-
1
-
-
84869505278
-
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
-
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
-
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
-
4
-
-
84987617568
-
BioCreative-IV virtual issue
-
bau039-9
-
Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, et al. BioCreative-IV virtual issue. Database. 2014;2014:bau039-9.
-
(2014)
Database
, vol.2014
-
-
Arighi, C.N.1
Wu, C.H.2
Cohen, K.B.3
Hirschman, L.4
Krallinger, M.5
Valencia, A.6
-
5
-
-
84865997531
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
12
-
-
84897915860
-
Knowledge-based extraction of adverse drug events from biomedical text
-
Kang N, Singh B, Bui C, Afzal Z, van Mulligen EM, Kors JA. Knowledge-based extraction of adverse drug events from biomedical text. BMC Bioinformatics. 2014;15:64.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 64
-
-
Kang, N.1
Singh, B.2
Bui, C.3
Afzal, Z.4
Mulligen, E.M.5
Kors, J.A.6
-
13
-
-
43749110484
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
24
-
-
37849006444
-
Rapid pattern development for concept recognition systems: application to point mutations
-
Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L. Rapid pattern development for concept recognition systems: application to point mutations. J Bioinform Comput Biol. 2007;5:1233-59.
-
(2007)
J Bioinform Comput Biol
, vol.5
, pp. 1233-1259
-
-
Caporaso, J.G.1
Baumgartner, W.A.2
Randolph, D.A.3
Cohen, K.B.4
Hunter, L.5
-
25
-
-
33751088706
-
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
-
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
-
27
-
-
84876207025
-
Combining joint models for biomedical event extraction
-
McClosky D, Riedel S, Surdeanu M, McCallum A, Manning CD. Combining joint models for biomedical event extraction. BMC Bioinformatics. 2012;13 Suppl 11:S9.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S9
-
-
McClosky, D.1
Riedel, S.2
Surdeanu, M.3
McCallum, A.4
Manning, C.D.5
-
28
-
-
0842283365
-
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
-
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
-
30
-
-
85104042765
-
Overview of BioNLP'09 shared task on event extraction
-
Kim J-D, Ohta T, Pyysalo S, Kano Y, Tsujii J. Overview of BioNLP'09 shared task on event extraction. In: BioNLP '09 Proc Work Curr Trends Biomed Nat Lang Process Shar Task. Association for Computational Linguistics. 2009. p. 1-9.
-
(2009)
BioNLP '09 Proc Work Curr Trends Biomed Nat Lang Process Shar Task. Association for Computational Linguistics
, pp. 1-9
-
-
Kim, J.-D.1
Ohta, T.2
Pyysalo, S.3
Kano, Y.4
Tsujii, J.5
-
31
-
-
84926140240
-
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
-
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
-
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
-
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
-
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
-
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
-
38
-
-
84865957320
-
The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships
-
Van Mulligen EM, Fourrier-Reglat A, Gurwitz D, Molokhia M, Nieto A, Trifiro G, et al. The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships. J Biomed Inform. 2012;45:879-84.
-
(2012)
J Biomed Inform
, vol.45
, pp. 879-884
-
-
Mulligen, E.M.1
Fourrier-Reglat, A.2
Gurwitz, D.3
Molokhia, M.4
Nieto, A.5
Trifiro, G.6
-
39
-
-
84900334705
-
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
-
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
-
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
-
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
-
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
-
45
-
-
0038005018
-
DAVID: Database for Annotation, Visualization, and Integrated Discovery
-
Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003;4:P3.
-
(2003)
Genome Biol
, vol.4
, pp. P3
-
-
Dennis, G.1
Sherman, B.T.2
Hosack, D.A.3
Yang, J.4
Gao, W.5
Lane, H.C.6
-
46
-
-
84880973546
-
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
-
47
-
-
79953205976
-
The value of data
-
Mons B, van Haagen H, Chichester C, Hoen P-B 't, den Dunnen JT, van Ommen G, et al. The value of data. Nat Genet. 2011;43:281-3.
-
(2011)
Nat Genet
, vol.43
, pp. 281-283
-
-
Mons, B.1
Haagen, H.2
Chichester, C.3
Hoen, P.-B.4
Dunnen, J.T.5
Ommen, G.6
-
48
-
-
51049088874
-
Overview of BioCreative II gene mention recognition
-
Smith L, Tanabe L, Ando R, Kuo C, Chung I, Hsu C, et al. Overview of BioCreative II gene mention recognition. Genome Biol. 2008;9:S2.
-
(2008)
Genome Biol
, vol.9
, pp. S2
-
-
Smith, L.1
Tanabe, L.2
Ando, R.3
Kuo, C.4
Chung, I.5
Hsu, C.6
-
49
-
-
84882760954
-
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
-
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
|