Text-mining solutions for biomedical research: enabling integrative biology

被引:149
作者
Rebholz-Schuhmann, Dietrich [1 ,2 ]
Oellrich, Anika [1 ]
Hoehndorf, Robert [3 ,4 ]
机构
[1] European Bioinformat Inst, Cambridge CB10 1SD, England
[2] Univ Zurich, Inst Comp Linguist, CH-8050 Zurich, Switzerland
[3] Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
[4] Univ Cambridge, Dept Physiol Dev & Neurosci, Cambridge CB2 3EG, England
关键词
PROTEIN-PROTEIN INTERACTIONS; KNOWLEDGE; INFORMATION; GENES; IDENTIFICATION; DISCOVERY; NETWORKS; TOOL; NORMALIZATION; RECOGNITION;
D O I
10.1038/nrg3337
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
In response to the unbridled growth of information in literature and biomedical databases, researchers require efficient means of handling and extracting information. As well as providing background information for research, scientific publications can be processed to transform textual information into database content or complex networks and can be integrated with existing knowledge resources to suggest novel hypotheses. Information extraction and text data analysis can be particularly relevant and helpful in genetics and biomedical research, in which up-to-date information about complex processes involving genes, proteins and phenotypes is crucial. Here we explore the latest advancements in automated literature analysis and its contribution to innovative research approaches.
引用
收藏
页码:829 / 839
页数:11
相关论文
共 105 条
[1]   Text mining for biology - the way forward: opinions from leading scientists [J].
Altman, Russ B. ;
Bergman, Casey M. ;
Blake, Judith ;
Blaschke, Christian ;
Cohen, Aaron ;
Gannon, Frank ;
Grivell, Les ;
Hahn, Udo ;
Hersh, William ;
Hirschman, Lynette ;
Jensen, Lars Juhl ;
Krallinger, Martin ;
Mons, Barend ;
O'Donoghue, Sean I. ;
Peitsch, Manuel C. ;
Rebholz-Schuhmann, Dietrich ;
Shatkay, Hagit ;
Valencia, Alfonso .
GENOME BIOLOGY, 2008, 9
[2]   Event extraction for systems biology by text mining the literature [J].
Ananiadou, Sophia ;
Pyysalo, Sampo ;
Tsujii, Jun'ichi ;
Kell, Douglas B. .
TRENDS IN BIOTECHNOLOGY, 2010, 28 (07) :381-390
[3]  
[Anonymous], 2004, Knowledge representation and reasoning
[4]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[5]   Utopia documents: linking scholarly literature with research data [J].
Attwood, T. K. ;
Kell, D. B. ;
McDermott, P. ;
Marsh, J. ;
Pettifer, S. R. ;
Thorne, D. .
BIOINFORMATICS, 2010, 26 (18) :i568-i574
[6]   PRINTS and its automatic supplement, prePRINTS [J].
Attwood, TK ;
Bradley, P ;
Flower, DR ;
Gaulton, A ;
Maudling, N ;
Mitchell, AL ;
Moulton, G ;
Nordle, A ;
Paine, K ;
Taylor, P ;
Uddin, A ;
Zygouri, C .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :400-402
[7]   Bio2RDF: Towards a mashup to build bioinformatics knowledge systems [J].
Belleau, Francois ;
Nolin, Marc-Alexandre ;
Tourigny, Nicole ;
Rigault, Philippe ;
Morissette, Jean .
JOURNAL OF BIOMEDICAL INFORMATICS, 2008, 41 (05) :706-716
[8]   Conceptual biology: Unearthing the gems [J].
Blagosklonny, MV ;
Pardee, AB .
NATURE, 2002, 416 (6879) :373-373
[9]   The Gene Ontology: enhancements for 2011 [J].
Blake, J. A. ;
Dolan, M. ;
Drabkin, H. ;
Hill, D. P. ;
Ni, L. ;
Sitnikov, D. ;
Burgess, S. ;
Buza, T. ;
Gresham, C. ;
McCarthy, F. ;
Pillai, L. ;
Wang, H. ;
Carbon, S. ;
Lewis, S. E. ;
Mungall, C. J. ;
Gaudet, P. ;
Chisholm, R. L. ;
Fey, P. ;
Kibbe, W. A. ;
Basu, S. ;
Siegele, D. A. ;
McIntosh, B. K. ;
Renfro, D. P. ;
Zweifel, A. E. ;
Hu, J. C. ;
Brown, N. H. ;
Tweedie, S. ;
Alam-Faruque, Y. ;
Apweiler, R. ;
Auchinchloss, A. ;
Axelsen, K. ;
Argoud-Puy, G. ;
Bely, B. ;
Blatter, M. -C. ;
Bougueleret, L. ;
Boutet, E. ;
Branconi-Quintaje, S. ;
Breuza, L. ;
Bridge, A. ;
Browne, P. ;
Chan, W. M. ;
Coudert, E. ;
Cusin, I. ;
Dimmer, E. ;
Duek-Roggli, P. ;
Eberhardt, R. ;
Estreicher, A. ;
Famiglietti, L. ;
Ferro-Rojas, S. ;
Feuermann, M. .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D559-D564
[10]  
Blaschke C, 1999, Proc Int Conf Intell Syst Mol Biol, P60