Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature

Genome Research

Volumn 12, Issue 1, 2002, Pages 203-214

  Raychaudhuri, Soumya ^a   Chang, Jeffrey T ^a   Sutphin, Patrick D ^a   Altman, Russ B ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACT REPORT; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DOCUMENT EXAMINATION; ENTROPY; GENE FUNCTION; GENETIC ASSOCIATION; INFORMATION PROCESSING; NOMENCLATURE; PRIORITY JOURNAL; SCIENTIFIC LITERATURE; STANDARDIZATION; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES, FUNGAL; RESEARCH; SACCHAROMYCES CEREVISIAE;

EID: 0036144742     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.199701     Document Type: Article

References (42)

1. The genome sequence of Drosophila melanogaster
2. Basic local alignment search tool
3. Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system
4. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
5. Selection of MEDLINE contents, the development of its thesaurus, and the indexing process
6. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
7. Characterization of single-nucleotide polymorphisms in coding regions of human genes
8. Accessing genetic information with high-density DNA arrays
9. SGD: Saccharomyces Genome Database
10. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
11. Constructing biological knowledge bases by extracting information from text sources
12. Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries
13. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
14. Indexing consistency in MEDLINE
15. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis
16. Developing NLP Tools for Genome Informatics: An Information Extraction Perspective
17. Better prediction of protein cellular localization sites with the k nearest neighbors classifier
18. The EMOTIF database
19. Medline for Health Professionals: How to Search PubMed on the Internet
20. Hidden Markov models in computational biology. Applications to protein modeling
21. A biochemical genomics approach for identifying genes by the activity of their products
22. MIPS: A database for genomes and protein sequences
23. Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts
24. Using maximum entropy for text classification
25. A pragmatic information extraction strategy for gathering data on genetic interactions
26. A simple introduction to maximum entropy models. Institute for Research in Cognitive Science, Technical Report
27. Functions of the gene products of
28. Information access. Building a 'GenBank' of the published literature
29. Two decades of statistical language modeling: Where do we go from here?
30. Large-scale analysis of the yeast genome by transposon tagging and gene disruption
31. Quantitative monitoring of gene expression patterns with a complementary DNA microarray
32. Genes, themes and microarrays: Using information retrieval for large-scale gene analysis
33. Detecting gene relations from Medline abstracts
34. EUCLID: Automatic classification of proteins in functional classes by their database annotations
35. Automatic extraction of protein interactions from scientific abstracts
36. Multiple independent defective suppressor-mutator transposon insertions in Arabidopsis: A tool for functional genomics
37. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
38. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis