PathNER – Systematic Identification of Biological Pathway Mentions

PathNER

:: DESCRIPTION

PathNER (Pathway Named Entity Recognition) is a tool for the identification of specific pathway mentions from biomedical literature.It’s implemented under the GATE framework, including two major components: rule-based detection and dictionary matching.

::DEVELOPER

Pathways and biological systems modelling group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 PathNER

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Oct 16;7 Suppl 3:S2. doi: 10.1186/1752-0509-7-S3-S2.
PathNER: a tool for systematic identification of biological pathway mentions in the literature.
Wu C, Schwartz JM, Nenadic G.

Moara 1.0.6 – Extract & Normalize Gene and Protein Mentions

Moara 1.0.6

:: DESCRIPTION

Moara is a software for gene mentions and normalization in biological texts.

::DEVELOPER

Moara team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows/Linux/MacOsX
  • Java
  • MySQL
  • Weka
  • SecondString
  • ABNER

:: DOWNLOAD

 Moara

:: MORE INFORMATION

Citation

Moara: a Java library for extracting and normalizing gene and protein mentions.
Neves ML, Carazo JM, Pascual-Montano A.
BMC Bioinformatics. 2010 Mar 26;11:157.