Literature DB >> 16882651

OSIRIS: a tool for retrieving literature about sequence variants.

Julio Bonis1, Laura Inés Furlong, Ferran Sanz.   

Abstract

UNLABELLED: Sequence variants, in particular single nucleotide polymorphisms (SNPs), are key elements for the identification of genes associated with complex diseases and with particular drug responses. The search for literature about sequence variation is hampered by the large number of allelic variants reported for many genes and by the variability in both gene and sequence variants nomenclatures. We describe OSIRIS, a search tool that integrates different sources of information with the aim to retrieve literature about sequence variation of a gene. In addition, it provides a method to link a dbSNP entry with the articles referring to it. AVAILABILITY: OSIRIS is available for public use at http://ibi.imim.es/

Mesh:

Year:  2006        PMID: 16882651     DOI: 10.1093/bioinformatics/btl421

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  11 in total

1.  Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.

Authors:  Emily Doughty; Attila Kertesz-Farkas; Olivier Bodenreider; Gary Thompson; Asa Adadey; Thomas Peterson; Maricel G Kann
Journal:  Bioinformatics       Date:  2010-12-07       Impact factor: 6.937

2.  Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.

Authors:  J Gregory Caporaso; Nita Deshpande; J Lynn Fink; Philip E Bourne; K Bretonnel Cohen; Lawrence Hunter
Journal:  Pac Symp Biocomput       Date:  2008

3.  tmVar: a text mining approach for extracting sequence variants in biomedical literature.

Authors:  Chih-Hsuan Wei; Bethany R Harris; Hung-Yu Kao; Zhiyong Lu
Journal:  Bioinformatics       Date:  2013-04-05       Impact factor: 6.937

4.  Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature.

Authors:  Ayush Singhal; Michael Simmons; Zhiyong Lu
Journal:  J Am Med Inform Assoc       Date:  2016-04-27       Impact factor: 4.497

5.  tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine.

Authors:  Chih-Hsuan Wei; Lon Phan; Juliana Feltz; Rama Maiti; Tim Hefferon; Zhiyong Lu
Journal:  Bioinformatics       Date:  2018-01-01       Impact factor: 6.937

Review 6.  Towards precision medicine: advances in computational approaches for the analysis of human variants.

Authors:  Thomas A Peterson; Emily Doughty; Maricel G Kann
Journal:  J Mol Biol       Date:  2013-08-17       Impact factor: 5.469

7.  MutationFinder: a high-performance system for extracting point mutation mentions from text.

Authors:  J Gregory Caporaso; William A Baumgartner; David A Randolph; K Bretonnel Cohen; Lawrence Hunter
Journal:  Bioinformatics       Date:  2007-05-11       Impact factor: 6.937

8.  Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

Authors:  Ayush Singhal; Michael Simmons; Zhiyong Lu
Journal:  PLoS Comput Biol       Date:  2016-11-30       Impact factor: 4.475

9.  MAGPEL: an autoMated pipeline for inferring vAriant-driven Gene PanEls from the full-length biomedical literature.

Authors:  Nafiseh Saberian; Adib Shafi; Azam Peyvandipour; Sorin Draghici
Journal:  Sci Rep       Date:  2020-07-23       Impact factor: 4.379

10.  OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature.

Authors:  Laura I Furlong; Holger Dach; Martin Hofmann-Apitius; Ferran Sanz
Journal:  BMC Bioinformatics       Date:  2008-02-05       Impact factor: 3.169

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