Literature retrieval and mining in bioinformatics: State of the art and challenges

Advances in Bioinformatics

Volumn 2012, Issue , 2012, Pages

  Manconi, Andrea ^a   Vargiu, Eloisa ^b,c   Armano, Giuliano ^b   Milanesi, Luciano ^a  

^a CNR   (Italy)

^b UNIVERSITY OF CAGLIARI   (Italy)

^c Barcelona Digital Technology Center   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84863649603     PISSN: 16878027     EISSN: 16878035     Source Type: Journal    
DOI: 10.1155/2012/573846     Document Type: Review

References (78)

1. Armano G., de Gemmis M., Semeraro G., Vargiu E., Intelligent Information Access 2010 SCI 301 Heidelberg, Germany Springer Studies in Computational Intelligence
2. Baeza-Yates R. A., Ribeiro-Neto B., Modern Information Retrieval 1999 Boston, Mass, USA Addison-Wesley Longman
3. Kobayashi M., Takeda K., Information retrieval on the web ACM Computing Surveys 2000 32 2 165 173
4. Bao S., Xue G., Wu X., Yu Y., Fei B., Su Z., Optimizing web search using social annotations 16th International World Wide Web Conference (WWW '07) May 2007 New York, NY, USA 501 510 (Pubitemid 47582279)
5. Manning C. D., Raghavan P., Schtze H., Introduction to Information Retrieval 2008 New York, NY, USA Cambridge University Press
6. Mayfield J., Finin T., Information retrieval on the semantic web: Integrating inference and retrieval Proceedings of the SIGIR Workshop on the Semantic Web August 2003
7. Berry M. W., Survey of Text Mining 2003 New York, NY, USA Springer
8. Sebastiani F., Machine learning in automated text categorization ACM Computing Surveys 2002 34 1 1 47
9. Mani I., Automatic Summarization 2001 Amsterdam, The Netherlands John Benjamins
10. Luhn H., The automatic creation of literature abstracts IBM Journal of Research and Development 1958 2 159 165
11. Baxendale P., Machine-made index for technical literaturean experiment IBM Journal of Research and Development 1958 2 354 361
12. Edmundson H. P., New methods in automatic extracting Journal of ACM 1969 16 264 285
13. Nenkova A., Automatic text summarization of newswire: lessons learned from the document understanding conference 3 Proceedings of the 20th National Conference on Artificial Intelligence 2005 AAAI Press 1436 1441 (Pubitemid 43006636)
14. Armano G., Giuliani A., Vargiu E., Studying the impact of text summarization on contextual advertising Proceedings of the 8th International Workshop on Text-based Information Retrieval 2011
15. Kocz A., Prabakarmurthi V., Kalita J., Summarization as feature selection for text categorization Proceedings of the 10th ACM International Conference on Information and Knowledge Management (CIKM '01) November 2001 New York, NY, USA 365 370 (Pubitemid 34974652)
16. Martin J., Clustering full text documents Proceedings of the Workshop on Data Engineering for Inductive Learning at (IJCAI '95) 1995
17. Willett P., Recent trends in hierarchic document clustering: a critical review Information Processing and Management 1988 24 5 577 597
18. Aone C., Bennett S. W., Gorlinsky J., Multi-media fusion through application of machine learning and nlp AAAI Spring Symposium Working Notes on Machine Learning in Information Access 1996
19. Fisher D. H., Knowledge acquisition via incremental conceptual clustering Machine Learning 1987 2 2 139 172
20. Liere R., Tadepalli P., Active learning with committees for text categorization Proceedings of the 14th National Conference on Artificial Intelligence (AAAI '97) July 1997 591 596
21. Cheeseman P., Kelly J., Self M., Stutz J., Taylor W., Freeman D., Readings in Knowledge Acquisition and Learning, chap. AutoClass: A Bayesian Classification System 1993 San Francisco, Calif, USA Morgan Kaufmann
22. Green C., Edwards P., Using machine learning to enhance software tools for internet information management Proceedings of the AAAI Workshop on Internetbased Information Systems 1996 48 55
23. Appelt D. E., Introduction to information extraction AI Communications 1999 12 3 161 172 (Pubitemid 30506805)
24. Soderland S., Fisher D., Aseltine J., Lehnert W., Crystal inducing a conceptual dictionary 2 Proceedings of the 14th International Joint Conference on Artificial Intelligence 1995 San Francisco, Calif, USA Morgan Kaufmann 1314 1319
25. Huffman S. B., Learning information extraction patterns from examples Connectionist, Statistical, and Symbolic Approaches to Learning for Natural Language Processing 1996 London, UK Springer 246 260 (Pubitemid 126054052)
26. Califf M. E., Mooney R. J., Relational learning of pattern-match rules for information extraction Proceedings of the 16th National Conference on Artificial Intelligence (AAAI '99), 11th Innovative Applications of Artificial Intelligence Conference (IAAI '99) July 1999 328 334
27. Freitag D., Machine learning for information extraction in informal domains Machine Learning 2000 39 169 202 (Pubitemid 30594820)
28. Bollacker K. D., Lawrence S., Giles C. L., Discovering relevant scientific literature on the Web IEEE Intelligent Systems and Their Applications 2000 15 2 42 47 (Pubitemid 30587665)
29. McNee S. M., Albert I., Cosley D., Gopalkrishnan P., Lam S. K., Rashid A. M., Konstan J. A., Riedl J., On the recommending of citations for research papers Proceedings of the 8th Conference on Computer Supported Cooperative Work (CSCW '02) November 2002 New York, NY, USA 116 125
30. Janssen W. C., Popat K., UpLib: a universal personal digital library system Proceedings of the 2003 ACM Symposium on Document Engineering November 2003 fra 234 242
31. Mahdavi F., Ismail M. A., Abdullah N., Semi-automatic trend detection in scholarly repository using semantic approach Proceedings of the World Academy of Science, Engineering and Technology 2009 Amsterdam, The Netherlands 224 226
32. Cannata N., Merelli E., Altman R. B., Erratum: time to organize the bioinformatics resourceome PLoS Computational Biology 2006 2 2 112
33. Bajpai A. K., Davuluri S., Haridas H., In search of the right literature search engine(s) Nature Preceding 2011
34. Yu H., Kim T., Oh J., Ko I., Kim S., Han W. S., Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS BMC Bioinformatics 2010 11 supplement 2 S6
35. Fontaine J. F., Barbosa-Silva A., Schaefer M., Huska M. R., Muro E. M., Andrade-Navarro M. A., MedlineRanker: flexible ranking of biomedical literature Nucleic Acids Research 2009 37 2 W141 W146
36. Wang J., Cetindil I., Ji S., Li C., Xie X., Li G., Feng J., Interactive and fuzzy search: a dynamic way to explore MEDLINE Bioinformatics 2010 26 18 2321 2327
37. Herbrich R., Graepel T., Obermayer K., B. Smola, S. Schoelkopf, Large margin rank boundaries for ordinal regression Advances in Large Margin Classifiers 2000 Cambridge, Mass, USA MIT Press
38. Lewis J., Ossowski S., Hicks J., Errami M., Garner H. R., Text similarity: an alternative way to search MEDLINE Bioinformatics 2006 22 18 2298 2304 (Pubitemid 44390887)
39. Coppernoll-Blach P., Quertle: the conceptual relationships alternative search engine for pubmed Journal of Medical Library Association 2011 99 2 176 177
40. Doms A., Schroeder M., GoPubMed: exploring PubMed with the gene ontology Nucleic Acids Research 2005 33 2 W783 W786 (Pubitemid 44530030)
41. Perez-Iratxeta C., Pérez A. J., Bork P., Andrade M. A., Update on XplorMed: a web server for exploring scientific literature Nucleic Acids Research 2003 31 13 3866 3868 (Pubitemid 37442266)
42. Rebholz-Schuhmann D., Kirsch H., Arregui M., Gaudan S., Riethoven M., Stoehr P., EBIMedtext crunching to gather facts for proteins from Medline Bioinformatics 2007 23 2 e237 e244 (Pubitemid 46189663)
43. Hoffmann R., Valencia A., A gene network for navigating the literature Nature Genetics 2004 36 7 664
44. Tanabe L., Scherf U., Smith L. H., Lee J. K., Hunter L., Weinstein J. N., MedMiner: an internet text-mining tool for biomedical information, with application to gene expression profiling BioTechniques 1999 27 6 1210 1217
45. Greenhalgh T., How to read a paper. The medline database BMJ 1997 315 7101 180 183 (Pubitemid 27303067)
46. Yeh A. S., Hirschman L., Morgan A. A., Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup Bioinformatics 2003 19 i331 339
47. Thomas J., Milward D., Ouzounis C., Pulman S., Carroll M., Automatic extraction of protein interactions from scientific abstracts Pacific Symposium on Biocomputing 2000 541 552
48. He M., Wang Y., Li W., PPI finder: a mining tool for human protein-protein interactions PLoS ONE 2009 4 2
49. Berardi M., Malerba D., Piredda R., Attimonelli M., Scioscia G., Leo P., 16 Biomedical Literature Mining for Biological Databases Annotation 2008
50. Craven M., Kumlien J., Constructing biological knowledge bases by extracting information from text sources Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology 1999 77 86
51. Swanson D. R., Smalheiser N. R., An interactive system for finding complementary literatures: a stimulus to scientific discovery Artificial Intelligence 1997 91 2 183 203 (Pubitemid 127371600)
52. Donaldson I., Martin J., de Bruijn B., Wolting C., Lay V., Tuekam B., Zhang S., Baskin B., Bader G. D., Michalickova K., Pawson T., Hogue C. W., PreBIND and Textomymining the biomedical literature for protein-protein interactions using a support vector machine BMC Bioinformatics 2003 4 1 11
53. Wiegers T. C., Davis A. P., Cohen K. B., Hirschman L., Mattingly C. J., Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics Database (CTD) BMC Bioinformatics 2009 10, article 326
54. Kemper B., Matsuzaki T., Matsuoka Y., Tsuruoka Y., Kitano H., Ananiadou S., Tsujii J., PathText: a text mining integrator for biological pathway visualizations Bioinformatics 2010 26 12 i374 i381
55. Oda K., Kim J. D., Ohta T., Okanohara D., Matsuzaki T., Tateisi Y., Tsujii J., New challenges for text mining: mapping between text and manually curated pathways BMC Bioinformatics 2008 9 supplement 3 S5
56. Herrgrd M. J., Swainston N., Dobson P., Dunn W. B., Arga K. Y., Arvas M., Bthgen N., Borger S., Costenoble R., Heinemann M., Hucka M., Le Novre N., Li P., Liebermeister W., Mo M. L., Oliveira A. P., Petranovic D., Pettifer S., Simeonidis E., Smallbone K., Spasi I., Weichart D., Brent R., Broomhead D. S., Westerhoff H. V., Kirdar B., Penttil M., Klipp E., Palsson B.., Sauer U., Oliver S. G., Mendes P., Nielsen J., Kell D. B., A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Nature Biotechnology 2008 26 10 1155 1160
57. Karamanis I., Lewi R., Seal R. D., E B., Integrating natural language processing with flybase curation Proceedings of the Pacific Symposium on Biocomputing 2007 Maui, Hawaii, USA 245 256
58. Kiritchenko S., Matwin S., Famili A. F., Hierarchical text categorization as a tool of associating genes with gene ontology codes Proceedings of the 2nd European Workshop on Data Mining and Text Mining for Bioinformatics 2004 26 30
59. Swanson D. R., Fish oil, Raynaud's syndrome, and undiscovered public knowledge Perspectives in Biology and Medicine 1986 30 1 7 18
60. Bruza P., Weeber M., Literature-based Discovery 2008 15 Heidelberg, Germany Springer
61. Hristovski D., Peterlin B., Mitchell J. A., Humphrey S. M., Using literature-based discovery to identify disease candidate genes International Journal of Medical Informatics 2005 74 24 289 298 (Pubitemid 40208459)
62. Chen L., Friedman C., Extracting phenotypic information from the literature via natural language processing Medinfo 2004 11 2 758 762
63. Srinivasan P., Rindflesch T., Exploring text mining from MEDLINE Proceedings of the AMIA Symposium 2002 722 726
64. Corney D. P. A., Buxton B. F., Langdon W. B., Jones D. T., BioRAT: extracting biological information from full-length papers Bioinformatics 2004 20 17 3206 3213 (Pubitemid 39619210)
65. Cheng D., Knox C., Young N., Stothard P., Damaraju S., Wishart D. S., PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites Nucleic Acids Research 2008 36 W399 W405
66. Ananiadou S., Kell D. B., Tsujii J. I., Text mining and its potential applications in systems biology Trends in Biotechnology 2006 24 12 571 579 (Pubitemid 44762220)
67. Nikitin A., Egorov S., Daraselia N., Mazo I., Pathway studiothe analysis and navigation of molecular networks Bioinformatics 2003 19 16 2155 2157 (Pubitemid 37408171)
68. Hur J., Schuyler A. D., States D. J., Feldman E. L., SciMiner: web-based literature mining tool for target identification and functional enrichment analysis Bioinformatics 2009 25 6 838 840
69. Jelier R., Schuemie M. J., Veldhoven A., Dorssers L. C. J., Jenster G., Kors J. A., Anni 2.0: a multipurpose text-mining tool for the life sciences Genome Biology 2008 9 6, article R96
70. Schuemie M., Jelier R., J J. K., Peregrine: lightweight gene name normalization by dictionary lookup Proceedings of the 2nd BioCreative Challenge Evaluation Workshop 2007 131 140
71. Tsuruoka Y., Tsujii J., Ananiadou S., Facta: a text search engine for finding associated biomedical concepts Bioinformatics 2008 24 21 2559 2560
72. Weeber M., Klein H., Aronson A. R., Mork J. G., de Jong-van den Berg L. T., Vos R., Msc: Text-based discovery in biomedicine: the architecture of the DAD-system Proceedings of the AMIA, the Annual Conference of the American Medical Informatics Association 2000 903 907
73. Deerwester S. C., Dumais S. T., Landauer T. K., Furnas G. W., Harshman R. A., Indexing by latent semantic analysis JASIS 1990 41 6 391 407
74. Miller G. A., Wordnet: a lexical database for english Communications of the ACM 1995 38 11 39 41
75. Krauthammer M., Nenadic G., Term identification in the biomedical literature Journal of Biomedical Informatics 2004 37 6 512 526 (Pubitemid 39487155)
76. Shah P. K., Perez-Iratxeta C., Bork P., Andrade M. A., Information extraction from full text scientific articles: where are the keywords? BMC Bioinformatics 2003 4, article no. 20
77. Hirschman L., Yeh A., Blaschke C., Valencia A., Overview of BioCreAtIvE: critical assessment of information extraction for biology BMC Bioinformatics 2005 6 1, article S1
78. Krallinger M., Morgan A., Smith L., Leitner F., Tanabe L., Wilbur J., Hirschman L., Valencia A., Evaluation of text-mining systems for biology: overview of the second biocreative community challenge Genome Biology 2008 9 2, article no. S1