Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot

BMC Bioinformatics

Volumn 6, Issue SUPPL.1, 2005, Pages

  Ehrler, Frédéric ^a,b   Geissbühler, Antoine ^b   Jimeno, Antonio ^a,c   Ruch, Patrick ^b  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^c CERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPETITIVE PERFORMANCE; CONFIDENCE ESTIMATION; GENE ONTOLOGY ANNOTATIONS; MEDICAL SUBJECT HEADINGS; NATURAL LANGUAGE PROCESSING; RECALL AND PRECISION; TEXT CATEGORIZATION; USER PERSPECTIVES;

EXPERIMENTS; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS; TEXT PROCESSING;

DATA MINING;

ACCURACY; ARTICLE; COMPETITION; GENE EXPRESSION; GENE SEQUENCE; GENETIC DATABASE; INTERMETHOD COMPARISON; LANGUAGE PROCESSING; LEARNING ALGORITHM; MEDICAL RESEARCH; PROTEIN ANALYSIS; RECALL; SCORING SYSTEM; SWISS-PROT; AUTOMATED PATTERN RECOGNITION; BIOLOGY; CLASSIFICATION; GENE; INFORMATION RETRIEVAL; NOMENCLATURE; PROCEDURES; PROTEIN DATABASE; WRITING;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENES; INFORMATION STORAGE AND RETRIEVAL; PATTERN RECOGNITION, AUTOMATED; TERMINOLOGY AS TOPIC; WRITING;

EID: 24644514269     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-S1-S23     Document Type: Article

References (45)

1. Hirschman L, Park J, Tsujii J, Wong L, Wu C: Accomplishments and challenges in literature data mining for biology. Bioinformatics 2002, 18(12):1553-1561.
2. Chinchor N: MUC-7 Named-Entity task Definition. MUC 1997.
3. Hull D: Xerox TREC-8 Question Answering Track Report. TREC-8 Report 2000.
4. Kantor P, Voorhees E: The TREC-5 Confusion Track: Comparing Retrieval Methods for Scanned Text. Information Retrieval 2000:165-76.
5. Ruch P: Using contextual spelling correction to improve retrieval effectiveness in degraded text collections. COLING 2002.
6. Mittendorf E, Schauble P: Measuring the Effects of Data Corruption on Information Retrieval. SDAIR Proceedings 1996.
7. Yang Y: Sampling strategies and learning efficiency in text categorization. Proceedings of the AAAI Spring Symposium on Machine Learning in Information Access 1996.
8. McCallum A, Nigam K: A comparison of event models for Naive Bayes text classification. AAAI-98 Workshop on Learning for Text Categorization 1998.
9. Joachims T: Making Large-Scale SVM Learning Practical. Advances in Kernel Methods - Support Vector Learning 1999.
10. Schapire R, Singer Y: BoosTexter: A Boosting-based System for Text Categorization. Machine Learning 2000, 39(2/3):135-168.
11. Apté C, Damerau F, Weiss S: Automated learning of decision rules for text categorization. ACM Transactions on Information Systems (TOIS) 1994, 12(3):233-251.
12. Hayes P, Weinstein S: A System for Content-Based Indexing of a Database of News Stories. Proceedings of the Second Annual Conference on Innovative Applications of Intelligence 1990.
13. Larkey L, Croft W: Combining classifiers in text categorization. SIGIR, ACM Press, New York, US; 1996:289-297.
14. Yang Y, Chute C: A linear least squares fit mapping method for information retrieval from natural language texts. COLING 1992:447-453.
15. Rasolofo Y, Savoy J: Term Proximity Scoring for Keyword-based Retrieval Systems. ECIR 2003:101-116.
16. Hull D, Grefenstette G, Schulze B, Gaussier E, Schutze H, Pedersen J: XEROX TREC-5 site report: Routing, Filtering, NLP, and Spanish tracks. TREC-5 NIST Special Publication 500-238 1997:167-180.
17. Strzalkowski T, Stein G, Wise GB, Carballo JP, Tapanainen P, Jarvinen T, Voutilainen A, Karlgren J: Natural Language Information Retrieval: TREC-7 Report. Text REtrieval Conference 1998:164-173.
18. Tan C, Wang Y, Lee C: The Use of BiGrams to Enhance Text Categorization. Information Processing and Management 2002, 38(4):529-546.
19. Kongovi M, Guzman J, Dasigi V: Text Categorization: An Experiment Using Phrases. ECIR 2002, LNCS 2291:213-220.
20. Tolle K, Chen H: Comparing noun phrasing techniques for use with medical digital library tools. Journal of the American Society for Information Science 2000, 51(4):352-370.
21. Mitra M, Buckley C, Singhal A, Cardie C: An analysis of Statistical and Syntactic Phrases. RIAO 1997:200-214.
22. Arampatzis A, van der Weide T, van Nommel P, Koster C: Linguistically Motivated Information Retrieval. Encyclopedia of Library and Information Sciece 2000, 69:.
23. Stolz W: A probabilistic procedure for grouping words into phrases. Language and Speech 1965, 8:.
24. Ruch P, Baud R, Bouillon P, Robert G: Minimal Commitment and Full Lexical Disambiguation: Balancing Rules and Hidden Markov Models. CoNLL 2000:111-116.
25. Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-8.
26. ConsortiuT TGO: Gene Ontology: tool for the unification of biology. Nature Genetics 2000, 25:25-29.
27. Ruch P, Chichester C, Cohen G, Coray G, Ehrler F, Ghorbel H, Müller H, Pallotta V: Report on the TREC 2003 Experiment: Genomic Track. TREC-12 2004 [http://trec.nist.gov/pubs/trec12/t12_proceedings.html].
28. Reynar J, Ratnaparkhi A: Entropy Approach to Identifying Sentence Boundaries. Proceedings of the ANLP 1997.
29. Ruch P, Baud R, Geissbḧler A: Using Lexical Disambiguation and Named-Entity Recognition to Improve Spelling Correction in the Electronic Patient Record. Art Intell Med 2003, 29(1-2):169-184.
30. Wagner R, Fisher M: The string-to-string correction problem. Journal of the Association of Computing Machinery 1974, 1:168-173.
31. Cohen W, Fienberg PRS: A Comparison of String Distance Metrics for Name-Matching Tasks. IIWeb 2003:73-78.
32. Krallinger M, Padron M: Prediction of GO annotation by Combining Entity Specific Sentence Sliding Windows Profiles. BioCreative Notebook Papers, CNB 2004 [http://www.pdg.cnb.uam.es/BioLink/workshop_BioCreative_04/ handout/].
33. Salton G, McGill M: Introduction to Modern Information Retrieval McGraw Hill Book; 1983.
34. Amati G, van Rijsbergen C: Probabilistic Models of Information Retrieval based on Measuring the Divergence from Randomness. ACM Transactions on Information Systems (TOIS) 2002, 20(4):357-389.
35. Singhal A, Buckley C, Mitra M: Pivoted document length normalization. ACM-SIGIR 1996:21-29.
36. Grabtree I, Soltysiak S: Identifying and Tracking Changing Interests. International Journal of Digital Libraries 1998, 2:38-53.
37. Klinkenberg R, Joachims T: Detecting Concept Drift with Support Vector Machines. Proceedings of ICML 2000:487-494.
38. Park Y, Byrd R, Boguraev B: Automatic Glossary Extraction: Beyond Terminology Identification. COLING 2002.
39. Verspoor K, Cohn J, Joslyn C, Mniszewski S: Protein Annotation as Term categorization in the Gene Ontology. BioCreative Notebook Papers, CNB 2004 [http://www.pdg.cnb.uam.es/BioLink/workshop_BioCreative_04/ handout/].
40. Couto F, Silva M, Coutinho P: FIGO: Findings GO Terms in UnStructured Text. BioCreative Notebook Papers, CNB 2004 [http://www.pdg.cnb.uam.es/ BioLink/workshop_BioCreative_04/handout/].
41. Hanish D, Fundel K, Mevissen H, Zimmer R, Fluck J: ProMiner: Organism-specific protein name detecion using approximate string matching. BioCreative Notebook Papers, CNB 2004 [http://www.pdg.cnb.uam.es/BioLink/workshop_BioCreative_04/handout/].
42. Crim J, McDonald R, Pereira F: Automatically Annotating Documents with Normalized Gene Lists. BioCreative Notebook Papers, CNB 2004 [http://www.pdg.cnb.uam.es/BioLink/workshop_BioCreative_04/handout/].
43. Hersh W, Bhupatiraju R: TREC GENOMICS Track Overview. TREC-12 2004 [http://trec.nist.gov/pubs/trec12/t12_proceedings.html].
44. Mizuta Y, Collier N: Zone Identification in Biology Articles as a Basis for Information Extraction. COLING Workshop on Natural Language Processing in Biomedicine and its Application (JNLPBA) 2004.
45. Tbahriti I, Chichester C, Lisacek F, Ruch P: Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE. COLING Workshop on Natural Language Processing in Biomedicine and its Application (JNLPBA) 2004.