{ "name": "Seadots project", "abstract": "This is a collection of OGC Blocks for the [SeaDOTs project](http://seadots-project.eu).\nIt defines the indicator model, property relationship schema, and supporting ontologies\nused across the three SeaDOTs Digital Twin demonstrators (Germany, Norway, Sweden).\nSee also: [iliad-apis-features](https://github.com/ogcincubator/iliad-apis-features) for data types and DT processes.\n", "sparqlEndpoint": "http://defs-hosted.opengis.net/fuseki-hosted/query", "modified": "2026-07-31T22:06:53.084332", "tooling": { "bblocks-postprocess": { "commitId": "\"f3952c38e56b44bfa91d3b3ddf5a320e0c4efa8a", "shortCommitId": "\"f3952c", "date": "2026-07-30T14:19:42+00:00\"" } }, "gitRepository": "https://github.com/ogcincubator/bblocks-seadots", "gitHubRepository": "https://github.com/ogcincubator/bblocks-seadots/blob/master/", "baseURL": "https://ogcincubator.github.io/bblocks-seadots/", "viewerURL": "https://ogcincubator.github.io/bblocks-seadots/", "validationReport": "https://ogcincubator.github.io/bblocks-seadots/build/tests/report.html", "validationReportJson": "https://ogcincubator.github.io/bblocks-seadots/build/tests/report.json", "imports": [ "https://opengeospatial.github.io/bblocks/register.json", "https://opengeospatial.github.io/ogcapi-sosa/build/register.json", "https://ogcincubator.github.io/geodcat-ogcapi-records/build/register.json", "https://ogcincubator.github.io/cross-domain-model/build/register.json", "https://ogcincubator.github.io/bblocks-sta/build/register.json", "https://ogcincubator.github.io/bblocks-stac/build/register.json", "https://ogcincubator.github.io/bblocks-openscience/build/register.json", "https://ogcincubator.github.io/bblocks-ogcapi-processes/build/register.json", "https://ogcincubator.github.io/iliad-apis-features/build/register.json" ], "bblocks": [ { "itemIdentifier": "ogc.hosted.seadots.area-of-interest", "name": "Marine Area of Interest", "abstract": "Simple GeoJSON Feature profile for a polygon delimiting a marine area of interest (AOI) used by experiments, monitoring programmes, or impact assessments. The polygon is carried only in the top-level GeoJSON `geometry`; `properties` carries a human-readable `title` and `description`.", "status": "under-development", "dateTimeAddition": "2026-05-19T00:00:00Z", "itemClass": "schema", "register": "ogc-marine-dt-seadots", "version": "0.1", "dateOfLastChange": "2026-07-31", "license": "https://creativecommons.org/licenses/by/4.0/", "tags": [ "AOI", "marine", "OGC Feature", "GeoJSON", "area-of-interest", "German demo", "Swedish demo", "Norwegian demo" ], "authors": [ { "name": "SeaDOTs Marine Data Team", "organization": "SINTEF Ocean (SeaDOTs)" } ], "dependsOn": [], "ldContext": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/area-of-interest/context.jsonld", "shaclRules": [], "standards": [ "https://datatracker.ietf.org/doc/html/rfc7946" ], "maturity": "development", "scope": "dev", "shaclShapes": {}, "schema": { "application/yaml": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/area-of-interest/schema.yaml", "application/json": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/area-of-interest/schema.json" }, "sourceSchema": "https://ogcincubator.github.io/bblocks-seadots/_sources/area-of-interest/schema.yaml", "sourceLdContext": "https://ogcincubator.github.io/bblocks-seadots/_sources/area-of-interest/context.jsonld", "resolvedSchemaProperties": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/area-of-interest/resolvedProperties.json", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/area-of-interest/", "validationPassed": true, "testOutputs": "https://github.com/ogcincubator/bblocks-seadots/blob/master/build/tests/hosted/seadots/area-of-interest/", "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/area-of-interest/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/area-of-interest/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.area-of-interest" } } }, { "itemIdentifier": "ogc.hosted.seadots.benthic-biomass-observations-imr", "name": "IMR Benthic Biomass Observations", "abstract": "GeoJSON FeatureCollection profile for raw IMR / MAREANO Marbunn benthic biomass observation point features across species and cruises. This block preserves individual sample records, while benthic-biomass-density-imr provides the aggregate per-taxon observation derived from those raw features.", "status": "under-development", "dateTimeAddition": "2026-05-26T00:00:00Z", "itemClass": "schema", "register": "ogc-marine-dt-seadots", "version": "0.1", "dateOfLastChange": "2026-07-31", "license": "https://creativecommons.org/licenses/by/4.0/", "tags": [ "IMR", "MAREANO", "Marbunn", "benthic", "raw data", "FeatureCollection", "cruise", "species" ], "authors": [ { "name": "SeaDOTs Marine Data Team", "organization": "SINTEF Ocean (SeaDOTs)" } ], "sources": [ { "title": "MAREANO Marbunn", "link": "https://marbunn-ekstern.hi.no/apps/marbunn/v1/" }, { "title": "Institute of Marine Research (IMR)", "link": "https://www.hi.no/" } ], "dependsOn": [], "ldContext": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/benthic-biomass-observations-imr/context.jsonld", "shaclRules": [], "standards": [ "https://datatracker.ietf.org/doc/html/rfc7946", "http://rs.tdwg.org/dwc/terms/" ], "maturity": "development", "scope": "dev", "shaclShapes": {}, "schema": { "application/yaml": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/benthic-biomass-observations-imr/schema.yaml", "application/json": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/benthic-biomass-observations-imr/schema.json" }, "sourceSchema": "https://ogcincubator.github.io/bblocks-seadots/_sources/benthic-biomass-observations-imr/schema.yaml", "sourceLdContext": "https://ogcincubator.github.io/bblocks-seadots/_sources/benthic-biomass-observations-imr/context.jsonld", "resolvedSchemaProperties": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/benthic-biomass-observations-imr/resolvedProperties.json", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/benthic-biomass-observations-imr/", "validationPassed": true, "testOutputs": "https://github.com/ogcincubator/bblocks-seadots/blob/master/build/tests/hosted/seadots/benthic-biomass-observations-imr/", "transforms": [ { "id": "to-benthic-biomass-density-mareano", "description": "Converts the raw IMR / MAREANO Marbunn observation FeatureCollection into the aggregate `benthic-biomass-density-mareano` observation profile. The source weights are converted to point densities in kg m-2 using explicit per-gear sampled-area assumptions, then spatially extrapolated over the AOI with inverse distance weighting (IDW). The assumptions are recorded in output provenance.\n", "type": "python", "ref": "https://ogcincubator.github.io/bblocks-seadots/_sources/benthic-biomass-observations-imr/transforms/to_benthic_biomass_density_mareano.py", "inputs": { "mediaTypes": [ { "mimeType": "application/json", "label": "JSON", "defaultExtension": "json" }, { "mimeType": "application/geo+json", "label": "GeoJSON", "defaultExtension": "geojson" } ] }, "outputs": { "mediaTypes": [ { "mimeType": "application/json", "label": "JSON", "defaultExtension": "json" }, { "mimeType": "application/geo+json", "label": "GeoJSON", "defaultExtension": "geojson" } ], "profiles": [ "bblocks://ogc.hosted.seadots.benthic-biomass-density-mareano" ] }, "code": "#!/usr/bin/env python3\n\"\"\"\nTransform IMR / MAREANO Marbunn raw observation points into the\n`benthic-biomass-density-mareano` aggregate observation shape.\n\nThe source FeatureCollection contains catch-sample weights in kilograms. The\ntarget block expects density in kg m-2, so this transformer first applies\nexplicit per-gear sampled-area assumptions to estimate point densities, then\nextrapolates each taxon over the AOI with inverse distance weighting (IDW).\n\nOGC Building Blocks Python transform compatibility:\n* when executed by the postprocessor, `input_data` is provided and this file\n assigns `output_data`;\n* when run standalone, it reads JSON from stdin and writes JSON to stdout.\n\"\"\"\nfrom __future__ import annotations\n\nimport datetime as dt\nimport json\nimport math\nimport sys\nfrom collections import defaultdict\nfrom typing import Any\n\n\nOBS_BLOCK = \"bblocks://ogc.hosted.seadots.benthic-biomass-observations-imr\"\nTARGET_BLOCK = \"bblocks://ogc.hosted.seadots.benthic-biomass-density-mareano\"\nTARGET_ID = \"https://example.org/norwegian-ses/benthic-biomass-density-mareano/from-imr-observations\"\n\n# Area assumptions are intentionally conservative and explicit. They are not a\n# replacement for cruise-level swept-area metadata.\nDEFAULT_GEAR_AREAS_M2 = {\n \"Small VV grab\": 0.1,\n \"VVgrab020\": 0.2,\n \"Large VV grab\": 0.25,\n \"Boxcorer\": 0.1,\n \"Bioboks\": 0.1,\n \"Beamtrawl\": 100.0,\n \"RP-sledge\": 50.0,\n \"Videograb\": 0.1,\n}\nFALLBACK_SAMPLE_AREA_M2 = 0.1\nIDW_POWER = 2.0\nIDW_GRID_SIZE = 25\n\n\ndef _as_number(value: Any) -> float | None:\n if isinstance(value, bool):\n return None\n if isinstance(value, (int, float)) and math.isfinite(float(value)):\n return float(value)\n if isinstance(value, str):\n try:\n parsed = float(value)\n except ValueError:\n return None\n return parsed if math.isfinite(parsed) else None\n return None\n\n\ndef _as_string(value: Any) -> str | None:\n if value is None:\n return None\n text = str(value).strip()\n return text or None\n\n\ndef _feature_species(props: dict[str, Any]) -> str | None:\n return (\n _as_string(props.get(\"scientificName\"))\n or _as_string(props.get(\"Scientific name\"))\n or _as_string(props.get(\"species\"))\n or _as_string(props.get(\"sourceSpeciesQuery\"))\n )\n\n\ndef _feature_equipment(props: dict[str, Any]) -> str | None:\n return _as_string(props.get(\"equipment\")) or _as_string(props.get(\"Equipment\"))\n\n\ndef _feature_cruise(props: dict[str, Any]) -> str | None:\n return _as_string(props.get(\"cruise\")) or _as_string(props.get(\"Cruise\"))\n\n\ndef _sample_area_m2(equipment: str | None) -> tuple[float, bool]:\n if equipment in DEFAULT_GEAR_AREAS_M2:\n return DEFAULT_GEAR_AREAS_M2[equipment], False\n return FALLBACK_SAMPLE_AREA_M2, True\n\n\ndef _bbox_polygon(source: dict[str, Any]) -> dict[str, Any]:\n props = source.get(\"properties\") or {}\n aoi = props.get(\"aoi\") or {}\n geometry = aoi.get(\"geometry\")\n if isinstance(geometry, dict) and geometry.get(\"type\") == \"Polygon\":\n return geometry\n\n bbox = source.get(\"bbox\") or aoi.get(\"bbox\")\n if isinstance(bbox, list) and len(bbox) >= 4:\n min_lon, min_lat, max_lon, max_lat = [float(v) for v in bbox[:4]]\n return {\n \"type\": \"Polygon\",\n \"coordinates\": [[\n [min_lon, min_lat],\n [max_lon, min_lat],\n [max_lon, max_lat],\n [min_lon, max_lat],\n [min_lon, min_lat],\n ]],\n }\n\n return {\"type\": \"Polygon\", \"coordinates\": [[[-5.0, 56.0], [33.0, 56.0], [33.0, 82.0], [-5.0, 82.0], [-5.0, 56.0]]]}\n\n\ndef _geometry_bbox(geometry: dict[str, Any]) -> tuple[float, float, float, float]:\n rings = geometry.get(\"coordinates\") or []\n points = []\n for ring in rings:\n if isinstance(ring, list):\n for point in ring:\n if isinstance(point, list) and len(point) >= 2:\n lon = _as_number(point[0])\n lat = _as_number(point[1])\n if lon is not None and lat is not None:\n points.append((lon, lat))\n if not points:\n return (-5.0, 56.0, 33.0, 82.0)\n lons = [p[0] for p in points]\n lats = [p[1] for p in points]\n return (min(lons), min(lats), max(lons), max(lats))\n\n\ndef _feature_xy(feature: dict[str, Any]) -> tuple[float, float] | None:\n geometry = feature.get(\"geometry\") or {}\n if geometry.get(\"type\") != \"Point\":\n return None\n coordinates = geometry.get(\"coordinates\") or []\n if len(coordinates) < 2:\n return None\n lon = _as_number(coordinates[0])\n lat = _as_number(coordinates[1])\n if lon is None or lat is None:\n return None\n return lon, lat\n\n\ndef _grid_points(bounds: tuple[float, float, float, float], size: int) -> list[tuple[float, float]]:\n min_lon, min_lat, max_lon, max_lat = bounds\n if size < 1 or min_lon == max_lon or min_lat == max_lat:\n return [((min_lon + max_lon) / 2, (min_lat + max_lat) / 2)]\n lon_step = (max_lon - min_lon) / size\n lat_step = (max_lat - min_lat) / size\n return [\n (min_lon + (col + 0.5) * lon_step, min_lat + (row + 0.5) * lat_step)\n for row in range(size)\n for col in range(size)\n ]\n\n\ndef _idw_area_mean(\n observations: list[tuple[float, float, float]],\n grid_points: list[tuple[float, float]],\n power: float,\n) -> float:\n if not observations:\n return 0.0\n if len(observations) == 1:\n return observations[0][2]\n\n estimates = []\n for gx, gy in grid_points:\n numerator = 0.0\n denominator = 0.0\n exact = None\n for ox, oy, value in observations:\n distance = math.hypot(gx - ox, gy - oy)\n if distance == 0:\n exact = value\n break\n weight = 1 / (distance ** power)\n numerator += weight * value\n denominator += weight\n estimates.append(exact if exact is not None else numerator / denominator)\n return sum(estimates) / len(estimates)\n\n\ndef _phenomenon_time(source: dict[str, Any], cruises: set[str]) -> str | dict[str, str] | None:\n props = source.get(\"properties\") or {}\n phenomenon_time = props.get(\"phenomenonTime\")\n if isinstance(phenomenon_time, dict) and phenomenon_time.get(\"start\") and phenomenon_time.get(\"end\"):\n return {\"start\": str(phenomenon_time[\"start\"]), \"end\": str(phenomenon_time[\"end\"])}\n if isinstance(phenomenon_time, str) and phenomenon_time:\n return phenomenon_time\n if cruises:\n ordered = sorted(cruises)\n return f\"{ordered[0]}/{ordered[-1]}\"\n return None\n\n\ndef transform(raw_json: str) -> str:\n source = json.loads(raw_json)\n if source.get(\"type\") != \"FeatureCollection\":\n raise ValueError(\"Expected a GeoJSON FeatureCollection from benthic-biomass-observations-imr\")\n\n grouped: dict[str, dict[str, Any]] = defaultdict(lambda: {\n \"weight_kg\": 0.0,\n \"area_m2\": 0.0,\n \"n_samples\": 0,\n \"n_weighted\": 0,\n \"fallback_area_samples\": 0,\n \"equipment\": set(),\n \"cruises\": set(),\n \"depths\": [],\n \"observations\": [],\n })\n all_cruises: set[str] = set()\n all_equipment: set[str] = set()\n ignored_features = 0\n\n for feature in source.get(\"features\") or []:\n if not isinstance(feature, dict):\n ignored_features += 1\n continue\n props = feature.get(\"properties\") or {}\n species = _feature_species(props)\n if not species:\n ignored_features += 1\n continue\n\n row = grouped[species]\n row[\"n_samples\"] += 1\n\n equipment = _feature_equipment(props)\n if equipment:\n row[\"equipment\"].add(equipment)\n all_equipment.add(equipment)\n\n cruise = _feature_cruise(props)\n if cruise:\n row[\"cruises\"].add(cruise)\n all_cruises.add(cruise)\n\n depth = _as_number(props.get(\"Bottom depth\"))\n if depth is not None:\n row[\"depths\"].append(depth)\n\n weight = _as_number(props.get(\"Weight\"))\n if weight is None:\n continue\n xy = _feature_xy(feature)\n area, used_fallback = _sample_area_m2(equipment)\n point_density = weight / area\n row[\"weight_kg\"] += weight\n row[\"area_m2\"] += area\n row[\"n_weighted\"] += 1\n if xy is not None:\n row[\"observations\"].append((xy[0], xy[1], point_density))\n if used_fallback:\n row[\"fallback_area_samples\"] += 1\n\n per_taxon = []\n geometry = _bbox_polygon(source)\n grid_points = _grid_points(_geometry_bbox(geometry), IDW_GRID_SIZE)\n total_weighted_samples = 0\n total_fallback_area_samples = 0\n for species, row in grouped.items():\n density = _idw_area_mean(row[\"observations\"], grid_points, IDW_POWER)\n observed_mean_density = row[\"weight_kg\"] / row[\"area_m2\"] if row[\"area_m2\"] > 0 else 0.0\n total_weighted_samples += int(row[\"n_weighted\"])\n total_fallback_area_samples += int(row[\"fallback_area_samples\"])\n depths = row[\"depths\"]\n per_taxon.append({\n \"scientificName\": species,\n \"density_kg_m2\": round(density, 8),\n \"habitat\": \"unclassified\",\n \"depthBand_m\": (\n f\"{round(min(depths))}-{round(max(depths))}\"\n if depths else \"unknown\"\n ),\n \"nSamples\": int(row[\"n_samples\"]),\n \"observedMeanDensity_kg_m2\": round(observed_mean_density, 8),\n })\n\n per_taxon.sort(key=lambda item: (-item[\"density_kg_m2\"], item[\"scientificName\"]))\n aggregate_density = round(sum(item[\"density_kg_m2\"] for item in per_taxon), 8)\n today = dt.date.today().isoformat()\n source_props = source.get(\"properties\") or {}\n source_prov = source_props.get(\"provenance\") or {}\n\n result = {\n \"id\": TARGET_ID,\n \"type\": \"Feature\",\n \"geometry\": geometry,\n \"properties\": {\n \"type\": \"Dataset\",\n \"title\": \"MAREANO benthic biomass density derived from IMR/Marbunn observations\",\n \"description\": (\n \"Per-taxon benthic biomass density estimate derived from raw IMR / \"\n \"MAREANO Marbunn catch-sample observations by converting catch \"\n \"weights to point densities and extrapolating over the AOI with IDW.\"\n ),\n \"created\": today,\n \"updated\": today,\n \"language\": {\"code\": \"en\"},\n \"license\": \"https://creativecommons.org/licenses/by/4.0/\",\n \"themes\": [{\n \"concepts\": [{\"id\": \"benthic-biomass\", \"label\": \"Benthic biomass density\"}],\n \"scheme\": \"https://id3.seadots.eu/themes\",\n }],\n \"keywords\": [\"MAREANO\", \"Marbunn\", \"IMR\", \"benthic biomass\", \"density\", \"transform\"],\n \"formats\": [{\"mediaType\": \"application/json\"}],\n \"conformsTo\": [\n \"http://www.w3.org/ns/sosa/Observation\",\n \"https://ogcincubator.github.io/geodcat-ogcapi-records/\",\n ],\n \"benthicBiomassDensity\": {\n \"name\": \"MAREANO benthic biomass density from IMR observations\",\n \"description\": \"Aggregate per-taxon density estimate transformed from raw Marbunn observation points using IDW interpolation over the AOI.\",\n \"role\": \"primary baseline\",\n \"source\": source.get(\"id\") or \"bblocks://ogc.hosted.seadots.benthic-biomass-observations-imr\",\n \"format\": \"application/json\",\n \"vocabularyTerm\": \"https://w3id.org/indicators/marine/obs/benthic-biomass-density-mareano\",\n \"observedProperty\": \"https://w3id.org/indicators/marine/obs/benthic-biomass-density-mareano\",\n \"phenomenonTime\": _phenomenon_time(source, all_cruises),\n \"data\": {\n \"units\": \"kg m-2\",\n \"samplePeriod\": _phenomenon_time(source, all_cruises),\n \"samplingProgramme\": \"MAREANO / IMR Marbunn\",\n \"perTaxon\": per_taxon,\n \"aggregateDensity_kg_m2\": aggregate_density,\n \"provenance\": {\n \"values\": \"mixed\",\n \"retrievalApiCall\": (source_props.get(\"source\") or {}).get(\"perSpeciesEndpoint\"),\n \"verifiedOn\": today,\n \"primarySource\": source_props.get(\"source\"),\n \"nearestAuthoritativeSource\": {\n \"url\": \"https://mareano.no/\",\n \"note\": \"Raw observations come from IMR / MAREANO Marbunn catch-sample point features.\",\n },\n \"verificationGap\": (\n \"Source observations provide catch weight in kg. The target block requires kg m-2. \"\n \"This transform first uses per-gear sampled-area assumptions rather than authoritative \"\n \"cruise-level swept-area metadata, then extrapolates point densities with IDW. \"\n \"Ordinary Kriging or Regression-Kriging would be preferable once variograms, \"\n \"environmental covariates and geostatistical dependencies are available.\"\n ),\n \"note\": (\n f\"Transformed {len(source.get('features') or [])} source features into \"\n f\"{len(per_taxon)} per-taxon rows. Ignored {ignored_features} malformed or \"\n f\"unnamed features. IDW grid={IDW_GRID_SIZE}x{IDW_GRID_SIZE}, power={IDW_POWER}, \"\n f\"weighted samples={total_weighted_samples}, samples using fallback area=\"\n f\"{total_fallback_area_samples}. Gear-area assumptions m2: \"\n f\"{json.dumps(DEFAULT_GEAR_AREAS_M2, sort_keys=True)}; fallback=\"\n f\"{FALLBACK_SAMPLE_AREA_M2}. Source fetched_utc=\"\n f\"{source_prov.get('fetched_utc', 'unknown')}.\"\n ),\n },\n },\n },\n },\n \"links\": [\n {\"rel\": \"describedby\", \"href\": TARGET_BLOCK, \"type\": \"application/schema+json\", \"title\": \"MAREANO Benthic Biomass Density Observation bblock\"},\n {\"rel\": \"derivedFrom\", \"href\": OBS_BLOCK, \"type\": \"application/schema+json\", \"title\": \"IMR Benthic Biomass Observations bblock\"},\n {\"rel\": \"cite-as\", \"href\": \"https://mareano.no/\", \"title\": \"MAREANO programme\"},\n {\"rel\": \"cite-as\", \"href\": \"https://www.hi.no/\", \"title\": \"Institute of Marine Research\"},\n ],\n }\n return json.dumps(result, indent=2, ensure_ascii=False)\n\n\ndef main() -> int:\n sys.stdout.write(transform(sys.stdin.read()))\n sys.stdout.write(\"\\n\")\n return 0\n\n\nif \"input_data\" in globals():\n output_data = transform(input_data)\nelif __name__ == \"__main__\":\n raise SystemExit(main())\n" } ], "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/benthic-biomass-observations-imr/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/benthic-biomass-observations-imr/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.benthic-biomass-observations-imr" } } }, { "itemIdentifier": "ogc.hosted.seadots.geoparquet-header", "name": "GeoParquet Header", "abstract": "Generic, reusable CSVW + GeoParquet 1.1 metadata header envelope shape (fileName, source, parquetSchema, geo). Dataset-specific GeoParquet profiles reference this schema via $ref rather than redefining the envelope inline.", "status": "under-development", "dateTimeAddition": "2026-07-31T00:00:00Z", "itemClass": "schema", "register": "ogc-marine-dt-seadots", "version": "0.1", "dateOfLastChange": "2026-07-31", "license": "https://creativecommons.org/licenses/by/4.0/", "tags": [ "geoparquet", "csvw", "schema", "envelope", "seadots" ], "authors": [ { "name": "SeaDOTs Marine Data Team", "organization": "SINTEF Ocean (SeaDOTs)" } ], "sources": [ { "title": "GeoParquet specification", "link": "https://geoparquet.org/" }, { "title": "PROJJSON schema", "link": "https://proj.org/en/stable/schemas/index.html" }, { "title": "CSVW (CSV on the Web)", "link": "https://www.w3.org/TR/tabular-data-primer/" } ], "ldContext": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/geoparquet-header/context.jsonld", "shaclRules": [], "standards": [ "https://geoparquet.org/" ], "maturity": "development", "scope": "dev", "shaclShapes": {}, "schema": { "application/yaml": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/geoparquet-header/schema.yaml", "application/json": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/geoparquet-header/schema.json" }, "sourceSchema": "https://ogcincubator.github.io/bblocks-seadots/_sources/geoparquet-header/schema.yaml", "sourceLdContext": "https://ogcincubator.github.io/bblocks-seadots/_sources/geoparquet-header/context.jsonld", "resolvedSchemaProperties": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/geoparquet-header/resolvedProperties.json", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/geoparquet-header/", "validationPassed": true, "testOutputs": "https://github.com/ogcincubator/bblocks-seadots/blob/master/build/tests/hosted/seadots/geoparquet-header/", "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/geoparquet-header/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/geoparquet-header/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.geoparquet-header" } } }, { "itemIdentifier": "ogc.hosted.seadots.obis-mareano-checklist", "name": "OBIS MAREANO Checklist", "abstract": "Raw OBIS checklist response for selected MAREANO dataset identifiers. The example preserves the OBIS API payload as returned by the checklist endpoint and is used as source material for derived SeaDOTs biomass-density proxy examples.", "status": "under-development", "dateTimeAddition": "2026-05-26T00:00:00Z", "itemClass": "schema", "register": "ogc-marine-dt-seadots", "version": "0.1", "dateOfLastChange": "2026-07-31", "license": "https://creativecommons.org/licenses/by/4.0/", "tags": [ "OBIS", "MAREANO", "checklist", "benthic", "Darwin Core" ], "authors": [ { "name": "SeaDOTs Marine Data Team", "organization": "SINTEF Ocean (SeaDOTs)" } ], "sources": [ { "title": "OBIS checklist API", "link": "https://api.obis.org/v3/checklist" } ], "dependsOn": [], "ldContext": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/obis-mareano-checklist/context.jsonld", "shaclRules": [], "standards": [ "http://rs.tdwg.org/dwc/terms/", "https://api.obis.org/" ], "maturity": "development", "scope": "dev", "shaclShapes": {}, "schema": { "application/yaml": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/obis-mareano-checklist/schema.yaml", "application/json": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/obis-mareano-checklist/schema.json" }, "sourceSchema": "https://ogcincubator.github.io/bblocks-seadots/_sources/obis-mareano-checklist/schema.yaml", "sourceLdContext": "https://ogcincubator.github.io/bblocks-seadots/_sources/obis-mareano-checklist/context.jsonld", "resolvedSchemaProperties": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/obis-mareano-checklist/resolvedProperties.json", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/obis-mareano-checklist/", "validationPassed": true, "testOutputs": "https://github.com/ogcincubator/bblocks-seadots/blob/master/build/tests/hosted/seadots/obis-mareano-checklist/", "transforms": [ { "id": "to-benthic-biomass-density-mareano", "description": "Converts an OBIS checklist or occurrence response for selected MAREANO datasets into a `benthic-biomass-density-mareano` proxy example. The source contains occurrence rows or occurrence record counts, not biomass; the output records normalized occurrence shares in the target density field, carries per-observation outputs when occurrence rows are present, and documents the limitation in provenance.\n", "type": "python", "ref": "https://ogcincubator.github.io/bblocks-seadots/_sources/obis-mareano-checklist/transforms/to_benthic_biomass_density_mareano.py", "inputs": { "mediaTypes": [ { "mimeType": "application/json", "label": "JSON", "defaultExtension": "json" } ] }, "outputs": { "mediaTypes": [ { "mimeType": "application/json", "label": "JSON", "defaultExtension": "json" }, { "mimeType": "application/geo+json", "label": "GeoJSON", "defaultExtension": "geojson" } ], "profiles": [ "bblocks://ogc.hosted.seadots.benthic-biomass-density-mareano" ] }, "code": "#!/usr/bin/env python3\n\"\"\"\nTransform an OBIS checklist or occurrence response into the\n`benthic-biomass-density-mareano` example shape.\n\nOBIS checklist and occurrence rows provide occurrence records, not biomass or\nsampled area. This transformer therefore emits an occurrence-weighted proxy for\n`density_kg_m2` so the result can be carried by the target bblock, and it\nrecords the limitation in provenance. When occurrence rows are provided, the\noutput also carries per-observation output rows.\n\nOGC Building Blocks Python transform compatibility:\n* when `input_data` is provided, assigns `output_data`;\n* when run standalone, reads JSON from stdin and writes JSON to stdout.\n\"\"\"\nfrom __future__ import annotations\n\nimport datetime as dt\nimport json\nimport sys\nfrom typing import Any\n\n\nSOURCE_ENDPOINT = (\n \"https://api.obis.org/v3/checklist?size=10&skip=20&datasetid=\"\n \"d556b9d4-7625-4aa2-894d-441eabae47f7,\"\n \"152259dc-9c20-4c1a-9644-8e4b509d4f73,\"\n \"14fa3c3e-259c-4af9-9314-eee1dc3a119b\"\n)\nOCCURRENCE_ENDPOINT = (\n \"https://api.obis.org/v3/occurrence?size=10&skip=20&datasetid=\"\n \"d556b9d4-7625-4aa2-894d-441eabae47f7,\"\n \"152259dc-9c20-4c1a-9644-8e4b509d4f73,\"\n \"14fa3c3e-259c-4af9-9314-eee1dc3a119b\"\n)\nSOURCE_BLOCK = \"bblocks://ogc.hosted.seadots.obis-mareano-checklist\"\nTARGET_BLOCK = \"bblocks://ogc.hosted.seadots.benthic-biomass-density-mareano\"\nCHECKLIST_TARGET_ID = \"https://example.org/norwegian-ses/benthic-biomass-density-mareano/obis-checklist-proxy\"\nOCCURRENCE_TARGET_ID = \"https://example.org/norwegian-ses/benthic-biomass-density-mareano/obis-occurrence-proxy\"\nOBSERVED_PROPERTY = \"https://w3id.org/indicators/marine/obs/benthic-biomass-density-mareano\"\n\nMAREANO_FOOTPRINT = {\n \"type\": \"Polygon\",\n \"coordinates\": [[\n [-5.0, 56.0],\n [33.0, 56.0],\n [33.0, 82.0],\n [-5.0, 82.0],\n [-5.0, 56.0],\n ]],\n}\n\n\ndef _as_int(value: Any, default: int = 0) -> int:\n if isinstance(value, bool):\n return default\n if isinstance(value, int):\n return value\n if isinstance(value, float):\n return int(value)\n if isinstance(value, str):\n try:\n return int(float(value))\n except ValueError:\n return default\n return default\n\n\ndef _as_float(value: Any) -> float | None:\n if isinstance(value, bool):\n return None\n if isinstance(value, (int, float)):\n return float(value)\n if isinstance(value, str):\n try:\n return float(value)\n except ValueError:\n return None\n return None\n\n\ndef _taxon_name(row: dict[str, Any]) -> str | None:\n value = row.get(\"acceptedNameUsage\") or row.get(\"scientificName\")\n if value is None:\n return None\n text = str(value).strip()\n return text or None\n\n\ndef _aphia_id(row: dict[str, Any]) -> int | None:\n value = row.get(\"aphiaID\") or row.get(\"acceptedNameUsageID\") or row.get(\"taxonID\")\n parsed = _as_int(value, -1)\n return parsed if parsed >= 0 else None\n\n\ndef _is_occurrence_row(row: dict[str, Any]) -> bool:\n return any(key in row for key in (\"occurrenceID\", \"basisOfRecord\", \"decimalLatitude\", \"decimalLongitude\", \"eventDate\"))\n\n\ndef _occurrence_output(row: dict[str, Any], density_proxy: float) -> dict[str, Any]:\n item = {\n \"id\": row.get(\"id\") or row.get(\"occurrenceID\"),\n \"occurrenceID\": row.get(\"occurrenceID\"),\n \"scientificName\": _taxon_name(row),\n \"density_kg_m2\": round(density_proxy, 10),\n \"eventDate\": row.get(\"eventDate\"),\n \"datasetName\": row.get(\"datasetName\"),\n \"samplingProtocol\": row.get(\"samplingProtocol\"),\n }\n aphia_id = _aphia_id(row)\n if aphia_id is not None:\n item[\"aphiaID\"] = aphia_id\n lon = _as_float(row.get(\"decimalLongitude\"))\n lat = _as_float(row.get(\"decimalLatitude\"))\n depth = _as_float(row.get(\"depth\") or row.get(\"minimumDepthInMeters\"))\n if lon is not None:\n item[\"decimalLongitude\"] = lon\n if lat is not None:\n item[\"decimalLatitude\"] = lat\n if depth is not None:\n item[\"depth_m\"] = depth\n return {k: v for k, v in item.items() if v is not None}\n\n\ndef transform(raw_json: str) -> str:\n source = json.loads(raw_json)\n rows = source.get(\"results\")\n if not isinstance(rows, list):\n raise ValueError(\"Expected OBIS checklist JSON with a results array\")\n\n usable_rows = [row for row in rows if isinstance(row, dict) and _taxon_name(row)]\n occurrence_mode = any(_is_occurrence_row(row) for row in usable_rows)\n if occurrence_mode:\n record_total = len(usable_rows)\n else:\n record_total = sum(_as_int(row.get(\"records\")) for row in usable_rows)\n if record_total <= 0:\n record_total = 1\n\n grouped: dict[str, dict[str, Any]] = {}\n observation_outputs = []\n for row in usable_rows:\n records = 1 if occurrence_mode else _as_int(row.get(\"records\"))\n density_proxy = records / record_total\n name = _taxon_name(row)\n if name not in grouped:\n grouped[name] = {\"records\": 0, \"row\": row}\n grouped[name][\"records\"] += records\n if occurrence_mode:\n observation_outputs.append(_occurrence_output(row, density_proxy))\n\n per_taxon = []\n for name, grouped_row in grouped.items():\n row = grouped_row[\"row\"]\n records = grouped_row[\"records\"]\n density_proxy = records / record_total\n item = {\n \"scientificName\": name,\n \"density_kg_m2\": round(density_proxy, 10),\n \"habitat\": \"marine benthic occurrence taxon\" if occurrence_mode else \"marine benthic checklist taxon\",\n \"depthBand_m\": \"occurrence depth varies\" if occurrence_mode else \"unknown\",\n \"nSamples\": records,\n \"obisRecords\": records,\n \"taxonRank\": row.get(\"taxonRank\"),\n }\n aphia_id = _aphia_id(row)\n if aphia_id is not None:\n item[\"aphiaID\"] = aphia_id\n per_taxon.append(item)\n\n per_taxon.sort(key=lambda item: (-item[\"density_kg_m2\"], item[\"scientificName\"]))\n aggregate_density = round(sum(item[\"density_kg_m2\"] for item in per_taxon), 10)\n today = dt.date.today().isoformat()\n\n result = {\n \"id\": OCCURRENCE_TARGET_ID if occurrence_mode else CHECKLIST_TARGET_ID,\n \"type\": \"Feature\",\n \"geometry\": MAREANO_FOOTPRINT,\n \"properties\": {\n \"type\": \"Dataset\",\n \"title\": \"MAREANO benthic biomass density proxy from OBIS occurrence data\" if occurrence_mode else \"MAREANO benthic biomass density proxy from OBIS checklist\",\n \"description\": (\n \"Occurrence-weighted proxy derived from OBIS records for selected \"\n \"MAREANO datasets. OBIS records do not provide biomass, sampled \"\n \"area or station geometry; this output is a schema-compatible proxy, not \"\n \"a physical biomass-density measurement.\"\n ),\n \"created\": today,\n \"updated\": today,\n \"language\": {\"code\": \"en\"},\n \"license\": \"https://creativecommons.org/licenses/by/4.0/\",\n \"themes\": [{\n \"concepts\": [{\"id\": \"benthic-biomass\", \"label\": \"Benthic biomass density\"}],\n \"scheme\": \"https://id3.seadots.eu/themes\",\n }],\n \"keywords\": [\"OBIS\", \"MAREANO\", \"occurrence\", \"benthic biomass\", \"proxy\"],\n \"formats\": [{\"mediaType\": \"application/json\"}],\n \"conformsTo\": [\n \"http://www.w3.org/ns/sosa/Observation\",\n \"https://ogcincubator.github.io/geodcat-ogcapi-records/\",\n ],\n \"benthicBiomassDensity\": {\n \"name\": \"OBIS occurrence proxy for MAREANO benthic biomass density\",\n \"description\": \"Per-taxon normalized OBIS occurrence records carried as a density proxy.\",\n \"role\": \"primary baseline proxy\",\n \"source\": OCCURRENCE_ENDPOINT if occurrence_mode else SOURCE_ENDPOINT,\n \"format\": \"application/json\",\n \"vocabularyTerm\": OBSERVED_PROPERTY,\n \"observedProperty\": OBSERVED_PROPERTY,\n \"phenomenonTime\": \"unknown\",\n \"data\": {\n \"units\": \"dimensionless occurrence share encoded in kg m-2 field\",\n \"samplePeriod\": \"unknown\",\n \"samplingProgramme\": \"OBIS / MAREANO\",\n \"perTaxon\": per_taxon,\n \"aggregateDensity_kg_m2\": aggregate_density,\n \"observationOutputs\": observation_outputs,\n \"provenance\": {\n \"values\": \"mixed\",\n \"retrievalApiCall\": OCCURRENCE_ENDPOINT if occurrence_mode else SOURCE_ENDPOINT,\n \"verifiedOn\": today,\n \"primarySource\": {\n \"name\": \"OBIS checklist API\",\n \"url\": OCCURRENCE_ENDPOINT if occurrence_mode else SOURCE_ENDPOINT,\n },\n \"nearestAuthoritativeSource\": {\n \"url\": \"https://obis.org/\",\n \"note\": \"OBIS occurrence/checklist endpoints for selected MAREANO dataset identifiers.\",\n },\n \"verificationGap\": (\n \"The source OBIS response contains occurrence records or occurrence record counts. \"\n \"It does not contain biomass, sampled area, station effort \"\n \"or physical density measurements. `density_kg_m2` is therefore a normalized \"\n \"occurrence-count proxy for testing target bblock interoperability.\"\n ),\n \"note\": (\n f\"Transformed {len(usable_rows)} OBIS {'occurrence' if occurrence_mode else 'checklist'} rows from a response with \"\n f\"total={source.get('total')} into a MAREANO biomass-density proxy example. \"\n f\"Proxy density is {'occurrence count' if occurrence_mode else 'records'} / \"\n f\"{'number of occurrence rows in this page' if occurrence_mode else 'sum(records in this page)'}; \"\n f\"aggregate={aggregate_density}.\"\n ),\n },\n },\n },\n },\n \"links\": [\n {\"rel\": \"describedby\", \"href\": TARGET_BLOCK, \"type\": \"application/schema+json\", \"title\": \"MAREANO Benthic Biomass Density Observation bblock\"},\n {\"rel\": \"derivedFrom\", \"href\": SOURCE_BLOCK, \"type\": \"application/schema+json\", \"title\": \"OBIS MAREANO Checklist bblock\"},\n {\"rel\": \"cite-as\", \"href\": \"https://obis.org/\", \"title\": \"OBIS\"},\n {\"rel\": \"cite-as\", \"href\": \"https://mareano.no/\", \"title\": \"MAREANO programme\"},\n ],\n }\n return json.dumps(result, indent=2, ensure_ascii=False)\n\n\ndef main() -> int:\n sys.stdout.write(transform(sys.stdin.read()))\n sys.stdout.write(\"\\n\")\n return 0\n\n\nif \"input_data\" in globals():\n output_data = transform(input_data)\nelif __name__ == \"__main__\":\n raise SystemExit(main())\n" } ], "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/obis-mareano-checklist/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/obis-mareano-checklist/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.obis-mareano-checklist" } } }, { "itemIdentifier": "ogc.hosted.seadots.ontology", "name": "Property relationship ontology", "abstract": "This ontology provides classes and properties to model property relationships with magnitude", "status": "under-development", "dateTimeAddition": "2026-04-17T00:00:00Z", "itemClass": "model", "register": "ogc-marine-dt-seadots", "version": "1.0", "dateOfLastChange": "2026-07-31", "dependsOn": [], "tags": [ "seadots", "ontology" ], "highlighted": true, "shaclShapes": { "ogc.hosted.seadots.ontology": [ "https://ogcincubator.github.io/bblocks-seadots/_sources/ontology/rules.shacl" ] }, "ontology": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/ontology/ontology.ttl", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/ontology/", "validationPassed": true, "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/ontology/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/ontology/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.ontology" } } }, { "itemIdentifier": "ogc.hosted.seadots.properties", "name": "Seadots Properties", "abstract": "Defines seadots properties", "status": "under-development", "dateTimeAddition": "2026-04-17T00:00:00Z", "itemClass": "model", "register": "ogc-marine-dt-seadots", "version": "1.0", "dateOfLastChange": "2026-07-31", "dependsOn": [], "tags": [ "seadots", "data model" ], "highlighted": true, "shaclShapes": {}, "ontology": "https://ogcincubator.github.io/bblocks-seadots/build/annotated/hosted/seadots/properties/ontology.ttl", "sourceFiles": "https://ogcincubator.github.io/bblocks-seadots/_sources/properties/", "validationPassed": true, "documentation": { "json-full": { "mediatype": "application/json", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/json-full/hosted/seadots/properties/index.json" }, "markdown": { "mediatype": "text/markdown", "url": "https://ogcincubator.github.io/bblocks-seadots/build/generateddocs/markdown/hosted/seadots/properties/index.md" }, "bblocks-viewer": { "mediatype": "text/html", "url": "https://ogcincubator.github.io/bblocks-seadots/bblock/ogc.hosted.seadots.properties" } } }, { "itemIdentifier": "ogc.hosted.seadots.property-relationship", "name": "Property relationship", "abstract": "Provides a common model for defining property relationships bound to the ontology", "status": "under-development", "dateTimeAddition": 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