Indicium

A standard for typed scientific claims bound to their evidence.

Quickstart Schema URI scheme

Indicium standardizes one thing: the binding of a scientific claim to typed evidence and to the source that evidence points to, with provenance. A claim minted by any tool that imports Indicium has the same structure as one minted by any other, merges with it, and never travels without its evidence trace.

One source of truth

One LinkML schema generates the pydantic models, JSON Schema, SHACL shapes, the OWL ontology and the JSON-LD context. The supplemental SHACL shapes (constraints LinkML cannot express) are kept by hand beside it.

Reused ontologies

Evidence types come from ECO, citation relations from CiTO, document types from DoCO, IAO and FaBiO, the assertion structure from SEPIO, provenance from PROV-O.

SHACL validation

validate_graph runs the SHACL shapes over any RDF graph and returns the report. Domain packages add their own shapes through the same call.

Reuse axes

Axis	Standard
Evidence type	ECO (Evidence & Conclusion Ontology)
Claim to citation relation	CiTO
Source and document type	DoCO and IAO
Article type	FaBiO
Assertion and evidence structure	SEPIO
Provenance	PROV-O
Claim structure	Bucur et al. 5-slot SuperPattern (K-CAP 2021)

What Indicium defines

Component	What it is
Claim	The 5-slot Bucur SuperPattern (context, subject, qualifier, relation, object) with ECO-typed evidence
Evidence	A typed evidence record grounding a claim
Source	A DoCO/FaBiO-typed document or artefact that an evidence record points to
CitationLink	A CiTO-typed link from a source to a claim
ClaimLink	A CiTO-typed relation between two claims (supports, disputes, refines, ...)
IndiciumDocument	The container that serialises a set of claims, evidence and sources

Install

pip install indicium-standard

The 2.0.0 upload to PyPI is pending. Until pip install indicium-standard finds it, install from the repository:

pip install "git+https://github.com/HolobiomicsLab/indicium"

The distribution is indicium-standard; the import package is indicium

The PyPI name indicium belongs to an unrelated, abandoned key-value-store package that also ships a top-level indicium module. Installing both into one environment clobbers the import. Always depend on indicium-standard.

Quickstart

import rdflib
from indicium import ASB_BASE, validate_graph

claim = f"""
@prefix asb: <{ASB_BASE}> .
<urn:claim:1> a asb:Claim ;
    asb:context "in vitro" ;
    asb:subject "compound A" ;
    asb:qualifier "inhibits" ;
    asb:relation "inhibits growth of" ;
    asb:object "cell line B" .
"""

conforms, report = validate_graph(rdflib.Graph().parse(data=claim, format="turtle"))
print(conforms)  # True

The Quickstart page continues with the typed model and the adapters.

Schema artefacts

Generated from the LinkML source, src/indicium/schema/indicium.yaml:

Artefact	File
JSON Schema	indicium.schema.json
OWL ontology	indicium.owl.ttl
SHACL shapes	indicium.shapes.ttl
JSON-LD context	context.jsonld

The SHACL file holds the generated shapes and the supplemental ones, so running a SHACL processor on it gives the verdict of validate_graph.

The name

Indicium (Latin) is "a sign or mark that points to the truth"; in law, the evidentiary indication. Every claim carries its indicia, the traces that justify believing it.