New challenges for text mining: Mapping between text and manually curated pathways

BMC Bioinformatics

Volumn 9, Issue SUPPL. 3, 2008, Pages

  Oda, Kanae ^a   Kim, Jin Dong ^a   Ohta, Tomoko ^a   Okanohara, Daisuke ^a   Matsuzaki, Takuya ^a   Tateisi, Yuka ^b   Tsujii, Jun'ichi ^a,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b KOGAKUIN UNIVERSITY   (Japan)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC CONSTRUCTION; BIOLOGICAL DOMAIN; CAUSAL RELATIONSHIPS; TEXT MINING;

DATA MINING;

I KAPPA B ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TOLL LIKE RECEPTOR;

AMINO ACID SEQUENCE; BINDING AFFINITY; BIOINFERENCE; CITATION ANALYSIS; CONFERENCE PAPER; DATA MINING; GENE EXPRESSION; GENE SEQUENCE; GENE TRANSLOCATION; INFORMATION PROCESSING; LIGAND BINDING; MACHINE LEARNING; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SYSTEM ANALYSIS; TEXT MINING; ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BOOK; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING; NOMENCLATURE; PUBLICATION;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DICTIONARIES AS TOPIC; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PERIODICALS AS TOPIC; TERMINOLOGY AS TOPIC; VOCABULARY, CONTROLLED;

EID: 44649178742     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S3-S5     Document Type: Conference Paper

References (26)

1. Bader GD Cary MP Sander C Pathguide: A pathway resource list Nucleic Acids Res 2006, 34:D504-506. 1347488 16381921 10.1093/nar/gkj126
2. Luciano JS Stevens RD e-Science and biological pathway semantics BMC Bioinformatics 2007, 8(Suppl 3):S3. 1892100 17493286 10.1186/ 1471-2105-8-S3-S3
3. Rzhetsky A Iossifov I Koike T Krauthammer M Kra P Morris M Yu H Duboue PA Weng W Wilbur WJ et al. GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data J Biomed Inform 2004, 37:43-53. 10.1016/j.jbi.2003.10.001 15016385
4. Park JC Kim HS Kim JJ Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar Pac Symp Biocomput 2001:396-407. 11262958
5. Rajagopalan D Agarwal P Inferring pathways from gene lists using a literature-derived network of biological relationships Bioinformatics 2005, 21:788-793. 10.1093/bioinformatics/bti069 15509611
6. Santos C Eggle D States DJ Wnt pathway curation using automated natural language processing: Combining statistical methods with partial and full parse for knowledge extraction Bioinformatics 2005, 21:1653-1658. 10.1093/bioinformatics/bti165 15564295
7. Ohta T Tateisi Y Mima H Tsujii J GENIA corpus: An annotated research abstract corpus in molecular biology domain Proceedings of the Human Language Technology Conference (HLT 2002) San Diego, California 2002:73-77.
8. Kim J Ohta T Tsujii J Corpus annotation for mining biomedical events from literature BMC Bioinformatics 2008, 9:10. 10.1186/1471-2105-9-10 18182099 2267702
9. Oda K Kitano H A comprehensive map of the toll-like receptor signaling network Mol Syst Biol 2006, 2:2006.0015. 1681489 16738560 10.1038/ msb4100057
10. Rune S Yoshida K Yakushiji A Miyao Y Matsubayashi Y Ohta T AKANE System: Protein-Protein Interaction Pairs in BioCreAtIvE2 Challenge, PPI-IPS subtask In the Proceedings of the Second BioCreative Challenge Evaluation Workshop; April Madrid, Spain 2007:1-3.
11. Morgan A Hirschman L Overview of BioCreative II Gene Normalization Proceedings of the Second BioCreative Challenge Evaluation Workshop Madrid, Spain 2007:7-16.
12. McDonald DM Chen H Su H Marshall BB Extracting gene pathway relations using a hybrid grammar: The Arizona Relation Parser Bioinformatics 2004, 20:3370-3378. 10.1093/bioinformatics/bth409 15256411
13. Yakushiji A Miyao Y Tateisi Y Tsujii J Biomedical Information Extraction with Predicate-Argument Structure Patterns the First International Symposium on Semantic Mining in Biomedicine Hinxton, Cambridgeshire, UK 2005:60-69.
14. Temkin JM Gilder MR Extraction of protein interaction information from unstructured text using a context-free grammar Bioinformatics 2003, 19:2046-2053. 10.1093/bioinformatics/btg279 14594709
15. Daraselia N Yuryev A Egorov S Novichkova S Nikitin A Mazo I Extracting human protein interactions from MEDLINE using a full-sentence parser Bioinformatics 2004, 20:604-611. 10.1093/bioinformatics/btg452 15033866
16. Krallinger M Leitner F Valencia A Assessment of the Second BioCreative PPI task: Automatic Extraction of Protein-Protein Interactions Proceedings of the Second BioCreative Challenge Evaluation Workshop Madrid, Spain 2007:41-54.
17. Wilson G Mani I Sundheim B Ferro L A multilingual approach to annotating and extracting temporal information Proceeding of the workshop on Temporal and spatial information processing 2001:7.
18. Kontos J Elmaoglou A Malagardi I ARISTA Causal Knowledge Discovery from Texts Proceedings of 5th International Conference, DS 2002 Springer Berlin/Heidelberg 2002:348-355. Nov 24-26; Lubeck, Germany
19. Kim J Ohta T Oda K Tsujii J From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC) 2008. to appear
20. Schulz S Kumar A Bittner T Biomedical ontologies: What part-of is and isn't J Biomed Inform 2006, 39:350-361. 10.1016/j.jbi.2005.11.003 16442850
21. Tsujii J Ananiadou S Thesaurus or logical ontology, which do we need for mining text? Language Resources and Evaluation 2005, 39:77-90. 10.1007/ s10579-005-2697-0
22. Krallinger M Malik R Valencia A Text mining and protein annotations: The construction and use of protein description sentences Genome Inform 2006, 17:121-130. 17503385
23. Miyao Y Ohta T Masuda K Tsuruoka Y Yoshida K Ninomiya T Tsujii J Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases Proceedings of COLING-ACL 2006 July; Sydney, Australia 2006:1017-1024.
24. Miyao Y Tsujii J Feature Forest Models for Probabilistic HPSG Parsing Computational Linguistics 2008.
25. Ohta T Tateisi Y Kim J Yakushiji A Tsujii J Linguistic and Biological Annotations of Biological Interaction Events Proceedings of The Fifth International Conference on Language Resource and Evaluation (LREC 2006) May; Genoa, Italy Calzolari N 2006:1405-1408.
26. Oda K Matsuoka Y Funahashi A Kitano H A comprehensive pathway map of epidermal growth factor receptor signaling Mol Syst Biol 2005, 1:2005.0010. 1681468 16729045 10.1038/msb4100014