Provenance

NCBI Taxonomy for source taxon, Cell Ontology for each declared cell type, UBERON for anatomical origin, Cellosaurus with RRID for a named established cell line, ChEBI for small molecules and medium components, and SBOL 3 for genetic constructs. A living component MUST identify source taxon using an NCBITaxon IRI and MUST identify each declared cell type using a CL IRI when an applicable CL term exists. A package MUST declare each ontology source by name, authoritative URI, and version or release, and a consumer MUST NOT silently substitute a different ontology release.

A named established cell line MUST use a Cellosaurus accession, SHOULD also be expressed as an RRID of the form RRID:CVCL_..., and the package MUST pin the Cellosaurus release used for resolution. The schema carries these as cell_line.accession, cell_line.rrid and cell_line.cellosaurus_release, with the accession matching CVCL_ followed by four or more upper-case alphanumerics. A primary, donor-derived or novel line absent from Cellosaurus MUST use CL plus NCBITaxon and MUST identify the derivation source and provenance. neurontile-asbuilt.wwd records the line the lot was built from as a context observation, wwd:source_line with value CVCL_1E52.

Passage number and population doublings SHOULD be recorded when scientifically applicable. biology.passage_number is a quantity on the population. The Core registry carries wwd:passage_number as a count in unit 1 with causal class context, defined as the number of passages a population has undergone on receipt, with a domain of 0 to 200. wwd:population_doublings is a separate term: a passage is an operation, a doubling is a quantity of proliferation, and the Hayflick limit is stated in doublings. Passage is a context quantity, observed and not chosen by the producer.

The design rule DFM-008 reads biology.passage_number together with derivation. A primary population at or past the failure threshold is reported as an ERROR stating that the cells are past the usual replicative limit, with the remedy to use an earlier passage or switch to an immortalized or iPSC-derived source with a renewable bank. At the warning threshold the finding is that primary cells at that passage may show reduced fusion and force, with the remedy to qualify the lot at this passage before committing a run. A DFM finding is advisory with respect to conformance and MUST NOT be reported as a conformance error.

DFM-012, at WARNING severity, reporting that the population declares no licensing block and that commercial derivative rights are undeclared. The remedy in the reference validator is to add biology[].licensing with commercial_derivative_rights, and the rule records that unknown is an honest answer while silence is not. Section 13.1 states the same rule as a normative reading obligation: silence is not permission, and a consumer MUST NOT infer any right from the absence of a licensing declaration. unknown is a conforming value and MUST NOT be treated as equivalent to permission.

Every declared biological population MUST declare custody as one of producer_supplied, customer_supplied or third_party_supplied. A population declared customer_supplied MUST identify the agreement it is held under, and a producer that names no such agreement is asserting a defence it cannot identify, so a conforming validator MUST reject the package. The reference validator reports that as DFM-014 at ERROR severity. Where custody is customer_supplied and a custody_ref is named, DFM-012 does not run on that population and the validator emits an INFO finding that the work is a service on customer material.

The realization. Every realization MUST have an identifier, MUST declare its identifier scheme and MUST reference the exact component design revision realized. The Core schemes are local, vendor.lot, gs1.gtin, gs1.lot, isbt128.din and isbt128.coi. A GTIN identifies a product type and MUST NOT alone identify a specific realization. WWD does not define these schemes and MUST NOT redefine their syntax or semantics, and a consumer MUST treat a scheme-qualified identifier as opaque unless it implements that scheme. A fuller reading of the provenance classes carried on values is at /standard/as-built.

WWD provenance MUST be representable as a directed graph of entities, activities and agents, each node with a stable identifier and type, and each edge declaring relation, from and to. The eight Core relations map one to one onto PROV-O. Provenance derivation MUST be acyclic, and acyclicity applies to time as well as to edges: an activity MUST NOT end before it starts, an activity MUST NOT consume an entity before the activity that produced it has run, and a realization MUST NOT be dated before the activities in its own lineage. A graph MUST support splits and merges, and a producer MUST NOT model biological genealogy as a single chain when pooling or splitting occurred. Master Cell Bank to Working Cell Bank to production lot lineage SHOULD be represented with distinct entities and activities.