Text-mining solutions for biomedical research: enabling integrative biology - PubMed

Affiliations

• PMID: 23150036
• DOI: 10.1038/nrg3337

Review

Text-mining solutions for biomedical research: enabling integrative biology

Dietrich Rebholz-Schuhmann et al. Nat Rev Genet. 2012 Dec.

Abstract

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.

Similar articles

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

  Bravo À, Piñero J, Queralt-Rosinach N, Rautschka M, Furlong LI. Bravo À, et al. BMC Bioinformatics. 2015 Feb 21;16:55. doi: 10.1186/s12859-015-0472-9. BMC Bioinformatics. 2015. PMID: 25886734 Free PMC article.

• Extracting biomedical events from pairs of text entities.

  Liu X, Bordes A, Grandvalet Y. Liu X, et al. BMC Bioinformatics. 2015;16 Suppl 10(Suppl 10):S8. doi: 10.1186/1471-2105-16-S10-S8. Epub 2015 Jul 13. BMC Bioinformatics. 2015. PMID: 26201478 Free PMC article.

• BioReader: a text mining tool for performing classification of biomedical literature.

  Simon C, Davidsen K, Hansen C, Seymour E, Barnkob MB, Olsen LR. Simon C, et al. BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):57. doi: 10.1186/s12859-019-2607-x. BMC Bioinformatics. 2019. PMID: 30717659 Free PMC article.

• Text mining resources for the life sciences.

  Przybyła P, Shardlow M, Aubin S, Bossy R, Eckart de Castilho R, Piperidis S, McNaught J, Ananiadou S. Przybyła P, et al. Database (Oxford). 2016 Nov 25;2016:baw145. doi: 10.1093/database/baw145. Print 2016. Database (Oxford). 2016. PMID: 27888231 Free PMC article. Review.

• Biomedical text mining and its applications in cancer research.

  Zhu F, Patumcharoenpol P, Zhang C, Yang Y, Chan J, Meechai A, Vongsangnak W, Shen B. Zhu F, et al. J Biomed Inform. 2013 Apr;46(2):200-11. doi: 10.1016/j.jbi.2012.10.007. Epub 2012 Nov 15. J Biomed Inform. 2013. PMID: 23159498 Review.

Cited by

• PCorral--interactive mining of protein interactions from MEDLINE.

  Li C, Jimeno-Yepes A, Arregui M, Kirsch H, Rebholz-Schuhmann D. Li C, et al. Database (Oxford). 2013 May 2;2013:bat030. doi: 10.1093/database/bat030. Print 2013. Database (Oxford). 2013. PMID: 23640984 Free PMC article.

• Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: exploring the use of literature-based discovery in primary care research.

  Vos R, Aarts S, van Mulligen E, Metsemakers J, van Boxtel MP, Verhey F, van den Akker M. Vos R, et al. J Am Med Inform Assoc. 2014 Jan-Feb;21(1):139-45. doi: 10.1136/amiajnl-2012-001448. Epub 2013 Jun 17. J Am Med Inform Assoc. 2014. PMID: 23775174 Free PMC article.

• Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion.

  Jonnagaddala J, Jue TR, Chang NW, Dai HJ. Jonnagaddala J, et al. Database (Oxford). 2016 Aug 7;2016:baw112. doi: 10.1093/database/baw112. Print 2016. Database (Oxford). 2016. PMID: 27504009 Free PMC article.

• Ferret: a sentence-based literature scanning system.

  Srinivasan P, Zhang XN, Bouten R, Chang C. Srinivasan P, et al. BMC Bioinformatics. 2015 Jun 20;16(1):198. doi: 10.1186/s12859-015-0630-0. BMC Bioinformatics. 2015. PMID: 26091670 Free PMC article.

• Constructing a database for the relations between CNV and human genetic diseases via systematic text mining.

  Yang X, Song Z, Wu C, Wang W, Li G, Zhang W, Wu L, Lu K. Yang X, et al. BMC Bioinformatics. 2018 Dec 31;19(Suppl 19):528. doi: 10.1186/s12859-018-2526-2. BMC Bioinformatics. 2018. PMID: 30598077 Free PMC article.

References

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Research Materials

  • NCI CPTC Antibody Characterization Program