PubSearch Update

1. PubSearch Update Lukas Mueller, TAIR

2. Pub* Handles download of literature data • PubFetch • PubSearch • PubTrack Provides simple user interface for annotation tasks and stores all relevant data Tracks objects, such as articles, through a pipeline

3. PubSearch • PubSearch is a literature annotation tool for biological data hosts • It provides a simple user interface and powerful features. • The PubSearch database stores the complete literature information of a model organism, along with the controlled vocabularies, gene and sequence information, and the associations between these data types. • Aim: download and install software and you are in the business of literature curation!

4. New Hires • Behzad Mahini • Started March 2003 • Will be responsible for PubSearch project • Extensive bioinformatics experience • Incyte • Torrey Mesa Research Institute

5. Publications • Submitting publication about PubSearch

6. PubSearch.org • Registered the domain name http://PubSearch.org

7. Software improvements • Added read-only/read-write accounts. Now accounts can be limited to just searching for data. • New commands for adding Communications or URL data types. • Generalized selection of references in the annotation page. All reference types have a uniform interface for selection. • We are working on the improvement of the search interface. The plan is to separate out different search functions, but this is not yet released. • The Sequence display now shows the associated genes to that sequence.

8. Installation • released a binary for outside consumption and sent that file to the GMOD site (http://www.gmod.org) • Simplified installation with installation script. • Modified Amigo browser, which allows selecting GO terms by clicking on them, not yet included

9. Workshop • “Literature Curation Howto” • Tomorrow during the morning session.

10. Acknowledgments • PubSearch programmers • Danny Yoo • Iris Xu • TAIR Curators • RGD: Simon Twigger