Inventory and existing field alignment deliverable (1.1A)

[schristley]

• [x] #3
• [x] #6
• [x] #12
• [x] #17
• [x] #16

Aim 1.1A critical metrics: the proportion of entities and DEs accommodated in the semantic model and standards

[bcorrie]

Created a Consolidate Field Mapping file in Schema/Harmonization directory that has AIRR, IEDB, IRAD, and VDJBase columns - these need to be reviewed but it is a start.

This is based on @rvita and @bpeters42 AIRR-IEDB mapping (as per #4) with columns added.

[bcorrie]

Created a separate issue (#5) for mapping common fields.

[bcorrie]

I also created a separate issue (#6) for generating the ontologies that are being used.

[rvita]

AIRR_IEDB_maps_RV.xlsx

[bpeters42]

Please do not use the sheet from Randi for anything but internal mapping, but rather: https://docs.google.com/spreadsheets/d/1kMmANqAhg2ujURdRnSZBV-R0KO5Rxv7h/edit#gid=460086649

On Thu, Oct 19, 2023 at 3:57 PM rvita @.***> wrote:

AIRR_IEDB_maps_RV.xlsx https://github.com/airr-knowledge/issues/files/13048304/AIRR_IEDB_maps_RV.xlsx

— Reply to this email directly, view it on GitHub https://github.com/airr-knowledge/issues/issues/1#issuecomment-1771813924, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IQL37XLFNFAWJTAEX3YAGV6RAVCNFSM6AAAAAA5APRI72VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZRHAYTGOJSGQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[bpeters42]

I should read before I write: The sheet Randi sent is based on the IEDB export terms, which should be our gold standards. My apologies to all and specifically for Randi for not checking before complaining. This is exactly what should be used.

On Thu, Oct 19, 2023 at 4:01 PM Bjoern Peters @.***> wrote:

Please do not use the sheet from Randi for anything but internal mapping, but rather:

https://docs.google.com/spreadsheets/d/1kMmANqAhg2ujURdRnSZBV-R0KO5Rxv7h/edit#gid=460086649

On Thu, Oct 19, 2023 at 3:57 PM rvita @.***> wrote:

AIRR_IEDB_maps_RV.xlsx https://github.com/airr-knowledge/issues/files/13048304/AIRR_IEDB_maps_RV.xlsx

— Reply to this email directly, view it on GitHub https://github.com/airr-knowledge/issues/issues/1#issuecomment-1771813924, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IQL37XLFNFAWJTAEX3YAGV6RAVCNFSM6AAAAAA5APRI72VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZRHAYTGOJSGQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[bcorrie]

@schristley based on discussion today, I think it might be better to move the last two items on the checklist above to become part of 1.1B (https://github.com/airr-knowledge/issues/milestone/6)

That way this milestone is mostly about documenting the inventory of our current repositories, which we are almost done, and move the gap analysis and new fields, objects, and ontologies to 1.1B.

Does that make sense?

[schristley]

@schristley based on discussion today, I think it might be better to move the last two items on the checklist above to become part of 1.1B (https://github.com/airr-knowledge/issues/milestone/6)

That way this milestone is mostly about documenting the inventory of our current repositories, which we are almost done, and move the gap analysis and new fields, objects, and ontologies to 1.1B.

Does that make sense?

I agree for #11. The last item of critical metrics I would leave here, but feel free to have a copy on the other deliverable. That really shouldn't be a bullet item at this point, plus we are still debating how best to record and track metrics #15

[schristley]

moved #11 to #9

[schristley]

gathering of critical metrics is moved to #15