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This repository provides documentation on the protocol proposed by the Gene Ontology Consortium for gene set / term enrichment tools.

Give us feedback!

At this stage nothing is set on stone, and we are looking for feedback, particularly from tool providers. Get involved or provide feedback by any of the following mechanisms:

  • Fork this project on github
  • Add issues or comments on the issue tracker
  • Email us gohelp AT geneontology DOT org

Background

An ontology enrichment analysis takes as input a set of genes (optionally associated with expression values) and returns a set of ontology terms over-represented (or under-represented) for that set.

There are a number of different tools and services that allow for this kind of analysis. The GO consortium aims to make it easier for users to use a variety of different tools through a common interface on the GO website, facilitated via a standard protocol. Tool providers implementing this protocol can be hooked in to the GO website, after registering their tool.

image

At this stage the protocol is not finalized, we are soliciting comments. Currently pantherdb.org implements an earlier version of this protocol, this is what is currently driving the new GO website on http://beta.geneontology.org

The protocol is designed to be simple to implement for basic implementations, yet more extensible for advanced uses.

Default GO client

The protocol allows any client to connected to any server provided the server implements the protocol. In addition, downstream components can be hooked in - e.g. a 3rd party visualization can be hooked.

The current GO client can be tested via:

Documentation

See:

Examples

See the examples/ directory

Check back later for more examples - or better yet, submit samples from your tool here!

Scripts and utilities

See the util/ directory

This contains standalone scripts for wrapping existing tools

History

This project subsumes a previous project to define a term enrichment format (TERF), intended for use as output of command line tools, allowing hooks within Galaxy. After initial feedback from GO advisors we decided to generalize this to a web-based protocol that could be used independent of the Galaxy environment. Part of this standard still includes a JSON exchange format.

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Documentation on REST API and JSON payload for term enrichment services

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