News FeedProject title: Gene Name Identification in Biomedical Text
Supervisor: Casey M. Bergman
CASE Partner: Matthew Cockerill, BioMedCentral
http://www.ls.manchester.ac.uk/postgraduate/ukoreu/
research/researchdegrees/studentships/project/?id=703
A BBSRC CASE PhD studentship is available to evaluate, develop and
integrate automated methods for gene name identification in
biomedical literature and datasets. Genes are the fundamental units
of structure and function for many biological processes, and millions
of research articles report results on experiments on gene function
that remain locked in the biological literature. Gene name
identification is an important research topic in bioinformatics that
will allow textual data to be fully integrated with other high-
throughput genomic data, but is a challenging task because of
ambiguity and variation in how genes are named and used in the
biological literature.
The goals of this project are to conduct a critical evaluation of
open source gene name identification systems in full-text articles
and associated supplemental data files, to integrate gene name
identification systems into general bioinformatics workflows, and to
develop real-time methods for gene name identification that will
assist authors in the publication process. The project will develop a
"gene name checker" that will allow biologists to easily edit gene
names and provide links to databases prior to publication. This
project will also establish best practice for gene name
identification, provide middleware for gene name identification, and
integrate gene name identification into the semantic web
infrastructure for the life sciences.
This project will provide training in bioinformatics, natural
language processing, genomics, data and text mining and the semantic
web. Students interested in computational biology and/or genomics
with a background in computer programming are particularly encouraged
to apply. This project is a collaboration between Drs. Casey Bergman
and Goran Nenadic at the University of Manchester and Dr. Matthew
Cockerill at BioMedCentral.