ensembl-mcp-server

Previous value: -"Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl for the source species. `invalid_species`: The species or target_species string was not recognized by Ensembl. `no_input`: Neither symbol nor id was provided. `conflicting_input`: Both symbol and id were provided. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl for the source species. `invalid_species`: The species or target_species string was not recognized by Ensembl. `target_not_compared`: Both species are valid, but target_species is outside the comparison Ensembl runs for the source species, and Ensembl's pan-taxonomic comparison does not hold both species or its species list could not be read. `no_input`: Neither symbol nor id was provided. `conflicting_input`: Both symbol and id were provided. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "not_found",
-  "invalid_species",
-  "no_input",
-  "conflicting_input"
-]New value: +[
+  "not_found",
+  "invalid_species",
+  "target_not_compared",
+  "no_input",
+  "conflicting_input"
+]

Previous value: -"Percent identity between the query and target gene sequences (0-100). Higher values indicate more conserved sequences."New value: +"Percent identity over the target protein's length (0-100): identical positions divided by the target protein's length. The query-side value differs when the two proteins differ in length."

Previous value: -"Percent positive (similar) positions in the alignment (0-100). Includes conservative substitutions as well as identical residues."New value: +"Percent positive positions over the target protein's length (0-100): identical residues plus conservative substitutions, divided by the target protein's length."

Previous value: -"Guidance when no homologs are found, the list was capped, or symbol enrichment is incomplete."New value: +"Guidance when the homologs come from Ensembl's pan-taxonomic comparison, no homologs are found, the list was capped, or symbol enrichment is incomplete."

Previous value: -"Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome_gene (gene pathways), Reactome (translation pathways), GO (Gene Ontology terms). Transcript/translation references may require all_levels=true or the specific feature ID. Omit to return every database within the selected scope."New value: +"Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), Uniprot/SWISSPROT (reviewed UniProt accession, on the translation), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome_gene (gene pathways), Reactome (translation pathways), GO (Gene Ontology terms). Transcript/translation references may require all_levels=true or the specific feature ID. Omit to return every database within the selected scope."

Previous value: -"Database name in Ensembl internal format (e.g. HGNC, Uniprot_gn, EntrezGene, MIM_GENE, RefSeq_mRNA)."New value: +"Database name in Ensembl internal format (e.g. HGNC, Uniprot_gn, Uniprot/SWISSPROT, EntrezGene, MIM_GENE, RefSeq_mRNA)."

Added value: +{
+  "description": "Detail Ensembl records for the assignment: its source (e.g. UniProt, GO_Central) or, for a projection, the ortholog it came from. Omitted when blank.",
+  "type": "string"
+}

Added value: +{
+  "description": "How Ensembl assigned the reference, e.g. DIRECT (from the external database), DEPENDENT (derived from another reference), PROJECTION (projected from an ortholog), SEQUENCE_MATCH, CHECKSUM.",
+  "type": "string"
+}

Added value: +{
+  "description": "Evidence codes supporting the reference — GO evidence codes on GO terms (e.g. IDA experimental, IEA electronic, ISS sequence similarity). Omitted when Ensembl lists none.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}

Added value: +{
+  "description": "Target translation stable ID. Pass to ensembl_get_sequence with type=\"protein\".",
+  "type": "string"
+}

Added value: +{
+  "description": "Target gene display name, when a bounded secondary lookup resolves it.",
+  "type": "string"
+}

Previous value: -"Guidance when no homologs are found or the list was capped."New value: +"Guidance when no homologs are found, the list was capped, or symbol enrichment is incomplete."

Added value: +{
+  "default": false,
+  "description": "Include references on child objects: a gene includes its transcripts and translations. Default false queries only the requested object level, independently of dbname.",
+  "type": "boolean"
+}

Previous value: -"Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome (pathway IDs), GO (Gene Ontology terms). Omit to return all available xrefs."New value: +"Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA (NCBI RefSeq transcript), Reactome_gene (gene pathways), Reactome (translation pathways), GO (Gene Ontology terms). Transcript/translation references may require all_levels=true or the specific feature ID. Omit to return every database within the selected scope."

Previous value: -"Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). A version suffix on an ENS… ID (ENSG00000139618.17) is dropped before the request. Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2)."New value: +"Ensembl stable gene (ENSG…), transcript (ENST…), or translation (ENSP…) ID. A version suffix on an ENS… ID (ENSG00000139618.17) is dropped before the request. Use ensembl_lookup_gene to get the stable ID from a gene symbol. References default to this object level; all_levels=true includes child objects."

Previous value: -"Machine-readable failure mode. Declared by this tool: `not_found`: The Ensembl stable ID was not found or has no cross-references. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: The Ensembl stable ID was not found. An empty cross-reference list remains successful. Other values are possible when a failure originates below the handler."

Previous value: -"Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). A version suffix on an ENS… ID is dropped before the lookup. Returns a succeeded/failed split; each item carries its query — the ID as submitted, version included — and each failed item a reason and recovery. Provide exactly one of symbol, id, ids, or symbols."New value: +"Batch submission: up to 1,000 Ensembl stable IDs (ENSG…, ENST…); resolves the first 20 distinct trimmed queries. batch.omitted names the remainder to resubmit. A version suffix on an ENS… ID is dropped before the lookup. Returns a succeeded/failed/omitted partition; each attempted item carries its query — the ID as submitted, version included — and each failed item a reason and recovery. Provide exactly one of symbol, id, ids, or symbols."

Previous value: -20New value: +1000

Previous value: -"Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split; each item carries its submitted query. Synonyms and former symbols resolve with matchedAlias; one shared by several genes fails with reason ambiguous and its candidates. Provide exactly one of symbol, id, ids, or symbols."New value: +"Batch submission: up to 1,000 gene symbols; resolves the first 20 distinct trimmed queries. batch.omitted names the remainder to resubmit. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed/omitted partition; each attempted item carries its submitted query. Synonyms and former symbols resolve with matchedAlias; one shared by several genes fails with reason ambiguous and its candidates. Provide exactly one of symbol, id, ids, or symbols."

Previous value: -20New value: +1000

Added value: +{
+  "description": "Canonical Ensembl transcript ID, including its version when supplied. Use for a primary protein sequence.",
+  "type": "string"
+}

Added value: +{
+  "description": "Parent gene stable ID for a transcript-ID lookup. Absent for other object types.",
+  "type": "string"
+}

Added value: +{
+  "description": "MANE Select RefSeq transcript accession, when supplied by Ensembl.",
+  "type": "string"
+}

Added value: +{
+  "description": "Canonical Ensembl transcript ID, including its version when supplied. Use for a primary protein sequence.",
+  "type": "string"
+}

Added value: +{
+  "description": "Parent gene stable ID for a transcript-ID lookup. Absent for other object types.",
+  "type": "string"
+}

Added value: +{
+  "description": "MANE Select RefSeq transcript accession, when supplied by Ensembl.",
+  "type": "string"
+}

Added value: +{
+  "description": "Queries past the first 20 distinct items, in first-occurrence order. Resubmit these separately.",
+  "items": {
+    "description": "A distinct submitted query not attempted in this call.",
+    "type": "string"
+  },
+  "type": "array"
+}

Added value: +{
+  "description": "Canonical Ensembl transcript ID, including its version when supplied. Use for a primary protein sequence.",
+  "type": "string"
+}

Added value: +{
+  "description": "Parent gene stable ID for a transcript-ID lookup. Absent for other object types.",
+  "type": "string"
+}

Added value: +{
+  "description": "MANE Select RefSeq transcript accession, when supplied by Ensembl.",
+  "type": "string"
+}

Previous value: -[
-  "succeeded",
-  "failed"
-]New value: +[
+  "omitted",
+  "succeeded",
+  "failed"
+]

Added value: +{
+  "description": "Canonical Ensembl transcript ID, including its version when supplied. Use for a primary protein sequence.",
+  "type": "string"
+}

Added value: +{
+  "description": "Parent gene stable ID for a transcript-ID lookup. Absent for other object types.",
+  "type": "string"
+}

Added value: +{
+  "description": "MANE Select RefSeq transcript accession, when supplied by Ensembl.",
+  "type": "string"
+}

Added value: +{
+  "description": "Guidance for resubmitting unattempted batch queries.",
+  "type": "string"
+}

Added value: +{
+  "description": "Reference and alternate alleles returned by VEP, separated by slashes.",
+  "type": "string"
+}

Previous value: -"Clinical significance terms from ClinVar (e.g. pathogenic, benign)."New value: +"Aggregate clinical significance terms for the colocated record; these do not classify the submitted allele."

Added value: +{
+  "additionalProperties": {
+    "items": {
+      "type": "string"
+    },
+    "type": "array"
+  },
+  "description": "Clinical significance terms keyed by the allele explicitly annotated in the colocated record. Missing alleles have no reported attribution.",
+  "propertyNames": {
+    "type": "string"
+  },
+  "type": "object"
+}

Added value: +{
+  "description": "Reference allele for the colocated clinical annotations, when reported.",
+  "type": "string"
+}

Previous value: -"Per-transcript consequence details, capped to max_transcript_consequences. High-impact variants may affect many transcripts; focus on canonical transcripts (isCanonical from ensembl_lookup_gene) for primary effect. transcriptConsequencesTotal reports the full count."New value: +"Per-transcript consequence details, capped to max_transcript_consequences. High-impact variants may affect many transcripts; canonical and maneSelect identify annotated primary transcripts. transcriptConsequencesTotal reports the full count."

Added value: +{
+  "description": "Whether Ensembl marks this consequence transcript as canonical. Omitted when not reported.",
+  "type": "boolean"
+}

Added value: +{
+  "description": "MANE Select RefSeq transcript accession, when supplied.",
+  "type": "string"
+}

Added value: +{
+  "description": "Allele this transcript consequence describes, in the upstream genomic orientation.",
+  "type": "string"
+}

Previous value: -"Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering."New value: +"Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Case-sensitive (lncRNA, not lncrna); remove the filter to inspect all matching feature types. Applied server-side by Ensembl. Not all feature types support biotype filtering."

Previous value: -"Ensembl stable gene ID (e.g. ENSG00000139618). Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be combined with symbol."New value: +"Ensembl stable gene ID (e.g. ENSG00000139618). A version suffix (ENSG00000139618.17) is accepted and dropped before the query. Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be combined with symbol."

Previous value: -"Source species (the species the query gene belongs to) in Ensembl internal format. Default is homo_sapiens. Use ensembl_list_species to discover valid values."New value: +"Source species (the species the query gene belongs to) in Ensembl internal format. Default is homo_sapiens. Use ensembl_list_species with nameContains (a genus or common name, e.g. mouse) to find valid values."

Previous value: -"Filter to homologs in a single target species (e.g. mus_musculus for mouse). Omit to return homologs across all available species. Use ensembl_list_species to discover valid values."New value: +"Filter to homologs in a single target species (e.g. mus_musculus for mouse). Omit to return homologs across all available species. Use ensembl_list_species with nameContains (a genus or common name) to find valid values."

Previous value: -"Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl. `no_input`: Neither symbol nor id was provided. `conflicting_input`: Both symbol and id were provided. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl for the source species. `invalid_species`: The species or target_species string was not recognized by Ensembl. `no_input`: Neither symbol nor id was provided. `conflicting_input`: Both symbol and id were provided. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "not_found",
-  "no_input",
-  "conflicting_input"
-]New value: +[
+  "not_found",
+  "invalid_species",
+  "no_input",
+  "conflicting_input"
+]

Previous value: -"Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."New value: +"Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries; on a :-1 region it extends the lower coordinate."

Previous value: -"Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries."New value: +"Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries; on a :-1 region it extends the higher coordinate."

Previous value: -"Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set. A region needs start at or below end, within the sequence region, and spans at most 10,000,000 bases."New value: +"Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode — an id containing a colon is a region. A version suffix on a stable ID (ENST00000380152.8) is dropped before the request. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set. Coordinates are whole numbers; start..end works as well as start-end, and a :1 or :-1 suffix picks the strand (13:32315086-32315100:-1 returns the reverse complement). A region needs start at or below end, within the sequence region, and spans at most 10,000,000 bases. Name chromosomes as Ensembl does (13, X, MT; chr13 also works); the mitochondrion is MT in vertebrates, mitochondrion_genome in Drosophila, and MtDNA in C. elegans. M and chrM are accepted only where Ensembl resolves them to the mitochondrion (Drosophila, for one); elsewhere they fail as invalid_region naming the mitochondrion of the species."

Previous value: -"Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region; optional for the species:chr:start-end form (the embedded species is used when the field is omitted). Optional for stable ID lookups — Ensembl infers species from the ID prefix."New value: +"Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region. For the species:chr:start-end form the species in id takes precedence and this field is ignored. Unused for stable ID lookups — Ensembl infers species from the ID prefix."

Previous value: -"Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID). Region ids are genomic-only — request cdna, cds, or protein from a transcript or protein stable ID."New value: +"Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID). Region ids are genomic-only — request cdna, cds, or protein from a transcript or protein stable ID. A protein ID (ENSP…) serves only its protein; a non-coding transcript has no protein or cds."

Previous value: -"Machine-readable failure mode. Declared by this tool: `not_found`: The stable ID or region was not found in Ensembl. `type_mismatch`: A non-genomic type (cdna, cds, or protein) was requested for a region id or a gene ID. `missing_species`: A bare chr:start-end region was given without a species. `invalid_region`: A region id has its start after its end, starts past the end of its sequence region, spans more than the 10,000,000-base maximum, or names a sequence region the species lacks. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: The stable ID or region was not found in Ensembl. `type_mismatch`: The requested type does not exist for the id: cdna, cds, or protein for a region id or a gene ID; genomic, cdna, or cds for a protein ID; or protein or cds for a non-coding transcript. `invalid_species`: The species of a region (the species field or the species prefix in id) was not recognized by Ensembl. `missing_species`: A bare chr:start-end region was given without a species. `invalid_region`: A region id is not in the [species:]chr:start-end form, has its start after its end, starts past the end of its sequence region, spans more than the 10,000,000-base maximum, names the mitochondrion M or chrM where Ensembl resolves that to another region or none, or names a sequence region the species lacks. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "not_found",
-  "type_mismatch",
-  "missing_species",
-  "invalid_region"
-]New value: +[
+  "not_found",
+  "type_mismatch",
+  "invalid_species",
+  "missing_species",
+  "invalid_region"
+]

Previous value: -"Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2)."New value: +"Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). A version suffix on an ENS… ID (ENSG00000139618.17) is dropped before the request. Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2)."

Previous value: -"The Ensembl stable ID that was queried."New value: +"The Ensembl stable ID as submitted, including any version suffix."

Added value: +{
+  "default": 50,
+  "description": "Maximum number of species to return, counted from offset. Default 50. Set to 0 to return every matching species from offset to the end, uncapped. totalCount always reports the full number of matches before this cap.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "default": 0,
+  "description": "0-based position in the name-sorted matches where the returned page starts. Default 0. Pass nextOffset from a previous response to fetch the following page; an offset at or past totalCount returns no species.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "description": "The max_results limit applied to this page.",
+  "type": "number"
+}

Added value: +{
+  "description": "Offset of the first species after this page — pass it as offset to fetch the next page. Present only when more species follow.",
+  "type": "number"
+}

Previous value: -"Guidance when the filter matches no species."New value: +"Guidance when the filter matches no species, the offset is past the end, or more species follow this page."

Added value: +{
+  "description": "Number of species returned on this page.",
+  "type": "number"
+}

Previous value: -"Species matching the filter criteria, sorted by internal name."New value: +"Species matching the filter criteria, sorted by internal name: at most max_results entries starting at offset."

Previous value: -"Total number of matching species after local filtering."New value: +"Total number of matching species after local filtering, before offset and max_results. Exceeds the returned species count when the list was paged."

Added value: +{
+  "description": "True when more matching species follow this page; request nextOffset to continue.",
+  "type": "boolean"
+}

Previous value: -"Ensembl stable gene ID (e.g. ENSG00000139618 or ENSG00000139618.7 with version). Species is not required for ID lookup."New value: +"Ensembl stable gene ID (e.g. ENSG00000139618). A version suffix on an ENS… ID (ENSG00000139618.19) is dropped before the lookup, which returns the current version. Species is not required for ID lookup."

Previous value: -"Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."New value: +"Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). A version suffix on an ENS… ID is dropped before the lookup. Returns a succeeded/failed split; each item carries its query — the ID as submitted, version included — and each failed item a reason and recovery. Provide exactly one of symbol, id, ids, or symbols."

Previous value: -"Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. Use ensembl_list_species to discover valid values."New value: +"Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. Use ensembl_list_species with nameContains (a genus or common name) to find valid values."

Previous value: -"Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species."New value: +"Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species. A synonym or former symbol (HER2, TB1) resolves too; one shared by several genes returns ambiguous with the candidates instead of gene."

Previous value: -"Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."New value: +"Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split; each item carries its submitted query. Synonyms and former symbols resolve with matchedAlias; one shared by several genes fails with reason ambiguous and its candidates. Provide exactly one of symbol, id, ids, or symbols."

Added value: +{
+  "additionalProperties": false,
+  "description": "Present instead of gene when a symbol is not a current gene name and is a synonym or former symbol of several genes.",
+  "properties": {
+    "candidates": {
+      "description": "Every gene the symbol maps to. Retry with id set to the intended one.",
+      "items": {
+        "additionalProperties": false,
+        "description": "A gene the symbol is a synonym or former symbol of.",
+        "properties": {
+          "assemblyName": {
+            "description": "Genome assembly name (e.g. GRCh38). All coordinates are relative to this assembly.",
+            "type": "string"
+          },
+          "biotype": {
+            "description": "Gene biotype (e.g. protein_coding, lncRNA, pseudogene).",
+            "type": "string"
+          },
+          "chromosome": {
+            "description": "Chromosome or sequence region name.",
+            "type": "string"
+          },
+          "description": {
+            "description": "Brief gene description from Ensembl.",
+            "type": "string"
+          },
+          "displayName": {
+            "description": "Gene symbol or display name (e.g. BRCA2, TP53).",
+            "type": "string"
+          },
+          "end": {
+            "description": "Gene end position on the chromosome (1-based).",
+            "type": "number"
+          },
+          "id": {
+            "description": "Ensembl gene stable ID (ENSG…). Use this as input to other Ensembl tools.",
+            "type": "string"
+          },
+          "species": {
+            "description": "Species in Ensembl internal format (e.g. homo_sapiens). Echoed from lookup.",
+            "type": "string"
+          },
+          "start": {
+            "description": "Gene start position on the chromosome (1-based).",
+            "type": "number"
+          },
+          "strand": {
+            "description": "Strand: 1 for forward, -1 for reverse.",
+            "type": "number"
+          },
+          "transcripts": {
+            "description": "Transcript list. Present only when expand_transcripts is true.",
+            "items": {
+              "additionalProperties": false,
+              "description": "A single transcript summary entry.",
+              "properties": {
+                "biotype": {
+                  "description": "Transcript biotype (e.g. protein_coding, lncRNA, retained_intron).",
+                  "type": "string"
+                },
+                "displayName": {
+                  "description": "Transcript display name.",
+                  "type": "string"
+                },
+                "end": {
+                  "description": "Transcript end position on the chromosome (1-based).",
+                  "type": "number"
+                },
+                "id": {
+                  "description": "Ensembl transcript stable ID (ENST…).",
+                  "type": "string"
+                },
+                "isCanonical": {
+                  "description": "True when this is the canonical transcript for the gene.",
+                  "type": "boolean"
+                },
+                "lengthInBp": {
+                  "description": "Transcript length in base pairs.",
+                  "type": "number"
+                },
+                "start": {
+                  "description": "Transcript start position on the chromosome (1-based).",
+                  "type": "number"
+                },
+                "strand": {
+                  "description": "Strand: 1 for forward, -1 for reverse.",
+                  "type": "number"
+                }
+              },
+              "required": [
+                "id",
+                "isCanonical"
+              ],
+              "type": "object"
+            },
+            "type": "array"
+          }
+        },
+        "required": [
+          "id"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "guidance": {
+      "description": "How to pick a candidate and retry by id.",
+      "type": "string"
+    },
+    "query": {
+      "description": "The submitted symbol.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "query",
+    "candidates",
+    "guidance"
+  ],
+  "type": "object"
+}

Previous value: -"IDs/symbols that could not be resolved, with per-item query and error fields."New value: +"IDs/symbols that did not resolve to one gene, in input order."

Previous value: -{}New value: +false

Previous value: -"A failed lookup entry with query (the submitted ID or symbol) and error (reason string) fields."New value: +"One unresolved ID or symbol."

Added value: +{
+  "description": "Every gene the symbol maps to. Present only when reason is ambiguous.",
+  "items": {
+    "additionalProperties": false,
+    "description": "A gene the symbol is a synonym or former symbol of.",
+    "properties": {
+      "assemblyName": {
+        "description": "Genome assembly name (e.g. GRCh38). All coordinates are relative to this assembly.",
+        "type": "string"
+      },
+      "biotype": {
+        "description": "Gene biotype (e.g. protein_coding, lncRNA, pseudogene).",
+        "type": "string"
+      },
+      "chromosome": {
+        "description": "Chromosome or sequence region name.",
+        "type": "string"
+      },
+      "description": {
+        "description": "Brief gene description from Ensembl.",
+        "type": "string"
+      },
+      "displayName": {
+        "description": "Gene symbol or display name (e.g. BRCA2, TP53).",
+        "type": "string"
+      },
+      "end": {
+        "description": "Gene end position on the chromosome (1-based).",
+        "type": "number"
+      },
+      "id": {
+        "description": "Ensembl gene stable ID (ENSG…). Use this as input to other Ensembl tools.",
+        "type": "string"
+      },
+      "species": {
+        "description": "Species in Ensembl internal format (e.g. homo_sapiens). Echoed from lookup.",
+        "type": "string"
+      },
+      "start": {
+        "description": "Gene start position on the chromosome (1-based).",
+        "type": "number"
+      },
+      "strand": {
+        "description": "Strand: 1 for forward, -1 for reverse.",
+        "type": "number"
+      },
+      "transcripts": {
+        "description": "Transcript list. Present only when expand_transcripts is true.",
+        "items": {
+          "additionalProperties": false,
+          "description": "A single transcript summary entry.",
+          "properties": {
+            "biotype": {
+              "description": "Transcript biotype (e.g. protein_coding, lncRNA, retained_intron).",
+              "type": "string"
+            },
+            "displayName": {
+              "description": "Transcript display name.",
+              "type": "string"
+            },
+            "end": {
+              "description": "Transcript end position on the chromosome (1-based).",
+              "type": "number"
+            },
+            "id": {
+              "description": "Ensembl transcript stable ID (ENST…).",
+              "type": "string"
+            },
+            "isCanonical": {
+              "description": "True when this is the canonical transcript for the gene.",
+              "type": "boolean"
+            },
+            "lengthInBp": {
+              "description": "Transcript length in base pairs.",
+              "type": "number"
+            },
+            "start": {
+              "description": "Transcript start position on the chromosome (1-based).",
+              "type": "number"
+            },
+            "strand": {
+              "description": "Strand: 1 for forward, -1 for reverse.",
+              "type": "number"
+            }
+          },
+          "required": [
+            "id",
+            "isCanonical"
+          ],
+          "type": "object"
+        },
+        "type": "array"
+      }
+    },
+    "required": [
+      "id"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Added value: +{
+  "description": "What went wrong for this item.",
+  "type": "string"
+}

Added value: +{
+  "description": "The submitted ID or symbol.",
+  "type": "string"
+}

Added value: +{
+  "description": "not_found: nothing matched. ambiguous: the symbol is a synonym of several genes, listed in candidates. unavailable: Ensembl did not answer the synonym lookup for this symbol after retries, so whether it matches is unknown — retry it.",
+  "enum": [
+    "not_found",
+    "ambiguous",
+    "unavailable"
+  ],
+  "type": "string"
+}

Added value: +{
+  "description": "The next step for this item.",
+  "type": "string"
+}

Added value: +[
+  "query",
+  "reason",
+  "error",
+  "recovery"
+]

Previous value: -"Gene records for IDs/symbols that resolved successfully. Same shape as gene."New value: +"Records for IDs/symbols that resolved to one gene, in input order."

Previous value: -{}New value: +false

Previous value: -"A resolved gene record with the same shape as the gene output field."New value: +"A resolved gene record carrying its submitted query."

Added value: +{
+  "description": "Genome assembly name (e.g. GRCh38). All coordinates are relative to this assembly.",
+  "type": "string"
+}

Added value: +{
+  "description": "Gene biotype (e.g. protein_coding, lncRNA, pseudogene).",
+  "type": "string"
+}

Added value: +{
+  "description": "Chromosome or sequence region name.",
+  "type": "string"
+}

Added value: +{
+  "description": "Brief gene description from Ensembl.",
+  "type": "string"
+}

Added value: +{
+  "description": "Gene symbol or display name (e.g. BRCA2, TP53).",
+  "type": "string"
+}

Added value: +{
+  "description": "Gene end position on the chromosome (1-based).",
+  "type": "number"
+}

Added value: +{
+  "description": "Ensembl gene stable ID (ENSG…). Use this as input to other Ensembl tools.",
+  "type": "string"
+}

Added value: +{
+  "description": "The submitted symbol, present when it matched a synonym or former symbol rather than the current gene name; displayName holds the current name.",
+  "type": "string"
+}

Added value: +{
+  "description": "The submitted ID or symbol this record resolved from.",
+  "type": "string"
+}

Added value: +{
+  "description": "Species in Ensembl internal format (e.g. homo_sapiens). Echoed from lookup.",
+  "type": "string"
+}

Added value: +{
+  "description": "Gene start position on the chromosome (1-based).",
+  "type": "number"
+}

Added value: +{
+  "description": "Strand: 1 for forward, -1 for reverse.",
+  "type": "number"
+}

Added value: +{
+  "description": "Transcript list. Present only when expand_transcripts is true.",
+  "items": {
+    "additionalProperties": false,
+    "description": "A single transcript summary entry.",
+    "properties": {
+      "biotype": {
+        "description": "Transcript biotype (e.g. protein_coding, lncRNA, retained_intron).",
+        "type": "string"
+      },
+      "displayName": {
+        "description": "Transcript display name.",
+        "type": "string"
+      },
+      "end": {
+        "description": "Transcript end position on the chromosome (1-based).",
+        "type": "number"
+      },
+      "id": {
+        "description": "Ensembl transcript stable ID (ENST…).",
+        "type": "string"
+      },
+      "isCanonical": {
+        "description": "True when this is the canonical transcript for the gene.",
+        "type": "boolean"
+      },
+      "lengthInBp": {
+        "description": "Transcript length in base pairs.",
+        "type": "number"
+      },
+      "start": {
+        "description": "Transcript start position on the chromosome (1-based).",
+        "type": "number"
+      },
+      "strand": {
+        "description": "Strand: 1 for forward, -1 for reverse.",
+        "type": "number"
+      }
+    },
+    "required": [
+      "id",
+      "isCanonical"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Added value: +[
+  "id",
+  "query"
+]

Previous value: -"Single gene record. Present for symbol or id lookups."New value: +"Single gene record. Present for an id lookup, or a symbol lookup that resolved to one gene."

Added value: +{
+  "description": "The submitted symbol, present when it matched a synonym or former symbol rather than the current gene name; displayName holds the current name.",
+  "type": "string"
+}

Previous value: -"Species in Ensembl internal format. Default is homo_sapiens. For non-human variants, set the appropriate species (e.g. mus_musculus for mouse). Use ensembl_list_species to discover valid values."New value: +"Species in Ensembl internal format. Default is homo_sapiens. For non-human variants, set the appropriate species (e.g. mus_musculus for mouse). Use ensembl_list_species with nameContains (a genus or common name) to find valid values."

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_notation`: The variant notation is malformed or cannot be parsed by VEP. `not_found`: The variant location falls outside any known transcript or assembly region. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_notation`: The variant notation is malformed or cannot be parsed by VEP. `not_found`: The variant location falls outside any known transcript or assembly region. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "invalid_notation",
-  "not_found"
-]New value: +[
+  "invalid_notation",
+  "not_found",
+  "invalid_species"
+]

Previous value: -"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."New value: +"Genomic region as chr:start-end with species set (e.g. 13:32315086-32400268), or species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268), with start at or below end. Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. The mitochondrion is MT in vertebrates, mitochondrion_genome in Drosophila, and MtDNA in C. elegans; M and chrM are accepted only where Ensembl resolves them to the mitochondrion (Drosophila, for one) and otherwise fail as invalid_region naming the mitochondrion of the species. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."

Previous value: -"Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values."New value: +"Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Required for a bare chr:start-end region; for the species:chr:start-end form the species in region takes precedence and this field is ignored. Use ensembl_list_species with nameContains (a genus or common name, e.g. mouse) to find valid values."

Previous value: -[
-  "species",
-  "region"
-]New value: +[
+  "region"
+]

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed, contains invalid coordinates, or spans more than the 5,000,000-base maximum. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed, has its start greater than its end, names the mitochondrion M or chrM where Ensembl resolves that to another region or none, contains coordinates outside the sequence region, or spans more than the 5,000,000-base maximum. `invalid_species`: The species (the species field or the region's species prefix) was not recognized by Ensembl. `missing_species`: A bare chr:start-end region was given without a species. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "invalid_region",
-  "invalid_species"
-]New value: +[
+  "invalid_region",
+  "invalid_species",
+  "missing_species"
+]

Previous value: -"The region queried, as provided."New value: +"The region queried, as provided minus any species prefix (reported as species)."

Previous value: -"The species queried."New value: +"The species queried: the region's species prefix when it has one, otherwise the species field."

Added value: +1

Previous value: -"Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set."New value: +"Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set. A region needs start at or below end, within the sequence region, and spans at most 10,000,000 bases."

Added value: +1

Added value: +{
+  "default": 10000,
+  "description": "Maximum number of characters in the returned window. Default 10000. Set to 0 to return everything from offset to the end, uncapped.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "default": 0,
+  "description": "0-based character offset where the returned window starts, counted in the resolved sequence (including any expand_5prime/expand_3prime flank). Default 0. Pass nextOffset from a truncated response to fetch the following window; an offset at or past the end returns an empty window.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Previous value: -"Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID)."New value: +"Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with coding transcript). protein: amino acid sequence (requires ENST… or ENSP… ID). Region ids are genomic-only — request cdna, cds, or protein from a transcript or protein stable ID."

Previous value: -[
-  {
-    "not": {
-      "required": [
-        "error"
-      ]
-    },
-    "required": [
-      "id",
-      "type",
-      "seq",
-      "length"
-    ]
-  },
-  {
-    "required": [
-      "error"
-    ]
-  }
-]New value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "id",
+      "type",
+      "seq",
+      "length",
+      "offset",
+      "truncated"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Previous value: -"Machine-readable failure mode. Declared by this tool: `not_found`: The stable ID or region was not found in Ensembl. `type_mismatch`: The requested sequence type is incompatible with the provided ID type. `missing_species`: A bare chr:start-end region was given without a species. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: The stable ID or region was not found in Ensembl. `type_mismatch`: A non-genomic type (cdna, cds, or protein) was requested for a region id or a gene ID. `missing_species`: A bare chr:start-end region was given without a species. `invalid_region`: A region id has its start after its end, starts past the end of its sequence region, spans more than the 10,000,000-base maximum, or names a sequence region the species lacks. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "not_found",
-  "type_mismatch",
-  "missing_species"
-]New value: +[
+  "not_found",
+  "type_mismatch",
+  "missing_species",
+  "invalid_region"
+]

Previous value: -"Sequence length in characters — nucleotides for genomic/cdna/cds, amino-acid residues for protein. Use this to budget context window usage before processing the sequence."New value: +"Full sequence length in characters, not the window size — nucleotides for genomic/cdna/cds, amino-acid residues for protein. Includes any expand_5prime/expand_3prime flank."

Added value: +{
+  "description": "Offset of the first character after this window — pass it as offset to fetch the next window. Present only when truncated.",
+  "type": "number"
+}

Added value: +{
+  "description": "Guidance about the window: how to continue when truncated, or why it is empty when the offset is past the end.",
+  "type": "string"
+}

Added value: +{
+  "description": "0-based character offset where this window starts.",
+  "type": "number"
+}

Previous value: -"The full sequence. DNA sequences use IUPAC nucleotide codes (ACGT + ambiguity codes). Protein sequences use single-letter amino acid codes. Large genomic sequences (e.g. 85 kb for BRCA2) are returned in full."New value: +"The requested window of the sequence: at most max_length characters starting at offset. DNA sequences use IUPAC nucleotide codes (ACGT + ambiguity codes); protein sequences use single-letter amino acid codes. Empty when offset is at or past the end."

Added value: +{
+  "description": "True when more sequence follows this window; request nextOffset to continue.",
+  "type": "boolean"
+}

Added value: +1

Added value: +1

Added value: +1

Added value: +1

Added value: +1

Previous value: -"Feature types to retrieve. Default is gene only. Requesting variation in a large region can return tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."New value: +"Feature types to retrieve — at least one. Default is gene only. Requesting variation in a large region can match tens of thousands of features. Include variation only for targeted small regions (single gene loci or smaller)."

Added value: +1

Added value: +{
+  "default": 100,
+  "description": "Maximum number of features to return. A gene-length region can hold tens of thousands of variation features; the default keeps the response compact. Set to 0 to return every feature uncapped. totalCount always reports the true number found before this cap.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Previous value: -"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."New value: +"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most 5,000,000 bases per region; split a larger area into smaller windows. Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."

Added value: +1

Added value: +1

Added value: +{
+  "description": "Genome assembly the coordinates are on (e.g. GRCh38). Omitted only when it could not be resolved, in which case the notice says so.",
+  "type": "string"
+}

Added value: +{
+  "description": "The max_results limit applied to the feature list.",
+  "type": "number"
+}

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed or contains invalid coordinates. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed, contains invalid coordinates, or spans more than the 5,000,000-base maximum. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler."

Previous value: -"Genomic features found in the requested region."New value: +"Genomic features found in the requested region, capped to max_results. totalCount reports the full count found before the cap."

Previous value: -"Warning or guidance about the result set."New value: +"Guidance about the result set: empty, large, capped, or missing assembly."

Added value: +{
+  "description": "Number of features returned after the max_results cap.",
+  "type": "number"
+}

Previous value: -"Number of features returned. Note: very large regions may return truncated results."New value: +"Total number of features found in the region before the max_results cap. Exceeds the returned features count when the list was capped."

Added value: +{
+  "description": "True when the feature list was capped at max_results.",
+  "type": "boolean"
+}

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "homologs",
+      "totalCount",
+      "queryId",
+      "querySpecies",
+      "queryType"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl. `no_input`: Neither symbol nor id was provided. `conflicting_input`: Both symbol and id were provided. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "not_found",
+            "no_input",
+            "conflicting_input"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "homologs",
-  "totalCount",
-  "queryId",
-  "querySpecies",
-  "queryType"
-]

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "id",
+      "type",
+      "seq",
+      "length"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `not_found`: The stable ID or region was not found in Ensembl. `type_mismatch`: The requested sequence type is incompatible with the provided ID type. `missing_species`: A bare chr:start-end region was given without a species. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "not_found",
+            "type_mismatch",
+            "missing_species"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "id",
-  "type",
-  "seq",
-  "length"
-]

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "xrefs",
+      "totalCount",
+      "queriedId"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `not_found`: The Ensembl stable ID was not found or has no cross-references. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "not_found"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "xrefs",
-  "totalCount",
-  "queriedId"
-]

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "species",
+      "totalCount"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode.",
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "species",
-  "totalCount"
-]

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    }
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `not_found`: The gene symbol or stable ID was not found in Ensembl. `invalid_species`: The species string was not recognized by Ensembl. `no_input`: Neither symbol, id, ids, nor symbols was provided. `conflicting_input`: More than one of symbol, id, ids, or symbols was provided. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "not_found",
+            "invalid_species",
+            "no_input",
+            "conflicting_input"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "results",
+      "totalCount"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `invalid_notation`: The variant notation is malformed or cannot be parsed by VEP. `not_found`: The variant location falls outside any known transcript or assembly region. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "invalid_notation",
+            "not_found"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "results",
-  "totalCount"
-]

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +false

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "features",
+      "totalCount",
+      "region",
+      "species"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode. Declared by this tool: `invalid_region`: The region string could not be parsed or contains invalid coordinates. `invalid_species`: The species string was not recognized by Ensembl. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "invalid_region",
+            "invalid_species"
+          ],
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

Removed value: -[
-  "features",
-  "totalCount",
-  "region",
-  "species"
-]

Added value: +{
+  "default": 25,
+  "description": "Maximum number of homologs to return. Broad orthology queries (e.g. BRCA2 across all species) can return 150+ homologs; the default keeps responses focused. Set to 0 to return every homolog uncapped. totalCount always reports the true number available before this cap.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "description": "The max_results limit applied to the homolog list.",
+  "type": "number"
+}

Previous value: -"Homologous genes found for the query gene."New value: +"Homologous genes found for the query gene, capped to max_results. totalCount reports the full count available before the cap."

Previous value: -"Guidance when no homologs are found."New value: +"Guidance when no homologs are found or the list was capped."

Added value: +{
+  "description": "Number of homologs returned after the max_results cap.",
+  "type": "number"
+}

Previous value: -"Total number of homologs returned."New value: +"Total number of homologs available before the max_results cap. Exceeds the returned homologs count when the list was capped."

Added value: +{
+  "description": "True when the homolog list was capped at max_results.",
+  "type": "boolean"
+}

Added value: +{
+  "default": false,
+  "description": "When true, return every PubMed ID for each colocated variant, overriding max_pubmed_ids_per_variant. Default false to keep responses compact.",
+  "type": "boolean"
+}

Added value: +{
+  "default": 10,
+  "description": "Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) cite 100+ papers; the default trims each list. Set to 0 to return every PubMed ID uncapped. pubmedTotal on each colocated variant reports the true pre-cap count. Ignored when include_all_colocated_pubmed is true.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "default": 10,
+  "description": "Maximum transcript consequences to return per VEP record. High-impact variants can affect 60+ transcripts; the default keeps the response focused on the top consequences. Set to 0 to return every transcript consequence uncapped. transcriptConsequencesTotal on each record always reports the true pre-cap count.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

Added value: +{
+  "description": "The max_transcript_consequences limit applied.",
+  "type": "number"
+}

Previous value: -"Guidance when no results are returned."New value: +"Guidance when no results are returned or when caps omitted detail."

Previous value: -"PubMed IDs for literature associated with this variant."New value: +"PubMed IDs for literature associated with this variant, capped to max_pubmed_ids_per_variant. pubmedTotal reports the full count when the list was capped."

Added value: +{
+  "description": "Total PubMed IDs available for this variant before the max_pubmed_ids_per_variant cap. Equals the returned pubmed length when the list was not capped.",
+  "type": "number"
+}

Previous value: -"Per-transcript consequence details. High-impact variants may affect many transcripts; focus on canonical transcripts (isCanonical from ensembl_lookup_gene) for primary effect."New value: +"Per-transcript consequence details, capped to max_transcript_consequences. High-impact variants may affect many transcripts; focus on canonical transcripts (isCanonical from ensembl_lookup_gene) for primary effect. transcriptConsequencesTotal reports the full count."

Added value: +{
+  "description": "Total transcript consequences available before the max_transcript_consequences cap. Equals the returned transcriptConsequences length when not capped.",
+  "type": "number"
+}

Added value: +{
+  "description": "Total transcript consequences returned across all records after the cap.",
+  "type": "number"
+}

Added value: +{
+  "description": "True when transcript consequences were capped at max_transcript_consequences.",
+  "type": "boolean"
+}

Previous value: -"Ensembl stable ID (ENSG…, ENST…, ENSP…) or region in the format species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) for region mode. For genomic region queries, species is also required."New value: +"Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-32400268) when the species field is set."

Previous value: -"Species in Ensembl internal format (e.g. homo_sapiens). Required for region mode (when id is a species:chr:start-end string). Optional for stable ID lookups — Ensembl infers species from the ID prefix."New value: +"Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region; optional for the species:chr:start-end form (the embedded species is used when the field is omitted). Optional for stable ID lookups — Ensembl infers species from the ID prefix."

Previous value: -"Variant in one of two formats: (1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; genomic: 13:g.32316462T>A; (2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T. For region+allele, strand is 1 (forward) or -1 (reverse); chromosome names use no \"chr\" prefix for vertebrates."New value: +"Variant in one of three formats: (1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; genomic: 13:g.32316462T>A; (2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T (strand is 1 for forward or -1 for reverse); (3) dbSNP rsID — e.g. rs334. Ensembl normalizes chromosome names; canonical vertebrate output omits the \"chr\" prefix, though a chr-prefixed name is also accepted."

Previous value: -"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Chromosome names use Ensembl format — no \"chr\" prefix for vertebrates (13, not chr13). For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."New value: +"Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also accepted. For large regions (>100 kb), limit to gene feature type to avoid overwhelming results."

Added value: +{
+  "description": "Parent transcript ID (ENST…) for exon features. An exon is reported once per parent transcript it belongs to, so the same exon ID can appear on multiple rows that differ only by this field — not duplicates.",
+  "type": "string"
+}

Added value: +{
+  "description": "Position (1-based) of an exon within its parent transcript.",
+  "type": "number"
+}

Previous value: -"Filter to a specific Ensembl division. EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. EnsemblPlants covers crop and model plant genomes. EnsemblFungi, EnsemblMetazoa, EnsemblProtists cover non-vertebrate model organisms. Omit to return all divisions."New value: +"Filter to a specific Ensembl division. EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. EnsemblPlants covers crop and model plant genomes. EnsemblFungi, EnsemblMetazoa, EnsemblProtists cover non-vertebrate model organisms. Omit to return the endpoint default division (vertebrates)."

Previous value: -"Ensembl stable gene ID (e.g. ENSG00000139618). Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be used together with symbol."New value: +"Ensembl stable gene ID (e.g. ENSG00000139618). Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be combined with symbol."

Previous value: -"Gene symbol in the source species (e.g. BRCA2, TP53). Requires species to be set. Cannot be used together with id."New value: +"Gene symbol in the source species (e.g. BRCA2, TP53). Species defaults to homo_sapiens; set species for other organisms. Cannot be combined with id."

Added value: +{
+  "description": "Sequence length in characters — nucleotides for genomic/cdna/cds, amino-acid residues for protein. Use this to budget context window usage before processing the sequence.",
+  "type": "number"
+}

Removed value: -{
-  "description": "Sequence length in characters (nucleotides or amino acids). Use this to budget context window usage before processing the sequence.",
-  "type": "number"
-}

Previous value: -[
-  "id",
-  "type",
-  "seq",
-  "lengthInBp"
-]New value: +[
+  "id",
+  "type",
+  "seq",
+  "length"
+]

Previous value: -"Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Cannot be combined with symbol or id."New value: +"Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."

Previous value: -"Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Required when using symbol. Default is homo_sapiens for symbol-based lookups. Use ensembl_list_species to discover valid values."New value: +"Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. Use ensembl_list_species to discover valid values."

Previous value: -"Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Requires species to be set. Case-insensitive in most species."New value: +"Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species."

Previous value: -"Batch lookup: up to 20 gene symbols. Requires species to be set. Returns a succeeded/failed split. Cannot be combined with symbol, id, or ids."New value: +"Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols."