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identifier slot for img ids #6

Closed ssarrafan closed 1 year ago

ssarrafan commented 1 year ago

Make an alternative identifiers slot for IMG IDs

@turbomam can you add more details here when the time comes to work on this please

turbomam commented 1 year ago

@ssarrafan can you answer any of these questions, or tell me who can?

ssarrafan commented 1 year ago

@ssarrafan can you answer any of these questions, or tell me who can?

  • What action is required?
  • What class should bear an IMG ID attribute?
  • What kind of thing should the IMG ID point to?

Here are some answers from @pvangay: What action is required? — not sure I understand this question What class should bear an IMG ID attribute? — I would think BioSample? What kind of thing should the IMG ID point to? — there are some redirects that take place here. based on a changesheet i helped with recently, the ID is provided in the slot but it’s ultimately used (by kitware I believe) in this url: identifiers.org/id — which then gets redirected to the proper IMG URL.
Thank you @pvangay for your help!

sujaypatil96 commented 1 year ago

Linked issue: https://github.com/linkml/linkml/issues/938

turbomam commented 1 year ago

@mslarae13 said probably links to IMG biosmaple identifiers

The point here is that IMG identifiers shouldn't go in a catch-all slot, but rather a qualified/attributes slot.

See https://data.dev.microbiomedata.org/details/sample/gold:Gb0126432

which links to https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=3300042765

It looks like that IMG page is about the results of assembling and taxon-calling

There's an NMDC link!

NMDC ID | nmdc:mga0jx8k09

What patterns does GOLD use for linking biosmaples to results?

ssarrafan commented 1 year ago

@turbomam Any update on this issue? Can this issue be closed today or by Tuesday?

ssarrafan commented 1 year ago

Discussed at squad meeting and moving to the backlog.

turbomam commented 1 year ago

@mslarae13 I have created a multivalued but otherwise under-specified img_identifiers slot for class Biosample . I am also migrating alternative_identifiers with prefixes of 'img.taxon' into the img_identifiers slot in https://github.com/microbiomedata/nmdc-schema/blob/issue-486-data-to-7-0/util/migrate_7.py

@ssarrafan what can you and I do to ensure that the right level of detail is provided by the requesting party at the time of issue creation?