from Nature Genetics Review

Biomediacal Literature Data-Mining and Text-Mining Applications

I will give a assessment soon

There are numerous literature collections (corpora), software modules and web-based applications for biomedical literature mining. Here we list some applications that can be accessed through web interfaces and a small subset of resources that are useful for developers of new literature-mining systems.

Web-based applications

Information retrieval

E-BioSci . . . . . . . . . . . . . . . . . . . .http://www.e-biosci.org

EBIMed . . . . . . . . . . . . . . . . . . . .http://www.ebi.ac.uk/Rebholz-srv/ebimed

Google Scholar . . . . . . . . . . . . .http://scholar.google.com

GoPubMed . . . . . . . . . . . . . . . . .http://www.gopubmed.org

MedMiner . . . . . . . . . . . . . . . . . .http://discover.nci.nih.gov/textmining

PubFinder . . . . . . . . . . . . . . . . . .http://www.glycosciences.de/tools/PubFinder

PubMed . . . . . . . . . . . . . . . . . . . .http://www.pubmed.org

Textpresso . . . . . . . . . . . . . . . . .http://www.textpresso.org

XplorMed . . . . . . . . . . . . . . . . . .http://www.ogic.ca/projects/xplormed

Entity recognition

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

Information extraction

iProLINK . . . . . . . . . . . . . . . . . . .http://pir.georgetown.edu/iprolink

JournalMine . . . . . . . . . . . . . . . .http://textmine.cu-genome.org

PreBIND . . . . . . . . . . . . . . . . . . . .http://prebind.bind.ca

PubGene . . . . . . . . . . . . . . . . . . .http://www.pubgene.org

Text mining

Arrowsmith . . . . . . . . . . . . . . . .http://arrowsmith.psych.uic.edu

Integration

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

G2D . . . . . . . . . . . . . . . . . . . . . . . .http://www.ogic.ca/projects/g2d_2

ProLinks . . . . . . . . . . . . . . . . . . . .http://dip.doe-mbi.ucla.edu/pronav

STRING . . . . . . . . . . . . . . . . . . . .http://string.embl.de

Text collections

Full text corpora

HighWire Press . . . . . . . . . . . . .http://highwire.stanford.edu

PubMed Central . . . . . . . . . . . .http://www.pubmedcentral.org

Tagged corpora

FetchProt . . . . . . . . . . . . . . . . . .http://fetchprot.sics.se

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

GENIA . . . . . . . . . . . . . . . . . . . . .http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA

PennBioIE . . . . . . . . . . . . . . . . . .http://bioie.ldc.upenn.edu

Yapex . . . . . . . . . . . . . . . . . . . . . .http://www.sics.se/humle/projects/prothalt

Information-extraction modules

Entity taggers

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

GAPSCORE . . . . . . . . . . . . . . . .http://bionlp.stanford.edu/gapscore

Part-of-speech taggers

Brill Tagger . . . . . . . . . . . . . . . . .http://www.cs.jhu.edu/~brill

TNT Tagger . . . . . . . . . . . . . . . . .http://www.coli.uni-saarland.de/~thorsten/tnt

TreeTagger . . . . . . . . . . . . . . . . .http://www.ims.uni-stuttgart.de/~schmid

Parsers

CASS . . . . . . . . . . . . . . . . . . . . . .http://www.vinartus.net/spa

Collins Parser . . . . . . . . . . . . . . .http://people.csail.mit.edu/mcollins

Stanford Parser . . . . . . . . . . . . .http://nlp.stanford.edu/software