GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.
The automatic recognition of gene names and their associated database identifiers from biomedical text has been widely studied in recent years, as these tasks play an important role in many downstream text-mining applications. Despite significant previous research, only a small number of tools are p...
| Publicado en: | BioMed Research International Vol. 2015; pp. 1 - 8 |
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| Autores principales: | , , |
| Formato: | Journal Article |
| Publicado: |
Wiley-Blackwell
8/25/2015
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109322387&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109322387 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 8/25/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109322387 109322387 NLM26380306 10.1155/2015/918710 NLM26380306 PMC4561873 109322387 ppf: 1 ppct: 7 formats: fmt: @attributes: type: P tig: atl: GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains. aug: au: Wei, Chih-Hsuan Kao, Hung-Yu Lu, Zhiyong affil: National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA sug: ab: The automatic recognition of gene names and their associated database identifiers from biomedical text has been widely studied in recent years, as these tasks play an important role in many downstream text-mining applications. Despite significant previous research, only a small number of tools are publicly available and these tools are typically restricted to detecting only mention level gene names or only document level gene identifiers. In this work, we report GNormPlus: an end-to-end and open source system that handles both gene mention and identifier detection. We created a new corpus of 694 PubMed articles to support our development of GNormPlus, containing manual annotations for not only gene names and their identifiers, but also closely related concepts useful for gene name disambiguation, such as gene families and protein domains. GNormPlus integrates several advanced text-mining techniques, including SimConcept for resolving composite gene names. As a result, GNormPlus compares favorably to other state-of-the-art methods when evaluated on two widely used public benchmarking datasets, achieving 86.7% F1-score on the BioCreative II Gene Normalization task dataset and 50.1% F1-score on the BioCreative III Gene Normalization task dataset. The GNormPlus source code and its annotated corpus are freely available, and the results of applying GNormPlus to the entire PubMed are freely accessible through our web-based tool PubTator. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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