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.

ArrayXPath – Biological Pathway-based analysis of Gene Expression data

ArrayXPath

:: DESCRIPTION

ArrayXPath is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG)

::DEVELOPER

SNUBI (Snubi’s Not Unics, Biomedical Informatics.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W460-4.
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.
Chung HJ1, Kim M, Park CH, Kim J, Kim JH.

PathwayMatrix – Visualizing Binary Relationships between Proteins in Biological Pathways

PathwayMatrix

:: DESCRIPTION

PathwayMatrix presents novel methods to visualize and interact with representations of signaling pathways. It provides visual anayltics tools that allow systems biologists and cancer researchers to find patterns in the relationships and reactions between proteins and protein complexes.

::DEVELOPER

Creative Coding Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

PathwayMatrix

:: MORE INFORMATION

Citation

PathwayMatrix: visualizing binary relationships between proteins in biological pathways.
Dang TN, Murray P, Forbes AG.
BMC Proc. 2015 Aug 13;9(Suppl 6 Proceedings of the 5th Symposium on Biological Data):S3. doi: 10.1186/1753-6561-9-S6-S3

ReactionFlow – Visualization tool for Causality Analysis in Biological Pathways

ReactionFlow

:: DESCRIPTION

ReactionFlow is a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway

::DEVELOPER

Creative Coding Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

ReactionFlow

:: MORE INFORMATION

Citation

ReactionFlow: an interactive visualization tool for causality analysis in biological pathways.
Dang TN, Murray P, Aurisano J, Forbes AG.
BMC Proc. 2015 Aug 13;9(Suppl 6 Proceedings of the 5th Symposium on Biological Data):S6. doi: 10.1186/1753-6561-9-S6-S6.

VitaPad 0.6.1c – Visualize and Analyze Biological Pathways

VitaPad 0.6.1c

:: DESCRIPTION

VitaPad is an application used to visualize biological pathways and map experimental data to them

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux/MacOsX
Java

:: DOWNLOAD

VitaPad

:: MORE INFORMATION

Citation

VitaPad: visualization tools for the analysis of pathway data.
Holford M, Li N, Nadkarni P, Zhao H.
Bioinformatics. 2005 Apr 15;21(8):1596-602. Epub 2004 Nov 25.

PiPa – Setup and Maintain a Database for Information on PPI and Biological Pathways

PiPa

:: DESCRIPTION

PiPa is a java-based tool to setup and maintain a database for information on Protein-Protein Interactions and biological Pathways integrated from multiple public databases.

::DEVELOPER

Wissensmanagement in der Bioinformatik

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows /MacOsX
Java

:: DOWNLOAD

PiPa

:: MORE INFORMATION

Citation

Arzt, S., Starlinger, J., Arnold, O., Kröger, S., Jaeger, S., and Leser, U. (2011).
PiPa: Custom Integration of Protein Interactions and Pathways
GI-Jahrestagung 2011, Workshop “Daten In den Lebenswissenschaften”.

BioPAX level 3 – Biological Pathway Exchange Language

BioPAX level 3

:: DESCRIPTION

BioPAX (Biological Pathway Exchange) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

::DEVELOPER

BioPAX Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

BioPAX

:: MORE INFORMATION

Citation:

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666

Paintomics 3 v0.4.5 – Painting Omics Data in Biological Pathways

Paintomics 3 v0.4.5

:: DESCRIPTION

Paintomics is a web tool for the integration and visualization of transcriptomics and metabolomics data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):137-9. Epub 2010 Nov 23.
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
García-Alcalde F, García-López F, Dopazo J, Conesa A.

MinPath 1.4 – Biological Pathway Reconstructions using Protein Family Predictions

MinPath 1.4

:: DESCRIPTION

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

MinPath

:: MORE INFORMATION

Citation:

Yuzhen Ye and Thomas G. Doak.
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.
PLoS Computational Biology, 5(8): e1000465 (2009)

CSO validator 20120216 – Curation Workflow for Biological Pathways

CSO validator 20120216

:: DESCRIPTION

CSO validator is an ontology-based validation tool that guides creating high-quality biological pathways in CSO (Cell System Ontology).

::DEVELOPER

CSO validator team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/windows/MacOsX
java

:: DOWNLOAD

CSO validator

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2471-2. doi: 10.1093/bioinformatics/btr395. Epub 2011 Jul 8.
CSO validator: improving manual curation workflow for biological pathways.
Jeong E, Nagasaki M, Ikeda E, Sekiya Y, Saito A, Miyano S.