Unit

UNIT 9.7 PubSearch and PubFetch: A Simple Management System for Semiautomated Retrieval and Annotation of Biological Information from the Literature

  1. Danny Yoo1,
  2. Iris Xu1,
  3. Tanya Z. Berardini1,
  4. Seung Yon Rhee1,
  5. Vijay Narayanasamy2,
  6. Simon Twigger2

Published Online: 1 MAR 2006

DOI: 10.1002/0471250953.bi0907s13

Current Protocols in Bioinformatics

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.

Author Information

  1. 1

    Carnegie Institution, Stanford, California

  2. 2

    Medical College of Wisconsin, Milwaukee, Wisconsin

Publication History

  1. Published Online: 1 MAR 2006
  2. Published Print: FEB 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.

Keywords:

  • literature curation;
  • ontology;
  • controlled vocabulary;
  • annotation;
  • genes;
  • relational database;
  • web application