Signaling

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Signaling Metrics

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 ontology structure documentation

Draft organization of ideas

Signaling branch file Apr 6th 2009

In brief:

  • 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


Signaling Nomenclature

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.


Signaling Topics

SIGNALING TOPICS THAT REQUIRE MORE INPUT

Intracellular_signal_transduction

calcium signaling

Notch signaling

[SAPKs]

Signaling per pathway- go through each pathway to check correctness

ONGOING SIGNALING TOPICS

non 1:1 receptor:ligand binding DONE THE KEY BITS

function-process links in signaling

tidy-up

Downstream Processes

DONE SIGNALING TOPICS

cleaning up MAPKKK cascade DONE

Response to and signaling DONE

Multi-organism process signaling modulation terms

NF-KappaB signaling DONE

GPCR signaling DONE THE KEY BITS

Proposal to remove the process/pathway split in signaling. December 2010. DONE

RECEPTORS This is split into

Signaling and receptor-mediated endocytosis DONE THE KEY BITS

Receptor signaling proteinsDONE THE KEY BITS

Initiation of signal transduction: DONE

signaling regulation terms DONE

signal release/generation DONE

Signaling Conference Calls And Discussions

Discussions from the First Phase (up to March 2010)

EBI signaling meeting 2009

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.

Proposal circulated via the GO list.

Signaling demo February 2010

from Jen


Discussions from the Second Phase (March 2010 onwards)

March 15th 2010

March 25th 2010

Signaling April 19th 2010

May 10th 2010

July 19th 2010

October 11th 2010

October 18th 2010

December 9th 2010

January 10th 2011

July 18th 2011

December 21st 2011

April 2013

GO Signaling Workshop

Signaling Workshop February 2011



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.

Molecular Biology of the Cell

Signaling diagrams

More signaling diagrams


Community Input

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):

PHASE I:

  GOC:mtg_signal
  GO:0023004- GO:0023300, Jen Deegan subrange; signaling

PHASE II:

  GOC:signaling
  GOC:mtg_signaling_feb11:	GO content meeting, February 16th-17th 2011.
 
  GO:0038001- GO:0039000 Becky Foulger subrange; signaling



LINKS AND RESOURCES

Signaling Curation Manual