Add new slot `derived_from` by cthoyt · Pull Request #548 · mapping-commons/sssom

cthoyt · 2026-05-23T07:11:26Z

Resolves #537

This PR adds a new field derived_from that enables mapping inference (e.g., via chaining, inversion) to refer back to the mappings from which it was derived.

This was motivated by needs from the NFDI use case, and also would enable nearly full subsumption of the SeMRA data model by the SSSOM data model.

It's been a few weeks since I posted the issue outlining this proposal and got some feedback on slack, so I thought it was time to make a concrete contribution.

docs/ have been added/updated if necessary (added inference.md)
make test has been run locally
tests have been added/updated (if applicable)
CHANGELOG.md has been updated.

If you are proposing a change to the SSSOM metadata model, you must

provide a full, working and valid example in examples/
provide a link to the related GitHub issue in the see_also field of the linkml model
provide a link to a valid example in the see_also field of the linkml model
update the "Model changes across versions" (in src/docs/spec-models.md) accordingly
run SSSOM-Py test suite against the updated model

Implementations

gouttegd

Mostly looks good to me, but before this can be merged, either ts4nfdi/mapping-sameness-identifier#2 must be resolved or the PR must be amended to remove the bit about the appropriate CURIE/URI prefix for encoding MSIs as CURIEs being “left to the curators”.

cthoyt · 2026-05-24T13:12:51Z

@gouttegd thanks for the feedback. I agree that the introduction of MSIs here is problematic because of current unresolved discussions about MSI, so opted to remove references to it in the description.

I also switched to using example.com dummy URI prefixes in the examples

gouttegd

Looks good to me.

cthoyt · 2026-05-25T07:58:22Z

@matentzn ready for your final review

matentzn

Agree in principle with all this, but some quick fixes and RFCs

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

cthoyt · 2026-05-26T08:42:34Z

@matentzn @gouttegd ready for re-review

cthoyt · 2026-05-26T08:49:08Z

sorry nico, I deleted a comment about fixing the word CURIEs in the text that was resolved already but seemed to be hanging for some reason (github bug?)

gouttegd

A few last details, but otherwise still good.

matentzn

Some nits but basically done

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

matentzn

Great work! Thank you!

cthoyt marked this pull request as ready for review May 23, 2026 07:28

cthoyt requested review from gouttegd and matentzn and removed request for gouttegd May 23, 2026 07:51

cthoyt changed the title ~~Add derived from~~ Add new slot derived_from May 23, 2026

gouttegd reviewed May 23, 2026

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Comment thread examples/schema/derived_from.sssom.tsv

gouttegd mentioned this pull request May 23, 2026

Add support for derived_from gouttegd/sssom-java#19

Merged

Add derived_from field

4e5d541

cthoyt force-pushed the add-derived-from branch from 812e09a to 4e5d541 Compare May 24, 2026 12:48

cthoyt added 8 commits May 24, 2026 14:52

Fix descriptions of mappings

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Fix spurious whitespace

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Update derived_from.sssom.tsv

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Remove text about how to encode CURIE/URI prefix

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Remove recommendation to use MSI in description

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Update sssom_schema.yaml

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Update inference.md

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Use example.org dummy URI

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Update inference.md

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gouttegd reviewed May 24, 2026

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Update sssom_schema.yaml

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gouttegd previously approved these changes May 25, 2026

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cthoyt enabled auto-merge (squash) May 25, 2026 07:57

matentzn reviewed May 25, 2026

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Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

cthoyt dismissed gouttegd’s stale review via 780e106 May 25, 2026 17:29

cthoyt and others added 2 commits May 25, 2026 19:29

Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Update src/sssom_schema/schema/sssom_schema.yaml

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

cthoyt requested a review from gouttegd May 26, 2026 08:42

cthoyt added 2 commits May 26, 2026 10:47

Update inference.md

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Update inference.md

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mapping-commons deleted a comment from matentzn May 26, 2026

cthoyt added 2 commits May 26, 2026 10:49

Update inference.md

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Update inference.md

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gouttegd requested changes May 26, 2026

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Updates based on Damien's comments

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cthoyt requested a review from gouttegd May 26, 2026 09:54

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cthoyt enabled auto-merge (squash) May 26, 2026 10:12

matentzn requested changes May 26, 2026

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Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

cthoyt dismissed gouttegd’s stale review via 2d9a45f May 26, 2026 13:12

cthoyt and others added 6 commits May 26, 2026 15:12

Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Update src/docs/inference.md

788319d

Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Update cas CURIEs and labels

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Reformat

78cd6c2

Update src/docs/inference.md

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Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

cthoyt requested review from gouttegd and matentzn May 26, 2026 13:16

matentzn approved these changes May 26, 2026

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gouttegd approved these changes May 26, 2026

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cthoyt merged commit f087f5e into master May 26, 2026
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cthoyt deleted the add-derived-from branch May 26, 2026 13:25

This was referenced May 28, 2026

Trace how one mapping was derived from a( set of o)nther? #91

Closed

Distinguish core mappings from metadata and introduce core_mapping_id #361

Closed

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cthoyt commented May 23, 2026 •

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