Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR
Authors:
- K. Van AukenKAK. Van Auken
- P. FeyPFP. Fey
- T. Z. BerardiniTBT. Z. Berardini
- R. DodsonRDR. Dodson
- L. CooperLCL. Cooper
- D. LiDLD. Li
- J. ChanJCJ. Chan
- Y. LiYLY. Li
- S. BasuSBS. Basu
- H.-M. MullerHMH.-M. Muller
- R. ChisholmRCR. Chisholm
- E. HualaEHE. Huala
Open Access
- 1 January 2012
- journal article
- Published by Oxford University Press (OUP) in Database: The Journal of Biological Databases and Curation
- Vol. 2012, bas040
Abstract
WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we describe the curation workflow at WormBase, with particular emphasis on our use of text-mining tools (BioCreative 2012, Workshop Track II). We then describe the application of a specific component of that workflow, Textpresso for Cellular Component Curation (CCC), to Gene Ontology (GO) curation at dictyBase and TAIR (BioCreative 2012, Workshop Track III). We find that, with organism-specific modifications, Textpresso can be used by dictyBase and TAIR to annotate gene productions to GO's Cellular Component (CC) ontology.Keywords
This publication has 21 references indexed in Scilit:
- Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical ApproachFrontiers in Genetics, 2012
- Text mining for the biocuration workflowDatabase: The Journal of Biological Databases and Curation, 2012
- The Arabidopsis Information Resource (TAIR): improved gene annotation and new toolsNucleic Acids Research, 2011
- Disease Ontology: a backbone for disease semantic integrationNucleic Acids Research, 2011
- WormBase 2012: more genomes, more data, new websiteNucleic Acids Research, 2011
- Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curationBMC Bioinformatics, 2009
- The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotationsNucleic Acids Research, 2008
- Manual curation is not sufficient for annotation of genomic databasesBioinformatics, 2007
- Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological LiteraturePLOS Biology, 2004
- Building a cell and anatomy ontology of Caenorhabditis elegansComparative and Functional Genomics, 2003