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geneontology / project-management

Tracking project metadata in the GO as issues.
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Extend GPI format for more detailed information transfer (e.g. withdrawn/merged/split) resources to GO Central #83

Open kltm opened 1 year ago

kltm commented 1 year ago
Project link

https://github.com/orgs/geneontology/projects/TBD

Project description

Currently, the only information that can be carried by the GPI format is whether or not an identifier exists. We need to be able to QC and triage items in this window and optionally do automatic updates when possible of merges, track splits and withdrawn identifiers.

The mile-high problem here is that the SoT for identifiers is the resources/MODs, but the annotation/model SoT is GO Central. This introduces a lag and non-automated cleanup that was not previously an issue.

The initial discussion/proposal is at https://docs.google.com/document/d/1GXSKLKWJMNZmUOBbuMhgvPf4WCjDaKLCooOcUF0UMoE/edit

Originally from https://github.com/geneontology/pipeline/issues/239

Current ameliorating actions underway at:

https://github.com/geneontology/go-site/issues/2066 https://github.com/geneontology/go-site/issues/2061

PI

TBD

Product owner (PO)

TBD

Technical lead (TL)

TBD

Other personnel (OP)

TBD

Technical specs

TBD (template: https://docs.google.com/document/d/111UqtS3G0aJZpAijZYI3Da0t94OQpGePlPJsqZE4Tio/edit)

Other comments

N/A

kltm commented 1 year ago

From @cmungall data dictionary as linkml; maybe @sierra-moxon can help with finding the right properties and making the schema

pgaudet commented 1 year ago

@kltm proposes to have a proposal for the next GO meeting

kltm commented 1 year ago

Talking to @cmungall , from ontology, will propose:

is_obsolete: bool replaced_by: id (merge) n x consider: id (split)

kltm commented 1 year ago

Comment from @tberardini that we may want to consider adding a "date" component to these additions.

pgaudet commented 2 months ago

Other format issues to be considered (outside the scope of this specific project, but need to consider GPI & GAF purposes and specs before implementing what is proposed in this project:

from a GPI file thread on Slack