Anni 2.1 – Text-mining tool for the Life Sciences

Anni 2.1

:: DESCRIPTION

Anni provides an ontology-based interface to Medline and retrieves documents and associations for several classes of biomedical concepts, including genes, drugs and diseases, with proven text-mining technology.

::DEVELOPER

the Biosemantics Group.

:: SCREENSHOTS

Anni

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

Anni

:: MORE INFORMATION

Citation

Anni 2.0: a multipurpose text-mining tool for the life sciences.
Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA
Genome Biology 2008 Jun 12, 9(6):R96

PolySearch 2 – Text Mining system for extracting relationships between Human Diseases, Genes, Mutations, Drugs and Metabolites

PolySearch 2

:: DESCRIPTION

PolySearch2 is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.
Liu Y, Liang Y, Wishart D.
Nucleic Acids Res. 2015 Apr 29. pii: gkv383

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. doi: 10.1093/nar/gkn296. Epub 2008 May 16.
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS.

CoPub 5.2 – MedLine Text Mining tool

CoPub 5.2

:: DESCRIPTION

CoPub is a text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database.

::DEVELOPER

CoPub team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

CoPub update: CoPub 5.0 a text mining system to answer biological questions.
Fleuren WW, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, de Vlieg J, Alkema W.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W450-4. doi: 10.1093/nar/gkr310.

Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W.
CoPub: a literature-based keyword enrichment tool for microarray data analysis.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W406-10. Epub 2008 Apr 28.

MyMiner – Text Mining tools for Biology

MyMiner

:: DESCRIPTION

MyMiner is a free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems.

::DEVELOPER

MyMiner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2285-7. Epub 2012 Jul 12.
MyMiner: a web application for computer-assisted biocuration and text annotation.
Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar AV, Leitner F, Valencia A, Marcelle C.

PubTator – Text Mining tool for Assisting Biocuration

PubTator

:: DESCRIPTION

PubTator is a Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques. As an all-in-one system, PubTator provides one-stop service for annotating PubMed citations.

::DEVELOPER

Zhiyong Lu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wei CH, Kao HY, Lu Z.,
PubTator: a Web-based text mining tool for assisting Biocuration,
Nucleic acids research, 2013, 41 (W1): W518-W522. doi: 10.1093/nar/gkt44

tmVar – Text Mining approach for Extracting Sequence Variants in Biomedical Literature

tmVar

:: DESCRIPTION

tmVar is a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS).

::DEVELOPER

Chih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao, Ph.D. and Zhiyong Lu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 tmVar

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1433-9. doi: 10.1093/bioinformatics/btt156. Epub 2013 Apr 5.
tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Wei CH, Harris BR, Kao HY, Lu Z.

FACTA+ 0.8.1 – Text Mining from MEDLINE

FACTA+ 0.8.1

:: DESCRIPTION

FACTA+ (Finding Associated Concepts with Text Analysis) is an advanced text mining tool that helps you discover associations between biomedical concepts from MEDLINE articles. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner — the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds.

::DEVELOPER

Yoshimasa Tsuruoka

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yoshimasa Tsuruoka, Jun’ichi Tsujii, and Sophia Ananiadou. 2008.
FACTA: a text search engine for finding associated biomedical concepts,
Bioinformatics, Vol. 24, No. 21, pp. 2559-2560.

Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun’ichi Tsujii, and Sophia Ananiadou. 2011.
Discovering and visualizing indirect associations between biomedical concepts,
Bioinformatics, Vol. 27 ISMB 2011, pp. i111-i119.

E3Miner – Text Mining tool for Ubiquitin-protein Ligases

E3Miner

:: DESCRIPTION

E3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about E3s with their underlying mechanisms. This tool integrates available E3 data not only from the published literature but also from the biological databases, using natural language processing techniques.

:: DEVELOPER

NLP*CL LaboratoryKAIST.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W416-22. doi: 10.1093/nar/gkn286. Epub 2008 May 15.
E3Miner: a text mining tool for ubiquitin-protein ligases.
Lee H, Yi GS, Park JC.