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PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature

Authors :
Vijay Narayanasamy
Danny Yoo
Simon N. Twigger
Iris Xu
Seung Y. Rhee
Tanya Z. Berardini
Source :
Current Protocols in Bioinformatics
Publication Year :
2006
Publisher :
Wiley, 2006.

Abstract

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

Details

ISSN :
1934340X and 19343396
Volume :
13
Database :
OpenAIRE
Journal :
Current Protocols in Bioinformatics
Accession number :
edsair.doi.dedup.....7989a47f70f5b47ac3667d3c117fb228
Full Text :
https://doi.org/10.1002/0471250953.bi0907s13