Table 1 Biomedical text-mining resources, servers and programs

Abbreviation Server

Biomedical abbreviation server

http://bionlp.stanford.edu/abbreviation/

AbGene

Protein name tagger

ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe

ABNER

Protein/Gene/DNA/RNA/cell tagger

http://www.cs.wisc.edu/~bsettles/abner/

AliasServer

Protein alias handler

http://cbi.labri.fr/outils/alias/index.php

ARGH

Biomedical acronym resolver

http://invention.swmed.edu/argh/

ARROWSMITH

Extended MEDLINE search tool

http://kiwi.uchicago.edu/

BioMail

PubMed updating and alerting service

http://biomail.sourceforge.net/biomail/

BioRAT

Biology information extraction tool

http://bioinf.cs.ucl.ac.uk/biorat/

BITOLA

Literature-based biomedical discovery system

http://www.mf.uni-lj.si/bitola/

Chilibot

Relationship extraction

http://www.chilibot.net

CrossRef Search

Full content search engine

http://www.crossref.org/crossrefsearch.html

GAPSCORE

Protein name tagger

http://bionlp.stanford.edu/gapscore

Geisha

Text-mining tool to assist microarray analysis

http://www.pdg.cnb.uam.es/blaschke/cgi-bin/geisha

GeneScene

Information extraction for regulatory pathways

http://genescene.arizona.edu/index.html

GOAnnotator

Annotation extraction from literature

http://xldb.fc.ul.pt/rebil/tools/goa/

Google Scholar

Scholar literature search engine

http://scholar.google.com/

iHOP

Information on hyperlinked proteins

http://www.pdg.cnb.uam.es/UniPub/iHOP/

iProLINK

Protein annotation and tagging

http://pir.georgetown.edu/iprolink

KAT

Annotate proteins from scientific references

http://www.bork.embl-heidelberg.de/kat/

KeX

Protein name tagger

http://www.hgc.jp/service/tooldoc/KeX

KinasePathway database

Tool for extraction of protein, gene and compound interactions from text

http://kinasedb.ontology.ims.u-tokyo.ac.jp

MedBlast

Document retrieval for sequences

http://medblast.sibsnet.org/

MedMiner

Extraction of sentences relevant to genes

http://discover.nci.nih.gov/textmining/main.jsp

microGENIE

Text-mining for microarrays

http://www.cs.vu.nl/microgenie

My NCBI

PubMed updating and alerting service

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed

NDPG

Scores the literature based coherence of gene clusters

None

NLProt

Protein name tagger

http://cubic.bioc.columbia.edu/services/nlprot/

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

PreBIND

Classifier of protein interaction documents

http://bind.ca/

PubCrawler

PubMed updating and alerting service

http://pubcrawler.gen.tcd.ie/

PubGene

Text-mining tool for microarrays

http://www.pubgene.org/

PubMatrix

Multiplex literature mining tool

http://pubmatrix.grc.nia.nih.gov/secure-bin/index.pl

PubMed Entrez

Biomedical citation retrieval system

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed

Relationship Extractor

Biomedical relationship extractor

http://www-personal.engin.umich.edu/~murthyr/Relationship_Extractor.html

SAWTED

Text-enhanced remote homolog detector

http://www.sbg.bio.ic.ac.uk/~sawted/

Scopus

Scientific literature database and search

http://www.scopus.com/scopus/home

Textpresso

C. elegans literature information retrieval and extraction tool

http://www.textpresso.org/

XplorMed

Explores bibliographic MEDLINE searches

http://www.bork.embl-heidelberg.de/xplormed

Yapex

Protein name tagger

http://ellis.sics.se:8080/cgi-bin/Yapex/yapex.cgi