Validating candidate gene-mutation relations in MEDLINE abstracts via crowdsourcing

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7348 LNBI, Issue , 2012, Pages 83-91

  Burger, John D ^a   Doughty, Emily ^b   Bayer, Sam ^a   Tresner Kirsch, David ^a   Wellner, Ben ^a   Aberdeen, John ^a   Lee, Kyungjoon ^c   Kann, Maricel G ^b   Hirschman, Lynette ^a  

^a MITRE CORPORATION   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

annotation; Crowdsourcing; mutations; text mining

Indexed keywords

ANNOTATION; BIOMEDICAL LITERATURE; CROWDSOURCING; CURATION; GENE LISTS; GOLD STANDARDS; HUMAN INTELLIGENCE; MECHANICAL TURKS; MEDLINE; MULTIPLE GENES; MUTATIONS; SCALABLE APPROACH; TEXT MINING;

ABSTRACTING; DATA MINING; DATABASE SYSTEMS; EXPERIMENTS;

GENES;

EID: 84863914239     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-31040-9_8     Document Type: Conference Paper

References (19)

1. Amberger, J., Bocchini, C.A., Scott, A.F., Hamosh, A.: McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 37(Database issue), 793-796 (2009)
2. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29(1), 308-311 (2001)
3. Thorisson, G.A., Lancaster, O., Free, R.C., Hastings, R.K., Sarmah, P., Dash, D., Brahmachari, S.K., Brookes, A.J.: HGVbaseG2P: a central genetic association database. Nucleic Acids Res. 37(Database issue), D797-D802 (2009)
4. Stenson, P.D., Ball, E.V., Howells, K., Phillips, A.D., Mort, M., Cooper, D.N.: The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Human Genomics 4(2), 69-72 (2009)
5. Samuels, M.E., Rouleau, G.A.: The case for locus-specific databases. Nat. Rev. Genet. 12(6), 378-379 (2011)
6. Klein, R.J., Zeiss, C., Chew, E.Y., Tsai, J.Y., Sackler, R.S., Haynes, C., Henning, A.K., SanGiovanni, J.P., Mane, S.M., Mayne, S.T., Bracken, M.B., Ferris, F.L., Ott, J., Barnstable, C., Hoh, J.: Complement factor H polymorphism in age-related macular degeneration. Science 308(5720), 385-389 (2005)
7. Denny, J.C., Ritchie, M.D., Basford, M.A., Pulley, J.M., Bastarache, L., Brown-Gentry, K., Wang, D., Masys, D.R., Roden, D.M., Crawford, D.C.: PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics 26(9), 1205-1210 (2010)
8. Tatonetti, N.P., Dudley, J.T., Sagreiya, H., Butte, A.J., Altman, R.B.: An integrative method for scoring candidate genes from association studies: application to warfarin dosing. BMC Bioinformatics 11(suppl. 9), S9 (2010)
9. Caporaso, J.G., Baumgartner Jr., W.A., Randolph, D.A., Cohen, K.B., Hunter, L.: MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics 23(14), 1862-1865 (2007)
10. Doughty, E., Kertesz-Farkas, A., Bodenreider, O., Thompson, G., Adadey, A., Peterson, T., Kann, M.G.: Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature. Bioinformatics 27(3), 408-415 (2011)
11. Winnenburg, R., Plake, C., Schroeder, M.: Improved mutation tagging with gene identifiers applied to membrane protein stability prediction. BMC Bioinformatics 10(suppl. 8), S3 (2009)
12. Rebholz-Schuhmann, D., Marcel, S., Albert, S., Tolle, R., Casari, G., Kirsch, H.: Automatic extraction of mutations from Medline and cross-validation with OMIM. Nucleic Acids Res. 32(1), 135-142 (2004)
13. Horn, F., Lau, A.L., Cohen, F.E.: Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. Bioinformatics 20(4), 557-568 (2004)
14. Erdogmus, M., Sezerman, O.U.: Application of automatic mutation-gene pair extraction to diseases. J. Bioinform. Comput. Biol. 5(6), 1261-1275 (2007)
15. Aronson, A.R.: Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. In: Proc. AMIA Symp., pp. 17-21 (2001)
16. Aberdeen, J., Bayer, S., Yeniterzi, R., Wellner, B., Clark, C., Hanauer, D., Malin, B., Hirschman, L.: The MITRE Identification Scrubber Toolkit: design, training, and assessment. International Journal of Medical Informatics 79(12), 849-859 (2010)
17. Callison-Burch, C., Dredze, M.: Creating speech and language data with Amazon's Mechanical Turk NAACL HLT. In: 2010 Workshop on Creating Speech and Language Data with Amazon's Mechanical Turk. Association for Computational Linguistics, Los Angeles (2010)
18. Yetisgen-Yildiz, M., Solti, I., Xia, F., Halgrim, S.: Preliminary Experiments with Amazon's Mechanical Turk for Annotating Medical Named Entities. In: NAACL HLT 2010 Workshop on Creating Speech and Language Data with Amazon's Mechanical Turk, pp. 180-183. Assn for Comp. Ling, Los Angeles (2010)
19. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31(1), 365-370 (2003)