Transcript PubSearch_update_CSHL

PubSearch Update
Lukas Mueller, TAIR
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
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!
New Hires
• Behzad Mahini
– Started March 2003
– Will be responsible for PubSearch project
– Extensive bioinformatics experience
• Incyte
• Torrey Mesa Research Institute
Publications
• Submitting publication about PubSearch
PubSearch.org
• Registered the domain name
http://PubSearch.org
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.
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
Workshop
• “Literature Curation Howto”
• Tomorrow during the morning session.
Acknowledgments
• PubSearch programmers
– Danny Yoo
– Iris Xu
• TAIR Curators
• RGD: Simon Twigger