rickard KL, Rosse C. Representing complexity in part-whole relationships within the Foundational Model of Anatomy. Proc AMIA Symp. 2003.
23. http://www.geneontology.org/doc-/GO.usage.html#sensu
24. http://www.geneontology.org/GO.synonyms.html
25. http://www.ebi.ac.uk/GOA/
26. Lill R, Stuart RA, Drygas ME, Nargang FE, Neupert W. Import of cytochrome c heme lyase into mitochondria: a novel pathway into the intermembrane space. EMBO J. 1992 Feb;11(2):449-56.
27. Kumar A, Smith B. The Unified Medical Language System and the Gene Ontology: Some Critical Reflections. (Lecture Notes in Computer Science. 2821) 2003: 135-148.