SourceForge meeting 2015-03-11

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'modified amino acid' merged into 'amino acid derivative'

A heads up that ChEBI effected the high-level change of merging CHEBI:25359 'modified amino acid' into CHEBI:83821 'amino acid derivative'

(http://www.ebi.ac.uk/chebi/searchId.do?chebiId=25359)

and that this change has now percolated to our files, resulting in dangling parent warnings.

This change only affects 5 terms. I think David OS was working on this, I haven't checked if there are tickets about this anywhere. If not, shall we edit these axioms manually, while we wait for the broader issue described below to be resolved:

https://www.ebi.ac.uk/panda/jira/browse/GO-161

Protein family binding term requests

Once and for all, clarify. This also follows up on Paola's email from Monday.

 http://wiki.geneontology.org/index.php/Ontology_meeting_2015-03-05#How_to_define_protein_families_in_enzyme_binding_terms
 So the resolution is NOT to allow for protein family binding terms. If so, do we want to email the GO list 
 and/or mention policy/procedure briefly at the next annotation call.

dph- I sent all of the pending requests to Paul T. I will report on his results.

Pending SF request: https://sourceforge.net/p/geneontology/ontology-requests/11523/ https://sourceforge.net/p/geneontology/ontology-requests/11541/

And there is one protein binding term in the TG queue.

What's a protein complex and what isn't?

Spindle isn't, spindle midzone is. https://sourceforge.net/p/geneontology/ontology-requests/11521/

Spindle, GO:0005819: The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

Spindle midzone, GO:0051233: The area in the center of the spindle where the spindle microtubules from opposite poles overlap.

Related! Guidelines on protein complexes

See Paola's email 'Fwd: protein complexes' dated today March 11th.

(Lower priority) future mini-projects

Do we have resources (and willingness) to work on autophagy, or on gene expression?

For autophagy, e.g. is this correct: autophagy is_a 'cellular catabolic process'? Should it be autophagy has_part cellular catabolic process?

For gene expression, see a recent thread here: https://sourceforge.net/p/geneontology/ontology-requests/11535/