What the papers say: Text mining for genomics and systems biology

Table 2 Some freely available software for NLP tasks in the biological domain

Name	URL	Task
AbGene [28]	ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe/AbGene	NER
ABNER [29]	http://pages.cs.wisc.edu/~bsettles/abner/	NER
AkanePPI [30]	http://www-tsujii.is.s.u-tokyo.ac.jp/~satre/akane/	PPI
BANNER [31]	http://banner.sourceforge.net/	NER
BioTagger-GM	http://www.seas.upenn.edu/~strctlrn/BioTagger/BioTagger.html	NER
GENIA [32]	http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/tagger/	NER
Graph Kernel [33]	http://mars.cs.utu.fi/PPICorpora/GraphKernel.html	PPI
LINNAEUS [34]	http://linnaeus.sourceforge.net/	NER
JNET [35]	http://julielab.de/	NER
JSBD	http://julielab.de/	SEN
LingPipe	http://alias-i.com/lingpipe/	NER
MedPOS [36]	http://ii-public.nlm.nih.gov/MMTx/MedPost_SKR.shtml	POS
NLProt [37]	http://cubic.bioc.columbia.edu/services/nlprot/	NER
OpenDMAP [38]	http://opendmap.sourceforge.net/	PPI
OSCAR3[39]	http://sourceforge.net/projects/oscar3-chem/	NER
POSBIOTM-NER [40]	http://isoft.postech.ac.kr/Research/BioNER/POSBIOTM/NER/main.html	NER
Sptoolkit	http://text0.mib.man.ac.uk:8080/scottpiao/sent_detector	SEN
Whatizit [41]	http://www.ebi.ac.uk/webservices/whatizit/	NER/PPI

Task refers to the part of a text-mining pipeline that the software can be used for. Abbreviations: NER, named entity recognition; POS, part of speech tagger; PPI, protein-protein interaction extraction; SEN, sentencisation

ISSN: 1479-7364