SEPIO evidence links and skill reliance¶

Indicium 2.0.0 corrects two SEPIO bindings before its first package release. The JSON keys stay the same; their RDF predicates change. The LinkML schema defines both bindings, and the packaged JSON-LD context is generated from it.

JSON key	RDF predicate in 2.0.0	Meaning
`supports_claim`	`sepio:0000427` (`is_evidence_line_for`)	Evidence line → the Claim it evaluates
`for_claim`	`indicium:for_claim`	Local evidence-line-to-Claim link
`asserts`	`indicium:asserts`	Downstream skill or consuming resource → a Claim it relies on

Here sepio:, ro: and eco: expand to http://purl.obolibrary.org/obo/SEPIO_, http://purl.obolibrary.org/obo/RO_ and http://purl.obolibrary.org/obo/ECO_. The packaged context marks these underscore-ending bases with @prefix: true for JSON-LD 1.1 expansion.

Why these bindings fit¶

The SEPIO ontology, whose version IRI is the 2023-06-13 release, declares sepio:0000006 (has_evidence_line) as the inverse of sepio:0000427. Its domain is the union of proposition (sepio:0000000) and assertion (sepio:0000001); its range is evidence line (sepio:0000002). Reversing that relation therefore gives an evidence line → proposition or assertion link. Indicium's Evidence already binds to the evidence-line class, and a Claim describes the scientific proposition being evaluated. This selection does not add an OWL equivalence between asb:Claim and either SEPIO class.

The old supports_claim binding, sepio:0000007 (has_supporting_evidence_line), is a subproperty of has_evidence_line and runs in the other direction. sepio:0000376 (evidence_item_for) links an evidence item to an evidence line, so it does not fit an Evidence → Claim edge. sepio:0000440 and sepio:0000441 also run from an assertion toward evidence, rather than from an evidence line toward a Claim.

The old asserts binding, sepio:0000130 (authored_by), concerns the agent that generated information. A skill can rely on a Claim without authoring it. sepio:0000030 (asserts_proposition) requires a SEPIO assertion as its subject, while sepio:0000109 (expresses) describes a document stating a proposition or assertion in its content. Neither captures reliance alone. indicium:asserts consequently has no external equivalence or close mapping. It is a schema-declared extension slot with range Claim; the core model does not introduce a Skill class or attach this slot to Claim.

The regression fixture in tests/fixtures/sepio/ preserves the relevant OWL axioms and lists its source version, SHA-256 and CC BY 3.0 attribution.

Target and evidence direction¶

supports_claim retains its historical name and its LinkML alias for_claim. They refer to the same intended target but remain two independent JSON fields and two distinct RDF predicates. If both are populated, callers should use the same Claim IRI. The generated model does not copy one field into the other or enforce agreement. Neither field alone establishes supporting polarity.

Direction belongs on the evidence line as sepio:0000183, with one of:

Value	Direction
`sepio:0000403`	supporting
`sepio:0000404`	disputing
`sepio:0000405`	inconclusive

For example, a disputing line still identifies the Claim it evaluates:

@prefix asb: <https://w3id.org/asb#> .
@prefix indicium: <https://w3id.org/indicium/> .
@prefix sepio: <http://purl.obolibrary.org/obo/SEPIO_> .

<urn:example:claim> a asb:Claim ;
    asb:context "in vitro" ; asb:subject "A" ;
    asb:qualifier "inhibits" ; asb:relation "inhibits" ; asb:object "B" .
<urn:example:evidence> a sepio:0000002 ;
    sepio:0000427 <urn:example:claim> ;
    sepio:0000183 sepio:0000404 ;
    indicium:quote_exact "A does not inhibit B" .
<urn:example:skill> indicium:asserts <urn:example:claim> .

A SEPIO exporter may additionally emit the inverse claim sepio:0000006 evidence. Only when the evidence direction is known to be supporting may it use claim sepio:0000007 evidence. Do not reverse an old incorrect triple mechanically and infer support from the JSON key's name. An absent direction remains unspecified.

ASB validation annotations¶

ASB's validation bridge already emits sepio:0000183 with the three direction values above, and ro:0002558 → eco:0000501 for automatic assertion evidence. These annotations are unchanged. They are separate from Indicium's Claim lifecycle (claim_status) and ECO evidence classification (eco_code).

@prefix asbval: <https://w3id.org/asb/validation#> .
@prefix sepio: <http://purl.obolibrary.org/obo/SEPIO_> .
@prefix ro: <http://purl.obolibrary.org/obo/RO_> .
@prefix eco: <http://purl.obolibrary.org/obo/ECO_> .

<urn:example:assessment> a asbval:ClaimAssessment ;
    sepio:0000183 sepio:0000403 ;
    ro:0002558 eco:0000501 .

The core LinkML model has no dedicated ASB assessment class or direction slot. Non-closed SHACL permits these external annotations but does not validate their values on assessment nodes. ASB owns that validation contract and its assessment-class alignment to SEPIO's evidence-line domain. Passing Indicium SHACL does not certify an ASB validation record. sepio:0000174 denotes the statement class, not a qualifier property.

https://w3id.org/indicium/context.jsonld does not resolve yet; the URI scheme page says where to load the context from until it does.

Updating consumers¶

Keep JSON keys supports_claim, for_claim and asserts. Refresh embedded context copies from indicium-standard 2.0.0, then regenerate RDF that was expanded with the earlier context. In such old RDF, Evidence → Claim edges using SEPIO_0000007 need SEPIO_0000427, and skill-reliance edges using SEPIO_0000130 need indicium:asserts. Restrict any migration to those known uses: legitimate claim-side support and authorship triples must retain their SEPIO predicates. Records referring to the central context need no key rewrite; their expanded RDF and any cached context still need refreshing.

The packaged context is available without an HTTP request through importlib.resources.files('indicium.schema').joinpath('context.jsonld'). See URI scheme for namespace documentation and instance IDs.