Mutation Miner (ISMB 2005)

Introduction

Biological researchers today have access to vast amounts of exponentially growing research data in a structured form within several publicly accessible databases. A large proportion of salient information is however still hidden within individual research papers, since costly manual database curation efforts are overwhelmed by the scale of new information being generated. In the domain of protein engineering, critical units of information required from the literature include: the identity of the mutated protein, the identity and position of wild type residues that are mutated, the identity of the resulting mutant residues and the impacts of the mutations on functional properties of the proteins.
Mutation Miner is a system designed to automate the extraction of mutations and textual annotations describing the impacts of mutations on protein properties (mutation annotations) from full text scientific literature. Furthermore, the system retrieves and carries out bioinformatic analyses on mutated sequences providing the mapped coordinates of mutants on a selected structure. Integration of multiple formatted mutation annotations with associated residue coordinates facilitates their rendering with structure visualization tools. We describe the architecture and tools that support Mutation Miner (Text mining-NLP, Sequence Analysis, Structure Visualization) and present performance evaluations that demonstrate the feasibility of this approach.

Mutation Miner Poster at ISMB 2005

Reference

Christopher J. O. Baker and René Witte, Mutation Miner. 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005), June 25-29, 2005, Detroit, Michigan, USA.

Bibtex entry (also for download):

@InProceedings{BakerWitte_ISMB2005,
  author = 	 {Christopher J. O. Baker and Ren{\'e} Witte},
  title = 	 {{Mutation Miner}},
  booktitle =	 {13th Annual International conference on 
       Intelligent Systems for Molecular Biology (ISMB 2005)},
  year =	 {2005},
  address =	 {Detroit, Michigan, USA},
  month =	 {June 25--29}
}

You can also visit the webpage of the 13th Annual International conference on Intelligent Systems for Molecular Biology.

Software

For downloading our open source software, please refer to the successor project, Open Mutation Miner (OMM).