CamEds Ontology meeting 2012-06-19

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FOR EDITORS' CALL TOMORROW

David mentioned that the Managers' calls will now take place on the 1st and 3rd Wed. of the month? Is this right? So we know when to schedule the Editors' calls exactly.

Also has Jane heard of any follow-up to the RHEA/GO call? See http://wiki.geneontology.org/index.php/Ontology_meeting_2012-06-20


PROTEIN BINDING (BECKY)

I joined Emily and Marjin's meeting on Thursday to give an overview of Marjin's work on making a curation aid for protein binding terms. Some ontology questions came up from the meeting:


MORE SPECIFIC PROTEIN BINDING TERMS

  • Q: Can we continue to add more specific protein binding terms in, E.g. for more enzymes?


PROTEIN FAMILIES

  • Q: Should we use 'family' in protein binding names? We're not currently consistent:
SMC protein binding ; GO:0043221
p53 binding ; GO:0002039

hedgehog family protein binding ; GO:0097108
neurexin family protein binding ; GO:0042043


PROTEIN COMPLEX SUBUNIT BINDING

  • Q: Can we represent binding to a protein complex subunit? E.g. if a protein binds to a RNA polymerase subunit, which GO term would you currently use?
RNA polymerase binding ; GO:0070063
RNA polymerase II core binding ; GO:0000993


PROTEIN BINDING VS PROTEIN COMPLEX BINDING

AI: We're not consistent in the parentage of 'protein binding' vs 'protein complex binding' at the moment. Presumably the following term should have a protein complex binding parent:

ion channel binding ; GO:0044325
Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel   across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.


GENE PRODUCT BINDING

  • Q Are these GO terms valid:
Ku70 binding
MDM2 binding
MDM4 binding
Hsp272 protein binding
Hsp70 protein binding
Hsp90 protein binding


MULTI-STEP ENZYME REACTIONS (BECKY)


MISFOLDED GLYCOPROTEIN CATABOLISM

  • Q: Is this a valid term request: misfolded or incompletely synthesized glycoprotein catabolic process GO:NEW

[1]


CELL CYCLE

  • Q: Is there any funding in the budget for a cell cycle workshop?
  • Q: Who should attend the workshop?


ACETATE DERIVATIVES

These terms are on my XP-making list:

GO:0030635    acetate derivative metabolic process
GO:0030636    acetate derivative biosynthetic process
GO:0030637    acetate derivative catabolic process

The only specific child of these terms (which looks wrong according to the ChEBI structure) is the polyketide metabolism terms (LOTS of children).

Based on the annotations to the 3 acetate derivative terms, I created 2 new, more specific terms:

GO:0030635    acetate derivative metabolic process	0
GO:0030636    acetate derivative biosynthetic process	1 TAS SGD annotation from PMID:15042596*
GO:0030637    acetate derivative catabolic process	0
ID: GO:1900619 Label: acetate ester metabolic process
ID: GO:1900620 Label: acetate ester biosynthetic process

Any objections to me deleting the acetate derivative terms? It looks on a limb anyway- I'm sure there's more things derived from acetate that aren't under this node.




ID: GO:1900619 Label: acetate ester metabolic process ID: GO:1900620 Label: acetate ester biosynthetic process acetate ester; CHEBI:47622