Wednesday, March 13, 2013

Bioinformatics 101: Literature / Text Mining

Search Engines:
  • PubMed
    • popular, free tool provided by NCBI to search biomedical journal articles
    • includes links to connected NCBI resources (GEO, RefSeq, etc.)
  • Google Scholar
    • popular, free tool to search the scientific literature
    • provides citation information
    • allows authors to create their own bibliographies (which provide author-level citation metrics) 
Gene-Centric Information:
  • NCBI Gene
    • free tool curated by the NCBI
    • includes literature citations, Gene Ontology categories, alternative and official gene symbols, etc.
  • iHOP (Information Hyperlinked Over Proteins)
    • free text-mining program that predicts interactions between genes
  • PolySearch
    • free text-mining program that predicts interactions between genes, diseases, drugs, metabolites, SNPs, pathways, and/or tissues
  • IPA (Ingenuity Pathway Analysis)
    • commercial program curating information about genes, metabolites, etc.
    • most popular use is for functional enrichment analysis, but it can also be used as a general tool for searching the literature

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