{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"title": "annotationReport",
"type": "object",
"properties": {
"reports": {
"type": "array",
"items": {
"type": "object",
"properties": {
"annotation": {
"type": "object",
"properties": {
"gene_id": {
"type": "string",
"format": "integer",
"title": "NCBI GeneID"
},
"symbol": {
"type": "string",
"title": "Gene symbol"
},
"description": {
"type": "string",
"title": "Gene name"
},
"name": {
"type": "string"
},
"tax_id": {
"type": "string",
"format": "integer",
"title": "NCBI Taxonomy ID for the organism"
},
"taxname": {
"type": "string",
"title": "Taxonomic name of the organism"
},
"common_name": {
"type": "string",
"title": "Common name of the organism"
},
"type": {
"title": "Deprecated",
"type": "string",
"default": "UNKNOWN",
"enum": [
"UNKNOWN",
"tRNA",
"rRNA",
"snRNA",
"scRNA",
"snoRNA",
"PROTEIN_CODING",
"PSEUDO",
"TRANSPOSON",
"miscRNA",
"ncRNA",
"BIOLOGICAL_REGION",
"OTHER"
]
},
"gene_type": {
"type": "string",
"title": "Gene locus type"
},
"rna_type": {
"type": "string",
"default": "rna_UNKNOWN",
"enum": [
"rna_UNKNOWN",
"premsg",
"tmRna"
]
},
"orientation": {
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"locus_tag": {
"type": "string"
},
"reference_standards": {
"type": "array",
"items": {
"type": "object",
"properties": {
"gene_range": {
"title": "The range of this Gene record on this genomic region.",
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "NCBI Accession.version of the sequence"
},
"range": {
"type": "array",
"items": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
}
}
}
},
"type": {
"title": "Type of genomic region",
"type": "string",
"default": "UNKNOWN",
"enum": [
"UNKNOWN",
"REFSEQ_GENE",
"PSEUDOGENE",
"BIOLOGICAL_REGION",
"OTHER"
]
}
}
}
},
"genomic_regions": {
"type": "array",
"items": {
"type": "object",
"properties": {
"gene_range": {
"title": "The range of this Gene record on this genomic region.",
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "NCBI Accession.version of the sequence"
},
"range": {
"type": "array",
"items": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
}
}
}
},
"type": {
"title": "Type of genomic region",
"type": "string",
"default": "UNKNOWN",
"enum": [
"UNKNOWN",
"REFSEQ_GENE",
"PSEUDOGENE",
"BIOLOGICAL_REGION",
"OTHER"
]
}
}
}
},
"transcripts": {
"type": "array",
"items": {
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "RefSeq transcript accession with version"
},
"name": {
"type": "string",
"title": "RefSeq transcript name"
},
"length": {
"type": "integer",
"title": "RefSeq transcript length in nucleotides"
},
"cds": {
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "NCBI Accession.version of the sequence"
},
"range": {
"type": "array",
"items": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
}
}
}
},
"genomic_locations": {
"type": "array",
"items": {
"type": "object",
"properties": {
"genomic_accession_version": {
"type": "string"
},
"sequence_name": {
"type": "string"
},
"genomic_range": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
},
"exons": {
"type": "array",
"items": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
}
}
}
}
},
"ensembl_transcript": {
"type": "string",
"title": "Ensembl transcript accession with version"
},
"protein": {
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "RefSeq protein accession with version"
},
"name": {
"type": "string",
"title": "Protein name"
},
"length": {
"type": "integer",
"title": "Protein length in amino acids"
},
"isoform_name": {
"type": "string",
"title": "Protein isoform name"
},
"ensembl_protein": {
"type": "string",
"title": "Ensembl protein accession with version"
},
"mature_peptides": {
"type": "array",
"items": {
"type": "object",
"properties": {
"accession_version": {
"type": "string"
},
"name": {
"type": "string"
},
"length": {
"type": "integer"
}
}
}
}
}
},
"type": {
"title": "Indicates transcript protein-coding potential and whether it was computationally predicted",
"type": "string",
"default": "UNKNOWN",
"enum": [
"UNKNOWN",
"PROTEIN_CODING",
"NON_CODING",
"PROTEIN_CODING_MODEL",
"NON_CODING_MODEL"
]
},
"select_category": {
"type": "string",
"default": "SELECT_UNKNOWN",
"enum": [
"SELECT_UNKNOWN",
"REFSEQ_SELECT",
"MANE_SELECT",
"MANE_PLUS_CLINICAL"
]
}
}
}
},
"proteins": {
"type": "array",
"items": {
"type": "object",
"properties": {
"accession_version": {
"type": "string",
"title": "RefSeq protein accession with version"
},
"name": {
"type": "string",
"title": "Protein name"
},
"length": {
"type": "integer",
"title": "Protein length in amino acids"
},
"isoform_name": {
"type": "string",
"title": "Protein isoform name"
},
"ensembl_protein": {
"type": "string",
"title": "Ensembl protein accession with version"
},
"mature_peptides": {
"type": "array",
"items": {
"type": "object",
"properties": {
"accession_version": {
"type": "string"
},
"name": {
"type": "string"
},
"length": {
"type": "integer"
}
}
}
}
}
}
},
"chromosomes": {
"type": "array",
"items": {
"type": "string"
}
},
"swiss_prot_accessions": {
"type": "array",
"items": {
"type": "string"
}
},
"ensembl_gene_ids": {
"type": "array",
"items": {
"type": "string"
}
},
"omim_ids": {
"type": "array",
"items": {
"type": "string"
}
},
"synonyms": {
"type": "array",
"items": {
"type": "string"
}
},
"annotations": {
"type": "array",
"items": {
"type": "object",
"properties": {
"assembly_accession": {
"type": "string",
"title": "Genome assembly accession"
},
"assembly_name": {
"type": "string",
"title": "Genome assembly name"
},
"annotation_name": {
"type": "string",
"title": "Genome annotation name"
},
"annotation_release_date": {
"type": "string",
"title": "Genome annotation release date"
},
"genomic_locations": {
"type": "array",
"items": {
"type": "object",
"properties": {
"genomic_accession_version": {
"type": "string"
},
"sequence_name": {
"type": "string"
},
"genomic_range": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
},
"exons": {
"type": "array",
"items": {
"type": "object",
"properties": {
"begin": {
"type": "string",
"format": "integer",
"title": "Sequence start position"
},
"end": {
"type": "string",
"format": "integer",
"title": "Sequence stop position"
},
"orientation": {
"title": "Direction relative to the genome",
"type": "string",
"default": "none",
"enum": [
"none",
"plus",
"minus"
]
},
"order": {
"type": "integer",
"title": "The position of this sequence in a group of sequences"
},
"ribosomal_slippage": {
"type": "integer",
"title": "When ribosomal slippage is desired, fill out slippage amount between this and previous range."
}
}
}
}
}
}
}
}
}
}
}
},
"query": {
"items": {
"type": "string"
},
"type": "array"
},
"warning": {
"type": "object",
"properties": {
"gene_warning_code": {
"type": "string",
"default": "UNKNOWN_GENE_WARNING_CODE",
"enum": [
"UNKNOWN_GENE_WARNING_CODE",
"ACCESSION_VERSION_MISMATCH",
"REPLACED_GENE_ID",
"DISCONTINUED_GENE_ID",
"UNRECOGNIZED_GENE_ID",
"UNRECOGNIZED_GENE_SYMBOL",
"UNRECOGNIZED_ACCESSION",
"UNRECOGNIZED_TAX_TOKEN",
"NO_GENE_ANNOTATION_FOUND",
"ABOVE_SPECIES_TAXON"
]
},
"reason": {
"type": "string"
},
"message": {
"type": "string"
},
"replaced_id": {
"type": "object",
"properties": {
"requested": {
"type": "string"
},
"returned": {
"type": "string"
}
}
},
"unrecognized_identifier": {
"type": "string"
}
}
},
"errors": {
"type": "array",
"items": {
"type": "object",
"properties": {
"assembly_error_code": {
"type": "string",
"default": "UNKNOWN_ASSEMBLY_ERROR_CODE",
"enum": [
"UNKNOWN_ASSEMBLY_ERROR_CODE",
"INVALID_BIOPROJECT_IDS",
"NO_ASSEMBLIES_FOR_BIOPROJECTS",
"INVALID_TAXON",
"MISSING_SEARCH_FIELD",
"INVALID_BIOSAMPLE_IDS",
"NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS",
"NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES",
"INVALID_WGS_ACCESSIONS",
"NO_ASSEMBLIES_FOR_WGS_ACCESSIONS"
]
},
"gene_error_code": {
"type": "string",
"default": "UNKNOWN_GENE_ERROR_CODE",
"enum": [
"UNKNOWN_GENE_ERROR_CODE",
"INCOMPLETE_LOOKUP_SYMBOL",
"INVALID_TAXON_GENE_ARGUMENT"
]
},
"organelle_error_code": {
"type": "string",
"default": "UNKNOWN_ORGANELLE_ERROR_CODE",
"enum": [
"UNKNOWN_ORGANELLE_ERROR_CODE",
"INVALID_ORGANELLE_TAXON",
"NO_ORGANELLES_FOR_ACCESSION"
]
},
"virus_error_code": {
"type": "string",
"default": "UNKNOWN_VIRUS_ERROR_CODE",
"const": "UNKNOWN_VIRUS_ERROR_CODE"
},
"taxonomy_error_code": {
"type": "string",
"default": "UNKNOWN_TAXONOMY_ERROR_CODE",
"enum": [
"UNKNOWN_TAXONOMY_ERROR_CODE",
"INVALID_TAXONOMY_TAXON"
]
},
"sequence_error_code": {
"type": "string",
"default": "UNKNOWN_SEQUENCE_ERROR_CODE",
"enum": [
"UNKNOWN_SEQUENCE_ERROR_CODE",
"INVALID_SEQUENCE_ACCESSION"
]
},
"reason": {
"type": "string"
},
"message": {
"type": "string"
},
"invalid_identifiers": {
"type": "array",
"items": {
"type": "string"
}
}
}
}
},
"row_id": {
"type": "string"
}
}
}
},
"messages": {
"type": "array",
"items": {
"type": "object",
"properties": {
"error": {
"type": "object",
"properties": {
"assembly_error_code": {
"type": "string",
"default": "UNKNOWN_ASSEMBLY_ERROR_CODE",
"enum": [
"UNKNOWN_ASSEMBLY_ERROR_CODE",
"INVALID_BIOPROJECT_IDS",
"NO_ASSEMBLIES_FOR_BIOPROJECTS",
"INVALID_TAXON",
"MISSING_SEARCH_FIELD",
"INVALID_BIOSAMPLE_IDS",
"NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS",
"NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES",
"INVALID_WGS_ACCESSIONS",
"NO_ASSEMBLIES_FOR_WGS_ACCESSIONS"
]
},
"gene_error_code": {
"type": "string",
"default": "UNKNOWN_GENE_ERROR_CODE",
"enum": [
"UNKNOWN_GENE_ERROR_CODE",
"INCOMPLETE_LOOKUP_SYMBOL",
"INVALID_TAXON_GENE_ARGUMENT"
]
},
"organelle_error_code": {
"type": "string",
"default": "UNKNOWN_ORGANELLE_ERROR_CODE",
"enum": [
"UNKNOWN_ORGANELLE_ERROR_CODE",
"INVALID_ORGANELLE_TAXON",
"NO_ORGANELLES_FOR_ACCESSION"
]
},
"virus_error_code": {
"type": "string",
"default": "UNKNOWN_VIRUS_ERROR_CODE",
"const": "UNKNOWN_VIRUS_ERROR_CODE"
},
"taxonomy_error_code": {
"type": "string",
"default": "UNKNOWN_TAXONOMY_ERROR_CODE",
"enum": [
"UNKNOWN_TAXONOMY_ERROR_CODE",
"INVALID_TAXONOMY_TAXON"
]
},
"sequence_error_code": {
"type": "string",
"default": "UNKNOWN_SEQUENCE_ERROR_CODE",
"enum": [
"UNKNOWN_SEQUENCE_ERROR_CODE",
"INVALID_SEQUENCE_ACCESSION"
]
},
"reason": {
"type": "string"
},
"message": {
"type": "string"
},
"invalid_identifiers": {
"type": "array",
"items": {
"type": "string"
}
}
}
},
"warning": {
"type": "object",
"properties": {
"gene_warning_code": {
"type": "string",
"default": "UNKNOWN_GENE_WARNING_CODE",
"enum": [
"UNKNOWN_GENE_WARNING_CODE",
"ACCESSION_VERSION_MISMATCH",
"REPLACED_GENE_ID",
"DISCONTINUED_GENE_ID",
"UNRECOGNIZED_GENE_ID",
"UNRECOGNIZED_GENE_SYMBOL",
"UNRECOGNIZED_ACCESSION",
"UNRECOGNIZED_TAX_TOKEN",
"NO_GENE_ANNOTATION_FOUND",
"ABOVE_SPECIES_TAXON"
]
},
"reason": {
"type": "string"
},
"message": {
"type": "string"
},
"replaced_id": {
"type": "object",
"properties": {
"requested": {
"type": "string"
},
"returned": {
"type": "string"
}
}
},
"unrecognized_identifier": {
"type": "string"
}
}
}
}
}
},
"total_count": {
"type": "integer",
"title": "The total count of available genes (ignoring the page_size parameter)."
},
"next_page_token": {
"type": "string",
"title": "A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages."
}
}
}