BioNoculars: Extracting protein-protein interactions from biomedical text

ACL 2007 - Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing

Volumn , Issue , 2007, Pages 89-96

  Madkour, Amgad ^a   Darwish, Kareem ^a   Hassan, Hany ^a   Hassan, Ahmed ^a   Emam, Ossama ^a  

^a IBM Center for Advanced Studies in Cairo   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; GRAPHIC METHODS; TRANSLATION (LANGUAGES);

BIOMEDICAL TEXT; DOMAIN INDEPENDENTS; EXTRACTION PATTERNS; GRAPH-BASED; MEDICAL DOCUMENTS; MUTUAL REINFORCEMENT; PROTEIN-PROTEIN INTERACTIONS; VITAL SOURCES;

PROTEINS;

EID: 85037353106     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (33)

1. Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. 2000. Gene ontology: tool for the unification of biology. Nature Genetics,volume 25 pp.25-29.
2. BioCreative. 2004. [Online].
3. Blaschke C., M. A. Andrade, C. Ouzounis, and A. Valencia. 1999. Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. ISMB99, pp. 60-67.
4. Blaschke, C. and A. Valencia. 2001. Can Bibliographic Pointers for Known Biological Protein Interactions as a Case Study. Comparative and Functional Ge-nomics,vol. 2: 196-206.
5. Cherry, J. M., C. Adler, C. Ball, S. A. Chervitz, S. S. Dwight, E. T. Hester, Y. Jia, G. Juvik, T. Roe, M. Schroeder, S. Weng, and D. Botstein. 1998. SGD: Saccharomyces Genome Database. Nucleic Acids Research, 26, 73-9.
6. Chun, H. W., Y. Tsuruka, J. D. Kim, R. Shiba, N. Nagata, T. Hishiki, and J. Tsujii. 2006. Extraction of Gene-Disease Relations from MEDLINE Using Domain Dictionaries and Machine Learning. Pacific Symposium on Biocomputing 11:4-15.
7. Collier, N., C. Nobata, and J. Tsujii. 2000. Extracting the Names of Genes and Gene Products with a Hidden Markov Model. COLING, 2000, pp. 201207.
8. Cooper, J. and A. Kershenbaum. 2005. Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information. BMC Bioinformatics.
9. DIPPPI http://www2.informatik.hu-berlin.de/ haken-ber/corpora. 2006.
10. Ferrucci, D. and A. Lally. 2004. UIMA: an architectural approach to unstructured information processing in the corporate research environment. Natural Language Engineering 10, No. 3-4, 327-348.
11. Fukuda, K., T. Tsunoda, A. Tamura, and T. Takagi. 1998. Toward information extraction: identifying protein names from biological papers. PSB, pages 705716.
12. Hakenberg, J., C. Plake, U. Leser, H. Kirsch, and D. Rebholz-Schuhmann. 2005. LLL’05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata. Proc Learning Language in Logic Workshop (LLL’05) at ICML 2005, pp. 38-45. Bonn, Germany.
13. Hanisch, D., J. Fluck, HT. Mevissen, and R. Zimmer. 2003. Playing biologys name game: identifying protein names in scientific text. PSB, pages 403414.
14. Hao, Y., X. Zhu, M. Huang, and M. Li. 2005. Discovering patterns to extract protein-protein interactions from the literature: Part II. Bioinformatics, Vol. 00 no. 0 2005 pages 1-7.
15. Hassan, H., A. Hassan, and O. Emam. 2006. Unsupervised Information Extraction Approach Using Graph Mutual Reinforcement. Proceedings of Empirical Methods for Natural Language Processing (EMNLP).
16. Humphreys B. L. and D. A. B. Lindberg. 1993. The UMLS project: making the conceptual connection between users and the information they need. Bulletin of the Medical Library Association, 1993; 81(2): 170.
17. Jörg Hakenberg, Conrad Plake, Ulf Leser. 2005. Genic Interaction Extraction with Alignments and Finite State Automata. Proc Learning Language in Logic Workshop (LLL’05) at ICML 2005, pp. 38-45. Bonn, Germany (August 2005)
18. Kazama, J., T. Makino, Y. Ohta, and J. Tsujii. 2002. Tuning Support Vector Machines for Biomedical Named Entity Recognition. ACL Workshop on NLP in Biomedical Domain, pages 18.
19. Kleinberg, J. 1998. Authoritative sources in a hy-perlinked environment. In Proc. Ninth Ann. ACM-SIAM Symp. Discrete Algorithms, pages 668-677, ACM Press, New York.
20. Koike A. and T. Takagi. 2004. Gene/protein/family name recognition in biomedical literature. BioLINK 2004: Linking Biological Literature, Ontologies, and Database, pp. 9-16.
21. Koike, A., Y. Niwa, and T. Takagi 2005. Automatic extraction of gene/protein biological functions from biomedical text. Bioinformatics, Vol. 21, No. 7.
22. Leroy, G. and H. Chen. 2005. Genescene: An Ontology-enhanced Integration of Linguistic and Co-Occurance based Relations in Biomedical Text. JASIST Special Issue on Bioinformatics.
23. Mack, R. L., S. Mukherjea, A. Soffer, N. Uramoto, E. W. Brown, A. Coden, J. W. Cooper, A. Inokuchi, B. Iyer, Y. Mass, H. Matsuzawa, L. V. Subramaniam. 2004. Text analytics for life science using the Unstructured Information Management Architecture. IBM Systems Journal 43(3): 490-515.
24. Mika, S. and B. Rost. 2004. NLProt: extracting protein names and sequences from papers. Nucleic Acids Research, 32 (Web Server issue): W634W637.
25. Saric, J., L. J. Jensen, R. Ouzounova, I. Rojas, and P. Bork. 2004. Extracting regulatory gene expression networks from PUBMED. Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, Barcelona, Spain, pp.191-198.
26. Saric, J., L. J. Jensen, R. Ouzounova, I. Rojas, and P. Bork. 2006. Extraction of regulatory gene/protein networks from Medline. Bioinformatics Vol.22 no 6,pp. 645-650.
27. Schmid, H. 1994. Probabilistic Part-of-Speech Tagging Using Decision Trees. In the International Conference on New Methods in Language Processing, Manchester, UK.
28. Settles, B. 2004. Biomedical Named Entity Recognition Using Conditional Random Fields and Rich Feature Sets. In Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA), Geneva, Switzerland, pages 104-107.
29. Settles, B. 2005. ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text. Bioinformatics, 21(14): 3191-3192.
30. Tanabe L., and W. J. Wilbur. 2002. Tagging gene and protein names in biomedical text. Bioinformatics, 18(8):11241132.
31. Temkin, J. M. and M. R. Gilder. 2003. Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 19(16):2046-2053.
32. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. 2000. DIP: the Database of Interacting Proteins. Nucleic Acids Res 28: 289291.
33. Yamamoto, K., T. Kudo, A. Konagaya, Y. Matsumoto. 2003. Protein Name Tagging for Biomedical Annotation in Text. Proceedings of the ACL 2003 Workshop on Natural Language Processing in Biomedicine, pp. 65-72.