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