Difference between revisions of "Requesting a New Complex ID from ComplexPortal"

From GO Wiki
Jump to: navigation, search
m
Line 1: Line 1:
Users can request complex IDs from IntAct by filling the Complex submission template and emailing it to intact-help@ebi.ac.uk or bmeldal@ebi.ac.uk with as much detail as possible.
+
Users can request complex IDs from Complex Portal by sending a message via the yellow tile on the [https://www.ebi.ac.uk/complexportal/home Homepage] "Request Complex for curation" or emailing complexportal@ebi.ac.uk with as much detail as possible.
  
==[https://www.ebi.ac.uk/intact/ IntAct] Complex submission template==
+
==Complex submission template==
 
   
 
   
 
* Please supply as much information as possible to allow us to make your term.
 
* Please supply as much information as possible to allow us to make your term.
Line 11: Line 11:
 
   
 
   
 
===Participants===
 
===Participants===
* [http://www.uniprot.org/ UniProt] IDs for proteins (and their binding regions and stoichiometry - if available)
+
* [http://www.uniprot.org UniProt] IDs for proteins (and their binding regions and stoichiometry - if available)
* [https://www.ebi.ac.uk/chebi/ ChEBI] IDs for small molecules (and stoichiometry - if available)
+
* [https://www.ebi.ac.uk/chebi ChEBI] IDs for small molecules (and stoichiometry - if available)
* [http://rnacentral.org/ RNAcentral] IDs for ncRNAs (and stoichiometry - if available)
+
* [http://rnacentral.org RNAcentral] IDs for ncRNAs (and stoichiometry - if available)
 
   
 
   
 
===Evidence===
 
===Evidence===
* PMID for papers showing that the complex exists (if you are familiar with IntAct please add the IntAct interaction AC if applicable)
+
* PMID for papers showing that the complex exists
* '''Note:''' It should be evidence for all or most of the participants, not lots of binaries and not from high throughput experiments.
+
* Optional: Cross-reference to a evidence database, e.g. from [https://www.ebi.ac.uk/intact IntAct], [https://www.ebi.ac.uk/pdbe PDBe] or [https://www.ebi.ac.uk/pdbe/emdb/searchForm.html/ EMDB]
+
* '''Note:''' The interaction evidence should include all or almost all complex members, not lots of binaries and not from high throughput experiments.
===Additional information===
 
PMIDs that show what the complex does and where (so we can add MF & BP GO terms, see below).
 
 
   
 
   
 
===Description===
 
===Description===
A nice, concise description would help, similar to that required for GO term submissions :)
+
* A nice, concise description would help, similar to that required for GO term submissions.
 
===Properties===
 
Any additional information such as molecular weight of the COMPLEX, size, buried surface area, stokes radius, binding regions…
 
 
   
 
   
 
===GO annotations===
 
===GO annotations===
Any terms that apply to the COMPLEX:
+
Any terms that apply to the COMPLEX (as far as it's known):
CC for the complex class and the cellular location (e.g. nucleus, plasma membrane…)
+
* CC for the complex (child of GO:0032991 protein-containing complex)
MFs & BPs: as many as applicable
+
* CC for cellular location (e.g. nucleus, plasma membrane…)
Please supply PMIDs if possible
+
* MF: at least the central function of the complex
+
* BPs: the process(es) the complex is involved in
===Xrefs (if applicable)===
+
* Please supply PMIDs
* [https://www.wwpdb.org/ wwPDB]
 
* [https://enzyme.expasy.org/ EC number] (for enzymes)
 
 
   
 
   
----
 
 
==Using Intact Helpdesk for new complex requests==
 
Alternatively, new complexes can now also be requested directly from the yellow tile on the new CP homepage (www.ebi.ac.uk/complexportal) but that's just a helpdesk message until we get round to create a form behind that tile.
 
  
 
== Review Status ==
 
== Review Status ==
  
Last reviewed: July 5, 2017
+
Last reviewed: Nov 17, 2020
  
 
[[Category:GO Editors]][[Category:Ontology]]
 
[[Category:GO Editors]][[Category:Ontology]]

Revision as of 03:01, 17 November 2020

Users can request complex IDs from Complex Portal by sending a message via the yellow tile on the Homepage "Request Complex for curation" or emailing complexportal@ebi.ac.uk with as much detail as possible.

Complex submission template

Complex names

  • Most commonly known name (recommended name):
  • Synonyms (could be any and many!):

Participants

  • UniProt IDs for proteins (and their binding regions and stoichiometry - if available)
  • ChEBI IDs for small molecules (and stoichiometry - if available)
  • RNAcentral IDs for ncRNAs (and stoichiometry - if available)

Evidence

  • PMID for papers showing that the complex exists
  • Optional: Cross-reference to a evidence database, e.g. from IntAct, PDBe or EMDB
  • Note: The interaction evidence should include all or almost all complex members, not lots of binaries and not from high throughput experiments.

Description

  • A nice, concise description would help, similar to that required for GO term submissions.

GO annotations

Any terms that apply to the COMPLEX (as far as it's known):

  • CC for the complex (child of GO:0032991 protein-containing complex)
  • CC for cellular location (e.g. nucleus, plasma membrane…)
  • MF: at least the central function of the complex
  • BPs: the process(es) the complex is involved in
  • Please supply PMIDs


Review Status

Last reviewed: Nov 17, 2020