Large-scale testing of bibliome informatics using Pfam protein families

Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006

Volumn , Issue , 2006, Pages 76-87

  Maguitman, Ana G ^a   Rechtsteiner, Andreas ^b   Verspoor, Karin ^b   Strauss, Charlie E ^b   Rocha, Luis M ^a  

^a INDIANA UNIVERSITY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-CHEMICALS; BIOMEDICAL LITERATURE; GOLD STANDARDS; INFORMATICS; LARGE SCALE TESTING; LARGE SCALE TESTS; LITERATURE MINING; PROTEIN FAMILY; SHANNON'S ENTROPY; TEST SETS; VECTOR SPACE MODELS;

ABSTRACTING; MINING; STANDARDS;

PROTEINS;

ALGORITHM; ARTICLE; BIOLOGY; EVALUATION; PROTEIN DATABASE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN;

EID: 36348936988     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. R. Baeza-Yates and B. Ribiero-Neto, Modern Information Retrieval. Pearson Education, 1999.
2. K. G, Becker, D. A. Hosack, G. Dennis, R. A. Lempicki, T. J. Bright, C. Cheadle, and J. Engel. PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics, 4(1):61, Dec 2003.
3. E. B. Camon, D. G, Barrell, E. C. Dimmer, V. Lee, M. Magrane, J. Maslen, D. Binns, and R. Apweiler. An evaluation of go annotation retrieval for biocreative and goa. BMC Bioinformatics, 6 Suppl 1 :S 15, 2005.
4. J. Challacombe, A. Rechtsteiner, R. Gottardo, L. M. Rocha, E P. Brown, T. Shenk, M. Altherr, and T. Brettin. Evaluation of the host transcriptions] response to human cytomegalovirus infection. Physiological Genomics., 18(1):51-62, 2004.
5. M. E. Colosimo, A. A. Morgan, A. S. Yeh, J, B. Colombe, and L. Hirschmah. Data preparation and interannotator agreement: Biocreative task 1 b. BMC Bioinformatics, 6 Suppl 1:512, 2005.
6. R. O. Duda, P. E. Hart, and D. G. Stork. Pattern Classification. Wiley, New York, NY, 2nd edition, 2000.
7. S. Dumais. Enhancing performance in latent semantic indexing, 1990.
8. W. Hersh, R. T. Bhupatiraju, and S. Corley. Enhancing access to the Bibliome: the TREC Genomics Track. Medinfo, 11(Pt 2):773-777, 2004.
9. L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia. Overview of biocreative: critical assessment of information extraction for biology. BMCBioinformatics, 6 Suppl 1:S1, 2005.
10. R. Homayouni, K. Heinrich, L. Wei, and M. W. Berry. Gene clustering by Latent Semantic Indexing of MEDLINE Abstracts. Bioinformatics, 21(1): 104-115, 2005.
11. T. K. Jenssen, A. Laegreid, J. Komorowski, and E. Hovig. A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28(1):21- 28, 2001.
12. G. J. Klir and M. J. Wierman. Uncertainty-Based Information: Elements of Generalized Information Theory. Studies in Fuzziness and Soft Computing. Physica-Verlag, 1999.
13. D. R. Masys, J. B. Welsh, J. Lynn Fink, M. Gribskov, I. Klacansky, and J. Corbeil. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics, 17(4):319-26, 2001.
14. A. Rechtsteiner. Mullivariate Analysis Of Gene Expression Data And Functional Information: Automated Methods For Functional Genomics. PhD thesis, Portland State University, 2005.
15. A. Rechtsteiner and L. M. Rocha. MeSH key terms for validation and annotation of gene expression clusters. In Currents in Computational Molecular Biology. RECOMB 2004, pages 212-213, 2004.
16. A. Rechtsteiner, L. M. Rocha, and C. E. Strauss. Clustering of protein families in literature keyword space. In Currents in Computational Molecular Biology. RECOMB 2005, Boston, MA, 2005.
17. L. M. Rocha, T. Simas, A. Rechtsteiner, M. DiGiacomo, and R. Luce. Mylibrary@lanl: Proximity and semi-metric networks for a collaborative and recommender web service. In The 2005 IEEESWIOACM International Conference on Web Intelligence (WJ 2005), pages 565-571, Compiegne, France, Sep 2005.
18. H. Shatkay and R. Feldman. Mining the biomedical literature in the genomic era: An overview. Journal of Computational Biology, 10(6):821-856, 2003.
19. SIB/EBI. UniProf Swiss-Prot. http://www.ebi.ac.uk/swissprot/2004.
20. E. L. Sonnhammer, S. R. Eddy, and R. Durbin. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28(3):405-420, Jul 1997.
21. P. Srinivasan. MeSHmap: a text mining tool for MEDLINE. Proc AMIA Symp, pages 642-646, 2001.
22. L. Tanabe, U. Scherf, L. H. Smith, J. K. Lee, L. Hunter, and J. N. Weinstein. Med- Miner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques, 27(6): 1210-1214, Dec 1999.
23. K. Verspoor, J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L. M. Rocha, and T. Simas. Protein annotation as term categorization in the gene ontology using word proximity networks. BMC Bioinformatics, 6 Suppl 1 :S20, 2005.