Manager Call 2020-03-04: Difference between revisions
Jump to navigation
Jump to search
m (→Agenda) |
No edit summary |
||
Line 14: | Line 14: | ||
* A [https://docs.google.com/document/d/1jpvnBX7h_zeVJO9-OJadMHcJyQNvd2CPyZvkvkWyQf4 Google doc] with the proposed changes and some comments is available for people to review. | * A [https://docs.google.com/document/d/1jpvnBX7h_zeVJO9-OJadMHcJyQNvd2CPyZvkvkWyQf4 Google doc] with the proposed changes and some comments is available for people to review. | ||
* There are a few points where we still need a final decision (marked in red). | * There are a few points where we still need a final decision (marked in red). | ||
** Will we allow >1 reference? Yes, this is the most practical decision. | |||
** Dates/times ok as specified in the document? Answer:yes | |||
** For annotation identifiers in the initial import, should we enforce that the identifier prefix be in the db-xref.yaml? These will need to be in the yaml file if the identifiers will persist. Seth thinks they should since they won't be replaced with GO annotation identifiers. | |||
** Are the new headers ok: Yes | |||
** For ECO codes in the properties, if they persist we will need to perform a check. | |||
** For entity types in the GPI, do we want to require groups to go to protein coding gene or non-encoding RNA encoding gene? To what level do we want to require people to annotate? We will require ncRNA and not allow transcript. Otherwise we will follow the existing document. | |||
* Kimberly will present this on Tuesday's annotation call. | |||
===GO meeting Paris=== | ===GO meeting Paris=== | ||
Page ready to be shared: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics | Page ready to be shared: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics | ||
Registration here: https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 | Registration here: https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101 | ||
* People should start registering for the meeting. | |||
Pasteur: bioinformatics hub to be cited as co-organizer of the GO User Meeting. | Pasteur: bioinformatics hub to be cited as co-organizer of the GO User Meeting. | ||
==Discussion== | ==Discussion== |
Revision as of 12:54, 4 March 2020
Agenda
- Agenda: Laurent-Philippe
- Minutes: David
- Present: David, Paul T, Seth, Laurent-Philippe, Kimberly, Pascale, Chris, Huaiyu
- Regrets: Judy
Discussion points
Caltech f2f, 24-28 Feb
Summary
- One deliverable from the meeting was GPAD/GPI 2.0 specs.
- A Google doc with the proposed changes and some comments is available for people to review.
- There are a few points where we still need a final decision (marked in red).
- Will we allow >1 reference? Yes, this is the most practical decision.
- Dates/times ok as specified in the document? Answer:yes
- For annotation identifiers in the initial import, should we enforce that the identifier prefix be in the db-xref.yaml? These will need to be in the yaml file if the identifiers will persist. Seth thinks they should since they won't be replaced with GO annotation identifiers.
- Are the new headers ok: Yes
- For ECO codes in the properties, if they persist we will need to perform a check.
- For entity types in the GPI, do we want to require groups to go to protein coding gene or non-encoding RNA encoding gene? To what level do we want to require people to annotate? We will require ncRNA and not allow transcript. Otherwise we will follow the existing document.
- Kimberly will present this on Tuesday's annotation call.
GO meeting Paris
Page ready to be shared: http://wiki.geneontology.org/index.php/2020_Paris_GOC_Meeting_Logistics Registration here: https://www.eventbrite.com/e/gene-ontology-main-meeting-tickets-97870099101
- People should start registering for the meeting.
Pasteur: bioinformatics hub to be cited as co-organizer of the GO User Meeting.
Discussion
Noctua/NEO
- Loading UniProt Viral + bacterial GPI: This came up again from the multi-organism working group. They want to start making GO-CAM models. Can the loading of the GPI file be prioritized and assigned?
Paper identifying missing 'is_a' relations
David https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa106/5739437
Some missing relations are not: is it a version problem ? or maybe they aren't using the inferred version of the ontology ?
Is there any missing link that could be useful for the ontology ?
Non-GO editors people making PR in the ontology tracker
https://github.com/geneontology/go-ontology/issues/17091
Isn't our policy that *only* GO editors work on the ontology ? Or do we want to allow some other users to make PRs?