DUFMech LinkML schema

FamilyRecord

A source-derived family projection; SEEDED is not scientific review.

Field	Range	Cardinality	Description
id	string	Required	`^Pfam:PF[0-9]{5}$`
pfam_id	string	Required	`^PF[0-9]{5}$`
name	string	Required
short_name	string	Required
interpro_id	string	Optional	`^InterPro:IPR[0-9]{6}$`
seed_status	SeedStatus	Required
characterization_status	CharacterizationStatus	Required
curation_status	CurationStatus	Required
review_id	string	Optional	Retained completed record report; required with matching content and history for REVIEWED. `^(reports/yaml_record_review/[A-Za-z0-9_.-]+[.]md\|reviews/structured/[A-Za-z0-9][A-Za-z0-9._-]{0,159}/review[.]yaml)$`
curation_history	string	Optional	Stable directory containing canonical append-only history for this family. `^history/records/PF[0-9]{5}$`
curation_events	CurationEvent	Optional	Read-only index derived from validated canonical history sidecars, never an authoring surface.
description	string	Optional	Imported source description, not a verified functional assertion.
source_url	uri	Required
counters	FamilyCounters	Optional
provenance	SnapshotProvenance	Required
score_provenance	SnapshotProvenance	Optional
assertions	FunctionalAssertion	Optional
discussions	Discussion	Optional
datasets	Dataset	Optional
cross_corpus_links	CrossCorpusLink	Optional

Human-owned overlay. Imported identity and counters cannot be overridden.

Field	Range	Cardinality	Description
pfam_id	string	Required	`^PF[0-9]{5}$`
curation_status	CurationStatus	Required
review_id	string	Optional	`^(reports/yaml_record_review/[A-Za-z0-9_.-]+[.]md\|reviews/structured/[A-Za-z0-9][A-Za-z0-9._-]{0,159}/review[.]yaml)$`
curation_history	string	Optional	`^history/records/PF[0-9]{5}$`
assertions	FunctionalAssertion	Optional
discussions	Discussion	Optional
datasets	Dataset	Optional
cross_corpus_links	CrossCorpusLink	Optional

Generated record-level view of a canonical sidecar event; the referenced history record is authoritative.

Field	Range	Cardinality	Description
timestamp	string	Required	Preserve the canonical UTC timestamp spelling and precision through model serialization. `^20[0-9]{2}-`
curator	string	Required
action	string	Required
outcome	string	Required
summary	string	Required
history_record	string	Required	`^history/records/PF[0-9]{5}/[A-Za-z0-9_.-]+[.]ya?ml$`
event_index	integer	Required
llm_assisted	boolean	Required

Field	Range	Cardinality
proteins	integer	Optional
matches	integer	Optional
proteomes	integer	Optional
taxa	integer	Optional
structures	integer	Optional
alphafold_models	integer	Optional
domain_architectures	integer	Optional

Field	Range	Cardinality	Description
snapshot_id	string	Required
path	string	Required	`^data/worklists/[A-Za-z0-9_-]+[.]json$`
sha256	string	Required	`^[a-f0-9]{64}$`
generated_at	string	Required	`^\d{4}-\d{2}-\d{2}T.*(Z\|[+-]\d{2}:\d{2})$`
source_url	uri	Optional	Upstream URL when the snapshot is acquired rather than locally derived.

Scoped experimental or computational claim, not implied by a DUF name.

Field	Range	Cardinality	Description
assertion_id	string	Required	`^[A-Za-z0-9_-]+$`
statement	string	Required
evidence_kind	EvidenceKind	Required
scope	string	Required	Exact family/subfamily/protein scope and limits of generalization.
evidence	ClaimEvidence	Required

A primary-source quotation retained locally for an independently checkable claim.

Field	Range	Cardinality	Description
reference	string	Required	`^(PMID:[0-9]+\|doi:10[.][0-9]{4,9}/\S+\|https://\S+)$`
source_url	uri	Required
snippet	string	Required
explanation	string	Required
cache_path	string	Required	`^evidence/[A-Za-z0-9_./-]+[.]txt$`
cache_sha256	string	Required	`^[a-f0-9]{64}$`

SeedStatus: UNKNOWN_CANDIDATE, KNOWN_HISTORICAL_DUF, EX_DUF, FALSE_POSITIVE_TEXT_HIT
CharacterizationStatus: UNSCORED, UNKNOWN_CANDIDATE, KNOWN_HISTORICAL_DUF, PARTIALLY_CHARACTERIZED
CurationStatus: SEEDED, IN_PROGRESS, REVIEWED
EvidenceKind: EXPERIMENTAL, COMPUTATIONAL, CONTEXTUAL