Format reference
Glossary
Every term the specification defines, in one table, with the section it comes from and the page that reads it in depth. Then the registry terms and the legal value sets.
Definition
The WWD 0.1 draft defines its terms in a terminology section and in the normative sections that introduce them, and it fixes a Core property registry in which every term carries a quantity kind, a canonical unit, a value shape and a causal class. This page lists every defined term with its definition, the section it is defined in, and the page on this site that reads it in depth, followed by the registry terms and the closed vocabularies the format states.
A WWD term has one meaning across the manifest, the design document and the results document. Section 2 of the draft carries the terminology list. The remaining terms are introduced by the sections that make them normative, and the section column below points at the one that does.
A term naming a measurable characteristic sits in the Core property registry instead, where it fixes a quantity kind, a canonical unit, a value shape and a causal class. Those terms are in the second table. The closed vocabularies, the legal sets a value may be drawn from, follow both.
Terms
Alphabetical. Definition, defining section, and the page that reads the term in depth.
| Term | Definition | Section | Read in depth |
|---|---|---|---|
| Acceptance criterion | A requirement whose satisfaction contributes to realization disposition. | 2 | acceptance-criteria |
| Assembly | A component that contains or positions other components. | 2 | interfaces |
| Assumed provenance | An explicit modeling or authoring assumption without direct evidence. | 2 | as-built |
| Backing | The mechanism by which a field's value is obtained. | 2 | fields |
| Binding | The association among a property, field, domain, frame, and component or region. | 2 | fields |
| Causal role | Whether a quantity was determined by the producer or by the living system; one of control, response, context, or derived. | 2, 7.8 | causal-roles |
| Component | An identified designed living article or assembly described by WWD. | 2 | wwd-file-format |
| Composition | An ordered mapping from identified constituents to nonnegative fractions, each stated with unit 1. | 12.5 | fields |
| Conformance class | A named set of sections a package or implementation claims against, claimed by class and version. | 22 | conformance |
| Connection | A declared join naming exactly two ports, both of which must resolve. | 14.7 | interfaces |
| Context | A quantity observed but not chosen by the producer; a covariate. | 2, 7.8 | causal-roles |
| Control | A quantity the producer sets by a stated means. | 2, 7.8 | causal-roles |
| Decision rule | The stated procedure by which a sample statistic is compared with a criterion limit; one of point_estimate, test, confidence_bound or tolerance_interval. | 15.3 | acceptance-criteria |
| Derived quantity | A field, dimension, state value or result whose causal role is derived, which must declare the inputs it was computed from and the rule that computed it. | 7.12 | causal-roles |
| Design document | The manifest-designated JSON document containing the WWD Core data model. | 2 | wwd-file-format |
| Design rule | A named, deterministic assertion over values in the package, carrying an identifier, an assertion, declared inputs and a severity of error or warning. | 7.14 | dfm |
| Designed provenance | Declared intent, target, nominal value, or prescribed state. | 2 | as-built |
| Director | The unit vector d of a uniaxial alignment value, nematic so that d and -d are exactly equivalent. | 12.3 | fields |
| Disposition | The lot outcome derived from the applicable criterion results and policy, never stored as an unexplained independent fact. | 16, 16.1 | acceptance-criteria |
| Draft package | A package that declares itself incomplete by setting draft to true in the manifest, a declaration that must not be represented in the design document. | 3.5 | wwd-file-format |
| Extension | Namespaced semantics outside WWD Core, identified by a versioned URI. | 2 | conformance |
| External asset | A logical package asset whose bytes are obtained through one or more external URIs and verified by content integrity. | 2 | geometry |
| Field | A function assigning a value to each point in a declared spatial-temporal domain. | 2 | fields |
| Fixture | A component that carries the apparatus a measurement is read from, declared as a component rather than as a note on a method. | 14.6 | interfaces |
| Frame | An identified coordinate system with origin, ordered axes, handedness, units, and transforms. | 2, 5.1 | geometry |
| Inferred provenance | A value estimated from other evidence by a stated method. | 2 | as-built |
| Interface | A declared boundary or connection through which mechanical load, electrical signals, or fluid may pass. | 2, 14.1 | interfaces |
| Internal asset | A byte sequence embedded in the package and listed in the manifest. | 2 | geometry |
| Library | A document declaring reusable parts, components, interfaces, assay methods and protocol fragments, each with an identifier stable across every design that uses it. | 7.13 | wwd-file-format |
| Manifest | The required wwd/manifest.json binding document that identifies package contents, relationships, versions, extensions, and integrity metadata. | 2, 3.2 | wwd-file-format |
| Measured provenance | A value obtained from an identified observation or assay. | 2 | as-built |
| Measured result | An as-built observation or statistic linked to exactly one acceptance criterion. | 2, 16 | as-built |
| Model | A solver-neutral statement of physical behavior, parameters, initial conditions, and boundary conditions. | 2, 18.2 | - |
| Named dimension | A declared dimension independent of the bounding box, identifying its geometric targets, nominal quantity, and tolerance or permitted interval. | 5.4 | geometry |
| Opaque asset | An asset a rewriter is directed to preserve despite not understanding its semantics. | 2 | geometry |
| Order parameter | The scalar S of a uniaxial alignment value, lying in the closed interval from zero to one, where zero is isotropic orientation and one is perfect alignment with the director. | 12.3 | fields |
| Package | The complete ZIP byte sequence carrying a WWD manifest and zero or more embedded assets. | 2, 3.1 | wwd-file-format |
| Port | A named point on a part that a connection may attach to; every declared interface of a component is a port of that component. | 14.7 | interfaces |
| Process deviation | A difference between a control as designed and the same control as measured, distinguishing a departure in execution from a change in design. | 2 | as-built |
| Property | A scientific characteristic with fixed meaning, quantity kind, and value shape. | 2, 7.9 | fields |
| Protocol | An ordered sequence of steps, each of which imposes stated controls on a stated target over a stated interval. | 7.11 | causal-roles |
| Provenance activity | A process occurring over time that uses or generates entities. | 2, 17 | provenance |
| Provenance agent | A person, organization, or software agent bearing responsibility. | 2, 17 | provenance |
| Provenance entity | A physical, digital, or conceptual thing with fixed aspects. | 2, 17 | provenance |
| Realization | An identified physical specimen, unit, batch, or lot made against a design revision. | 2, 16 | provenance |
| Region | An identified subset of component space, geometry, topology, or membership. | 2, 7.3 | geometry |
| Required extension | An extension without which the producer declares correct processing impossible. | 2, 19 | conformance |
| Requirement | An as-designed, testable condition on a component, region, interface, field, state, or performance measurand. | 2, 7.6 | acceptance-criteria |
| Response | A quantity the living system determines, targetable and measurable and never directly settable. | 2, 7.8 | causal-roles |
| Revision | A design revision, which must identify its immediate predecessor when one exists and must distinguish editorial republication from semantic revision. | 4.2 | as-built |
| Run | An identified execution of a model by a particular solver configuration. | 2, 18.3 | - |
| Sampling plan | The part of a criterion declaring sample size, sampling unit, source population or lot, selection method, stratification, replacement policy, and whether testing is destructive. | 15.2, 15.6 | acceptance-criteria |
| Scalar-or-field slot | One property location whose value may use quantity-string constant syntax or a field object without changing the surrounding model. | 2, 8 | fields |
| Simulated provenance | A value generated computationally from a model run. | 2 | as-built |
| Simulation result | An output generated by a run and therefore having simulated provenance. | 2, 18.4 | - |
| Uncertainty | A statement attached to a value identifying its kind, standard deviation, standard uncertainty, relative uncertainty, confidence interval, tolerance interval or a referenced uncertainty field, and carrying the numbers that kind requires. | 9 | acceptance-criteria |
| Used extension | Any extension present, whether required or optional. | 2, 19 | conformance |
| Yield | A statement of how many tested units met a named criterion, which must identify that criterion and must agree with the sample size reported by the corresponding measurement. | 15.6, 16.1 | acceptance-criteria |
A term outside this table is not defined by WWD 0.1. Biological identity, unit syntax, genetic construct semantics and provenance graph vocabulary are delegated to NCBI Taxonomy, the Cell Ontology, UBERON, Cellosaurus, ChEBI, UDUNITS-2, SBOL 3 and PROV-O, and WWD does not redefine what those name.
Core property registry terms
62 terms, each fixing a quantity kind, a canonical unit and a causal class. Adding a term is additive; redefining one is forbidden.
A registry term carries its causal class with it, so a package cannot declare cell density
a response or twitch force a control. By class: control 27, response 26, context 8, derived 1.
| Term | Quantity kind | Unit | Causal class | Definition |
|---|---|---|---|---|
| wwd:active_electrode_fraction | fraction | 1 | response | Fraction of electrodes meeting a stated activity threshold. |
| wwd:anchor_spacing | length | mm | control | Distance between the mechanical anchors a tissue develops tension against. |
| wwd:burst_duration | event_duration | s | response | Duration of a single-electrode burst under the stated detection settings. |
| wwd:burst_rate | event_rate | 1/min | response | Rate of single-electrode bursts, averaged over the declared analysis population. |
| wwd:capillary_density | areal_density | 1/mm2 | response | Vessel count per unit cross-sectional area. |
| wwd:cell_alignment | order_parameter | 1 | response | Degree of cell-body alignment, expressed as for wwd:fiber_alignment. |
| wwd:coating_areal_density | areal_mass_density | ug/cm2 | control | Mass of adhesion coating applied per unit substrate area, such as laminin or fibronectin. |
| wwd:compaction_ratio | ratio | 1 | response | Final dimension as a fraction of the as-cast dimension after cell-driven matrix remodelling. |
| wwd:conduction_velocity | velocity | cm/s | response | Propagation speed of an excitation wave across the construct. |
| wwd:contraction_frequency | frequency | Hz | response | Spontaneous contraction rate. |
| wwd:cross_sectional_area | area | mm2 | response | Area of the load-bearing cross-section, perpendicular to the axis along which force is developed and reported. |
| wwd:culture_co2_fraction | fraction | 1 | control | Volume fraction of carbon dioxide in the incubator or vessel headspace. |
| wwd:culture_oxygen_fraction | fraction | 1 | control | Volume fraction of oxygen in the incubator or vessel headspace. |
| wwd:culture_temperature | temperature | degC | control | Incubation temperature during culture. |
| wwd:days_in_vitro | time | d | context | Days elapsed since plating or seeding, the conventional developmental clock for cultures. |
| wwd:differentiation_batch | categorical | 1 | context | Identifier of the independent differentiation run a population came from. |
| wwd:donor_id | categorical | 1 | context | Pseudonymous donor identifier. MUST NOT carry direct personal identifiers. |
| wwd:ecm_stiffness | modulus | kPa | control | Elastic modulus of the extracellular matrix the cells are embedded in or plated on, as prepared. |
| wwd:electrode_count | count | 1 | control | Number of electrodes in the array serving one sampling unit. |
| wwd:electrode_diameter | length | mm | control | Diameter of one electrode's exposed contact area. |
| wwd:electrode_impedance | impedance | kohm | context | Electrode impedance magnitude at a stated frequency and in a stated electrolyte. |
| wwd:electrode_pitch | length | mm | control | Centre-to-centre spacing of adjacent electrodes in an array. |
| wwd:fatigue_retention | fraction | 1 | response | Fraction of initial force retained after a stated fatigue protocol. |
| wwd:fiber_alignment | order_parameter | 1 | response | Degree of fiber alignment expressed as a director plus an order parameter S in [0,1]. |
| wwd:half_relaxation_time | signal_duration | ms | response | Interval from peak twitch force to half of that peak during relaxation. |
| wwd:matrix_composition | categorical | 1 | control | Identity of the matrix formulation, by reference to a protocol or a ChEBI/vendor identifier. |
| wwd:matrix_concentration | mass_concentration | mg/mL | control | Total mass of matrix solids per unit volume of the cast mixture, before compaction. |
| wwd:matrix_formulation | composition | 1 | control | Proportions of the identified constituents of the matrix, as nonnegative fractions summing to one. |
| wwd:mean_firing_rate | frequency | Hz | response | Mean spike rate across analysed electrodes. |
| wwd:mechanical_preload | force | uN | control | Static tension applied to a tissue before functional measurement. |
| wwd:medium_formulation | categorical | 1 | control | Identity of the culture medium formulation, by reference to a protocol or vendor catalogue identifier. |
| wwd:microbial_growth | categorical | 1 | response | Outcome of a sterility test: growth or no growth, under a stated medium, temperature and incubation period. |
| wwd:mycoplasma | categorical | 1 | response | Outcome of a mycoplasma test under a stated detection method. |
| wwd:network_burst_duration | event_duration | s | response | Duration of a network-wide synchronous burst, from the first to the last spike of the burst under the stated detection settings. |
| wwd:network_burst_participation | fraction | 1 | response | Fraction of electrodes taking part in a network burst. |
| wwd:network_burst_rate | event_rate | 1/min | response | Rate of network-wide synchronous bursts. |
| wwd:oxygen_tension | pressure | kPa | control | Partial pressure of oxygen in the culture environment. |
| wwd:passage_number | count | 1 | context | Number of passages a population has undergone on receipt. |
| wwd:passive_tension | force | uN | response | Static tension a tissue develops against its anchors at rest, before stimulation. |
| wwd:peak_twitch_force | force | uN | response | Peak force of a single twitch contraction under a stated stimulation protocol. |
| wwd:photostimulation_irradiance | irradiance | mW/mm2 | control | Optical power per unit area delivered at the tissue surface. |
| wwd:photostimulation_wavelength | wavelength | nm | control | Peak wavelength of light delivered for optogenetic stimulation. |
| wwd:pillar_stiffness | spring_constant | uN/um | control | Lateral bending stiffness of a compliant post used to anchor a tissue and to read out its force from deflection. |
| wwd:population_doublings | count | 1 | context | Cumulative population doublings a population has undergone. |
| wwd:print_nozzle_temperature | temperature | degC | control | Extrusion nozzle temperature during bioprinting. |
| wwd:purity | fraction | 1 | response | Fraction of cells expressing the stated identity marker set. |
| wwd:reagent_lot | categorical | 1 | context | Lot identifier of a medium component, matrix, coating or supplement, as supplied. |
| wwd:recovery_duration | elapsed_time | h | control | Time a component is held under stated conditions after unpacking, before acceptance measurement. |
| wwd:seeding_density_areal | areal_density | cells/mm2 | control | Cell count per unit area of substrate at the moment of plating. |
| wwd:seeding_density_volumetric | number_density | cells/mL | control | Cell count per unit volume of a cast or cell-laden gel at the moment of casting. |
| wwd:specific_force | stress | kPa | derived | Active force normalised by the cross-sectional area that generated it. |
| wwd:spontaneous_beat_rate | frequency | Hz | response | Spontaneous beat rate of a cardiac construct. |
| wwd:stimulation_amplitude | electric_field_strength | V/cm | control | Applied field strength during electrical stimulation. |
| wwd:stimulation_duty_cycle | fraction | 1 | control | Fraction of the stimulation period during which the stimulus is on. |
| wwd:stimulation_frequency | frequency | Hz | control | Pulse repetition rate during electrical stimulation. |
| wwd:stimulation_pulse_width | signal_duration | ms | control | Duration of one stimulation pulse. |
| wwd:substrate_modulus | modulus | kPa | control | Elastic modulus of the non-living substrate or scaffold body the cells are plated on or cast against, as prepared. |
| wwd:tetanic_force | force | uN | response | Peak force under fused tetanic stimulation. |
| wwd:time_to_peak_force | signal_duration | ms | response | Interval from stimulus onset to peak twitch force. |
| wwd:transit_duration | elapsed_time | h | context | Time elapsed between despatch and unpacking. |
| wwd:unloaded_shortening | ratio | 1 | response | Fractional shortening of an unloaded construct during contraction. |
| wwd:viability | fraction | 1 | response | Fraction of cells scored viable by a stated assay. |
The property registry in full, with domains and literature references
Closed vocabularies
The legal sets a reader looking up a term usually wants next.
| Vocabulary | Section | Status | Values |
|---|---|---|---|
| provenance | 7.7 | closed | designed, simulated, measured, inferred, assumed |
| causal_role | 7.8 | closed | control, response, context, derived |
| uncertainty_kind | 13.2 | closed | none, stddev, standard_uncertainty, relative, confidence_interval, tolerance_interval, field_ref |
| modality | 14 | closed | chemical, electrical, fluidic, informational, mechanical, optical, thermal |
| interface_role | 14 | open | mechanical: anchor, attachment_loop, bearing_surface, bonded_face, clamp_zone, load_boundary, tendon_end | electrical: combined, ground, recording, reference, stimulation | fluidic: inlet, outlet, perfusion_channel, port, reservoir, sterile_barrier | optical: combined, illumination, imaging_access, optical_readout, photostimulation |
| commercial_derivative_rights | 13.1 | closed | permitted, prohibited, service_only, requires_license, unknown |
| result_status | 16 | closed | pass, fail, marginal, not_evaluated |
| conformance_class | 22 | closed | WWD-Package-Core, WWD-Design-Core, WWD-Field-Evaluator, WWD-As-Built, WWD-Simulation, WWD-Manufacturing-Ready |
A closed vocabulary refuses an unknown value. interface_role is closed per
modality where a worked case exists and open for chemical, informational and thermal, where
0.1 has none. The registry file carries all 46 vocabularies:
causal_role, provenance, component_kind, biological_role, derivation, differentiation_method, use_restriction, custody, commercial_derivative_rights, material_role, region_kind, shipping_state, sampling_unit, sampling_selection, uncertainty_kind, interpolation, domain_kind, out_of_domain, backing, stimulation_waveform, fluidic_flow_direction, modality, interface_kind, interface_role, statistic, comparator, criticality, decision_rule_kind, tests_axis, result_status, realization_scheme, asset_role, prov_entity_kind, prov_activity_kind, prov_agent_kind, prov_relation, protocol_step_kind, rule_severity, tensor_kind, order_basis, conformance_class, port_kind, port_compatibility, connection_kind, population_of, quantity_kind.
Continue
Where each group of terms is read in depth.
- The WWD file format. Package, manifest, design document, results document.
- Property fields. Field, backing, binding, scalar-or-field slot, director and order parameter.
- Causal roles. Control, response, context, derived, protocol and derived quantities.
- Acceptance criteria. Requirement, criterion, sampling plan, decision rule, disposition and yield.
- As-built. The five provenance classes, the realization and the revision.
- Provenance. Entities, activities, agents and the material chain a package carries.
- Interfaces. Interface, port, connection, fixture and assembly.
- Geometry and payloads. Frame, region, named dimension, internal, external and opaque assets.
- Design rules. The shipped rules and producer-authored rules.
- Conformance. The six classes, extensions and refusal behaviour.
- The Core registries. Properties, assay methods and every closed vocabulary.
- The WWD 0.1 draft specification. All normative sections with anchors.