Previous value: -"Opt into conservative cross-repo content dedup (default false). On top of the always-on exact-DOI dedup, folds records that are the SAME dataset deposited under different (or no) DOIs — e.g. a Zenodo mirror of a figshare deposit, GEO<->ArrayExpress — into one record, annotating the survivor with the folded copies under mirrors[]. Conservative: a merge needs a shared file checksum OR identical (normalized-title, first-author-surname, year); title-only or partial matches never merge. Intra-page / best-effort only (a mirror on a different page is not collapsed), so a page may return fewer than size items; pagination is unaffected."New value: +"Opt into conservative cross-repo content dedup (default false). On top of the always-on exact-DOI dedup, folds records that are the SAME dataset deposited under different (or no) DOIs — e.g. a Zenodo mirror of a figshare deposit, GEO<->ArrayExpress — into one record, annotating the survivor with the folded copies under mirrors[]. Conservative: a merge needs a shared file checksum OR identical (normalized-title, first-author name, year); title-only or partial matches never merge. Intra-page / best-effort only (a mirror on a different page is not collapsed), so a page may return fewer than size items; pagination is unaffected."

Added value: +false

Added value: +false

Added value: +false

Added value: +false

Added value: +false

Added value: +{
+  "additionalProperties": {
+    "type": "string"
+  },
+  "title": "Errors",
+  "type": "object"
+}

Added value: +{
+  "additionalProperties": {
+    "type": "string"
+  },
+  "title": "Truncated",
+  "type": "object"
+}

Added value: +false

Added value: +{
+  "additionalProperties": {
+    "type": "string"
+  },
+  "title": "Errors",
+  "type": "object"
+}

Added value: +{
+  "additionalProperties": {
+    "type": "string"
+  },
+  "title": "Truncated",
+  "type": "object"
+}

Added value: +1

Added value: +{
+  "items": {
+    "type": "string"
+  },
+  "title": "Unverified",
+  "type": "array"
+}

Previous value: -"When true, probe 5 sources (zenodo, datacite, omics, literature, huggingface) and attach a 'health' field ({status: up|down, latency_ms, detail}) to those entries; the remaining 7 sources get health: null. Default false: returns the static catalog with no network."New value: +"When true, probe 5 sources (zenodo, datacite, omics, literature, huggingface) and attach a 'health' field ({status: up|down, latency_ms, detail}) to those entries; every other source gets health: null. Default false: returns the static catalog with no network."

Previous value: -"Restrict fan-out to these sources (default: all). Available: zenodo, dataone, cellxgene, datacite, dandi, omics, literature, huggingface, omicsdi, openml, pdb, uniprot, gwas"New value: +"Restrict fan-out to these sources (default: all). Available: zenodo, dataone, gbif, cellxgene, datacite, dandi, omics, literature, huggingface, datagov, nasacmr, omicsdi, openml, pdb, uniprot, gwas, biostudies"

Added value: +{
+  "anyOf": [
+    {
+      "type": "number"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Confidence"
+}

Added value: +{
+  "description": "Echo of an ontology-typed search param that was supplied but matched NO term,\nso the query ran WITHOUT that expansion.\n\nDistinct from ``SearchResult.errors``: an entry there means the ontology LOOKUP\nFAILED (HTTP/parse) and the two are mutually exclusive per field. An entry here\nmeans the lookup SUCCEEDED and legitimately returned no match — the common case\nfor a common name the registry does not index (NCBI Taxonomy has no ``yeast``,\n``oak`` or ``cedar``; UBERON has no bare ``root``).\n\nWithout this echo the response for a silently-dropped param is byte-identical to\none where the param was never passed, so the caller cannot tell that the filter\nthey asked for was not applied.",
+  "properties": {
+    "field": {
+      "title": "Field",
+      "type": "string"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "note": {
+      "title": "Note",
+      "type": "string"
+    },
+    "ontology": {
+      "title": "Ontology",
+      "type": "string"
+    }
+  },
+  "required": [
+    "field",
+    "input",
+    "ontology",
+    "note"
+  ],
+  "title": "UnresolvedEntity",
+  "type": "object"
+}

Added value: +{
+  "items": {
+    "$ref": "#/$defs/UnresolvedEntity"
+  },
+  "title": "Unresolved",
+  "type": "array"
+}

Previous value: -"Restrict fan-out to these sources (default: all). Available: zenodo, dataone, cellxgene, datacite, dandi, omics, literature, huggingface, omicsdi, openml, pdb, gwas"New value: +"Restrict fan-out to these sources (default: all). Available: zenodo, dataone, cellxgene, datacite, dandi, omics, literature, huggingface, omicsdi, openml, pdb, uniprot, gwas"

Previous value: -"When true, probe each source's base endpoint and attach a 'health' field ({status: up|down, latency_ms, detail}) to each source. Default false: returns the static catalog with no network."New value: +"When true, probe 5 sources (zenodo, datacite, omics, literature, huggingface) and attach a 'health' field ({status: up|down, latency_ms, detail}) to those entries; the remaining 7 sources get health: null. Default false: returns the static catalog with no network."

Previous value: -[
-  "schema",
-  "preview",
-  "head",
-  "sql"
-]New value: +[
+  "schema",
+  "preview",
+  "head",
+  "sql",
+  "peek"
+]

Added value: +{
+  "description": "When true, attach an RDA-grounded FAIRness assessment under fair{}: a 0–100 overall score plus findable/accessible/interoperable/reusable sub-scores, the count of indicators evaluated, and actionable gaps each naming its RDA FAIR Data Maturity Model indicator id. Pure/local — no network call. Only the machine-evaluable subset is scored (never fabricates what the metadata cannot show).",
+  "type": "boolean"
+}

Previous value: -"Optional export to render onto the result. 'croissant' attaches a file-level Croissant JSON-LD manifest (croissant field); 'ro-crate' attaches a minimal RO-Crate 1.1 manifest (ro_crate field)."New value: +"Optional export to render onto the result. 'croissant' attaches a file-level Croissant JSON-LD manifest (croissant field); 'ro-crate' attaches a minimal RO-Crate 1.1 manifest (ro_crate field); 'provenance' attaches a one-call RO-Crate 1.1 data-availability dossier (provenance field) bundling version-currency, licence+SPDX, FAIR score, retraction status, and the source/DOI/ID chain — it auto-attaches fair{} and trust{} so the dossier is complete in one call (unknown signals are reported as unknown, never as a clean claim)."

Previous value: -[
-  "croissant",
-  "ro-crate"
-]New value: +[
+  "croissant",
+  "ro-crate",
+  "provenance"
+]

Added value: +{
+  "description": "When true, attach trust signals (retraction status via Crossref) to the result under trust{}. One extra Crossref call; only meaningful for DOI-bearing records (a DataCite data DOI Crossref does not register leaves retracted=null = unknown, never a false clean claim).",
+  "type": "boolean"
+}

Added value: +{
+  "description": "When set, attach a licence-compatibility advisory under license_compat{} for an intended use of the record. Supported intents: 'commercial', 'redistribute', 'modify', 'ml-training' (training = a derivative+commercial use, our stated interpretation). The verdict is ALLOW/REVIEW/DENY computed from a bundled choosealicense.com licence matrix keyed on the normalized SPDX id, naming the governing clause — a metadata-derived advisory, NOT legal advice. An unrecognized or absent licence yields REVIEW (never a fabricated ALLOW/DENY); an unknown intent is an error.",
+  "type": "string"
+}

Added value: +{
+  "description": "FAIRness assessment attached on resolve(fair=True). PURE-function output:\na 0–100 overall score plus 0–100 per-dimension sub-scores, grounded in the\nmachine-evaluable subset of the RDA FAIR Data Maturity Model. ``assessed`` is\nthe count of indicators actually evaluated (transparency — we never score what\nthe metadata can't show). ``gaps`` are failed-indicator reasons, each naming its\nRDA indicator id and framed as a metadata-exposure gap, not a value judgement.",
+  "properties": {
+    "accessible": {
+      "title": "Accessible",
+      "type": "integer"
+    },
+    "assessed": {
+      "title": "Assessed",
+      "type": "integer"
+    },
+    "findable": {
+      "title": "Findable",
+      "type": "integer"
+    },
+    "gaps": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Gaps",
+      "type": "array"
+    },
+    "interoperable": {
+      "title": "Interoperable",
+      "type": "integer"
+    },
+    "reusable": {
+      "title": "Reusable",
+      "type": "integer"
+    },
+    "score": {
+      "title": "Score",
+      "type": "integer"
+    }
+  },
+  "required": [
+    "score",
+    "findable",
+    "accessible",
+    "interoperable",
+    "reusable",
+    "assessed"
+  ],
+  "title": "FairAssessment",
+  "type": "object"
+}

Added value: +{
+  "description": "Licence-compatibility advisory attached on resolve(use=<intent>). PURE-function\noutput: an ALLOW / REVIEW / DENY verdict for an intended use of the resolved record,\ncomputed from a bundled licence matrix (choosealicense.com flag vocabulary) keyed on\nthe normalized SPDX id. ``spdx_id`` is None exactly when the licence was unrecognized\nor absent (→ REVIEW, never a fabricated ALLOW/DENY). ``reason`` names the governing\nclause; ``disclaimer`` states this is a metadata-derived advisory, not legal advice.",
+  "properties": {
+    "disclaimer": {
+      "title": "Disclaimer",
+      "type": "string"
+    },
+    "license_raw": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "title": "License Raw"
+    },
+    "reason": {
+      "title": "Reason",
+      "type": "string"
+    },
+    "spdx_id": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "title": "Spdx Id"
+    },
+    "use": {
+      "title": "Use",
+      "type": "string"
+    },
+    "verdict": {
+      "enum": [
+        "ALLOW",
+        "REVIEW",
+        "DENY"
+      ],
+      "title": "Verdict",
+      "type": "string"
+    }
+  },
+  "required": [
+    "use",
+    "verdict",
+    "spdx_id",
+    "license_raw",
+    "reason",
+    "disclaimer"
+  ],
+  "title": "LicenseVerdict",
+  "type": "object"
+}

Added value: +{
+  "description": "A same-dataset copy folded into this record by content dedup (resolve the\nmirror's id to reach the original deposit). Only populated when a search ran\nwith the opt-in ``collapse_mirrors`` flag.",
+  "properties": {
+    "doi": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Doi"
+    },
+    "id": {
+      "title": "Id",
+      "type": "string"
+    },
+    "source": {
+      "title": "Source",
+      "type": "string"
+    }
+  },
+  "required": [
+    "source",
+    "id"
+  ],
+  "title": "Mirror",
+  "type": "object"
+}

Added value: +{
+  "description": "Integrity/provenance signals attached on resolve(trust=True). All nullable:\nNone = not checked or not determinable (e.g. a DOI Crossref doesn't register) —\nNEVER a negative claim. A *found* Crossref work yields definitive booleans.",
+  "properties": {
+    "concern": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Concern"
+    },
+    "retracted": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Retracted"
+    },
+    "retraction_doi": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Retraction Doi"
+    }
+  },
+  "title": "TrustSignals",
+  "type": "object"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/FairAssessment"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/LicenseVerdict"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "items": {
+    "$ref": "#/$defs/Mirror"
+  },
+  "title": "Mirrors",
+  "type": "array"
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Provenance"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/TrustSignals"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "description": "Optional assay/method name. Resolved via EDAM topics (EBI OLS); the query is expanded with the canonical name + exact synonyms (e.g. 'ChIP-seq' also matches 'ChIP-sequencing'/'ChIP-exo'). An unknown term yields no expansion; an OLS failure surfaces in errors. The expansion is echoed in assay_expansion.",
+  "type": "string"
+}

Added value: +{
+  "description": "Optional chemical/compound name. Resolved via ChEBI (EBI OLS); the query is expanded with the canonical name + exact synonyms (e.g. 'caffeine' also matches '1,3,7-trimethylxanthine'), capped to a bounded number of synonyms. An unknown term yields no expansion; an OLS failure surfaces in errors. The expansion is echoed in chemical_expansion.",
+  "type": "string"
+}

Added value: +{
+  "default": false,
+  "description": "Opt into conservative cross-repo content dedup (default false). On top of the always-on exact-DOI dedup, folds records that are the SAME dataset deposited under different (or no) DOIs — e.g. a Zenodo mirror of a figshare deposit, GEO<->ArrayExpress — into one record, annotating the survivor with the folded copies under mirrors[]. Conservative: a merge needs a shared file checksum OR identical (normalized-title, first-author-surname, year); title-only or partial matches never merge. Intra-page / best-effort only (a mirror on a different page is not collapsed), so a page may return fewer than size items; pagination is unaffected.",
+  "type": "boolean"
+}

Added value: +{
+  "description": "Optional disease/phenotype name. Resolved via MeSH (NCBI E-utilities); the query is expanded with the canonical descriptor + entry-term synonyms (e.g. 'breast cancer' also matches 'Breast Neoplasms'). The expansion is echoed in mesh_expansion.",
+  "type": "string"
+}

Added value: +{
+  "default": false,
+  "description": "Opt into diverse multi-query recall expansion: an LLM generates up to a few deliberately-diverse reformulations of your query, each is fanned out across all sources, and the deduped union is re-ranked against your original query — surfacing relevant records a single keyword query would miss. Costs N× the upstream calls (bounded). Requires an LLM endpoint (LLM_API_BASE); with none configured the search runs as a normal single query and notes it in errors['multi_query']. The variants used are echoed in query_expansion. Composes with understand=. NOTE: multi_query=true ALWAYS applies semantic re-ranking of the window internally regardless of rank=; the rank= param has no effect in this mode.",
+  "type": "boolean"
+}

Added value: +{
+  "default": false,
+  "description": "Opt into a whole-search RO-Crate 1.1 Run Crate (default false). Attaches provenance_crate{} — a machine-readable manifest documenting this search: the query, the sources queried, the ontology expansions that fired, the per-source errors (a partial search is disclosed), and per-hit provenance for every result (version-currency, licence + normalized SPDX, FAIR score). Per-hit RETRACTION is omitted — it would need one Crossref call per hit; use per-record resolve(format=provenance) for that. Covers THIS search page only (intra-page; each page of a paginated search gets its own crate).",
+  "type": "boolean"
+}

Previous value: -"Restrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature, huggingface, dataone, omicsdi"New value: +"Restrict fan-out to these sources (default: all). Available: zenodo, dataone, cellxgene, datacite, dandi, omics, literature, huggingface, omicsdi, openml, pdb, gwas"

Added value: +{
+  "description": "Optional tissue/anatomy name. Resolved via UBERON (EBI OLS); the query is expanded with the canonical term + exact synonyms (e.g. 'liver' also matches 'iecur'/'jecur'). The expansion is echoed in tissue_expansion.",
+  "type": "string"
+}

Added value: +{
+  "default": false,
+  "description": "Opt into LLM query understanding: a free-text query is rewritten into a keyword core + structured params (organism/disease/tissue/chemical/assay, kind, year) before fan-out; extracted entities are validated by the same ontology resolvers (a hallucinated entity that doesn't resolve is simply dropped), explicit params you pass always win, and the interpretation is echoed in query_understanding. Requires an LLM endpoint (LLM_API_BASE); with none configured the search runs unchanged and notes it in errors['understand'].",
+  "type": "boolean"
+}

Added value: +{
+  "description": "Echo of EDAM assay-synonym expansion that fired for a search (transparency).",
+  "properties": {
+    "canonical_name": {
+      "title": "Canonical Name",
+      "type": "string"
+    },
+    "edam_id": {
+      "title": "Edam Id",
+      "type": "string"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "synonyms": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Synonyms",
+      "type": "array"
+    }
+  },
+  "required": [
+    "input",
+    "edam_id",
+    "canonical_name",
+    "synonyms"
+  ],
+  "title": "AssayExpansion",
+  "type": "object"
+}

Added value: +{
+  "description": "Echo of ChEBI chemical-synonym expansion that fired for a search (transparency).",
+  "properties": {
+    "canonical_name": {
+      "title": "Canonical Name",
+      "type": "string"
+    },
+    "chebi_id": {
+      "title": "Chebi Id",
+      "type": "string"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "synonyms": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Synonyms",
+      "type": "array"
+    }
+  },
+  "required": [
+    "input",
+    "chebi_id",
+    "canonical_name",
+    "synonyms"
+  ],
+  "title": "ChemicalExpansion",
+  "type": "object"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/FairAssessment"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/LicenseVerdict"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "items": {
+    "$ref": "#/$defs/Mirror"
+  },
+  "title": "Mirrors",
+  "type": "array"
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Provenance"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/TrustSignals"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "description": "FAIRness assessment attached on resolve(fair=True). PURE-function output:\na 0–100 overall score plus 0–100 per-dimension sub-scores, grounded in the\nmachine-evaluable subset of the RDA FAIR Data Maturity Model. ``assessed`` is\nthe count of indicators actually evaluated (transparency — we never score what\nthe metadata can't show). ``gaps`` are failed-indicator reasons, each naming its\nRDA indicator id and framed as a metadata-exposure gap, not a value judgement.",
+  "properties": {
+    "accessible": {
+      "title": "Accessible",
+      "type": "integer"
+    },
+    "assessed": {
+      "title": "Assessed",
+      "type": "integer"
+    },
+    "findable": {
+      "title": "Findable",
+      "type": "integer"
+    },
+    "gaps": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Gaps",
+      "type": "array"
+    },
+    "interoperable": {
+      "title": "Interoperable",
+      "type": "integer"
+    },
+    "reusable": {
+      "title": "Reusable",
+      "type": "integer"
+    },
+    "score": {
+      "title": "Score",
+      "type": "integer"
+    }
+  },
+  "required": [
+    "score",
+    "findable",
+    "accessible",
+    "interoperable",
+    "reusable",
+    "assessed"
+  ],
+  "title": "FairAssessment",
+  "type": "object"
+}

Added value: +{
+  "description": "Licence-compatibility advisory attached on resolve(use=<intent>). PURE-function\noutput: an ALLOW / REVIEW / DENY verdict for an intended use of the resolved record,\ncomputed from a bundled licence matrix (choosealicense.com flag vocabulary) keyed on\nthe normalized SPDX id. ``spdx_id`` is None exactly when the licence was unrecognized\nor absent (→ REVIEW, never a fabricated ALLOW/DENY). ``reason`` names the governing\nclause; ``disclaimer`` states this is a metadata-derived advisory, not legal advice.",
+  "properties": {
+    "disclaimer": {
+      "title": "Disclaimer",
+      "type": "string"
+    },
+    "license_raw": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "title": "License Raw"
+    },
+    "reason": {
+      "title": "Reason",
+      "type": "string"
+    },
+    "spdx_id": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "title": "Spdx Id"
+    },
+    "use": {
+      "title": "Use",
+      "type": "string"
+    },
+    "verdict": {
+      "enum": [
+        "ALLOW",
+        "REVIEW",
+        "DENY"
+      ],
+      "title": "Verdict",
+      "type": "string"
+    }
+  },
+  "required": [
+    "use",
+    "verdict",
+    "spdx_id",
+    "license_raw",
+    "reason",
+    "disclaimer"
+  ],
+  "title": "LicenseVerdict",
+  "type": "object"
+}

Added value: +{
+  "description": "Echo of MeSH-synonym expansion that fired for a search (transparency).",
+  "properties": {
+    "canonical_name": {
+      "title": "Canonical Name",
+      "type": "string"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "mesh_ui": {
+      "title": "Mesh Ui",
+      "type": "string"
+    },
+    "synonyms": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Synonyms",
+      "type": "array"
+    }
+  },
+  "required": [
+    "input",
+    "mesh_ui",
+    "canonical_name",
+    "synonyms"
+  ],
+  "title": "MeshExpansion",
+  "type": "object"
+}

Added value: +{
+  "description": "A same-dataset copy folded into this record by content dedup (resolve the\nmirror's id to reach the original deposit). Only populated when a search ran\nwith the opt-in ``collapse_mirrors`` flag.",
+  "properties": {
+    "doi": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Doi"
+    },
+    "id": {
+      "title": "Id",
+      "type": "string"
+    },
+    "source": {
+      "title": "Source",
+      "type": "string"
+    }
+  },
+  "required": [
+    "source",
+    "id"
+  ],
+  "title": "Mirror",
+  "type": "object"
+}

Added value: +{
+  "description": "Transparency echo of A2.P2 multi-query recall expansion (search multi_query=true).\n\nWhen enabled and an LLM endpoint is configured, the LLM generates deliberately-diverse\nreformulations of the query; each variant is fanned out across all sources, and the\ndeduped union is re-ranked against the ORIGINAL query. ``variants`` lists the RAW variants\nactually fanned out, the original query first. Each variant received the same ontology\nexpansion (shown by the ``*_expansion`` echoes); results are the deduped union re-ranked\nagainst ``input``.",
+  "properties": {
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "variants": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Variants",
+      "type": "array"
+    }
+  },
+  "required": [
+    "input",
+    "variants"
+  ],
+  "title": "QueryExpansion",
+  "type": "object"
+}

Added value: +{
+  "description": "Echo of the LLM query-understanding rewrite that fired (transparency, A2.P1).\n\nThe LLM proposes; explicit caller params win; the ontology resolvers then VALIDATE the\nproposed entities. ``applied`` lists the fields the caller left None that were FED into\nthis search as parameters — for ontology entities (organism/disease/tissue/chemical/\nassay) this means \"passed to the resolver\", NOT \"resolved\": whether it actually expanded\nis shown by the corresponding ``*_expansion`` echo (None there ⇒ the entity did not\nresolve, and was never silently treated as a match). ``overridden`` lists fields the LLM\nproposed but the caller had set explicitly (so the LLM's value was ignored).",
+  "properties": {
+    "applied": {
+      "additionalProperties": true,
+      "title": "Applied",
+      "type": "object"
+    },
+    "extracted": {
+      "additionalProperties": true,
+      "title": "Extracted",
+      "type": "object"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "keyword_core": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "title": "Keyword Core"
+    },
+    "overridden": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Overridden",
+      "type": "array"
+    }
+  },
+  "required": [
+    "input",
+    "keyword_core"
+  ],
+  "title": "QueryUnderstanding",
+  "type": "object"
+}

Added value: +{
+  "description": "Echo of UBERON tissue-synonym expansion that fired for a search (transparency).",
+  "properties": {
+    "canonical_name": {
+      "title": "Canonical Name",
+      "type": "string"
+    },
+    "input": {
+      "title": "Input",
+      "type": "string"
+    },
+    "synonyms": {
+      "items": {
+        "type": "string"
+      },
+      "title": "Synonyms",
+      "type": "array"
+    },
+    "uberon_id": {
+      "title": "Uberon Id",
+      "type": "string"
+    }
+  },
+  "required": [
+    "input",
+    "uberon_id",
+    "canonical_name",
+    "synonyms"
+  ],
+  "title": "TissueExpansion",
+  "type": "object"
+}

Added value: +{
+  "description": "Integrity/provenance signals attached on resolve(trust=True). All nullable:\nNone = not checked or not determinable (e.g. a DOI Crossref doesn't register) —\nNEVER a negative claim. A *found* Crossref work yields definitive booleans.",
+  "properties": {
+    "concern": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Concern"
+    },
+    "retracted": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Retracted"
+    },
+    "retraction_doi": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Retraction Doi"
+    }
+  },
+  "title": "TrustSignals",
+  "type": "object"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/AssayExpansion"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/ChemicalExpansion"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/MeshExpansion"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Provenance Crate"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/QueryExpansion"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/QueryUnderstanding"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/TissueExpansion"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "description": "Optional export to render onto the result. 'croissant' attaches a file-level Croissant JSON-LD manifest (croissant field); 'ro-crate' attaches a minimal RO-Crate 1.1 manifest (ro_crate field).",
+  "enum": [
+    "croissant",
+    "ro-crate"
+  ],
+  "type": "string"
+}

Added value: +{
+  "description": "Usage/impact signals, each a separate axis — NO blended score. All\nnullable: a source that does not expose an axis leaves it None.",
+  "properties": {
+    "citations": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Citations"
+    },
+    "downloads": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Downloads"
+    },
+    "likes": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Likes"
+    },
+    "views": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Views"
+    }
+  },
+  "title": "Metrics",
+  "type": "object"
+}

Added value: +{
+  "items": {
+    "type": "string"
+  },
+  "title": "Access Modes",
+  "type": "array"
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Croissant"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "boolean"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Is Latest"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Last Updated"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/Metrics"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Ro Crate"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Superseded By"
+}

Previous value: -"Restrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature, huggingface"New value: +"Restrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature, huggingface, dataone, omicsdi"

Added value: +{
+  "items": {
+    "type": "string"
+  },
+  "title": "Access Modes",
+  "type": "array"
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Croissant"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "boolean"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Is Latest"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Last Updated"
+}

Added value: +{
+  "anyOf": [
+    {
+      "$ref": "#/$defs/Metrics"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null
+}

Added value: +{
+  "anyOf": [
+    {
+      "additionalProperties": true,
+      "type": "object"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Ro Crate"
+}

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Superseded By"
+}

Added value: +{
+  "description": "Usage/impact signals, each a separate axis — NO blended score. All\nnullable: a source that does not expose an axis leaves it None.",
+  "properties": {
+    "citations": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Citations"
+    },
+    "downloads": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Downloads"
+    },
+    "likes": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Likes"
+    },
+    "views": {
+      "anyOf": [
+        {
+          "type": "integer"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Views"
+    }
+  },
+  "title": "Metrics",
+  "type": "object"
+}

Added value: +{
+  "items": {
+    "type": "string"
+  },
+  "title": "Resumed",
+  "type": "array"
+}

Added value: +{
+  "default": false,
+  "description": "When true, probe each source's base endpoint and attach a 'health' field ({status: up|down, latency_ms, detail}) to each source. Default false: returns the static catalog with no network.",
+  "type": "boolean"
+}

Added value: +{
+  "properties": {
+    "name": {
+      "title": "Name",
+      "type": "string"
+    },
+    "orcid": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Orcid"
+    }
+  },
+  "required": [
+    "name"
+  ],
+  "title": "Creator",
+  "type": "object"
+}

Added value: +{
+  "properties": {
+    "award": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Award"
+    },
+    "funder": {
+      "title": "Funder",
+      "type": "string"
+    }
+  },
+  "required": [
+    "funder"
+  ],
+  "title": "FundingRef",
+  "type": "object"
+}

Added value: +"#/$defs/Creator"

Removed value: -"string"

Added value: +{
+  "items": {
+    "$ref": "#/$defs/FundingRef"
+  },
+  "title": "Funding",
+  "type": "array"
+}

Added value: +{
+  "description": "Opaque pagination token from a prior search's next_cursor. When set, all other search params are read from the cursor.",
+  "type": "string"
+}

Added value: +{
+  "description": "Keep only results of this kind.",
+  "enum": [
+    "dataset",
+    "sequencing_run",
+    "study",
+    "publication",
+    "software"
+  ],
+  "type": "string"
+}

Added value: +{
+  "description": "Keep results with year >= this.",
+  "type": "integer"
+}

Added value: +{
+  "description": "Keep results with year <= this.",
+  "type": "integer"
+}

Added value: +{
+  "default": "relevance",
+  "description": "Result ordering. 'relevance' (default) = upstream/merged order. 'semantic' re-ranks the fetched page by embedding similarity to the query (needs EMBEDDING_API_BASE; degrades to relevance order with an errors['semantic'] note if unconfigured). In semantic mode pagination is window-based (each page consumes its full fetched window).",
+  "enum": [
+    "relevance",
+    "semantic"
+  ],
+  "type": "string"
+}

Previous value: -"Restrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature"New value: +"Restrict fan-out to these sources (default: all). Available: zenodo, datacite, omics, literature, huggingface"

Removed value: -[
-  "query"
-]

Added value: +{
+  "properties": {
+    "name": {
+      "title": "Name",
+      "type": "string"
+    },
+    "orcid": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Orcid"
+    }
+  },
+  "required": [
+    "name"
+  ],
+  "title": "Creator",
+  "type": "object"
+}

Added value: +"#/$defs/Creator"

Removed value: -"string"

Added value: +{
+  "items": {
+    "$ref": "#/$defs/FundingRef"
+  },
+  "title": "Funding",
+  "type": "array"
+}

Added value: +{
+  "properties": {
+    "award": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ],
+      "default": null,
+      "title": "Award"
+    },
+    "funder": {
+      "title": "Funder",
+      "type": "string"
+    }
+  },
+  "required": [
+    "funder"
+  ],
+  "title": "FundingRef",
+  "type": "object"
+}