Coordinate Provenance¶
A coordinate is a spatial interpretation of locality evidence. It may be reported directly with a sample, resolved from an explicit named site, or withheld because the source supports only a region. Bijux Pollenomics records which of those paths produced—or refused—a point.
This matters because every marker is visually exact. Without provenance, a regional study extent and a source-published excavation coordinate would look equally precise on a map.
Current Evidence Posture¶
The cross-species map-readiness review currently reports 234 direct coordinate-backed entries, two indirectly geocoded entries, 21 unresolved entries, and seven entries refused from mapping. These are readiness units in the governed species/site review, not a count of all recovered samples: many samples can share a reviewed locality, and samples without defensible linkage must not inherit it.
The asymmetry across species is material. Horse accounts for 207 of the direct entries, goat for 27, while several other species currently have no direct coordinate-backed entry. The public collection should expose that unevenness rather than let the strongest species imply equal spatial resolution for all animal evidence.
From Locality To Mapping Posture¶
flowchart TD
A[Reviewed sample locality] --> B{Source supplies coordinates?}
B -->|yes| C[Preserve source pair and locator]
B -->|no| D{One explicit named site?}
D -->|yes| E[Named-site resolution with method]
D -->|no| F{Region, transect, or multiple sites?}
F -->|yes| G[Refuse point mapping]
F -->|no| H[Keep geography unresolved]
C --> I[Coordinate provenance record]
E --> I
I --> J{Basis and linkage complete?}
J -->|yes| K[mappable_point]
J -->|no| H
G --> L[Non-point context]
H --> LA region centroid is not a compromise point. It is a different geographic claim and remains refused from point publication. Likewise, a source that names multiple caves or a transregional dispersal route cannot be represented by one marker until sample-to-site evidence separates the component locations.
Point eligibility is conjunctive: identity, locality linkage, coordinate basis, mapping posture, and product-specific rules must all pass. Confidence cannot compensate for a missing link earlier in the chain.
Confidence Is Not Decimal Precision¶
| Confidence | Coordinate basis | Public interpretation |
|---|---|---|
exact |
direct published coordinates or an explicit archive pair | source-backed point at the reported resolution |
approximate |
one explicit named place resolved through a documented method | cautious named-site point; not a source-supplied pair |
inferred |
indirect derivation | retained for non-public context, not point publication |
withheld |
region-only, aggregate, or unresolved geography | no public point |
unknown |
basis has not been normalized | no claim of coordinate precision |
exact describes provenance, not archaeological certainty to an arbitrary
number of decimal places. approximate is allowed only when the named place is
explicit and the resolution method remains visible. A mapping posture of
mappable_point is still required for either confidence class to publish.
The display should preserve that distinction. An approximate named-site resolution needs a visibly different interpretation from a source-published pair even if both use the same marker geometry. Decimal formatting must not suggest more precision than the source or resolution method supports.
Spatial Precision Has Several Components¶
A single confidence label cannot describe every spatial limitation:
| Component | Governing question |
|---|---|
| subject linkage | does this coordinate belong to the sample, a shared site, a project, or another object? |
| coordinate basis | was the pair reported, resolved from a name, derived, representative, or substituted? |
| source precision | what spatial resolution and numeric precision did the source actually provide? |
| resolution uncertainty | could the named-place or feature match select another location? |
| representation | does the product show a point, polygon, aggregate, or withheld geometry? |
| boundary sensitivity | could coordinate or boundary uncertainty change scope or threshold membership? |
The defensible spatial claim is bounded by all six. A source-reported pair may still be project-owned; an exact arithmetic transform may preserve a broadly located observation; an approximate point can remain useful without becoming an exact excavation coordinate.
Decimal Places Are Not An Uncertainty Model¶
Coordinate formatting describes numeric representation, not positional accuracy. Extra decimals can be introduced by reference-system conversion, centroid calculation, or serialization without adding source evidence.
A quantitative spatial analysis uses an uncertainty envelope only when its basis is governed—for example, a reported accuracy, source precision, feature geometry, or reviewed resolution radius. Otherwise it retains a qualitative precision class and refuses calculations that require a numeric error bound.
| Available support | Permitted uncertainty treatment |
|---|---|
| source supplies accuracy or uncertainty | retain the value, unit, confidence meaning, and locator |
| governed polygon or feature geometry | use that geometry under its versioned authority |
| reviewed named-place resolution radius | use the declared method and radius as qualified uncertainty |
| only rounded or highly precise decimals | retain representation; do not infer metres of accuracy |
| region-only locality | use region or non-point context; do not manufacture a point envelope |
Threshold and containment results must state whether plausible uncertainty can change the classification. When no defensible envelope exists, the correct posture is qualitative or withheld, not zero uncertainty.
Point Geometry Is Not The Observation¶
A point is a representation chosen for a product. The underlying observation may be a specimen, core, archaeological site, registry feature, field visit, or resolved place name. Those units cannot be merged merely because each has a latitude and longitude.
| Point owner | What the pair locates | Common overreading |
|---|---|---|
| sample | source-backed or reviewed sample locality | exact excavation position when only a site anchor is known |
| pollen sequence | sampling or core location as supplied by its source | uniform temporal coverage across sequences |
| archaeological site | site or registry feature | a dated event or direct biological observation |
| density cell | an aggregate spatial unit | one site at the cell centroid |
| field observation | one recorded visit or sample event | representative coverage of the surrounding lake or region |
Distance and containment operate on the represented geometry; scientific interpretation operates on the observation and its role. Both identities must remain available.
The Coordinate Record¶
Each animal coordinate-provenance row preserves:
- project accession, species, and site label;
- original and resolved place text;
- source artifact path and locator;
- coordinate basis and mapping posture;
- latitude and longitude as source-preserving text;
- resolution method and gazetteer or curated anchor;
- confidence class and rationale;
- paper or supplement linkage;
- associated chronology and interpretation notes;
- an explicit support-gap note when point publication is refused.
For samples whose own supplementary rows contain coordinates, the sample lineage supplies the coordinate basis directly. For broader project leads, coordinate provenance remains a separate reviewed record so a project-level anchor cannot silently become sample-level geography.
Coordinate Claim Identity¶
The numeric pair is an attribute of a spatial claim, not its identifier. The claim remains addressable through the governed subject, reported locality, basis, method, source locator, precision, and revision. Two equal pairs can therefore represent different evidence, while a reference-system conversion can produce a different pair for the same governed claim.
| Change | Database treatment |
|---|---|
| formatting or exact CRS conversion | new representation linked to the same spatial claim |
| corrected axis order or source transcription | corrected claim with explicit predecessor relation |
| new source-backed coordinate replaces a named-site resolution | stronger evidence claim; preserve the earlier curated claim |
| locality ownership changes | reevaluate whether the coordinate still belongs to the governed subject |
| point becomes withheld | retain the spatial evidence and publish a non-point or exclusion state |
This model prevents geometry history from disappearing when the current map shows only the accepted representation.
Coordinate Reuse Contract¶
A downstream export that retains latitude and longitude but drops their basis has converted reviewed evidence into unexplained geometry. Reuse should retain:
| Required field | Question it preserves |
|---|---|
| governing sample or site ID | Which observation owns this point? |
| original and resolved place text | What place was reported and what was interpreted? |
| source artifact and locator | Where is the supporting statement or pair? |
| coordinate basis and method | Was the point supplied, curated, or resolved? |
| confidence and mapping posture | May it appear as a point, and with what qualification? |
| spatial precision or caveat | How narrowly may distance or containment be interpreted? |
| product and admission decision | Why is the point visible in this scope? |
Coordinate reference conversion and decimal formatting may change representation, but they must not change basis, confidence, or supported precision. A transformed pair remains the same governed spatial claim only when its lineage to the original pair is retained.
Axis, Range, And Reference-System Contract¶
Coordinate serialization has two conventions that must not be confused:
| Surface | Order |
|---|---|
| named record fields and human-readable tables | latitude, then longitude |
| GeoJSON coordinate arrays | longitude, then latitude |
The normalized animal pair is accepted only when both values are present,
latitude lies within -90..90, and longitude lies within -180..180. The
source text is retained beside the numeric representation so parsing and
rounding remain inspectable.
Reference-system conversion is a separate lineage event. For example, the SVAR collector transforms source geometry from EPSG:3006 to EPSG:4326 before publication. That operation changes coordinate representation, not lake identity, source geometry ownership, or sampling suitability. A reusable transformation therefore retains source CRS, target CRS, method, source geometry identity, and any rounding applied.
flowchart LR
Source["source pair or geometry<br/>source CRS"] --> Validate["axis and range validation"]
Validate --> Transform["declared CRS transformation"]
Transform --> Record["named latitude / longitude"]
Record --> GeoJSON["GeoJSON longitude, latitude"]
Source --> Lineage["basis, source text, and geometry identity"]
Lineage --> GeoJSONSpatial Relations Are Derived Claims¶
A distance, containment result, or nearest-neighbour label is not stored truth about either endpoint. It is a derived claim whose lineage includes both coordinates and the operation applied to them:
flowchart LR
Left["endpoint A: identity, basis, precision"] --> Relation["distance or containment rule"]
Right["endpoint B: identity, basis, precision"] --> Relation
Rule["CRS, method, and threshold"] --> Relation
Relation --> Result{"supported result?"}
Result -->|yes| Qualified["qualified spatial relation"]
Result -->|boundary-sensitive| Review["threshold-sensitive review"]
Result -->|no| Refusal["relation withheld"]The result cannot be more precise than its weakest endpoint. A 20 km band around a registry representative point and an approximate named-site point is a qualified proximity test, not an exact statement about the physical distance between a coring location and a specimen. When coordinate uncertainty could change threshold membership, the result is boundary-sensitive rather than simply inside or outside.
Every reusable spatial relation should retain:
- both governing endpoint identities;
- each coordinate basis, confidence, and supported precision;
- the coordinate reference system and distance or containment method;
- the threshold, band, or polygon snapshot used; and
- whether uncertainty can change the classification.
Recomputing that relation after either endpoint changes is required. Copying a previous distance into a revised product would preserve a number while losing the claim that made it meaningful.
Spatial Analysis Needs A Relation Packet¶
Before classifying two records as near, inside, outside, or nearest, retain:
| Relation member | Required evidence |
|---|---|
| endpoint identities | typed sample, site, lake, boundary, or field-observation keys |
| endpoint geometries | coordinate or geometry claims with basis, CRS, precision, and revision |
| scientific roles | direct evidence, context, framing, decision support, or field observation |
| operation | distance metric, containment predicate, boundary snapshot, threshold, and tie behavior |
| uncertainty result | whether plausible endpoint or boundary uncertainty can change the classification |
| interpretation ceiling | the exact spatial statement supported without claiming time overlap or causation |
flowchart TD
Geometry["numeric geometry available"] --> Ownership{"endpoint ownership known?"}
Ownership -->|no| Refuse["withhold spatial relation"]
Ownership -->|yes| Precision{"basis and precision compatible?"}
Precision -->|no| Refuse
Precision -->|yes| Boundary{"uncertainty crosses threshold?"}
Boundary -->|yes| Sensitive["boundary-sensitive result"]
Boundary -->|no| Supported["qualified spatial result"]This packet prevents a technically correct distance calculation from becoming an unsupported scientific association. Spatial compatibility is only one input to a cross-domain comparison; temporal and evidence-role compatibility remain independent requirements.
Classify Coordinate Changes¶
| Change | Scientific interpretation |
|---|---|
| formatting or numeric type only | representation change if numeric meaning is identical |
| axis-order correction | geometry correction; recompute containment, distance, and membership |
| declared CRS transformation | representation change only when the full transform lineage is retained |
| new source-backed pair replaces geocoding | evidence-strength and geometry change |
| site anchor changes after locality review | locality-linked geometry change; reassess admission |
| precision or confidence becomes weaker | interpretation change even if the numeric pair is unchanged |
An unchanged marker is not proof of an unchanged spatial claim. Basis, confidence, locality ownership, and boundary snapshot can change the meaning or eligibility of the same pair.
Geometry Admission And Relation Admission Differ¶
A point may be defensible for locating an object yet unfit for a particular distance, containment, or association claim. The geometry decision governs the endpoint; the relation decision governs an operation over two endpoints.
| Decision | Required packet | Result |
|---|---|---|
| geometry admission | subject, locality owner, pair, CRS, basis, method, precision, and evidence locator | allowed representation of one object |
| containment admission | geometry packet plus boundary identity, snapshot, and spatial predicate | qualified membership in one geography |
| distance admission | two geometry packets plus distance method and uncertainty posture | qualified numeric relation |
| association admission | admitted spatial relation plus independent temporal and evidence-role support | bounded cross-domain claim |
Thus “has a point” is not a transferable permission. Each downstream spatial operation names its endpoints, method, evidence requirements, and refusal conditions.
Why Points Are Withheld¶
Common refusal conditions include:
- only a country, basin, region, or cultural area is supported;
- one recovered row still aggregates multiple named sites;
- the paper describes a transect or dispersal extent rather than a sample site;
- a site name is present but the sample-to-site linkage is unresolved;
- an apparent coordinate lacks its source locator or resolution rationale.
Withholding does not delete the evidence. The region or named places remain in the curation and review surfaces, where they can support broader context and identify the missing source work needed for a future point.
Spatial representations by support¶
| Supported claim | Defensible representation |
|---|---|
| source-backed sample or site coordinate | point, with basis and confidence available |
| one explicit place resolved approximately | qualified point when product rules allow it |
| region, basin, country, or transect | polygon, aggregate, label, or non-point context |
| multiple unresolved candidate sites | review surface, never one synthesized point |
| no defensible geography | explicit exclusion or unresolved count |
Read A Distance Carefully¶
Distance is derived from geometry, so its usefulness is bounded by both endpoints. An exact lake centroid and an approximate named-site point produce an approximate distance relation. A region-only sample has no defensible point distance even if a centroid is technically available. Ranking and proximity views should carry endpoint identity, basis, precision, distance method, and the threshold or band used.
Auditing A Mapped Sample¶
The species-owned record is
data/adna/species/<species-slug>/normalized/coordinate_provenance.json.
Compare its sample and locality linkage with sample_sites.json, then inspect
the cross-species review surfaces:
data/adna/governance/coordinate_caveat_surface.jsongroups direct, place-resolved, and still-weak geography;data/adna/governance/cross_species_map_readiness.jsonreports publication readiness across animal species;data/adna/governance/unresolved_site_ledger.jsonandoverbroad_site_ledger.jsonexpose geography that cannot support a point.
Read locality evidence when the underlying place claim is in question, and point publication rules for the full admission boundary.