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IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

The BioPAX community standard for pathway data sharing.

Emek Demir1, Michael P Cary, Suzanne Paley

  • 1Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

Nature Biotechnology
|September 11, 2010
PubMed
Summary
This summary is machine-generated.

Biological Pathway Exchange (BioPAX) is a standard language for sharing biological pathway data. It overcomes data fragmentation, enabling easier collection, interpretation, and sharing for biological discovery.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Biological pathway data is rapidly growing in volume.
  • Fragmentation of pathway information across incompatible databases hinders data utilization.
  • Existing data formats limit the collection, indexing, interpretation, and sharing of pathway information.

Purpose of the Study:

  • To introduce Biological Pathway Exchange (BioPAX) as a standardized language for biological pathways.
  • To address the challenge of fragmented and incompatible pathway data formats.
  • To facilitate the collection, indexing, interpretation, and sharing of molecular and cellular pathway data.

Main Methods:

  • Development of a community-driven standard language, BioPAX.
  • BioPAX enables representation of metabolic and signaling pathways, molecular and genetic interactions, and gene regulation networks.
  • Integration of data from multiple databases into a computable format.

Main Results:

  • BioPAX standardizes the representation of biological pathways.
  • Millions of interactions from thousands of pathways across various organisms are now available through BioPAX.
  • Pathway data is now more accessible and easier to manage.

Conclusions:

  • BioPAX effectively solves the problem of pathway data fragmentation.
  • The availability of large amounts of computable pathway data supports visualization, analysis, and biological discovery.
  • BioPAX facilitates broader access and utilization of biological pathway information.