Improved mutation tagging with gene identifiers applied to membrane protein stability prediction.

ABSTRACT:

Background

The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach to study structure-function relationships in biomedical data sets.

Results

We developed a rule- and regular expression-based protein point mutation retrieval pipeline for PubMed abstracts, which shows an F-measure of 87% for the mutation retrieval task on a benchmark dataset. In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks. Vice versa, we could show that gene recognition improved from 77% to 91% F-measur

SUBMITTER: Winnenburg R 

PROVIDER: S-EPMC2745585 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature