Literature DB >> 17990498

GeneRIF quality assurance as summary revision.

Zhiyong Lu1, K Bretonnel Cohen, Lawrence Hunter.   

Abstract

Like the primary scientific literature, GeneRIFs exhibit both growth and obsolescence. NLM's control over the contents of the Entrez Gene database provides a mechanism for dealing with obsolete data: GeneRIFs are removed from the database when they are found to be of low quality. However, the rapid and extensive growth of Entrez Gene makes manual location of low-quality GeneRIFs problematic. This paper presents a system that takes advantage of the summary-like quality of GeneRIFs to detect low-quality GeneRIFs via a summary revision approach, achieving precision of 89% and recall of 77%. Aspects of the system have been adopted by NLM as a quality assurance mechanism.

Mesh:

Year:  2007        PMID: 17990498      PMCID: PMC2652871          DOI: 10.1142/9789812772435_0026

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  7 in total

1.  Gene indexing: characterization and analysis of NLM's GeneRIFs.

Authors:  Joyce A Mitchell; Alan R Aronson; James G Mork; Lillian C Folk; Susanne M Humphrey; Janice M Ward
Journal:  AMIA Annu Symp Proc       Date:  2003

2.  Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record.

Authors:  Patrick Ruch; Robert Baud; Antoine Geissbühler
Journal:  Artif Intell Med       Date:  2003 Sep-Oct       Impact factor: 5.326

Review 3.  Summarization from medical documents: a survey.

Authors:  Stergos Afantenos; Vangelis Karkaletsis; Panagiotis Stamatopoulos
Journal:  Artif Intell Med       Date:  2005-02       Impact factor: 5.326

4.  Finding GeneRIFs via gene ontology annotations.

Authors:  Zhiyong Lu; K Bretonnel Cohen; Lawrence Hunter
Journal:  Pac Symp Biocomput       Date:  2006

5.  Automatically generating gene summaries from biomedical literature.

Authors:  Xu Ling; Jing Jiang; Xin He; Qiaozhu Mei; Chengxiang Zhai; Bruce Schatz
Journal:  Pac Symp Biocomput       Date:  2006

6.  Overview of BioCreAtIvE task 1B: normalized gene lists.

Authors:  Lynette Hirschman; Marc Colosimo; Alexander Morgan; Alexander Yeh
Journal:  BMC Bioinformatics       Date:  2005-05-24       Impact factor: 3.169

7.  MILANO--custom annotation of microarray results using automatic literature searches.

Authors:  Ran Rubinstein; Itamar Simon
Journal:  BMC Bioinformatics       Date:  2005-01-20       Impact factor: 3.169

  7 in total
  27 in total

1.  Manual curation is not sufficient for annotation of genomic databases.

Authors:  William A Baumgartner; K Bretonnel Cohen; Lynne M Fox; George Acquaah-Mensah; Lawrence Hunter
Journal:  Bioinformatics       Date:  2007-07-01       Impact factor: 6.937

2.  Evaluating relevance ranking strategies for MEDLINE retrieval.

Authors:  Zhiyong Lu; Won Kim; W John Wilbur
Journal:  J Am Med Inform Assoc       Date:  2008-10-24       Impact factor: 4.497

Review 3.  Community challenges in biomedical text mining over 10 years: success, failure and the future.

Authors:  Chung-Chi Huang; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-05-01       Impact factor: 11.622

4.  Insight into bacterial virulence mechanisms against host immune response via the Yersinia pestis-human protein-protein interaction network.

Authors:  Huiying Yang; Yuehua Ke; Jian Wang; Yafang Tan; Sebenzile K Myeni; Dong Li; Qinghai Shi; Yanfeng Yan; Hui Chen; Zhaobiao Guo; Yanzhi Yuan; Xiaoming Yang; Ruifu Yang; Zongmin Du
Journal:  Infect Immun       Date:  2011-09-12       Impact factor: 3.441

5.  Extraction of semantic biomedical relations from text using conditional random fields.

Authors:  Markus Bundschus; Mathaeus Dejori; Martin Stetter; Volker Tresp; Hans-Peter Kriegel
Journal:  BMC Bioinformatics       Date:  2008-04-23       Impact factor: 3.169

6.  A framework for annotating human genome in disease context.

Authors:  Wei Xu; Huisong Wang; Wenqing Cheng; Dong Fu; Tian Xia; Warren A Kibbe; Simon M Lin
Journal:  PLoS One       Date:  2012-12-10       Impact factor: 3.240

7.  Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Authors:  Peter B McGarvey; Hongzhan Huang; Raja Mazumder; Jian Zhang; Yongxing Chen; Chengdong Zhang; Stephen Cammer; Rebecca Will; Margie Odle; Bruno Sobral; Margaret Moore; Cathy H Wu
Journal:  PLoS One       Date:  2009-09-25       Impact factor: 3.240

8.  GeneRIF indexing: sentence selection based on machine learning.

Authors:  Antonio J Jimeno-Yepes; J Caitlin Sticco; James G Mork; Alan R Aronson
Journal:  BMC Bioinformatics       Date:  2013-05-31       Impact factor: 3.169

9.  Chapter 16: text mining for translational bioinformatics.

Authors:  K Bretonnel Cohen; Lawrence E Hunter
Journal:  PLoS Comput Biol       Date:  2013-04-25       Impact factor: 4.475

10.  TSGene: a web resource for tumor suppressor genes.

Authors:  Min Zhao; Jingchun Sun; Zhongming Zhao
Journal:  Nucleic Acids Res       Date:  2012-10-12       Impact factor: 16.971

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