Ontology meeting 2012-06-27

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30-minute meeting


ATTENDEES: Paola, Jane, Chris, Heiko, Harold


Chris needs to add some bits on the methods.


The EBI GO Editors will meet with ChEBI curators for an hour every week until all issues highlighted by David and Tanya will be resolved.

LEGO model

Chris will give us a presentation on specifications of the LEGO model.

To get examples:

 svn checkout http://owltools.googlecode.com/svn/trunk/Lego Lego

Discussion: At the recent Caltech meeting, some work was done on the LEGO model. Chris showed some examples of this based on insulin receptor's involvement (and subsequent signaling events) in Dauer stage in worm's life cycle - this was in UML so we can't display it, but the model will be polished and presented again at the next GOC meeting. We also went through how that model would be represented in OWL. In this particular example, a set of instances would be created for every individual kinase activation in the signaling pathway, and an ID assigned to each event. The model can handle differences in individual species, and would be built going through annotation process rather than as part of routine ontology editing. Some details are not ironed out yet - some relationships still need some work. The general idea is to show things that are generic, without specifying gene products. The level of representation in GO provides a nested structure, but doesn't say what the gene products are. So the annotator can unfold the expressions, and fill the slots as appropriate. How do we begin to transition from where we are now? There needs to be more documentation on how col. 16 relates to the LEGO model. It will be a bigger issue for discussion, possibly for the GO managers. In the meantime, how should this model influence the way we edit the ontology now? It actually doesn't impact so much what we're doing now, though at some point we might focus e.g. on signaling again and look at things from this perspective... We need to revisit this, the LEGO model will be more polished by the next GOC meeting and until then we can keep it in the back of our minds.

AI: Chris suggests that we could use an ontology project, e.g. apoptosis, to take something that is really difficult to capture with the current ontology and create a mock model to represent it. Paola will find an example, of e.g. apoptosis crossing over signaling, when the apoptosis ontology node has been fully revisited.

go-xp-chebi errors

After updating the transport terms with the new relation 'transports_or_maintains_localization_of' on Friday , there are two new redundant terms in the Jenkins build.

EquivalentClasses(GO:0015803 'branched-chain aliphatic amino acid transport' GO:1900755 'branched-chain amino-acid anion transport' )

EquivalentClasses(GO:0015708 'silicate transport' GO:0051207 'silicic acid transport' )

This are genuine equivalent classes, which need to be merged.

Judging from the annotations, GO:1900755 can be safely merged into GO:0015803, as GO:1900755 seems to have no direct annotations. Similar GO:0015708 has only one annotation and GO:0051207 has none.

AI: Jane fill fix these.