Table 1

Biomedical text-mining resources, servers and programs
Name
 Description
 URL
 Published reference or URL*
Abbreviation Server
 Biomedical abbreviation server
 http://bionlp.stanford.edu/abbreviation/ webcite
 [35]
AbGene
 Protein name tagger
 ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe webcite
 [29]
ABNER
 Protein/Gene/DNA/RNA/cell tagger
 http://www.cs.wisc.edu/~bsettles/abner/ webcite
 [31]
AliasServer
 Protein alias handler
 http://cbi.labri.fr/outils/alias/index.php webcite
 [37]
ARGH
 Biomedical acronym resolver
 http://invention.swmed.edu/argh/ webcite
 [88]
ARROWSMITH
 Extended MEDLINE search tool
 http://kiwi.uchicago.edu/ webcite
 [84]
BioMail
 PubMed updating and alerting service
 http://biomail.sourceforge.net/biomail/ webcite
 [12]
BioRAT
 Biology information extraction tool
 http://bioinf.cs.ucl.ac.uk/biorat/ webcite
 [81]
BITOLA
 Literature-based biomedical discovery system
 http://www.mf.uni-lj.si/bitola/ webcite
 [86]
Chilibot
 Relationship extraction
 http://www.chilibot.net webcite
 [57]
CrossRef Search
 Full content search engine
 http://www.crossref.org/crossrefsearch.html webcite
 [8]
GAPSCORE
 Protein name tagger
 http://bionlp.stanford.edu/gapscore webcite
 [23]
Geisha
 Text-mining tool to assist microarray analysis
 http://www.pdg.cnb.uam.es/blaschke/cgi-bin/geisha webcite
 [67]
GeneScene
 Information extraction for regulatory pathways
 http://genescene.arizona.edu/index.html webcite
 [59]
GOAnnotator
 Annotation extraction from literature
 http://xldb.fc.ul.pt/rebil/tools/goa/ webcite
 [51]
Google Scholar
 Scholar literature search engine
 http://scholar.google.com/ webcite
 [6]
iHOP
 Information on hyperlinked proteins
 http://www.pdg.cnb.uam.es/UniPub/iHOP/ webcite
 [40]
iProLINK
 Protein annotation and tagging
 http://pir.georgetown.edu/iprolink webcite
 [55]
KAT
 Annotate proteins from scientific references
 http://www.bork.embl-heidelberg.de/kat/ webcite
 [52]
KeX
 Protein name tagger
 http://www.hgc.jp/service/tooldoc/KeX webcite
 [33]
KinasePathway database
 Tool for extraction of protein, gene and compound interactions from text
 http://kinasedb.ontology.ims.u-tokyo.ac.jp webcite
 [46]
MedBlast
 Document retrieval for sequences
 http://medblast.sibsnet.org/ webcite
 [63]
MedMiner
 Extraction of sentences relevant to genes
 http://discover.nci.nih.gov/textmining/main.jsp webcite
 [69]
microGENIE
 Text-mining for microarrays
 http://www.cs.vu.nl/microgenie webcite
 [76]
My NCBI
 PubMed updating and alerting service
 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed webcite
 [11]
NDPG
 Scores the literature based coherence of gene clusters
 None
 [66]
NLProt
 Protein name tagger
 http://cubic.bioc.columbia.edu/services/nlprot/ webcite
 [25]
NPG search engine
 Nature Publishing Group search engine
 http:/ / search.nature.com/ search/ ?sp_a=sp1001702d&sp_t=advanced&sp_x _1=ujournal&sp-p=all&sp webcite
 [9]
PreBIND
 Classifier of protein interaction documents
 http://bind.ca/ webcite
 [44]
PubCrawler
 PubMed updating and alerting service
 http://pubcrawler.gen.tcd.ie/ webcite
 [13]
PubGene
 Text-mining tool for microarrays
 http://www.pubgene.org/ webcite
 [72]
PubMatrix
 Multiplex literature mining tool
 http://pubmatrix.grc.nia.nih.gov/secure-bin/index.pl webcite
 [74]
PubMed Entrez
 Biomedical citation retrieval system
 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed webcite
 [3]
Relationship Extractor
 Biomedical relationship extractor
 http://www-personal.engin.umich.edu/~murthyr/Relationship_Extractor.html webcite
 [90]
SAWTED
 Text-enhanced remote homolog detector
 http://www.sbg.bio.ic.ac.uk/~sawted/ webcite
 [61]
Scopus
 Scientific literature database and search
 http://www.scopus.com/scopus/home webcite
 [93]
Textpresso
 C. elegans literature information retrieval and extraction tool
 http://www.textpresso.org/ webcite
 [48]
XplorMed
 Explores bibliographic MEDLINE searches
 http://www.bork.embl-heidelberg.de/xplormed webcite
 [91]
Yapex
 Protein name tagger
 http://ellis.sics.se:8080/cgi-bin/Yapex/yapex.cgi webcite
 [27]

An overview of some of the available text-mining, information-extraction, information-retrieval and selective dissemination of information services currently available. *References to articles describing each tool are given; where no article has been published, the reference is to the URL.

Krallinger and Valencia Genome Biology 2005 6:224   doi:10.1186/gb-2005-6-7-224