Ontology meeting 2016-03-17
Attendees: Paola, David H, Harold, Tanya, Heiko, Chris, Judy, Paul T
Minutes: Paola
Follow-up: ETINES
http://wiki.geneontology.org/index.php/Ontology_meeting_2016-03-10#ETINES
Any issue we should discuss as a group?
We took a look at the spreadsheet. Cellular terms: Chris thought we had a placeholder pattern for those, and wondered do we need to just have that again? Actually situation is more complex than that, we still have a ton of cellular x terms without logical defs. AI: make a ticket to have a design pattern. It seems there already are GH tickets to discuss most of the general issues in the spreadsheet. Chris: maybe we could clean up as much as we can and then roll out even if it’s not perfect/all done. AI: all to check and try to clean up a bit more.
Cytoplasmic transport
https://github.com/geneontology/go-ontology/issues/12323
-> cytosolic transport? Use of occurs in?
People often use cytoplasmic as a qualifier when they mean cytosolic. So DOS’ proposal would be ok. But, we need to have a system in place to do a sanity check (see DH’s example) - we need to clarify what we mean. So the safest thing may be to have both terms and “weekly deprecate” cytoplasmic transport… But actually, the term only has a few dozens direct annotations. The number is small enough that we could look at them. DH will look at human, rat and mouse; Tanya will look at worm, fly and Arabidpsis. Chris added a note in the ticket.
Vesicular transport
vesicular transport proposal
Proposal for new relation - allowing merge of 'vesicle transport' and 'vesicle mediated transport' branches:
https://github.com/geneontology/go-ontology/issues/12317#issuecomment-194775043
A distinction needs to be made on whether or not things are inside a vesicle and the vesicle is moving, or if things are moving in and out of the vesicle. We need to be able to distinguish the two cases. Discussion on what relationship would better represent these cases. ‘mediated by’ should mean that it’s not necessary and sufficient for the process to happen, but as it is now, it’s probably not enough to distinguish between cases; definition is broad enough to cover both. AI: DOS to figure our how to best solve this one way or the other.
The nature of GO biological_process
Comment on email thread discussion. Alex would like to use GO to describe e.g. tumorigenesis but NOT have the terms in GO. Have people used GO elsewhere to describe diseases? e.g. angiogenesis during cancer would NOT be a subclass of go angiogenesis. As long as that’s the case, we could be fine with it. In Paul T’s proposal, what is normal and what isn’t becomes what has the cell evolved to do. AI: let’s take it to other GO tops and check that we’re all on the same line. May also wish to bring to a managers call. The GO editors second Paul t’s proposal.