Sites that are devoted to genes, proteins, and other bioinformatic resources:

• SENT
  WEb-based tool for semantic features in text
• PIE
  extracts protein interaction information from input text.
• NextBio
  finds genes, articles and public gene expression data that are related to query term.
• Whatizit
• MarkerInfoFinder
• babelomic
• ORegAnno
  An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
• Biorag
  Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c.elegans genes that are represented in Unigene clusters.
• Ontogene
  focuses on the extraction of semantic relations (e.g. bind, activate, block) between specific biological entities (such as Genes and Proteins) from the scientifical literature
• GeneLibrarian
  a platform to provide users well-organized information about any specific group of genes (e.g. one cluster of genes from a microarray chip) they might be interested in.
• Bio Resource for Array Genes
  a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c.elegans genes.
• CBioC: Collaborative Bio Curation
  allows anyone to search for and vote on statements related to a particular protein, gene, disease, or interaction extracted from PubMed articles.
• Medminer
  site for extracting information about gene-gene and gene-drug interactions from the abstracts of papers in Medline.
• MedGene
  links genes and diseases in Medline by a variety of statistical measures.
• Pubmatrix
  allows the searcher to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table
• Pubgene
  the PubGene Webtools allow users to analyze gene expression data with literature network information, browse literature neighbors of a given gene, search literature articles for a set of genes, search ontology terms related to a given gene, search MeSH terms found with a set of genes, and search for official nomenclature.
• HAPI
  the High-density Array Pattern Interpreter (HAPI) will accept gene expression array data in tab-delimited format for clusters of up to 250 genes and create keyword hierarchies from the published literature linked to those genes. Keyword hierarchies are intended to help interpret the biological similarities of the genes in the cluster.
• MedBlast
  searching articles related to a biological sequence.
• Chilibot
  Mining MEDLINE for gene/protein/keyword relationships.
• Genes2Diseases(G2D)
  a database of candidate genes for mapped inherited human diseases.
• GoMiner
  organizes a list of genes for biological interpretations in the context of the Gene Ontology.
• Semantic Gene Organizer (SGO)
  helps identify gene-gene and keyword-gene associations using gene concepts (via latent semantic indexing [LSI]) in Medline.
• GNF SymAtlas
  database of genes and expression data
• Organism and Bioinformatics Resources
  large collection of organism biology and bioinformatics resources
• Harvester
  caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information.
• DRAGON
  a collection of programs for analysis and extraction of biological data.
• IHOP
  search for abstract sentences that mention a specific gene, and create a gene network of co-mentioned genes.
• PILGRM for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). /http://pilgrm.princeton.edu/
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