Federation and sagebrain-model

kg-pipeline federates with two different sibling repositories, for two different reasons. See Build and validation for how the SCDM and ontology-crosswalk layers below actually get built.

Partner	Kind	What kg-pipeline links to it	Gate
Sage Common Data Model (SCDM)	Sibling schema, cross-portal Organization/Program/Person	institutionRef/consortiumRef/investigatorRef/contributorRef edges	Program edges: reviewed. Organization edges and Person stubs: not gated (see note below)
MONDO/UBERON crosswalks	Ontology-anchoring for sagebrain-model	Ontology-crosswalk federation edges	Human-reviewed; every shipped row is currently unreviewed
sagebrain-model	Sibling domain ontology	The private assay-metadata layer only — see below	confidence: high rows only (automatic, not reviewed)
governanceDUO	Sibling access-control graph	Nothing asserted directly — see "The D9 join" below	N/A — the join is structural, not a mapping

A Program edge requires a human-reviewed crosswalk row; an Organization edge mints automatically from a stable registry id; a Person edge is flagged cckp:provisional true instead.

SCDM and the ontology crosswalks

kg-pipeline's own 5 portal classes have no direct entity overlap with sagebrain-model — that overlap is one layer down, handled by the private assay-metadata layer described next.

The private assay-metadata layer

A separate pipeline stage extracts access-controlled per-file annotations and links them into sagebrain-model's own classes, reusing its declared vocabulary rather than inventing new predicates. It applies the MONDO/UBERON crosswalks automatically wherever a row's confidence is high (an exact label match) — no human review, unlike the Program and public ontology-crosswalk links above — and publishes only to a private staging folder (see Publishing and deposit).

The D9 join with governanceDUO

governanceDUO is a sibling access-control graph — who may access what, under which conditions. It owns the gov: namespace and its own closed gov:SynapseEntity shape, which requires Synapse ACL metadata this pipeline doesn't have.

kg-pipeline deliberately does not assert gov:SynapseEntity, even though both graphs land in the same Neptune store: doing so would fail governanceDUO's closed shape and duplicate a fact it already owns (see the D9 alignment plan). The join works anyway — this pipeline's canonical Synapse IRI is the same base governanceDUO and sagebrain-model use, so a shared id needs no shared type.

Where to look next

For	See
The SCDM federation design	scdm_alignment.md
The MONDO/UBERON crosswalk-promotion design	mondo_uberon_federation_promotion.md
Why kg-pipeline doesn't assert gov:SynapseEntity	kg_pipeline_sagebrain_alignment.md