메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Extraction of relations between genes and diseases from text and large-scale data analysis: Implications for translational research

Author keywords

Big data; Biocuration; Corpus development; Disease; Information extraction; Machine learning; Text mining; Translational bioinformatics

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIG DATA; BIOINFORMATICS; DATA INTEGRATION; DATA REDUCTION; DISEASES; GENES; INFORMATION ANALYSIS; INFORMATION RETRIEVAL; LEARNING SYSTEMS; NATURAL LANGUAGE PROCESSING SYSTEMS; QUALITY CONTROL;

EID: 84931264092     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0472-9     Document Type: Article
Times cited : (239)

References (51)
  • 1
    • 84869505278 scopus 로고    scopus 로고
    • Text-mining solutions for biomedical research: enabling integrative biology
    • Rebholz-Schuhmann D, Oellrich A, Hoehndorf R. Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet. 2012;13:829-39.
    • (2012) Nat Rev Genet , vol.13 , pp. 829-839
    • Rebholz-Schuhmann, D.1    Oellrich, A.2    Hoehndorf, R.3
  • 2
    • 84883742021 scopus 로고    scopus 로고
    • Improving data and knowledge management to better integrate health care and research
    • Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, et al. Improving data and knowledge management to better integrate health care and research. J Intern Med. 2013;274:321-8.
    • (2013) J Intern Med , vol.274 , pp. 321-328
    • Cases, M.1    Furlong, L.I.2    Albanell, J.3    Altman, R.B.4    Bellazzi, R.5    Boyer, S.6
  • 3
    • 84865064690 scopus 로고    scopus 로고
    • Mining the pharmacogenomics literature-a survey of the state of the art
    • Hahn U, Cohen KB, Garten Y, Shah NH. Mining the pharmacogenomics literature-a survey of the state of the art. Brief Bioinform. 2012;13:460-94.
    • (2012) Brief Bioinform , vol.13 , pp. 460-494
    • Hahn, U.1    Cohen, K.B.2    Garten, Y.3    Shah, N.H.4
  • 5
    • 84865997531 scopus 로고    scopus 로고
    • Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies
    • Pakhomov S, McInnes BT, Lamba J, Liu Y, Melton GB, Ghodke Y, et al. Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. J Biomed Inform. 2012;45:862-9.
    • (2012) J Biomed Inform , vol.45 , pp. 862-869
    • Pakhomov, S.1    McInnes, B.T.2    Lamba, J.3    Liu, Y.4    Melton, G.B.5    Ghodke, Y.6
  • 6
    • 84865989623 scopus 로고    scopus 로고
    • A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text
    • Xu R, Wang Q. A knowledge-driven conditional approach to extract pharmacogenomics specific drug-gene relationships from free text. J Biomed Inform. 2012;45:827-34.
    • (2012) J Biomed Inform , vol.45 , pp. 827-834
    • Xu, R.1    Wang, Q.2
  • 7
    • 84858300305 scopus 로고    scopus 로고
    • Discovery and explanation of drug-drug interactions via text mining
    • Percha B, Garten Y, Altman RB. Discovery and explanation of drug-drug interactions via text mining. Pac Symp Biocomput 2012:410-21.
    • (2012) Pac Symp Biocomput , pp. 410-421
    • Percha, B.1    Garten, Y.2    Altman, R.B.3
  • 8
    • 79959655291 scopus 로고    scopus 로고
    • Using a shallow linguistic kernel for drug-drug interaction extraction
    • Segura-Bedmar I, Martínez P, de Pablo-Sánchez C. Using a shallow linguistic kernel for drug-drug interaction extraction. J Biomed Inform. 2011;44:789-804.
    • (2011) J Biomed Inform , vol.44 , pp. 789-804
    • Segura-Bedmar, I.1    Martínez, P.2    Pablo-Sánchez, C.3
  • 9
    • 70349452436 scopus 로고    scopus 로고
    • Automatic summarization of MEDLINE citations for evidence-based medical treatment: a topic-oriented evaluation
    • Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC. Automatic summarization of MEDLINE citations for evidence-based medical treatment: a topic-oriented evaluation. J Biomed Inform. 2009;42:801-13.
    • (2009) J Biomed Inform , vol.42 , pp. 801-813
    • Fiszman, M.1    Demner-Fushman, D.2    Kilicoglu, H.3    Rindflesch, T.C.4
  • 10
    • 78650939621 scopus 로고    scopus 로고
    • Automatic integration of drug indications from multiple health resources
    • New York, New York, USA: ACM Press.
    • Névéol A, Lu Z. Automatic integration of drug indications from multiple health resources. In: Proc ACM Int Conf Heal informatics - IHI '10. New York, New York, USA: ACM Press; 2010. p. 666.
    • (2010) Proc ACM Int Conf Heal informatics - IHI '10 , pp. 666
    • Névéol, A.1    Lu, Z.2
  • 11
    • 84942412129 scopus 로고    scopus 로고
    • Extraction of potential adverse drug events from medical case reports
    • Gurulingappa H, Mateen-Rajput A, Toldo L. Extraction of potential adverse drug events from medical case reports. J Biomed Semantics. 2012;3:15.
    • (2012) J Biomed Semantics , vol.3 , pp. 15
    • Gurulingappa, H.1    Mateen-Rajput, A.2    Toldo, L.3
  • 13
    • 43749110484 scopus 로고    scopus 로고
    • Extraction of semantic biomedical relations from text using conditional random fields
    • Bundschus M, Dejori M, Stetter M, Tresp V, Kriegel H-P. Extraction of semantic biomedical relations from text using conditional random fields. BMC Bioinformatics. 2008;9:207.
    • (2008) BMC Bioinformatics , vol.9 , pp. 207
    • Bundschus, M.1    Dejori, M.2    Stetter, M.3    Tresp, V.4    Kriegel, H.-P.5
  • 14
    • 46249127253 scopus 로고    scopus 로고
    • Identifying gene-disease associations using centrality on a literature mined gene-interaction network
    • Ozgür A, Vu T, Erkan G, Radev DR. Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics. 2008;24:i277-85.
    • (2008) Bioinformatics , vol.24 , pp. i277-i285
    • Ozgür, A.1    Vu, T.2    Erkan, G.3    Radev, D.R.4
  • 15
    • 84865981409 scopus 로고    scopus 로고
    • A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions
    • Hakenberg J, Voronov D, Nguyên VH, Liang S, Anwar S, Lumpkin B, et al. A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. J Biomed Inform. 2012;45:842-50.
    • (2012) J Biomed Inform , vol.45 , pp. 842-850
    • Hakenberg, J.1    Voronov, D.2    Nguyên, V.H.3    Liang, S.4    Anwar, S.5    Lumpkin, B.6
  • 16
    • 56649109912 scopus 로고    scopus 로고
    • The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes
    • Vincze V, Szarvas G, Farkas R, Móra G, Csirik J. The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes. BMC Bioinformatics. 2008;9 Suppl 11:S9.
    • (2008) BMC Bioinformatics , vol.9 , pp. S9
    • Vincze, V.1    Szarvas, G.2    Farkas, R.3    Móra, G.4    Csirik, J.5
  • 17
    • 56649091414 scopus 로고    scopus 로고
    • Recognizing speculative language in biomedical research articles: a linguistically motivated perspective
    • Kilicoglu H, Bergler S. Recognizing speculative language in biomedical research articles: a linguistically motivated perspective. BMC Bioinformatics. 2008;9 Suppl 11:S10.
    • (2008) BMC Bioinformatics , vol.9 , pp. S10
    • Kilicoglu, H.1    Bergler, S.2
  • 20
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen T-K, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet. 2001;28:21-8.
    • (2001) Nat Genet , vol.28 , pp. 21-28
    • Jenssen, T.-K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 21
    • 27544448536 scopus 로고    scopus 로고
    • Implementing the iHOP concept for navigation of biomedical literature
    • Hoffmann R, Valencia A. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics. 2005;21 Suppl 2:ii252-8.
    • (2005) Bioinformatics , vol.21 , pp. ii252-ii258
    • Hoffmann, R.1    Valencia, A.2
  • 22
    • 65349157361 scopus 로고    scopus 로고
    • Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility study
    • Wang X, Hripcsak G, Markatou M, Friedman C. Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility study. J Am Med Inform Assoc , 16:328-37.
    • J Am Med Inform Assoc , vol.16 , pp. 328-337
    • Wang, X.1    Hripcsak, G.2    Markatou, M.3    Friedman, C.4
  • 23
    • 33847294345 scopus 로고    scopus 로고
    • RelEx-relation extraction using dependency parse trees
    • Fundel K, Küffner R, Zimmer R. RelEx-relation extraction using dependency parse trees. Bioinformatics. 2007;23:365-71.
    • (2007) Bioinformatics , vol.23 , pp. 365-371
    • Fundel, K.1    Küffner, R.2    Zimmer, R.3
  • 25
    • 33751088706 scopus 로고    scopus 로고
    • Extraction of gene-disease relations from Medline using domain dictionaries and machine learning
    • Chun H, Tsuruoka Y, Kim J, Shiba R, Nagata N, Hishiki T, et al. Extraction of gene-disease relations from Medline using domain dictionaries and machine learning. Pac Symp Biocomput 2006;4.
    • (2006) Pac Symp Biocomput , pp. 4
    • Chun, H.1    Tsuruoka, Y.2    Kim, J.3    Shiba, R.4    Nagata, N.5    Hishiki, T.6
  • 26
    • 84876238575 scopus 로고    scopus 로고
    • Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations
    • Liu H, Hunter L, Kešelj V, Verspoor K. Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations. PLoS One. 2013;8:e60954.
    • (2013) PLoS One , vol.8 , pp. e60954
    • Liu, H.1    Hunter, L.2    Kešelj, V.3    Verspoor, K.4
  • 28
    • 0842283365 scopus 로고    scopus 로고
    • The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text
    • Rindflesch TC, Fiszman M. The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform. 2003;36:462-77.
    • (2003) J Biomed Inform , vol.36 , pp. 462-477
    • Rindflesch, T.C.1    Fiszman, M.2
  • 29
    • 0035753772 scopus 로고    scopus 로고
    • Evaluating the UMLS as a source of lexical knowledge for medical language processing
    • Friedman C, Liu H, Shagina L, Johnson S, Hripcsak G. Evaluating the UMLS as a source of lexical knowledge for medical language processing. Proc AMIA Symp 2001;189-193.
    • (2001) Proc AMIA Symp , pp. 189-193
    • Friedman, C.1    Liu, H.2    Shagina, L.3    Johnson, S.4    Hripcsak, G.5
  • 31
    • 84926140240 scopus 로고    scopus 로고
    • Combining tree structures, flat features and patterns for biomedical relation extraction
    • Association for Computational Linguistics.
    • Chowdhury MFM, Lavelli A. Combining tree structures, flat features and patterns for biomedical relation extraction. In EACL '12 Proc 13th Conf Eur Chapter Assoc Comput Linguist. Association for Computational Linguistics; 2012:420-429.
    • (2012) EACL '12 Proc 13th Conf Eur Chapter Assoc Comput Linguist , pp. 420-429
    • Chowdhury, M.F.M.1    Lavelli, A.2
  • 32
    • 85144480129 scopus 로고    scopus 로고
    • Dependency tree kernels for relation extraction
    • Morristown, NJ, USA: Association for Computational Linguistics.
    • Culotta A, Sorensen J. Dependency tree kernels for relation extraction. In: Proc 42nd Annu Meet Assoc Comput Linguist - ACL '04. Morristown, NJ, USA: Association for Computational Linguistics; 2004. p. 423-es.
    • (2004) Proc 42nd Annu Meet Assoc Comput Linguist - ACL '04 , pp. 423-es
    • Culotta, A.1    Sorensen, J.2
  • 34
    • 71549135535 scopus 로고    scopus 로고
    • Protein-protein interaction extraction by leveraging multiple kernels and parsers
    • Miwa M, Saetre R, Miyao Y, Tsujii J. Protein-protein interaction extraction by leveraging multiple kernels and parsers. Int J Med Inform. 2009;78:e39-46.
    • (2009) Int J Med Inform , vol.78 , pp. e39-46
    • Miwa, M.1    Saetre, R.2    Miyao, Y.3    Tsujii, J.4
  • 35
    • 77951201715 scopus 로고    scopus 로고
    • Walk-weighted subsequence kernels for protein-protein interaction extraction
    • Kim S, Yoon J, Yang J, Park S. Walk-weighted subsequence kernels for protein-protein interaction extraction. BMC Bioinformatics. 2010;11:107.
    • (2010) BMC Bioinformatics , vol.11 , pp. 107
    • Kim, S.1    Yoon, J.2    Yang, J.3    Park, S.4
  • 36
    • 37549050918 scopus 로고    scopus 로고
    • Kernel approaches for genic interaction extraction
    • Kim S, Yoon J, Yang J. Kernel approaches for genic interaction extraction. Bioinformatics. 2008;24:118-26.
    • (2008) Bioinformatics , vol.24 , pp. 118-126
    • Kim, S.1    Yoon, J.2    Yang, J.3
  • 37
    • 84865064690 scopus 로고    scopus 로고
    • Mining the pharmacogenomics literature-a survey of the state of the art
    • Hahn U, Cohen K. Mining the pharmacogenomics literature-a survey of the state of the art. Brief Bioinform. 2012;13(4):460-94.
    • (2012) Brief Bioinform , vol.13 , Issue.4 , pp. 460-494
    • Hahn, U.1    Cohen, K.2
  • 39
    • 84900334705 scopus 로고    scopus 로고
    • A knowledge-driven approach to extract disease-related biomarkers from the literature
    • Bravo A, Cases M, Queralt-Rosinach N, Sanz F, Furlong LI. A knowledge-driven approach to extract disease-related biomarkers from the literature. Biomed Res Int. 2014;2014:253128.
    • (2014) Biomed Res Int , vol.2014 , pp. 253128
    • Bravo, A.1    Cases, M.2    Queralt-Rosinach, N.3    Sanz, F.4    Furlong, L.I.5
  • 40
    • 78149236787 scopus 로고    scopus 로고
    • DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks
    • Bauer-Mehren A, Rautschka M, Sanz F, Furlong LI. DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks. Bioinformatics. 2010;26:2924-6.
    • (2010) Bioinformatics , vol.26 , pp. 2924-2926
    • Bauer-Mehren, A.1    Rautschka, M.2    Sanz, F.3    Furlong, L.I.4
  • 42
    • 84872217237 scopus 로고    scopus 로고
    • The extraction of pharmacogenetic and pharmacogenomic relations--a case study using PharmGKB
    • Buyko E, Beisswanger E, Hahn U. The extraction of pharmacogenetic and pharmacogenomic relations--a case study using PharmGKB. Pac Symp Biocomput 2012;376-87.
    • (2012) Pac Symp Biocomput , pp. 376-387
    • Buyko, E.1    Beisswanger, E.2    Hahn, U.3
  • 43
    • 84878514642 scopus 로고    scopus 로고
    • Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing
    • Xu R, Wang Q. Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing. BMC Bioinformatics. 2013;14:181.
    • (2013) BMC Bioinformatics , vol.14 , pp. 181
    • Xu, R.1    Wang, Q.2
  • 44
    • 84864266208 scopus 로고    scopus 로고
    • The neurobiology of depression-revisiting the serotonin hypothesis. I. Cellular and molecular mechanisms
    • Albert PR, Benkelfat C, Descarries L. The neurobiology of depression-revisiting the serotonin hypothesis. I. Cellular and molecular mechanisms. Philos Trans R Soc Lond B Biol Sci. 2012;367:2378-81.
    • (2012) Philos Trans R Soc Lond B Biol Sci , vol.367 , pp. 2378-2381
    • Albert, P.R.1    Benkelfat, C.2    Descarries, L.3
  • 46
    • 84880973546 scopus 로고    scopus 로고
    • Crowdsourcing for bioinformatics
    • Good BM, Su AI. Crowdsourcing for bioinformatics. Bioinformatics. 2013;29:1925-33.
    • (2013) Bioinformatics , vol.29 , pp. 1925-1933
    • Good, B.M.1    Su, A.I.2
  • 49
    • 84882760954 scopus 로고    scopus 로고
    • Using rule-based natural language processing to improve disease normalization in biomedical text
    • Kang N, Singh B, Afzal Z, van Mulligen EM, Kors JA. Using rule-based natural language processing to improve disease normalization in biomedical text. J Am Med Inform Assoc. 2012;20:876-81.
    • (2012) J Am Med Inform Assoc , vol.20 , pp. 876-881
    • Kang, N.1    Singh, B.2    Afzal, Z.3    Mulligen, E.M.4    Kors, J.A.5
  • 50
    • 79955806959 scopus 로고    scopus 로고
    • Enabling Recognition of Diseases in Biomedical Text with Machine Learning: Corpus and Benchmark
    • Leaman R, Miller C. Enabling Recognition of Diseases in Biomedical Text with Machine Learning: Corpus and Benchmark. In: Proc 3rd Int Symp Lang Biol Med. 2009. p. 82-9.
    • (2009) Proc 3rd Int Symp Lang Biol Med. , pp. 82-89
    • Leaman, R.1    Miller, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.