UNIT 9.7 PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature
Published Online: 1 MAR 2006
Copyright © 2006 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Yoo, D., Xu, I., Berardini, T. Z., Yon Rhee, S., Narayanasamy, V. and Twigger, S. 2006. PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature. Current Protocols in Bioinformatics. 13:9.7:9.7.1–9.7.27.
- Published Online: 1 MAR 2006
- Published Print: FEB 2006
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.
- literature curation;
- controlled vocabulary;
- relational database;
- web application