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.

SIOMICS 3.0 – Systematic Identification Of Motifs In ChIP-Seq data

SIOMICS 3.0

:: DESCRIPTION

SIOMICS is a software developed to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments. The output of the software is the ranked motifs and motif modules (significantly co-occurring motif combinations). The statistical evaluation of the predicted motifs and motif modules is also provided.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

SIOMICS

:: REQUIREMENTS

  • Linux/ Windows
  • Python
  • Tkinter
  • Java

:: DOWNLOAD

 SIOMICS

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Mar;42(5):e35. doi: 10.1093/nar/gkt1288. Epub 2013 Dec 9.
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
Ding J, Hu H, Li X.