CamEds Ontology meeting 2012-06-19
- 1 FOR EDITORS' CALL TOMORROW
- 2 PROTEIN BINDING (BECKY)
- 3 MULTI-STEP ENZYME REACTIONS (BECKY)
- 4 MISFOLDED GLYCOPROTEIN CATABOLISM
- 5 CELL CYCLE
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?
- 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)
- Q: How should we represent multi-step enzyme reactions in GO?
- E.g: EC:184.108.40.206 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/13/72.html).
MISFOLDED GLYCOPROTEIN CATABOLISM
- Q: Is this a valid term request: misfolded or incompletely synthesized glycoprotein catabolic process GO:NEW
- Q: Is there any funding in the budget for a cell cycle workshop?
- Q: Who should attend the workshop?
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