Re: Corpora: protein name list

From: Philip Resnik (resnik@umiacs.umd.edu)
Date: Thu Nov 01 2001 - 17:46:06 MET

  • Next message: Michael Rundell: "Corpora: corpora: evidence and intuition"

    > I am collecting protein name list for bioinformatics research.
    > Does anyone know of public protein name list?

    You might find GenBank useful (http://www.ncbi.nlm.nih.gov/Genbank/).
    In particular, there is a protein database "compiled from a variety of
    sources, including SwissProt, PIR, PRF, PDB" (see the information at
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein).
    Also, the SWISS-PROT database can be downloaded; see the "downloading"
    link at http://www.expasy.ch/sprot/sprot-top.html. Either of these
    should provide a source from which a protein name list could be
    extracted.

    You might also be interested in a nice paper by Vasileios
    Hatzivassiloglou, Pablo A. Duboue and Andrey Rzhetsky: Disambiguating
    Proteins, Genes, and RNA in Text: A Machine Learning Approach, in
    Proceedings of the 9th International Conference on Intelligent Systems
    for Molecular Biology, Tivoli Gardens, Denmark, July 21--25, 2001
    (http://www.cs.columbia.edu/~pablo/publications/ISMB2001disambiguation.pdf).
    They apply supervised learning techniques to disambiguation of textual
    references, which you might find important since many appearances of
    items on a protein name list might actually be references to the
    related gene, etc. (I myself am exploring the use of named-entity
    tagging techniques for similar purposes.)

    I hope this helps. I'd be grateful if you'd post or forward any
    useful replies you receive!

    Best,

      Philip

      ----------------------------------------------------------------
      Philip Resnik, Assistant Professor
      Department of Linguistics and Institute for Advanced Computer Studies

      1401 Marie Mount Hall UMIACS phone: (301) 405-6760
      University of Maryland Linguistics phone: (301) 405-8903
      College Park, MD 20742 USA Fax: (301) 314-2644 / (301) 405-7104
      http://umiacs.umd.edu/~resnik E-mail: resnik@umiacs.umd.edu



    This archive was generated by hypermail 2b29 : Thu Nov 01 2001 - 17:49:29 MET