Text-mining

MILANO - Microarray Literature-based Annotation
http://bioinformatics.ekmd.huji.ac.il/milano

Gene set analysis: automated search in PubMed to find out co-occurrences of search terms

URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016)

iHOP - Information Hyperlinked over Proteins
http://www.ihop-net.org

Functional relationships: protein-interactions, literature co-occurrences, pathologies and phenotypes

Genie
http://cbdm.mdc-berlin.de/~genie

Rank genes or species for a specific PubMed query

MimMiner
http://www.cmbi.ru.nl/MimMiner

A text-mining approach for identifying (including ranking and clustering) gene/protein-phenotype relationships

CoPub
http://services.nbic.nl/copub/portal http://services.nbic.nl/copub5

Literature mining for co-occurring biomedical concepts: GO, disease, tissue, pathology, pathway, drug, etc.

PolySearch
http://wishart.biology.ualberta.ca/polysearch

Associations among queries

MEDIE
http://www.nactem.ac.uk/tsujii/medie

Biomedical correlations from literature

OpenDMAP - Open source Direct Memory Access Parser
http://opendmap.sourceforge.net

Concept analysis and information extraction by processing texts

BITOLA - Biomedical Discovery Support System
http://ibmi.mf.uni-lj.si/bitola

Literature based biological associations: disease, tissue, pathology, pathway, drug, etc.

Genes2Fans
http://actin.pharm.mssm.edu/genes2FANs

Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc.

MeSHy
http://bat.ina.certh.gr/tools/meshy

Mining PubMed information using frequencies of occurrences and concurrences of MeSH terms

aGeneApart
http://www.esat.kuleuven.be/ageneapart

Identifies the text based gene prioritization for human dysmorphy

100

Ali Baba - PubMed as a Graph
http://alibaba.informatik.hu-berlin.de

Search and visualize gene/protein functional associations: gene expression, tissue specificity, disease, pathways, protein-interactions, etc.

100

Chilibot - Mining PubMed for relationships
http://www.chilibot.net

Find relationships between proteins/genes/keywords by searching PubMed

100

DPBE - Dragon Plant Biology Explorer
http://research.i2r.a-star.edu.sg/DRAGON/ME2

Functional associations of Arabidopsis genes: literature keywords, GO, pathways, enzymes, gene/protein-interactions, etc.

100

URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016)

DTFAM - Dragon TF Association Miner
http://research.i2r.a-star.edu.sg/DRAGON/TFAM

Functional associations: literature keywords, GO, diseases, transcription factors, etc.

100

URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016)

eGIFT - Extracting Gene Information From Text
http://biotm.cis.udel.edu/eGIFT

Find relationships (informative terms: iTerms) for gene(s) from literature

100

GenCLiP - Gene Cluster with Literature Profiles
http://www.bioinformatics.org/genclip http://genclip.sourceforge.net http://www.genclip.com

A literature mining tool to identify pathogenesis profiles and specific pathways, including co-occurrence networks

100

GeneRanker
http://cbioc.eas.asu.edu/generanker http://www.generanker.org

Identify and annotate gene-disease relationship by mining the biomedical literature

100

Both the given URLs are not working, as on 10 Feb 2015 (confirmed on 15 Nov 2016)
URL not working as on 3 Nov 2016
URL not working as on 3 Nov 2016
Both the given URLs are not working as on 15 Nov 2016 (confirmed on 23 Feb 2017)

godisease
http://www.godisease.com

Gene associations: diseases, GO, protein-isoforms, etc., and any user keyword

100

Medline Ranker
http://cbdm.mdc-berlin.de/~medlineranker

Rank abstracts a specific PubMed query

100

PLAN2L - Plant annotation to literature
http://zope.bioinfo.cnio.es/plan2l

Integrated text mining and literature-derived bio-entity relationships in Arabidopsis thaliana

100

pubmed2ensembl
http://www.pubmed2ensembl.org

Gene related publication information, including GO, gene expression, domains and external references

100

PubNet - Publication Network Graph Utility
http://pubnet.gersteinlab.org

Literature derived networks based on MeSH terms, co-authors and shared location

100