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An evolving semantic profile

This is a proposed composition architecture, not a final project ontology or an approved set of mappings. Individual resource versions, scientific definitions, rights and compatibility still need review. The project should compose established community semantics rather than replace them.

Proposed composition: I-ADOPT variable structure connects biological, environmental and observation resources; explicit relations connect space, time and units; provenance accompanies reviewed harmonization recipes.

Provisional semantic composition, not an implemented universal ontology. Figure source.

Complementary responsibilities

Variable structure: I-ADOPT describes property, object of interest, optional matrix/context and constraints. It does not supply every component concept or all units, methods and observation metadata.

Biological entities and attributes: NCBITaxon, PCO, OBA/PATO, PO and UBERON provide different taxonomic, group, attribute and anatomical resources. Preserve their identifiers and definitions; no blanket equivalence between their classes is proposed.

Environmental context: ENVO and SWEET address overlapping but distinct environmental needs. Their assessed coverage does not imply automatic alignments.

Observation model: OBOE, SOSA/SSN and BCO offer different observation/sampling structures. They should be compared against actual source records and intended uses.

Relationships and quantitative context: RO can supply specifically defined relations; GeoSPARQL, OWL-Time and QUDT/UO contribute space, time and units. Relations, classes and quantity kinds must not be silently interchanged.

Provenance and execution: PROV-O can record derivation. Versioned recipes must separately state and justify scientific operations with QA and applicable human review.

Domain overlays

Overlay Candidate resources Boundary
Biodiversity Darwin Core, Humboldt, TCS Exchange, inventories and taxonomic concepts remain distinct
Food/agriculture AgrO, Crop Ontology, MIAPPE/PPEO, FoodOn No validated food-security outcome implied
Genomics MIxS, GO, SO, ChEBI Sequence/sample context is not ecological abundance
Traits OBA, PATO, TO, VT, ETS Trait, variable and measurement remain distinct
Interactions RO, GloBI, SFWO Asserted interactions retain participants, context and source evidence

Food and water tracks continue to use shared immutable resources and independent reviewed assumptions. This profile does not enable the undefined third track or promote a domain rule into the shared core.

The diagnostic recommended_portfolio.json is a coverage heuristic for human inspection. It does not implement this architecture, approve a mapping or select one semantic system to replace the others.

Inventory and limits · Review process · Pipeline integration