| 1 | 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 |
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URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016) |
| 2 | iHOP - Information Hyperlinked over Proteins
http://www.ihop-net.org | | Functional relationships: protein-interactions, literature co-occurrences, pathologies and phenotypes |
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| 3 | Genie
http://cbdm.mdc-berlin.de/~genie | | Rank genes or species for a specific PubMed query |
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| 4 | MimMiner
http://www.cmbi.ru.nl/MimMiner | | A text-mining approach for identifying (including ranking and clustering) gene/protein-phenotype relationships |
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| 5 | 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. |
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| 6 | PolySearch
http://wishart.biology.ualberta.ca/polysearch | | Associations among queries |
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| 7 | MEDIE
http://www.nactem.ac.uk/tsujii/medie | | Biomedical correlations from literature |
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| 8 | OpenDMAP - Open source Direct Memory Access Parser
http://opendmap.sourceforge.net | | Concept analysis and information extraction by processing texts |
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| 9 | BITOLA - Biomedical Discovery Support System
http://ibmi.mf.uni-lj.si/bitola | | Literature based biological associations: disease, tissue, pathology, pathway, drug, etc. |
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| 10 | Genes2Fans
http://actin.pharm.mssm.edu/genes2FANs | | Functional association networks: protein-interactions, pathways, miRNAs, phenotypes, domains, metabolites, etc. |
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| 11 | MeSHy
http://bat.ina.certh.gr/tools/meshy | | Mining PubMed information using frequencies of occurrences and concurrences of MeSH terms |
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| 12 | aGeneApart
http://www.esat.kuleuven.be/ageneapart | | Identifies the text based gene prioritization for human dysmorphy |
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| 13 | 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. |
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| 14 | Chilibot - Mining PubMed for relationships
http://www.chilibot.net | | Find relationships between proteins/genes/keywords by searching PubMed |
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| 15 | 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. |
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URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016) |
| 16 | DTFAM - Dragon TF Association Miner
http://research.i2r.a-star.edu.sg/DRAGON/TFAM | | Functional associations: literature keywords, GO, diseases, transcription factors, etc. |
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URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016) |
| 17 | | Find relationships (informative terms: iTerms) for gene(s) from literature |
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| 18 | 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 |
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| 19 | GeneRanker
http://cbioc.eas.asu.edu/generanker http://www.generanker.org | | Identify and annotate gene-disease relationship by mining the biomedical literature |
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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) |
| 20 | godisease
http://www.godisease.com | | Gene associations: diseases, GO, protein-isoforms, etc., and any user keyword |
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| 21 | Medline Ranker
http://cbdm.mdc-berlin.de/~medlineranker | | Rank abstracts a specific PubMed query |
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| 22 | PLAN2L - Plant annotation to literature
http://zope.bioinfo.cnio.es/plan2l | | Integrated text mining and literature-derived bio-entity relationships in Arabidopsis thaliana |
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| 23 | pubmed2ensembl
http://www.pubmed2ensembl.org | | Gene related publication information, including GO, gene expression, domains and external references |
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| 24 | PubNet - Publication Network Graph Utility
http://pubnet.gersteinlab.org | | Literature derived networks based on MeSH terms, co-authors and shared location |
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