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Created on: 12-Oct-2012   Last updated on: 12-Oct-2012  |  How to cite this?
Total resources - 24
A list of resources for text-mining
Sravanthi Davuluri and Akhilesh Bajpai (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
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
1

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
46
Genie
http://cbdm.mdc-berlin.de/~genie
Rank genes or species for a specific PubMed query
65
MimMiner
http://www.cmbi.ru.nl/MimMiner
A text-mining approach for identifying (including ranking and clustering) gene/protein-phenotype relationships
86
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.
87
PolySearch
http://wishart.biology.ualberta.ca/polysearch
Associations among queries
87
MEDIE
http://www.nactem.ac.uk/tsujii/medie
Biomedical correlations from literature
98
OpenDMAP - Open source Direct Memory Access Parser
http://opendmap.sourceforge.net
Concept analysis and information extraction by processing texts
98
BITOLA - Biomedical Discovery Support System
http://ibmi.mf.uni-lj.si/bitola
Literature based biological associations: disease, tissue, pathology, pathway, drug, etc.
99
Genes2Fans
http://actin.pharm.mssm.edu/genes2FANs
Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc.
99
MeSHy
http://bat.ina.certh.gr/tools/meshy
Mining PubMed information using frequencies of occurrences and concurrences of MeSH terms
99
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
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