short term: programmatically tag the origin of MIxS terms when imported into NMDC schema

[turbomam]

CC @cmungall @wdduncan

Sample MIxS term in NMDC shema

see also microbiomedata/nmdc-server#555

especially the discussion of MIxS' lat_lon field

[turbomam]

Implement with conforms_to or annotations?

semantics too loose?

• in_subset
• see_also

probably not

• quick and dirty parse of slot_uri, from_schema, imported_from, exact_mappings etc.
• owner (deprecated)

[wdduncan]

tagging @mslarae13

[cmungall]

I think in_subset is good

…

On Wed, Feb 2, 2022 at 1:42 PM Mark A. Miller ***@***.***> wrote: Implement with conforms_to or annotations? semantics too loose? - in_subset - see_also probably not - quick and dirty parse of slot_uri, from_schema, imported_from, exact_mappings etc. - owner (deprecated) — Reply to this email directly, view it on GitHub <#252 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOLWZFCTIPNGLYYKFGTUZGQLHANCNFSM5NNFBYAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[turbomam]

I implemented with source: http://w3id.org/mixs/terms in mixs.yaml

When creating the Bioscales tempalte, we found that the LinkML source attribute conflicts with a reserved source annotation in DataHarmonizer, so this might not be a good long term solution.

[turbomam]

What are DataHarmonizer's reserved field names

[turbomam]

@ssarrafan : I think @pkalita-lbl and Damion resolved the over-eager interpretation of LinkML's source field. We still need to have better policies for DataHarmonizer vs. LinkML attributes

[mslarae13]

@turbomam
Just checking, does this relate to the discussion we had yesterday about "annotating" the NMDC schema slots with "where they came from"?

Example, geo_loc_name being MIxS & location being gold ?

[turbomam]

Just checking, does this relate to the discussion we had yesterday about "annotating" the NMDC schema slots with "where they came from"?

@mslarae13 @ssarrafan

Yes, but I'm not convinced I did it in a sustainable way, or that I used the most appropriate LinkML slot to make the annotations. Will look into it more in the beginning of August.

[ssarrafan]

Just checking, does this relate to the discussion we had yesterday about "annotating" the NMDC schema slots with "where they came from"?

@mslarae13 @ssarrafan

Yes, but I'm not convinced I did it in a sustainable way, or that I used the most appropriate LinkML slot to make the annotations. Will look into it more in the beginning of August.

I'm tempted to tag this as interim fix and close it but will move it to August for you @turbomam. FYI @mslarae13

[mslarae13]

Just checking, does this relate to the discussion we had yesterday about "annotating" the NMDC schema slots with "where they came from"?

@mslarae13 @ssarrafan
Yes, but I'm not convinced I did it in a sustainable way, or that I used the most appropriate LinkML slot to make the annotations. Will look into it more in the beginning of August.

I'm tempted to tag this as interim fix and close it but will move it to August for you @turbomam. FYI @mslarae13

@ssarrafan I agree interim fix. Can we get a ticket started for the "preferred solution" per Mark's comment

[ssarrafan]

@sujaypatil96 @turbomam can this interim fix issue be closed?

I'm moving to Sept sprint but if you plan to not work on it in the next 2 weeks let me know so I can remove and add the backlog label