Gene product report

Gene record identifiers, genomic locations, transcripts, and products

Gene product report

Gene record identifiers, genomic locations, transcripts, and products

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

ncbi_dataset/data/product_report.jsonl

Each line of the gene product 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 product reports from JSON Lines to tabular formats.

Sample report

{
  "commonName": "human",
  "description": "alpha-1-B glycoprotein",
  "geneId": "1",
  "proteinCount": 1,
  "symbol": "A1BG",
  "taxId": "9606",
  "taxname": "Homo sapiens",
  "transcriptCount": 1,
  "transcriptTypeCounts": [
    {
      "count": 1,
      "type": "PROTEIN_CODING"
    }
  ],
  "transcripts": [
    {
      "accessionVersion": "NM_130786.4",
      "cds": {
        "accessionVersion": "NM_130786.4",
        "range": [
          {
            "begin": "56",
            "end": "1543"
          }
        ]
      },
      "ensemblTranscript": "ENST00000263100.8",
      "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"
        }
      ],
      "length": 3382,
      "protein": {
        "accessionVersion": "NP_570602.2",
        "ensemblProtein": "ENSP00000263100.2",
        "length": 495,
        "name": "alpha-1B-glycoprotein precursor"
      },
      "type": "PROTEIN_CODING"
    }
  ],
  "type": "PROTEIN_CODING"
}

ProductDescriptor 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	`GeneType`
`rnaType`	`rna-type`	RNA Type	`RnaType`
`transcripts repeated`	`transcript-`	Transcript	`Transcript`	RefSeq coding and non-coding transcript accessions
`transcriptCount`	`transcript-count`	Transcript Count	`uint32`
`proteinCount`	`protein-count`	Protein Count	`uint32`
`transcriptTypeCounts repeated`			`TranscriptTypeCount`

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`

MaturePeptide Structure

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

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	Description
`begin`	`start`	Start	`uint64`
`end`	`stop`	Stop	`uint64`
`orientation`	`orientation`	Orientation	`Orientation`
`order`	`order`	Order	`uint32`
`ribosomalSlippage`	coming soon	coming soon	`int32`	When ribosomal slippage is desired, fill out slippage amount between this and previous range.

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`

TranscriptTypeCount Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`type`			`Transcript.TranscriptType`
`count`	coming soon	coming soon	`uint32`

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`

Orientation Enumeration

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

RnaType Enumeration

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