Protein annotation as term categorization in the gene ontology using word proximity networks

BMC Bioinformatics

Volumn 6, Issue SUPPL.1, 2005, Pages

  Verspoor, Karin ^a   Cohn, Judith ^a   Joslyn, Cliff ^a   Mniszewski, Sue ^a   Rechtsteiner, Andreas ^a   Mocha, Luis M ^b,c   Simas, Tiago ^c  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b INDIANA UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVALUATION RESULTS; GENE ONTOLOGY; PARAMETER SETTING; PROTEIN ANNOTATION; PROXIMITY NETWORKS; SHOW THROUGH; UNSUPERVISED ALGORITHMS;

PROTEINS;

ACCURACY; ARTICLE; BIOINFORMATICS; DNA REPAIR; GENETIC ANALYSIS; HUMAN; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LEARNING ALGORITHM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; AUTOMATED PATTERN RECOGNITION; CLASSIFICATION; GENE; GENETIC DATABASE; PROCEDURES; WRITING;

PROTEIN;

DATABASES, GENETIC; GENES; PATTERN RECOGNITION, AUTOMATED; PROTEINS; WRITING;

EID: 33947330321     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-S1-S20     Document Type: Article

References (13)

1. The Gene Ontology Cosortium: Gene Ontology: Tool For the Unification of Biology. Nature Genetics 2000, 25(1):25-29.
2. Rocha LM: Semi-metric Behavior in Document Networks and its Application to Recommendation Systems. In Soft Computing Agents: A New Perspective for Dynamic Information Systems Edited by: Loia V. International Series Frontiers in Artificial Intelligence and Applications. IOS Press; 2002:137-163.
3. Joslyn C, Mniszewski S, Fulmer A, Heaton G: The Gene Ontology Categorizer. Bioinformatics 2004, 20(Suppl 1):I169-I177.
4. Witten IH, Moffat A, Bell T: Managing Gigabytes: Compressing and Indexing Documents and Images New York: Van Nostrand Reinhold; 1994.
5. Cunningham H, Maynard D, Bontcheva K, Tablan V: GATE: A Framework and Graphical Development Environment for Robust NLP Tools and Applications. Proceedings of the 40th Anniversary Meeting of the Association for Computational Linguistics (ACL'02); Philadelphia 2002:168-175.
6. Rocha LM, Bollen J: Biologically Motivated Distributed Designs for Adaptive Knowledge Management. In Design Principles for the Immune System and other Distributed Autonomous Systems Edited by: Segel L, Cohen I. Santa Fe Institute Series in the Sciences of Complexity. Oxford University Press; 2001:305-334.
7. Mordeson JN, Nair PS: Fuzzy Graphs and Fuzzy Hypergraphs Springer-Verlag; 2000.
8. Rocha LM: Automatic Conversation Driven by Uncertainty Reduction and Combination of Evidence for Recommendation Agents. In Systematic Organization of Information in Fuzzy Systems. NATO Science Series Edited by: Melo-Pinto P, Teodorescu HN, Fukuda T. IOS Press; 2003:249-265.
9. Shatkay, et al.: Genes, Themes and Microarrays Using Information Retrieval for Large-Scale Gene Analysis. In ISMB 2000 AAAI Press; 2000:317-328.
10. Joslyn C, Mniszewski S, Fulmer A, Heaton G: Structural Classification in the Gene Ontology. Proceedings of the Sixth Annual Bio-Ontologies Meeting (Bio-Ontologies 2003), Brisbane, Australia 2003.
11. Joslyn C: Poset Ontologies and Concept Lattices as Semantic Hierarchies. Conceptual Structures at Work, Lecture Notes in Artificial Intelligence 2004, 3127:287-302.
12. Deng M, Tu Z, Sun F, Chen R: Mapping Gene Ontology to Proteins Based on Protein-Protein Interaction Data. Bioinformatics 2004, 20(6):895-902.
13. Schroder, Bernd SW: Ordered Sets, Birkhauser, Boston 2003.