Annotation Conf. Call 2017-05-23
Bluejeans URL
https://bluejeans.com/993661940
Agenda
GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017
- Logistics: https://sites.google.com/view/goc2017
- 2017 Corvallis GOC Meeting Agenda
- Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry - especially the column about attending the GO dinner.
Noctua Models
- Presenter: Petra Fey (dictyBase)
- Rab8a regulates the exocyst-mediated kiss-and-run discharge of the Dictyostelium contractile vacuole
- Link to Noctua model
Minutes
- On call: Bob, Dave F, David H, Harold, Helen, Karen, Kimberly, Li, Moni, Pascale, Petra, Sabrina, Shur-Jen, Stan, Suzi, Tanya
GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017
- Please review the agenda
Noctua Models
- Petra presented a model for exocyst-mediated contractile vacuole discharge in Dicty
- Export GPAD link from Model menu in Noctua now using the most up-to-date reasoner (note that GAF is currently not available)
- Use of 'adjacent to' relation - this relation is used to qualify the relation between two things (e.g. cellular components), not between a process and a thing (component)
- 'adjacent to' entry in RO from Ontology Lookup Service
- In the model, we want to say that the regulation occurs in the part of the cytosol that is adjacent to the contractile vacuole membrane
- We do this by going to the View menu and exploding the view (evidence folded or all) and then make the appropriate connection between the two CC terms
- When we return to the folded view, then you see that the cytosol is removed from the original individual and is now a separate individual so that it can be specifically linked to contractile vacuole membrane
- Use of 'enabled by' relation - this relation is used between an entity and a Molecular Function (not an entity and a Biological Process)
- Curators need to make sure that they are articulating exactly which MF is linked to a specific BP
- Protein binding MF annotations
- Is the same protein binding individual appropriate as 'part of' each successive BP?
- Here, the curators needs to decide whether the evidence supports that the protein binding is 'part of' each process.
- Is Rab8A bound to the same protein throughout? Any other changes?
- Need to check the GPAD output for representation of Rab8A as 'part of' a process that is 'causally upstream of' a set of other processes
- With the MF refactoring, will this type of protein binding annotation still be used?
- In the MF refactoring, protein binding will generally be considered a mechanism to achieve a biological outcome, e.g. sequestration
- An update on the MF refactoring is scheduled for the Corvallis meeting.
- For protein binding annotations like this, we will want to make sure that there is an appropriate MF term to describe what Rab8A's activity is
- Is an annotation to protein complex binding more appropriate for this model?
- If you don't know what the relevant MF for an entity is, create a generic MF annotation in your Noctua model
- We need to discuss what evidence should be put on the generic MF annotation
- Note that the annotation extension information attached to the generic MF annotation may be quite useful to users
- For each gene product in a model, think of representing it as an annoton, i.e. an MF 'enabled by' a GP; that MF 'occurs in' a CC; and that MF has a causal relation to a BP
- The causal relations may be 'part of', 'causally upstream of', 'causally upstream of or within', etc.
- How will the CC contextual information for contractile vacuole discharge be represented in the GPAD?
- Probably as an annotation extension - but curators should check their GPAD annotations!
- Annotations to the exocyst complex
- Right now this is in the model as an independent annotation
- What is the appropriate MF for the exocyst complex?
- What are the desired annotations for Noctua?
- Any annotations can be made
- Curators would really like context-dependent relation selection
- Curators would also like to have a human readable (i.e. including term names, gene names, etc.) GPAD for QC