Table I.

Some examples of the online text-mining tools for biologists

PubGeneDesigned to identify relationships between genes based on their co-occurrence in the abstracts of scientific papers et al. (2001)
MedMinerFilters extract and organize relevant sentences in the literature based on the query given et al. (1999)
XploreMedAllows exploration of a set of abstracts derived from a MEDLINE search et al. (2003)
PubMatrixCompares a list of terms against another list of terms in PubMed et al. (2003)
AbXtractExtracts domain-specific information from the analysis of abstracts related to set of protein families and Valencia (1998)
VxInsightA general tool for revealing the implicit structure of the data in large databases et al. (2001)
SUISEKIExtracts protein-protein interactions from large collections of scientific text and Valencia (2001)
GISBiomedical text-mining system focused on gene-related information∼yuhc/gis/Chiang et al. (2004)
PreBINDLocates biomolecular interaction information in the scientific literature et al. (2003)
Genes2 DiseasesAnalyses relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases et al. (2002)
HAPILinks set of genes in the published literature by way of keyword hierarchies et al. (2001)
TextPressoAn information retrieval and extraction system for biological literature (Caenorhabditis elegans version) et al. (2004)
Dragon TF Association MinerFinds association between transcription factors, GO terms, and diseases. Has a module to filter out irrelevant documents et al. (2004)