Ontology meeting 2014-07-31: Difference between revisions
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===Is 'telomere maintenance via semi-conservative replication' a subclass of 'cellular homeostasis'?=== | ===Is 'telomere maintenance via semi-conservative replication' a subclass of 'cellular homeostasis'?=== | ||
Stemming from latest assert inferences job. Root is 'telomere maintenance' subclass of 'anatomical structure homeostasis'. Just double-checking that we're all ok with this as it sounds a bit weird, telomere being an anatomical structure. | Stemming from latest assert inferences job. Root is 'telomere maintenance' subclass of 'anatomical structure homeostasis'. Just double-checking that we're all ok with this as it sounds a bit weird, telomere being an anatomical structure. | ||
It does sound biologically unintuitive to others too, but this overall classification was implicitly agreed upon some time ago. David OS: a solution may be to tweak CARO (the Common Anatomy Reference Ontology). In CARO, anatomical entity is the most general class, and that includes spaces. A structure is a connected thing that has mass. Under that are cell and cell part. | |||
AI: David OS will add to the agenda for the next CARO meeting (to be held in September) to try and have a class at an intermediate level between cell and anatomical structure. | |||
===Review of Jira tickets (continued from last week)=== | ===Review of Jira tickets (continued from last week)=== | ||
Revision as of 12:54, 31 July 2014
Attendees: Paola, Harold, Heiko, Tanya, David OS, Chris, Jane
Minutes: Paola
Importing SO
We're still using CHEBI for some RNA logical defs - isn't it time we switched to SO? I needed something to define miRNA transport but no miRNA in CHEBI (although they do have many RNA types). See also this ticket: [1]
Some time ago, Chris, Karen, Colin and Mike Bada started working on a molecular sequence ontology (MSO). Lately progress has been slow. However, in principle there's no reason not to use what is in place so far; at least we could get the inferences right, and it would provide us with some structure. MSO is importing RNA terms from ChEBI at the moment, though ChEBI may not be the best solution for RNAs in the long run.
AI: Chris will email them to check on the status of the MSO, and see if we can start using that as an import file.
Is 'telomere maintenance via semi-conservative replication' a subclass of 'cellular homeostasis'?
Stemming from latest assert inferences job. Root is 'telomere maintenance' subclass of 'anatomical structure homeostasis'. Just double-checking that we're all ok with this as it sounds a bit weird, telomere being an anatomical structure.
It does sound biologically unintuitive to others too, but this overall classification was implicitly agreed upon some time ago. David OS: a solution may be to tweak CARO (the Common Anatomy Reference Ontology). In CARO, anatomical entity is the most general class, and that includes spaces. A structure is a connected thing that has mass. Under that are cell and cell part.
AI: David OS will add to the agenda for the next CARO meeting (to be held in September) to try and have a class at an intermediate level between cell and anatomical structure.
Review of Jira tickets (continued from last week)
Brief report on PAINT jamboree
Plan work for SF jamboree
Review and assign mini-projects, etc. Jane added a label 'jamboree' to ticket(s) of hers that she'd like us to discuss at the jamboree.