Interoperability

CSAG preserves scientific argument structure and exposes mappings to adjacent standards through its export formats.

Export fidelity

Format	Contract	Suitable for agent handoff
JSON	Lossless canonical artifact	Yes
RO-Crate (Research Object Crate)	Lossless bundle: byte-identical copies of the included files, each with a SHA-256 hash and byte count	Yes
JSON-LD (JSON for Linking Data) and RDF (Resource Description Framework) Turtle	Lossy semantic projection of CSAG identifiers and links	No; use for linked-data tooling
GraphML and TSV (tab-separated values)	Lossy analysis view with only the fields needed for graph or tabular analysis	No

Export commands print the fidelity level. A receiving agent validates the canonical JSON, or verifies the RO-Crate file hashes and then validates the included paper_extraction.json.

Provenance

ExtractionActivity, generated_by, derived_from, created_on, and created_by map to PROV-O (the W3C Provenance Ontology) and PAV (Provenance, Authoring and Versioning) patterns. Keep the source manuscript, schema version, validator version, and extraction parameters with each artifact.

CSAG field	Adjacent standard	Mapping note
ExtractionActivity	PROV-O prov:Activity	One extraction, validation, review, or export run.
Execution	PROV-O prov:Activity or workflow run record	A run that generated evidence, tested assertions, or produced artifacts.
created_on	PAV pav:createdOn	Timestamp for object creation.
created_by	PAV pav:createdBy	Person, service, or tool responsible for the record.
generated_by	PROV-O prov:wasGeneratedBy	Links records to an extraction activity.
derived_from	PROV-O prov:wasDerivedFrom	Links records to upstream CSAG objects or source records.

Evidence and entities

Evidence categories can be aligned with ECO (Evidence and Conclusion Ontology) terms when a curator has enough detail. Entity records can carry Biolink-compatible categories and external CURIEs (compact URIs) in xrefs or ontology_annotations.

CSAG field	Adjacent standard	Mapping note
EvidenceItem.evidence_type	ECO evidence classes	Use ECO only when the manuscript supports the specific evidence class.
EvidenceLink.polarity	SEPIO (Scientific Evidence and Provenance Information Ontology) evidence assertion relation	Keep support and refute semantics on the link, not on the evidence item.
Entity.entity_category	Biolink Model category	Map broad categories such as gene, organism, disease, or chemical to Biolink classes.
Entity.xrefs	OBO (Open Biological and Biomedical Ontology) Foundry and domain database identifiers	Store CURIEs or resolvable URIs for external database cross-references.
OntologyAnnotation	OBO, Biolink, or ECO term mapping	Records term ID, label, match type, and optional evidence code.
EntityMention	BioC or PubTator-style mention row	Keep mention offsets and normalized IDs as optional supplementary tables.

Entity normalization documents the default biomedical entity-normalization layer and the worked supplement under supplementary/entity-normalization/.

Citations and claims

Reference objects can represent CiTO (Citation Typing Ontology) citation relations. CSAG assertions can be exported as findings in the style of the Open Research Knowledge Graph (ORKG) and its reborn articles, and CSAG keeps context, evidence polarity, and inference steps explicit.

CSAG field	Adjacent standard	Mapping note
Reference	CiTO cited entity	Captures cited works used as background or evidence.
EvidenceItem.referenced_works	CiTO citation relation target	Use with EvidenceLink to say how the citation bears on a claim.
Assertion	ORKG reborn finding	Export as a finding only with context and grounding retained.
Context / Condition	ORKG reborn qualifiers	Preserve biological and experimental scope around findings.
InferenceStep	Argumentation reasoning step	Keeps multi-premise reasoning distinct from direct evidence links.
ResearchStateRecord / NextAction	Lab notebook or task-handoff state	Keeps the recorded read and follow-up actions separate from evidence polarity.

Restricted evidence

When source text cannot be redistributed:

1. Keep stable object IDs and source document IDs.
2. Keep section labels and page numbers when redistribution permits.
3. Replace TextSpan.exact_text with a redacted snippet or omit it.
4. Preserve offsets only when the source document is available to the reviewer.
5. Keep validation and quality reports so downstream users can audit structure without receiving protected source text.

RO-Crate packaging

csag export --format ro-crate packages paper_extraction.json with the validation, quality, and lint reports, the Markdown files, and the article JSON and section audit sidecars from the same directory, plus a matching entity-normalization supplement, when those files exist. The crate metadata records the CSAG schema and validator versions, validation profile, source extraction identifier, extraction and execution activities, and hashes for every copied file.

The exporter includes sidecars by presence and does not apply source-license restrictions. When source text cannot be redistributed, create the crate from a directory that contains only permitted files. The exporter refuses an output directory that is not empty. If a validation, quality, or lint report does not match its recorded input hash, the exporter stops instead of packaging that stale report.