Ontology meeting 2013-03-21

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MINUTES: Paola

ATTENDEES:


Cell cycle

1) Devote some time to bring Chris up to speed on the cell cycle meeting at EBI

2) Make a decision on cell cycle phases

3) Other follow-ups from last week: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-14#Cell_cycle


Annotation relations

We've been discussing with Tony and Rachael ways we might constraint the number of relationships available to an annotator making an annotation extension. Tony would rather not have protein2go have to reason within the session for speed reasons...could we make subsets based on the object type in c16 e.g. cell type, gene, protein?

(also message to Chris from Tony - have you done anything about the domain and range constraints yet? If not, do it :-))

Testing new OBO-Edit release

Jane to report on test obo/OWL round-trip.


interpro2go errors

  • I spoke with Tony and Rachael about the bad annotations being propagated from interpro2go mappings to terms in the 'do not annotate' anti-slim. Two conclusions:
    • They're quite keen to start including this subset in their DB (it's not there right now) which would catch these upstream
    • Sometimes for electronic annotations, mappings to terms in this subset are legitimate e.g. response to stress. We think we may need to split this set into 'do not use for manual annotation' and 'do not use for any annotation'. The latter would be for e.g. the x-part terms.


Web Presence

David to report on (copying over from last week) making a shared doc with proposed new upper structure for a/ Main web documentation b/ Internal documentation in the Drupal book style. We can then all edit and migrate existing web content across.


SF upgrade

Follow-up from here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#SF_upgrade

Jane to report on migration of categories.


Protein complexes

Harold to follow up on checking the protein complex xps before we incorporate (see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#Follow-up:_Protein_complexes).