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