Gene report

Gene record identifiers, genomic locations, transcripts, and products

Gene report

Gene record identifiers, genomic locations, transcripts, and products

The downloaded gene package contains a gene data report in JSON Lines format in the file:

ncbi_dataset/data/data_report.jsonl

Each line of the gene data report file is a hierarchical JSON object that represents a single gene record. The schema of the gene record is defined in the tables below where each row describes a single field in the report or a sub-structure, which is a collection of fields. The outermost structure of the report is GeneDescriptor.

Table fields that include a Table Field Mnemonic can be used with the dataformat command-line tool's --fields option. Refer to the dataformat CLI tool reference to see how you can use this tool to transform gene data reports from JSON Lines to tabular formats.

Sample report

{
  "annotations": [
    {
      "assembliesInScope": [
        {
          "accession": "GCF_000001405.40",
          "name": "GRCh38.p14"
        }
      ],
      "releaseDate": "2024-08-23",
      "releaseName": "GCF_000001405.40-RS_2024_08"
    },
    {
      "assembliesInScope": [
        {
          "accession": "GCF_009914755.1",
          "name": "T2T-CHM13v2.0"
        }
      ],
      "releaseDate": "2024-08-23",
      "releaseName": "GCF_009914755.1-RS_2024_08"
    }
  ],
  "chromosomes": [
    "19"
  ],
  "commonName": "human",
  "description": "alpha-1-B glycoprotein",
  "ensemblGeneIds": [
    "ENSG00000121410"
  ],
  "geneGroups": [
    {
      "id": "1",
      "method": "NCBI Ortholog"
    }
  ],
  "geneId": "1",
  "genomicRanges": [
    {
      "accessionVersion": "NC_000019.10",
      "range": [
        {
          "begin": "58345183",
          "end": "58353492",
          "orientation": "minus"
        }
      ]
    },
    {
      "accessionVersion": "NC_060943.1",
      "range": [
        {
          "begin": "61441599",
          "end": "61449907",
          "orientation": "minus"
        }
      ]
    }
  ],
  "nomenclatureAuthority": {
    "authority": "HGNC",
    "identifier": "HGNC:5"
  },
  "omimIds": [
    "138670"
  ],
  "orientation": "minus",
  "swissProtAccessions": [
    "P04217"
  ],
  "symbol": "A1BG",
  "synonyms": [
    "A1B",
    "ABG",
    "GAB",
    "HYST2477"
  ],
  "taxId": "9606",
  "taxname": "Homo sapiens",
  "transcripts": [
    {
      "accessionVersion": "NM_130786.4",
      "cds": {
        "accessionVersion": "NM_130786.4",
        "range": [
          {
            "begin": "56",
            "end": "1543"
          }
        ]
      },
      "ensemblTranscript": "ENST00000263100.8",
      "exons": {
        "accessionVersion": "NC_000019.10",
        "range": [
          {
            "begin": "58353404",
            "end": "58353492",
            "order": 1
          },
          {
            "begin": "58353292",
            "end": "58353327",
            "order": 2
          },
          {
            "begin": "58352928",
            "end": "58353197",
            "order": 3
          },
          {
            "begin": "58352283",
            "end": "58352555",
            "order": 4
          },
          {
            "begin": "58351391",
            "end": "58351687",
            "order": 5
          },
          {
            "begin": "58350370",
            "end": "58350651",
            "order": 6
          },
          {
            "begin": "58347353",
            "end": "58347640",
            "order": 7
          },
          {
            "begin": "58345183",
            "end": "58347029",
            "order": 8
          }
        ]
      },
      "genomicLocations": [
        {
          "exons": [
            {
              "begin": "58353404",
              "end": "58353492",
              "order": 1
            },
            {
              "begin": "58353292",
              "end": "58353327",
              "order": 2
            },
            {
              "begin": "58352928",
              "end": "58353197",
              "order": 3
            },
            {
              "begin": "58352283",
              "end": "58352555",
              "order": 4
            },
            {
              "begin": "58351391",
              "end": "58351687",
              "order": 5
            },
            {
              "begin": "58350370",
              "end": "58350651",
              "order": 6
            },
            {
              "begin": "58347353",
              "end": "58347640",
              "order": 7
            },
            {
              "begin": "58345183",
              "end": "58347029",
              "order": 8
            }
          ],
          "genomicAccessionVersion": "NC_000019.10",
          "genomicRange": {
            "begin": "58345183",
            "end": "58353492",
            "orientation": "minus"
          },
          "sequenceName": "Chromosome 19 Reference GRCh38.p14 Primary Assembly"
        },
        {
          "exons": [
            {
              "begin": "61449819",
              "end": "61449907",
              "order": 1
            },
            {
              "begin": "61449707",
              "end": "61449742",
              "order": 2
            },
            {
              "begin": "61449343",
              "end": "61449612",
              "order": 3
            },
            {
              "begin": "61448698",
              "end": "61448970",
              "order": 4
            },
            {
              "begin": "61447805",
              "end": "61448101",
              "order": 5
            },
            {
              "begin": "61446784",
              "end": "61447065",
              "order": 6
            },
            {
              "begin": "61443768",
              "end": "61444055",
              "order": 7
            },
            {
              "begin": "61441599",
              "end": "61443445",
              "order": 8
            }
          ],
          "genomicAccessionVersion": "NC_060943.1",
          "genomicRange": {
            "begin": "61441599",
            "end": "61449907",
            "orientation": "minus"
          },
          "sequenceName": "Chromosome 19 Alternate T2T-CHM13v2.0"
        }
      ],
      "genomicRange": {
        "accessionVersion": "NC_000019.10",
        "range": [
          {
            "begin": "58345183",
            "end": "58353492",
            "orientation": "minus"
          }
        ]
      },
      "length": 3382,
      "protein": {
        "accessionVersion": "NP_570602.2",
        "ensemblProtein": "ENSP00000263100.2",
        "length": 495,
        "name": "alpha-1B-glycoprotein precursor"
      },
      "type": "PROTEIN_CODING"
    }
  ],
  "type": "PROTEIN_CODING"
}

GeneDescriptor Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`geneId`	`gene-id`	NCBI GeneID	`uint64`	NCBI Gene ID	`2778`
`symbol`	`symbol`	Symbol	`string`	gene symbol	`GNAS`
`description`	`description`	Description	`string`	gene name	`GNAS complex locus`
`taxId`	`tax-id`	Taxonomic ID	`uint64`	NCBI Taxonomy ID for the organism	`9606`
`taxname`	`tax-name`	Taxonomic Name	`string`	Taxonomic name of the organism	`Homo sapiens`
`commonName`	`common-name`	Common Name	`string`	Common name of the organism	`human`
`type`	`gene-type`	Gene Type	`GeneDescriptor.GeneType`
`rnaType`	`rna-type`	RNA Type	`GeneDescriptor.RnaType`
`orientation`	`orientation`	Orientation	`Orientation`
`genomicRanges repeated`	`genomic-range-`	Genomic Range	`SeqRangeSet`
`referenceStandards repeated`	`ref-standard-`	Reference Standard	`GenomicRegion`	Clinical reference standard NG
`genomicRegions repeated`	`genomic-region-`	Genomic Region	`GenomicRegion`	Pseudogene, non-genic regulatory element and other genomic region NG
`transcripts repeated`	`transcript-`	Transcript	`Transcript`	RefSeq coding and non-coding transcript accessions
`proteins repeated`	`protein-`	Protein	`Protein`	Only for proteins directly annotated on the Gene, without any intermediary transcript
`chromosomes repeated`	`chromosomes`	Chromosomes	`string`		`1` `X,Y`
`nomenclatureAuthority`	`name-`	Nomenclature	`NomenclatureAuthority`
`swissProtAccessions repeated`	`swissprot-accessions`	SwissProt Accessions	`string`
`ensemblGeneIds repeated`	`ensembl-geneids`	Ensembl GeneIDs	`string`
`omimIds repeated`	`omim-ids`	OMIM IDs	`string`
`synonyms repeated`	`synonyms`	Synonyms	`string`
`replacedGeneId`	`replaced-gene-id`	Replaced NCBI GeneID	`uint64`	The NCBI Gene ID for the gene that was merged into the current gene record
`annotations repeated`	`annotation-`	Annotation	`Annotation`

AnnotatedAssemblies Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accession`	`accession`	Accession	`string`
`name`	`name`	Name	`string`

Annotation Structure

Field	Table Field Mnemonic	Table Column Name	Type
`releaseName`	`release-name`	Release Name	`string`
`releaseDate`	`release-date`	Release Date	`string`
`assembliesInScope repeated`	`assemblies-in-scope-`	Assemblies in Scope	`AnnotatedAssemblies`

GenomicLocation Structure

Field	Table Field Mnemonic	Table Column Name	Type
`genomicAccessionVersion`	`accession`	Accession	`string`
`sequenceName`	`seq-name`	Seq Name	`string`
`genomicRange`	`range-`		`Range`
`exons repeated`	`exon-`	Exons	`Range`

GenomicRegion Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`geneRange`	`gene-range-`	Gene Range	`SeqRangeSet`	The range of this Gene record on this genomic region.
`type`	`genomic-region-type`	Genomic Region Type	`GenomicRegion.GenomicRegionType`

MaturePeptide Structure

Field	Table Field Mnemonic	Table Column Name	Type
`accessionVersion`	`accession`	Accession	`string`
`name`	`name`	Name	`string`
`length`	`length`	Length	`uint32`

NomenclatureAuthority Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`authority`	`authority`	Authority	`string`	The nomenclature authority for this gene record	`HGNC`
`identifier`	`id`	ID	`string`	The nomenclature authority identifier for this gene record	`HGNC:4392`

Protein Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accessionVersion`	`accession`	Accession	`string`	RefSeq protein accession with version	`NP_001296812.1`
`name`	`name`	Name	`string`	Protein name	`protein ALEX`
`length`	`length`	Length	`uint32`	Protein length in amino acids	`626`
`isoformName`	`isoform`	Isoform	`string`	Protein isoform name	`isoform Alex`
`ensemblProtein`	`ensembl-protein`	Ensembl Protein	`string`	Ensembl protein accession with version	`ENSP00000302237.3`
`maturePeptides repeated`	`mat-peptide-`	Mature Peptide	`MaturePeptide`

Range Structure

A 1-based range on a sequence record.

Field	Table Field Mnemonic	Table Column Name	Type
`begin`	`start`	Start	`uint64`
`end`	`stop`	Stop	`uint64`
`orientation`	`orientation`	Orientation	`Orientation`
`order`	`order`	Order	`uint32`

SeqRangeSet Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accessionVersion`	`accession`	Sequence Accession	`string`	NCBI Accession.version of the sequence
`range repeated`	`range-`		`Range`	Series of intervals on above accession_version

Transcript Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accessionVersion`	`accession`	Accession	`string`	RefSeq transcript accession with version
`name`	`name`	Transcript Name	`string`	RefSeq transcript name	`transcript variant 12`
`length`	`length`	Transcript Length	`uint32`	RefSeq transcript length in nucleotides	`3180`
`cds`	`cds-`	CDS	`SeqRangeSet`
`genomicLocations repeated`	`genomic-location-`	Genomic	`GenomicLocation`
`ensemblTranscript`	`ensembl-transcript`	Ensembl Transcript	`string`	Ensembl transcript accession with version	`ENST00000306120.3`
`protein`	`protein-`	Protein	`Protein`
`type`	`transcript-type`	Type	`Transcript.TranscriptType`

GeneDescriptor.GeneType Enumeration

NB: GeneType values match Entrez Gene

Name	Number	Description
`UNKNOWN`	`0`
`tRNA`	`1`
`rRNA`	`2`
`snRNA`	`3`
`scRNA`	`4`
`snoRNA`	`5`
`PROTEIN_CODING`	`6`
`PSEUDO`	`7`	these will have NG or NR
`TRANSPOSON`	`8`
`miscRNA`	`9`
`ncRNA`	`10`
`BIOLOGICAL_REGION`	`11`	these will have NG
`OTHER`	`255`

GeneDescriptor.RnaType Enumeration

Name	Number	Description
`rna_UNKNOWN`	`0`
`premsg`	`1`
`tmRna`	`2`

GenomicRegion.GenomicRegionType Enumeration

Name	Number	Description
`UNKNOWN`	`0`
`REFSEQ_GENE`	`1`
`PSEUDOGENE`	`2`
`BIOLOGICAL_REGION`	`3`
`OTHER`	`4`

Orientation Enumeration

Name	Number	Description
`none`	`0`
`plus`	`1`
`minus`	`2`

Transcript.TranscriptType Enumeration

Name	Number	Description
`UNKNOWN`	`0`
`PROTEIN_CODING`	`1`
`NON_CODING`	`2`
`PROTEIN_CODING_MODEL`	`3`
`NON_CODING_MODEL`	`4`

Scalar Value Types

Protocol buffers type	Notes	C++	Python	Java	Go
`double`		`double`	`float`	`double`	`float64`
`float`		`float`	`float`	`float`	`float32`
`int32`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.	`int32`	`int`	`int`	`int32`
`int64`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.	`int64`	`int/long`	`long`	`int64`
`uint32`	Uses variable-length encoding.	`uint32`	`int/long`	`int`	`uint32`
`uint64`	Uses variable-length encoding.	`uint64`	`int/long`	`long`	`uint64`
`sint32`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.	`int32`	`int`	`int`	`int32`
`sint64`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.	`int64`	`int/long`	`long`	`int64`
`fixed32`	Always four bytes. More efficient than uint32 if values are often greater than 2^28.	`uint32`	`int`	`int`	`uint32`
`fixed64`	Always eight bytes. More efficient than uint64 if values are often greater than 2^56.	`uint64`	`int/long`	`long`	`uint64`
`sfixed32`	Always four bytes.	`int32`	`int`	`int`	`int32`
`sfixed64`	Always eight bytes.	`int64`	`int/long`	`long`	`int64`
`bool`		`bool`	`boolean`	`boolean`	`bool`
`string`	A string must always contain UTF-8 encoded or 7-bit ASCII text.	`string`	`str/unicode`	`String`	`string`
`bytes`	May contain any arbitrary sequence of bytes.	`string`	`str`	`ByteString`	`[]byte`

Generated November 25, 2024