Protein Residue Corpora

This page lists a collection of corpora related to extraction and annotation of protein residues, both plain amino acid mentions and mutation sites, in text. The main sourceforge download page is http://sourceforge.net/projects/bionlp-corpora/files/ProteinResidue

MutationFinder Corpora:

   MutationFinder-1.1-Corpus.tar.gz

Contains both the text and gold standard annotations of mutations. A development set and a test set are available. The corpora were developed for the evaluation of the MutationFinder tool (http://mutationfinder.sourceforge.net). These files were extracted from MutationFinder version 1.1, available at https://sourceforge.net/projects/mutationfinder/files/MutationFinder/MutationFinder-1.1/MutationFinder-1.1.tar.gz/download

Nagel Corpus:

   NagelCorpus.tar.gz

A set of 100 abstracts annotated by Kevin Nagel with protein, residue, organism triples.

Nagel K (2009) Automatic functional annotation of predicted active sites: combining PDB and literature mining. Cambridge, UK: University of Cambridge.

Protein Residue Full Text Corpus:

   ProteinResidueFullTextCorpus.tar.gz

A set of annotations of amino acid residues and mutations over a full-text corpus. The PMIDs of the source texts are provided; the source text itself is not due to copyright restrictions.

Protein Residue Relations Silver Corpus:

   ProteinResidueRelationsSilverCorpus.tar.gz

   ProteinResidueRelationsSilverCorpus_A1.tar.gz

This package includes annotations of protein-residue relations in 1520 PubMed abstracts, as well as the source text. This corpus is considered to be a "silver standard" corpus rather than a gold standard as the annotations were automatically generated and validated using physical information from the Protein Data Bank.

The package ending in "_A1" is in the A1 format of the BRAT Annotation tool (http://brat.nlplab.org/). Thanks to S.V. Ramanam of NPJoint http://npjoint.com/Cocoa_pre.html for producing this version.

Ravikumar K.E., Haibin, L., Cohn, JD, Wall, M.E., Verspoor, K.M. (2011) "Pattern Learning Through Distant Supervision for Extraction of Protein-Residue Associations in the Biomedical Literature". The Tenth International Conference on Machine Learning and Applications (ICMLA) 2011, Honolulu, Hawaii, USA, December, 2011.

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Maintained by Helen L. Johnson.
This file last modified Tuesday, 03-Jul-2012 00:51:45 UTC