SourceForge meeting 2013-10-30

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Scope of GO:0005615  ! extracellular space

#10434 Clarification for GO:0005615 (extracellular space)

This ticket requests that "comment for "extracellular space" be modified to clarify that it can also be used for secretions such as tears and saliva."

It is hard to see a justification for this in terms of useful annotation provided for end-users. Who is going to expect the contents of tears to be classified as components of an extracellular space? Isn't this the domain of anatomy ontologies? If a non-species specific term is needed, shouldn't the annotation be to an Uberon term?

part_of relationships for complexes

SF10283. Should a complex be described as being in a specific topology even if all of the members of the complex are not in that topology, example integral to membrane?

specific terms for amino acid modifications that vary among taxa

SF10413. Apparently in yeast S10 on a histone is equivalent to S14 in other organisms. How do we modify the definition of molecular function terms to represent this?


elevation/reduction in term names

Based on a SF item from Val. Elevation/reduction terms sound too much like a phenotype. Should they be changed to 'regulation' or is there a reason they're different? elevation of cytosolic calcium ion concentration ; GO:0007204 reduction of cytosolic calcium ion concentration ; GO:0051481 reduction of food intake in response to dietary excess ; GO:0002023

Function terms that refer to specific amino acids

histone kinase activity (H2B-S14 specific) SF# 10413

The term specifies modification of a specific amino acid in a histone, but the position of that amino acid changes from species to species. Should we broaden the current definition or make a new term?

Resurrecting obsolete terms

toluene biosynthesis SF# 10408

Turns out this process occurs. I need a refresher on how to un-obsolete a term.

[Paola] See http://wiki.geneontology.org/index.php/Curator_Guide:_Obsoletion#Restoring_obsolete_terms

("If you need to reinstate an obsolete term back into the ontologies, use the following: comment: Note that this term was reinstated from obsolete.")

I had to do this for 'caspase complex' recently, and asking the other editors, it seemed the only way was to hand-edit the term and delete the is_obsolete line; I couldn't find a function in OBO-Edit to do it.

schedule next signaling call

Monday 11th or Monday 25th November?