Concept-based query expansion for retrieving gene related publications from MEDLINE

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Matos, Sérgio ^a   Arrais, Joel P ^a   Maia Rodrigues, João ^b   Oliveira, José L ^a  

^a UNIVERSITY OF AVEIRO   (Portugal)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SOLUTIONS; BIOLOGICAL RESOURCES; EXPONENTIAL INCREASE; HIGH-THROUGHPUT METHOD; RELEVANT DOCUMENTS; RETRIEVED DOCUMENTS; SCIENTIFIC LITERATURE; SCIENTIFIC PUBLICATIONS;

DATA MINING; TOOLS;

GENES;

ARTICLE; DATA MINING; DOCUMENTATION; FACTUAL DATABASE; GENE; GENOMICS; INFORMATION RETRIEVAL; MEDLINE; METHODOLOGY; PUBLICATION; UNITED STATES;

ABSTRACTING AND INDEXING AS TOPIC; DATA MINING; DATABASES, FACTUAL; GENES; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; MEDLINE; PUBLICATIONS; PUBMED; UNITED STATES;

EID: 77951569837     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-212     Document Type: Article

References (32)

1. Altman R, Bergman C, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A. Text mining for biology - the way forward: opinions from leading scientists. Genome Biol 2008, 9(Suppl 2):S7. 10.1186/gb-2008-9-s2-s7, 2559991, 18834498.
2. Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7(2):119-129. 10.1038/nrg1768, 16418747.
3. Rebholz-Schuhmann D, Kirsch H, Couto F. Facts from text-is text mining ready to deliver?. PLoS Biol 2005, 3(2):e65. 10.1371/journal.pbio.0030065, 548955, 15719064.
4. Shatkay H. Hairpins in bookstacks: information retrieval from biomedical text. Brief Bioinform 2005, 6(3):222-238. 10.1093/bib/6.3.222, 16212771.
5. Krallinger M, Valencia A. Text-mining and information-retrieval services for molecular biology. Genome Biol 2005, 6(7):224. 10.1186/gb-2005-6-7-224, 1175978, 15998455.
6. Manning C, Raghavan P, Schütze H. Introduction to Information Retrieval 2008, New York: Cambridge University Press.
7. Kim JJ, Rebholz-Schuhmann D. Categorization of services for seeking information in biomedical literature: a typology for improvement of practice. Brief Bioinform 2008, 9(6):452-465. 10.1093/bib/bbn032, 18660511.
8. Weeber M, Kors JA, Mons B. Online tools to support literature-based discovery in the life sciences. Brief Bioinform 2005, 6(3):277-286. 10.1093/bib/6.3.277, 16212775.
9. Doms A, Schroeder M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 2005, (33 Web Server):W783-786. 10.1093/nar/gki470, 1160231, 15980585.
10. Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36(7):664. 10.1038/ng0704-664, 15226743.
11. Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U. AliBaba: PubMed as a graph. Bioinformatics 2006, 22(19):2444-2445. 10.1093/bioinformatics/btl408, 16870931.
12. Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P. EBIMed-text crunching to gather facts for proteins from Medline. Bioinformatics 2007, 23(2):e237-244. 10.1093/bioinformatics/btl302, 17237098.
13. Tsuruoka Y, Tsujii J, Ananiadou S. FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 2008, 24(21):2559-2560. 10.1093/bioinformatics/btn469, 2572701, 18772154.
14. Chen H, Sharp BM. Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics 2004, 5:147. 10.1186/1471-2105-5-147, 528731, 15473905.
15. 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 the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics: 17-21 July 2006 2006, 1017-1024. Sydney, Australia. Association for Computational Linguistics.
16. Arrais J, Santos B, Fernandes J, Carreto L, Santos MAS, Oliveira JL. GeneBrowser: an approach for integration and functional classification of genomic data. J Integr Bioinform 2007, 4(3).
17. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. Global functional profiling of gene expression. Genomics 2003, 81(2):98-104. 10.1016/S0888-7543(02)00021-6, 12620386.
18. Korotkiy M, Middelburg R, Dekker H, van Harmelen F, Lankelma J. A tool for gene expression based PubMed search through combining data sources. Bioinformatics 2004, 20(12):1980-1982. 10.1093/bioinformatics/bth183, 15044238.
19. Schuemie MJ, Kang N, Hekkelman ML, Kors JA. GeneE: gene and protein query expansion with disambiguation. Bioinformatics 2010, 26(1):147-148. 10.1093/bioinformatics/btp597, 19837720.
20. Arrais J, Rodrigues J, Oliveira J. Improving Literature Searches in Gene Expression Studies. Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22-24 October 2008; Salamanca, Spain 2009, 74-82. Berlin: Springer, Corchado JM, De Paz JF, Rocha MP, Fernández-Riverola F.
21. Chen L, Liu H, Friedman C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 2005, 21(2):248-256. 10.1093/bioinformatics/bth496, 15333458.
22. Schuemie MJ, Mons B, Weeber M, Kors JA. Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J Biomed Inform 2007, 40(3):316-324. 10.1016/j.jbi.2006.09.002, 17079192.
23. Koike A, Takagi T. Gene/protein/family name recognition in biomedical literature. Proceedings of BioLINK 2004: linking biological literature, ontologies, and databases: 6 May 2004; Boston 2004, 9-16. Association for Computational Linguistics.
24. Lu Y, Fang H, Zhai C. An empirical study of gene synonym query expansion in biomedical information retrieval. Inf Retr 2009, 12(1):51-68.
25. Stokes N, Li Y, Cavedon L, Zobel J. Exploring criteria for successful query expansion in the genomic domain. Inf Retr 2009, 12(1):17-50.
26. Pinto J, Dias O, Lourenço A, Carneiro S, Ferreira E, Rocha I, Rocha M. Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008): 22-24 October 2008; Salamanca, Spain 2009, 92-101. Berlin: Springer, Corchado JM, De Paz JF, Rocha MP, Fernández-Riverola F.
27. Arrais J, Pereira JE, Fernandes J, Oliveira JL. GeNS: a biological data integration platform. Proceedings of the International Conference on Bioinformatics and Biomedicine (ICBB 2009): 26-29 October 2009; Venice, Italy 2009, 850-855.
28. Qiu Y, Frei H-P. Concept based query expansion. Proceedings of the 16th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval: 27 June - 1 July 1993; Pittsburgh, PA 1993, 160-170. ACM.
29. Apache Lucene. , http://lucene.apache.org/
30. Entrez Programming Utilities. , http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/eutils_help.html
31. Hersh WR, Bhupatiraju RT, Ross L, Roberts P, Cohen AM, Kraemer DF. Enhancing access to the Bibliome: the TREC 2004 Genomics Track. J Biomed Discov Collab 2006, 13:1-3.
32. Lu Z, Kim W, Wilbur WJ. Evaluation of Query Expansion Using MeSH in PubMed. Inf Retr 2009, 12(1):69-80.