addedInput schema / properties / assay
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"
+}
addedInput schema / properties / chemical
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"
+}
addedInput schema / properties / collapse_mirrors
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"
+}
addedInput schema / properties / disease
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"
+}
addedInput schema / properties / multi_query
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"
+}
addedInput schema / properties / provenance
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"
+}
changedInput schema / properties / sources / description
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"
addedInput schema / properties / tissue
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"
+}
addedInput schema / properties / understand
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"
+}
addedOutput schema / $defs / AssayExpansion
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"
+}
addedOutput schema / $defs / ChemicalExpansion
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"
+}
addedOutput schema / $defs / DataResource / properties / fair
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/FairAssessment"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / $defs / DataResource / properties / license_compat
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/LicenseVerdict"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / $defs / DataResource / properties / mirrors
Added value: +{
+ "items": {
+ "$ref": "#/$defs/Mirror"
+ },
+ "title": "Mirrors",
+ "type": "array"
+}
addedOutput schema / $defs / DataResource / properties / provenance
Added value: +{
+ "anyOf": [
+ {
+ "additionalProperties": true,
+ "type": "object"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null,
+ "title": "Provenance"
+}
addedOutput schema / $defs / DataResource / properties / trust
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/TrustSignals"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / $defs / FairAssessment
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"
+}
addedOutput schema / $defs / LicenseVerdict
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"
+}
addedOutput schema / $defs / MeshExpansion
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"
+}
addedOutput schema / $defs / Mirror
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"
+}
addedOutput schema / $defs / QueryExpansion
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"
+}
addedOutput schema / $defs / QueryUnderstanding
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"
+}
addedOutput schema / $defs / TissueExpansion
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"
+}
addedOutput schema / $defs / TrustSignals
Added value: +{
+ "description": "Integrity/provenance signals attached on resolve(trust=True). All nullable:\nNone = not checked or not determinable (e.g. a DOI Crossref doesn't register) —\nNEVER a negative claim. A *found* Crossref work yields definitive booleans.",
+ "properties": {
+ "concern": {
+ "anyOf": [
+ {
+ "type": "boolean"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null,
+ "title": "Concern"
+ },
+ "retracted": {
+ "anyOf": [
+ {
+ "type": "boolean"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null,
+ "title": "Retracted"
+ },
+ "retraction_doi": {
+ "anyOf": [
+ {
+ "type": "string"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null,
+ "title": "Retraction Doi"
+ }
+ },
+ "title": "TrustSignals",
+ "type": "object"
+}
addedOutput schema / properties / assay_expansion
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/AssayExpansion"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / properties / chemical_expansion
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/ChemicalExpansion"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / properties / mesh_expansion
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/MeshExpansion"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / properties / provenance_crate
Added value: +{
+ "anyOf": [
+ {
+ "additionalProperties": true,
+ "type": "object"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null,
+ "title": "Provenance Crate"
+}
addedOutput schema / properties / query_expansion
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/QueryExpansion"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / properties / query_understanding
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/QueryUnderstanding"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
addedOutput schema / properties / tissue_expansion
Added value: +{
+ "anyOf": [
+ {
+ "$ref": "#/$defs/TissueExpansion"
+ },
+ {
+ "type": "null"
+ }
+ ],
+ "default": null
+}
