Difference between revisions of "Ontology meeting 2014-09-25"

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Attendees:
Attendees: David H, David OS, Paul T, Paola, Harold, Heiko, Chris, Tanya, Jane


Minutes:
Minutes:David H


=== Follow-up on 'transport' ===
=== Follow-up on 'transport' ===


See action items here - where are we? http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-11#Transport_terms_.28carried_over_from_last_week.29
See action items here - where are we? http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-11#Transport_terms_.28carried_over_from_last_week.29
Still looking at this.


===Accumulation of inferred links===
===Accumulation of inferred links===


Redundant links (i.e. where A is_a B and something is classified under both A and B) are causing problems in cell cycle - there's a lot of mess it's difficult to see what's going on. Let's discuss where we are with the workflow and removing these automatically. Could we possibly do a one-off removal for now?
Redundant links (i.e. where A is_a B and something is classified under both A and B) are causing problems in cell cycle - there's a lot of mess it's difficult to see what's going on. Let's discuss where we are with the workflow and removing these automatically. Could we possibly do a one-off removal for now?
Are we restricting to is_a? Yes. This is a guaranteed safe operation but it will end up removing asserted relations to generic terms that are further classified by reasoning. We do not want to remove the asserted relation. However, we can remove the ones that are placed there by inference and are redundant. This is the plan. We will run it manually the first couple of times just to make sure that everyone is happy with it. Then it will become part of the pipeline. A is_a B, B, is_a C, A is_a C, where A is_a C isInferred, then remove A is_a C
=== Inferences & Jenkins ===
See email thread [go-ontology] build-go-assert-inferences - Build # 92 - Failure!
It is possible to to manually trigger the assert inferences job. Chris showed how to look at the report in Jenkins. Action item: All of us get permission to trigger the build and then to look at the report if we are doing a lot of work. This way we can preemptively check for errors before the next Tuesday.
===negatively_regulates o part_of/positively_regulates o part_of===
Did you add these chains yet Chris? Need them for [https://sourceforge.net/p/geneontology/ontology-requests/11166/ SF 11166]
See email thread 'reasoner diff before and after' - as of just before the call, these don't seem to be in yet, but no-one objected so far (and Jane, Val and Paola ok'd them)
We checked the report and they look good, so we will go ahead and add the property chains. Chris will add them.
=== MF refactoring follow-up ===
Paul T., please see editors' comments at the end of this doc: https://docs.google.com/document/d/1y-6to0vwEJHc3i3wdPnJoCAq910auPQp5jBvafpJvL0/edit#heading=h.x7xjmjjghqb5
=== TG template for 'cell migration' ===
What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates'
=== GO into NCIt ===
* https://docs.google.com/document/d/1ozliyTh-QPyyUdYjk8P1mhygWCWtCnZKX9FNGvU-XlM/edit#
=== Monthly review of Jira tickets ===




[Category:Ontology]]
[[Category:Meetings]]
[[Category:Meetings]]
[[Category:Ontology]]

Latest revision as of 12:27, 25 September 2014

Attendees: David H, David OS, Paul T, Paola, Harold, Heiko, Chris, Tanya, Jane

Minutes:David H

Follow-up on 'transport'

See action items here - where are we? http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-11#Transport_terms_.28carried_over_from_last_week.29

Still looking at this.

Accumulation of inferred links

Redundant links (i.e. where A is_a B and something is classified under both A and B) are causing problems in cell cycle - there's a lot of mess it's difficult to see what's going on. Let's discuss where we are with the workflow and removing these automatically. Could we possibly do a one-off removal for now?

Are we restricting to is_a? Yes. This is a guaranteed safe operation but it will end up removing asserted relations to generic terms that are further classified by reasoning. We do not want to remove the asserted relation. However, we can remove the ones that are placed there by inference and are redundant. This is the plan. We will run it manually the first couple of times just to make sure that everyone is happy with it. Then it will become part of the pipeline. A is_a B, B, is_a C, A is_a C, where A is_a C isInferred, then remove A is_a C

Inferences & Jenkins

See email thread [go-ontology] build-go-assert-inferences - Build # 92 - Failure!

It is possible to to manually trigger the assert inferences job. Chris showed how to look at the report in Jenkins. Action item: All of us get permission to trigger the build and then to look at the report if we are doing a lot of work. This way we can preemptively check for errors before the next Tuesday.

negatively_regulates o part_of/positively_regulates o part_of

Did you add these chains yet Chris? Need them for SF 11166

See email thread 'reasoner diff before and after' - as of just before the call, these don't seem to be in yet, but no-one objected so far (and Jane, Val and Paola ok'd them)

We checked the report and they look good, so we will go ahead and add the property chains. Chris will add them.

MF refactoring follow-up

Paul T., please see editors' comments at the end of this doc: https://docs.google.com/document/d/1y-6to0vwEJHc3i3wdPnJoCAq910auPQp5jBvafpJvL0/edit#heading=h.x7xjmjjghqb5

TG template for 'cell migration'

What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates'

GO into NCIt

Monthly review of Jira tickets

[Category:Ontology]]