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Aims of the Signaling Project
- To revise and overhaul the signaling terms in GO, including those in process, function and component, and to connect up the signaling terms in various parts of the ontology.
- The signaling project was initiated by Jennifer Deegan, who worked with David Hill and subsequently a signaling working group. When Jen went on maternity leave in March 2010, Rebecca Foulger took over co-ordination of the signaling working group. This wiki reflects the work and ideas from both stages of the project.
- Here is an overview of where the signaling project is upto in May 2011.
High Level Organization of the Signaling Node
- Revising the signaling terms in GO required rearranging the high-level organization of the signaling node, to connect up the signaling terms that were scattered across the ontology and organize them in a more consistent way. Below are links to the ideas and discussions on the structure from Jen and the SWG's work:
Signaling branch file Apr 6th 2009
- The top level signaling term used to be 'signal transduction', under which were housed the signaling pathway term.
- In phase I of the signaling revisions, the node was split into signaling pathways and signaling processes (commited March 2010).
- By September 2010 it was clear that the process/pathway split was not working for annotation and was removed. The node instead was split into cellular, multicellular organism, and multiorganism signaling.
A summary of the high-level changes that have been put in place for the signaling terms is presented here
A summary of signaling nomenclature to describe how GO uses the phrases 'pathway' 'cascade' 'signal transduction', and how signaling fits in with the response terms, etc.
Glossary Of Signaling Terms
At the February 2011 Signaling workshop, it was agreed that GO will create a Signaling Glossary for terms and phrases that are commonly used in signaling term names, definitions and comments (but aren't actually GO terms themselves) to allow them to be standardized.
Downstream Processes DONE
Response to and signaling DONE THE KEY BITS
cascades Split into:
- Connecting Receptors and Cascades PRIORITY STARTED
- Naming Cascades
- Start and Stop Points of Cascades
- cAMP signaling
NF-KappaB signaling DONE
GPCR signaling DONE THE KEY BITS
non 1:1 receptor:ligand binding DONE THE KEY BITS
cleaning up MAPKKK cascade DONE THE KEY BITS
Proposal to remove the process/pathway split in signaling. December 2010. DONE
RECEPTORS This is split into
- RECEPTORS AND HAS PART DONE
- Transmembrane receptors DONE
- Signaling Receptors v. Transport Receptors DONE
- X-activated receptors DONE for growth factor receptors
- ligand-gated ion channels
- GPCRs : DONE THE KEY BITS ==
- Receptor clean-up
Signaling Conference Calls And Discussions
Discussions from the First Phase (up to March 2010)
Read about the discussions of signaling from April 2008 until July 2009.
Read about the discussions of signaling from July 2009.
Read about the discussions of signaling from November 2009.
Read about the discussions of signaling from December 2009.
Read about the discussions of signaling from January 2010.
Discussions from the Second Phase (March 2010 onwards)
GO Signaling Workshop
Signaling on Sourceforge
This is the list of signaling items on the sourceforge tracker, past and present. If you have an item that is not listed here then please feel free to add it.
Background: Text book views of signaling
Notes on general views of signaling from the standard text books are noted below.
If you have particular areas of expertise in signaling, or have general suggestions on how the terms could be improved then please add your name and brief details on the Community Input page
In preparation for the signaling workshop at the EBI in February 2011, three experts were also recruited, who are happy to provide feedback to the working group:
- Dr Andrea Townsend-Nicholson, UCL
- Dr Andrew Winter, BioGRID
- Dr Andrew Chatry-aramontri, BioGRID
Signaling DBXrefs and GO:IDs
The DBX-refs and GO IDs for the signaling overhaul are split according to those for the first phase (Jen Deegan and SWG) and the second phase (Rebecca and SWG):
GOC:mtg_signal GO:0023004- GO:0023300, Jen Deegan subrange; signaling
GOC:signaling GOC:mtg_signaling_feb11: GO content meeting, February 16th-17th 2011. GO:0038001- GO:0039000 Becky Foulger subrange; signaling