LEGO May 2, 2016

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Software Updates


Determining the Extent of Upstream/Downstream to Capture in GAF/GPAD

  • For an illustration, see:
    • Fatty acylation of Wnt is required for its secretion
    • Currently, worm, fly, fish, mouse, and human acyltransferases of the porcupine family are annotated to Wnt protein secretion or some variant (direct or regulation) of Wnt signaling pathway
    • The current GAF/GPAD output only includes, as an annotation extension, the immediate downstream process which in the illustrative model is 'Golgi to plasma membrane transport'
  • Is there/could there be a mechanism whereby curators indicate which annotons to include as causally_upstream of GAF/GPAD output for a given model?
  • What do we still need to get GAFs that can be used?
    • In the meantime we should just go for the default of including everything. It is easier to prune annotations that to add them in a second step later. This means that everything causally downstream of a gene's function will be annotated, but I don't think that it is that much different from the historical way of doing annotation.
    • We need to find a way to indicate attribution. I suggest that we use GO-curator xref-Noctua (dph-Noctua) in column 15.
  • Related to this, can new ontology terms be automatically generated from a model and curators given the option to add them to the ontology when they save their models?


  • More video tutorials? (Stacia)

current tutorials on Vimeo:

Models Discussion

cdc2 - Continuing Discussion from 2016-04-25


  • On call: Chris, David H., Heiko, Kimberly, Stacia, Suzi
  • Software Updates - none this week
  • GAF/GPAD outputs
    • We discussed the Wnt secretion model and how to create a model that will allow for the appropriate causally_upstream_of and regulates relations to be recovered in the GAF/GPAD output.
      • There are two issues here. The first is the ability for a curator to associate a gene product with a process that is transitively downstream in a given model, and to record a relation and evidence for that 'transitive' assertion. In the Wnt secretion model, the annotation wanted is an association with mom-1 and Wnt signaling pathway. The second is how do we indicate in a lossy GAF that this association represents a causally_upstream_of relation.
        • For the first issue, we dicussed computing transitive closure between the annoton that contains the gene product and the process that is several steps away. But then we needed a way to limit the associations to only those that we wanted to be output as lines in the gaf. We discussed two possibilities, the ability of an annotator to choose the processes that should be associated with a given annoton so that the gaf would be generated from selected individuals, or only creating models where we only put things that we wanted to be included. Both were unsatisfactory because in the first case, it is not possible to pick which piece of evidence in the transitive chain should be used for a line in the gaf and in the second case it kind of defeats the purpose of LEGO where we want to be able to get a full picture of the biology.
        • In the case of knowing how the gene product relates to the downstream process, we decided on the proposed qualifier model, where in the qualifier field of the gaf we would add a qualifier to express the relationship.
      • In the case of evidence, evidence for an activity may be different from evidence of the effect of that activity on a downstream process and often we will have a single piece of evidence (eg IMP) to support why we want to associate a gene product with something downstream. We'll need to explicitly add the relations and evidences for activities and downstream processes to have them correctly represented in the model and resulting output files. This will also make the model more complete because it will be possible to record all of the evidence for an assertion.
    • We also discussed the extent of what upstream processes might be included in a given model and to what extent known specificity plays into the decision to include commonly used cellular processes.
    • AI: Need to work out the qualifier proposal.
  • Documentation
    • Stacia and Kevin at SGD can help produce new training videos for the basic functionality of Noctua, including login, creating an annoton, adding relations, adding evidence, etc.