Seeking a New Biology Through Text Mining

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2008 Jul 11

PMID 18614002

Citations 32

Authors

Andrey Rzhetsky

Michael Seringhaus

Mark Gerstein

Affiliations

Soon will be listed here.

Abstract

Tens of thousands of biomedical journals exist, and the deluge of new articles in the biomedical sciences is leading to information overload. Hence, there is much interest in text mining, the use of computational tools to enhance the human ability to parse and understand complex text.

Citing Articles

PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge.

Wei C, Allot A, Lai P, Leaman R, Tian S, Luo L Nucleic Acids Res. 2024; 52(W1):W540-W546.

PMID: 38572754 PMC: 11223843. DOI: 10.1093/nar/gkae235.

Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification.

Erdengasileng A, Han Q, Zhao T, Tian S, Sui X, Li K Database (Oxford). 2022; 2022.

PMID: 35962559 PMC: 9375052. DOI: 10.1093/database/baac066.

Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability.

Leaman R, Wei C, Allot A, Lu Z PLoS Biol. 2020; 18(6):e3000716.

PMID: 32479517 PMC: 7289435. DOI: 10.1371/journal.pbio.3000716.

SBLC: a hybrid model for disease named entity recognition based on semantic bidirectional LSTMs and conditional random fields.

Xu K, Zhou Z, Gong T, Hao T, Liu W BMC Med Inform Decis Mak. 2018; 18(Suppl 5):114.

PMID: 30526592 PMC: 6284263. DOI: 10.1186/s12911-018-0690-y.

Automatic extraction of protein-protein interactions using grammatical relationship graph.

Yu K, Lung P, Zhao T, Zhao P, Tseng Y, Zhang J BMC Med Inform Decis Mak. 2018; 18(Suppl 2):42.

PMID: 30066644 PMC: 6069288. DOI: 10.1186/s12911-018-0628-4.

References

Jensen L, Saric J, Bork P . Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet. 2006; 7(2):119-29. DOI: 10.1038/nrg1768. View

Wilbur W, Hazard Jr G, Divita G, Mork J, Aronson A, Browne A . Analysis of biomedical text for chemical names: a comparison of three methods. Proc AMIA Symp. 1999; :176-80. PMC: 2232672. View

Ananiadou S, Kell D, Tsujii J . Text mining and its potential applications in systems biology. Trends Biotechnol. 2006; 24(12):571-9. DOI: 10.1016/j.tibtech.2006.10.002. View

Hendler J . Publishing on the semantic web. Nature. 2001; 410(6832):1023-4. DOI: 10.1038/35074206. View

Colosimo M, Morgan A, Yeh A, Colombe J, Hirschman L . Data preparation and interannotator agreement: BioCreAtIvE task 1B. BMC Bioinformatics. 2005; 6 Suppl 1:S12. PMC: 1869005. DOI: 10.1186/1471-2105-6-S1-S12. View

Bourne P . Will a biological database be different from a biological journal?. PLoS Comput Biol. 2005; 1(3):179-81. PMC: 1193993. DOI: 10.1371/journal.pcbi.0010034. View

Hamosh A, Scott A, Amberger J, Valle D, MCKUSICK V . Online Mendelian Inheritance in Man (OMIM). Hum Mutat. 1999; 15(1):57-61. DOI: 10.1002/(SICI)1098-1004(200001)15:1<57::AID-HUMU12>3.0.CO;2-G. View

Natarajan J, Berrar D, Dubitzky W, Hack C, Zhang Y, DeSesa C . Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line. BMC Bioinformatics. 2006; 7:373. PMC: 1557675. DOI: 10.1186/1471-2105-7-373. View

Krallinger M, Valencia A . Text-mining and information-retrieval services for molecular biology. Genome Biol. 2005; 6(7):224. PMC: 1175978. DOI: 10.1186/gb-2005-6-7-224. View

10.

Shatkay H, Hoglund A, Brady S, Blum T, Donnes P, Kohlbacher O . SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics. 2007; 23(11):1410-7. DOI: 10.1093/bioinformatics/btm115. View

11.

Cohen A, Hersh W . A survey of current work in biomedical text mining. Brief Bioinform. 2005; 6(1):57-71. DOI: 10.1093/bib/6.1.57. View

12.

Seringhaus M, Gerstein M . Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics. 2007; 8:17. PMC: 1781953. DOI: 10.1186/1471-2105-8-17. View

13.

Hirschman L, Morgan A, Yeh A . Rutabaga by any other name: extracting biological names. J Biomed Inform. 2003; 35(4):247-59. DOI: 10.1016/s1532-0464(03)00014-5. View

14.

Shiffrin R, Borner K . Mapping knowledge domains. Proc Natl Acad Sci U S A. 2004; 101 Suppl 1:5183-5. PMC: 387293. DOI: 10.1073/pnas.0307852100. View