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This material is based upon work supported by the National Science Foundation under Grant No.: EIA-0205448
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Mining the Bibliome
Works of Interest
 

Contents

  1. Affiliations
  2. Resources
  3. Readings

Affiliations

  • Links to the Institute for Research in Cognitive Science (IRCS) at the University of Pennsylvania.
  • Links to the National Science Foundation's Information Technology Research (ITR) program.
  • Links to the sister project entitled " Language, Learning and Modeling Biological Sequences ", funded via NSF ITR award EIA-0205456.

    Resources

  • [IUPAC]: The twenty essential nucleic acids and some other amino acids and symbols.
  • MedlinePlus: A site developed by the US National Library of Medicine and the National Institutes of Health which features an extensive medical encyclopedia, drug information, and a medical dictionary. (Ariel)
  • Merriam-Webster Medical Dictionary on the MedLine website (Ariel)
  • The National Library of Medicine's ChemIDplusLite provides access to nomenclature information for the identification of chemical substances cited in NLM databases.
  • Scirus: A great search engine for scientific information (Ariel)
  • BioTech: A site run by the University of Texas at Austin which includes a detailed chemical acronym database and life sciences dictionary. (Ariel)
  • Who Named It: This is a good way to tell if something is named after a person and should be tagged with /NNP. (Ari)
  • the NCI Metathesaurus (for cancer-related terms)

    three gene databases:

  • Terminology and ontology resources

    Readings

    POS

  • The POS manual,Part-of-Speech Tagging Guidelines for the Penn Treebank Project (3rd Revision, 2nd printing), Santorini & MacIntyre: PDF or zipped postScript file

    CYP450

    University of Pennsylvania's Information Technology Research/Extraction (ITR/E) Project, 'Mining the Bibliome':

  • Biomedical Annotation Database

    Dr. David Nelson of the University of Tennessee at Memphis:

  • Cytochrome P450 Homepage
  • Cytochrome P450s in humans
  • Human Cytochrome P450s
  • Superfamily name: Cytochrome P450

    The Plant Biotechnology Institute, National Research Council, Saskatoon, Saskatchewan, Canada:

  • P450s in Plants
  • P450s in other plants

    'Pharmacy Briefs', A Publication of The Pharmacy and Therapeuitcs Committee of Family Health Plan:

  • Cytochrome P450 Drug Metabolism and Interactions

    Christy Pardee, graduate student

  • Introduction to the Cytochrome P450 enzymes

    Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB):

  • Enzyme Nomenclature: Acting on NADH or NADPH

    The European Bioinformatics Institute:

  • EC Number search tool
  • Data bank information
  • Enzymes and Metabolic Pathways (EMP) database -- Inaccessible as of June 26, 2007

    Dr. Kirill Degtyarenko, member of the European Bioinformatics Institute:

  • List of EC numbers for P450 enzymes

    The Scripps Research Institute:

  • P450 proteins
  • Haem-thiolate proteins

    Sigma Aldrich:

  • Flavin-Containing Monooxygenase-1

    Swiss Institute of Bioinformatics:

  • Enzyme nomenclature database

    Cologne University BioInformatics Center:

  • Brenda: The Comprehensive Enzyme Information System

    The Midwest Cytochrome P450 Symposium from Purdue University:

  • Genes to Heme

    Oncology

    University of Pennsylvania's Information Technology Research/Extraction (ITR/E) Project, 'Mining the Bibliome':

  • Summary of the Oncology work
  • List of genes & malignancies also in Word Format
  • Paper submitted to HLT/NAACL 2004 (Human Language Technology conference / North American chapter of the Association for Computational Linguistics annual meeting). (Jan. '04, PDF, 8pp.) Pete White writes: "This manuscript has been submitted to [this workshop]. It is our information extraction group's latest summary of our work and thus represents the best current overall perspective of the project."
  • Some of our work at HGVS 2003 (Nov. '03, PowerPoint, 18pp.):
  • Pete White's presentation

    The Gene Ontology Consortium:

  • Gene Ontology (GO)

    The National Cancer Institute:

  • Cancer Genetics Overview
  • Cancer Topics

    American Cancer Society

  • Cancer Reference Information

    Cavenee and White:

  • The Genetic Basis of Cancer, Scientific American, March 1995 *

    Weinberg:

  • How cancer arises, Scientific American, September 1996 *

    Note

    * Some items listed here, marked with an asterisk, are available through this website only to annotators and other project members because of IPR restrictions.

    Treebanking

    Beatrice Santorini's textbooks

  • An introduction to syntactic theory
  • The syntax of natural language

    • University of Pennsylvania's Information Technology Research/Extraction (ITR/E) Project, 'Mining the Bibliome':

  • BioIE Wiki Treebanking Resources

    Information Extraction

    The University of Sheffield:

  • Information extraction from the Natural Language Processing Group
  • The TRESTLE Project [Added 2003-03-30]

    The Public Library of Science (PLOS) Biology, a peer-reviewed open-access journal:

  • Textpresso, An Ontology-Based Information Retrieval and Extraction System for Biological Literature