Signaling: Difference between revisions
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[[Category:Signaling]] | |||
Return to [[Main_Page|GOC Main Page]] | Return to [[Main_Page|GOC Main Page]] | ||
[[Signaling Metrics]] | [[Signaling Metrics]] | ||
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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. | 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. | ||
==<font color="navy">Signaling Topics</font color>== | ==<font color="navy">Signaling Topics</font color>== | ||
===<font color="blue">SIGNALING TOPICS THAT REQUIRE MORE INPUT</font color>=== | |||
[[Intracellular_signal_transduction]] | |||
[[calcium signaling]] | |||
[[Notch signaling]] | |||
[[ | [[http://wiki.geneontology.org/index.php/Stress-activated_protein_kinase_signaling_cascade_;_GO:0031098 SAPKs]] | ||
Signaling per pathway- go through each pathway to check correctness | |||
===<font color="blue">ONGOING SIGNALING TOPICS</font color>=== | |||
[[non 1:1 receptor:ligand binding]] <font color=" | [[non 1:1 receptor:ligand binding]] <font color="green">DONE THE KEY BITS</font color> | ||
[[function-process links in signaling]] | [[function-process links in signaling]] | ||
[[ | [[tidy-up]] | ||
[[Downstream Processes]] | |||
[http://gocwiki.geneontology.org/images/archive/0/03/20110110105524%21Signaling_proposal_dec10.pdf Proposal] to remove the process/pathway split in signaling. December 2010. <font color=" | ===<font color="blue">DONE SIGNALING TOPICS</font color>=== | ||
[[cleaning up MAPKKK cascade]] <font color="green">DONE</font color> | |||
[[Response to and signaling]] <font color="green">DONE</font color> | |||
[[Multi-organism process signaling modulation terms]] | |||
[[NF-KappaB signaling]] <font color="green">DONE</font color> | |||
[[GPCR signaling]] <font color="green">DONE THE KEY BITS</font color> | |||
[http://gocwiki.geneontology.org/images/archive/0/03/20110110105524%21Signaling_proposal_dec10.pdf Proposal] to remove the process/pathway split in signaling. December 2010. <font color="green">DONE</font color> | |||
[[RECEPTORS]] This is split into | [[RECEPTORS]] This is split into | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#RECEPTORS_AND_HAS_PART_:_STARTED RECEPTORS AND HAS PART] <font color="green"> | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#RECEPTORS_AND_HAS_PART_:_STARTED RECEPTORS AND HAS PART] <font color="green">DONE</font color> | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#TRANSMEMBRANE_RECEPTORS_:_DONE Transmembrane receptors] <font color=" | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#TRANSMEMBRANE_RECEPTORS_:_DONE Transmembrane receptors] <font color="green">DONE</font color> | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#SIGNALING_RECEPTORS_VS_CARGO_RECEPTORS_:_DONE Signaling Receptors v. Transport Receptors] <font color=" | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#SIGNALING_RECEPTORS_VS_CARGO_RECEPTORS_:_DONE Signaling Receptors v. Transport Receptors] <font color="green">DONE</font color> | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#X-ACTIVATED_RECEPTORS_:_STARTED X-activated receptors] <font color="green"> | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#X-ACTIVATED_RECEPTORS_:_STARTED X-activated receptors] <font color="green">DONE for growth factor receptors</font color> | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#LIGAND-GATED_ION_CHANNELS ligand-gated ion channels] | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#LIGAND-GATED_ION_CHANNELS ligand-gated ion channels] | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#GPCRs GPCRs] <font color="green">: | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#GPCRs GPCRs] <font color="green">: DONE THE KEY BITS </font color> == | ||
*[http://gocwiki.geneontology.org/index.php/RECEPTORS#DODGY_RECEPTOR_TERMS Receptor clean-up] | *[http://gocwiki.geneontology.org/index.php/RECEPTORS#DODGY_RECEPTOR_TERMS Receptor clean-up] | ||
[[Signaling and receptor-mediated endocytosis]] | [[Signaling and receptor-mediated endocytosis]] <font color="green">DONE THE KEY BITS</font color> | ||
[[Receptor signaling proteins]] | [[Receptor signaling proteins]]<font color="green">DONE THE KEY BITS</font color> | ||
[[Initiation of signal transduction]]: <font color=" | [[Initiation of signal transduction]]: <font color="green">DONE</font color> | ||
[[signaling regulation terms]] <font color=" | [[signaling regulation terms]] <font color="green">DONE</font color> | ||
[[signal release/generation]] | [[signal release/generation]] <font color="green">DONE</font color> | ||
==<font color="navy">Signaling Conference Calls And Discussions</font color> == | ==<font color="navy">Signaling Conference Calls And Discussions</font color> == | ||
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[[Signaling demo February 2010]] | [[Signaling demo February 2010]] | ||
[[Signaling to do list]] | [[Signaling to do list | from Jen]] | ||
Line 120: | Line 131: | ||
[[March 25th 2010]] | [[March 25th 2010]] | ||
[[April 19th 2010]] | [[Signaling April 19th 2010]] | ||
[[May 10th 2010]] | [[May 10th 2010]] | ||
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[[December 21st 2011]] | [[December 21st 2011]] | ||
[[April 2013]] | |||
*[[Signaling 2013-10-28|Oct 28]] | |||
*[[Signaling 2013-11-25|Nov 25]] | |||
==<font color="navy">GO Signaling Workshop</font color> == | ==<font color="navy">GO Signaling Workshop</font color> == | ||
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==<font color="navy">Signaling DBXrefs and GO:IDs</font color>== | ==<font color="navy">Signaling DBXrefs and GO:IDs</font color>== | ||
The DBX-refs and GO IDs for the signaling overhaul are split according to those for the first phase (Jen and SWG) and the second phase (Rebecca and SWG): | 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: | PHASE I: | ||
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==LINKS AND RESOURCES== | |||
[[Signaling Curation Manual]] | |||
Latest revision as of 17:44, 9 April 2014
Return to GOC Main Page
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
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
[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
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
- 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 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)
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.
Discussions from the Second Phase (March 2010 onwards)
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.
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