MicroBIGG-E report

MicroBIGG-E record accession, organism, location, and biosample information

MicroBIGG-E report

MicroBIGG-E record accession, organism, location, and biosample information

The downloaded MicroBIGG-E package contains a MicroBIGG-E data report in JSON lines format at the following location in the file:

ncbi_dataset/data/data_report.jsonl

Each line of the MicroBIGG-E data report file is a hierarchical JSON object that represents a single MicroBIGG-E record. The schema of the MicroBIGG-E 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 MicroBiggeReport.

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 MicroBIGG-E data reports from JSON Lines to tabular formats.

Sample report

{
  "amrFinderPlus": {
    "dbVersion": "2023-08-08.2",
    "type": "COMBINED",
    "version": "3.11.26"
  },
  "amrMethod": "BLASTP",
  "biosample": {
    "accession": "SAMN07179453",
    "assembly": "GCA_009287105.1",
    "geographicOrigin": "United Kingdom: United Kingdom",
    "source": "human",
    "type": "clinical"
  },
  "class": "COPPER",
  "closestReferenceSequenceComparison": {
    "accession": "CAA58527.1",
    "alignLength": 126,
    "name": "copper resistance system metallochaperone PcoC",
    "percentCoverage": 100.0,
    "percentIdentical": 99.21
  },
  "element": {
    "length": 126,
    "name": "copper resistance system metallochaperone PcoC",
    "referenceLength": 126,
    "symbol": "pcoC"
  },
  "location": {
    "accessionVersion": "AAMJFE010000009.1",
    "range": [
      {
        "begin": "20304",
        "end": "20684",
        "orientation": "plus"
      }
    ]
  },
  "readToAssemblyCoverage": {
    "assembly": 52,
    "contig": 55,
    "ratio": 1.05769
  },
  "subclass": "COPPER",
  "subtype": "METAL",
  "targetAcc": "PDT000214120.2",
  "taxonomy": {
    "group": "Salmonella enterica",
    "scientificName": "Salmonella enterica subsp. enterica serovar Rissen"
  },
  "type": "STRESS"
}

MicroBiggeReport Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`targetAcc`	`target-accession`	Target accession	`string`
`element`			`Element`
`location`			`SeqRangeSet`	The range of the gene
`type`	`type`	Type	`string`		`AMR` `STRESS`
`subtype`	`subtype`	Subtype	`string`		`AMR` `METAL`
`class`	`class`	Class	`string`		`GLYCOPEPTIDE` `COPPER/SILVER`
`subclass`	`subclass`	Subclass	`string`		`VANCOMYCIN` `COPPER/SILVER`
`amrMethod`	`amr-method`	AMR method	`string`		`EXACTP`
`isPlus`	`is-plus`	Is plus	`bool`
`closestReferenceSequenceComparison`			`ClosestReference`
`taxonomy`			`Taxonomy`
`biosample`			`Biosample`
`readToAssemblyCoverage`			`ReadToAssemblyCoverage`
`amrFinderPlus`			`AmrFinderPlus`
`genesOnContig repeated`	coming soon	coming soon	`string`
`genesOnIsolate repeated`	coming soon	coming soon	`string`

AmrFinderPlus Structure

Field	Table Field Mnemonic	Table Column Name	Type
`version`	`amrfinderplus-version`	AMRFinderPlus version	`string`
`type`	`amrfinderplus-type`	AMRFinderPlus type	`string`
`dbVersion`	`amrfinderplus-db-version`	AMRFinderPlus database version	`string`

Biosample Structure

Field	Table Field Mnemonic	Table Column Name	Type	Examples
`geographicOrigin`	`biosample-geo-origin`	BioSample geographic origin	`string`	`Denmark` `not determined`
`source`	`biosample-source`	BioSample source	`string`
`type`	`biosample-type`	BioSample type	`string`	`clinical` `environmental/other`
`accession`	`biosample-accession`	BioSample accession	`string`	`SAMN00808999`
`assembly`	`biosample-assembly`	BioSample assembly accession	`string`	`GCA_000395725.1`
`collectionDate`	`biosample-collection-date`	BioSample collection date	`string`

ClosestReference Structure

Field	Table Field Mnemonic	Table Column Name	Type
`accession`	`closest-ref-accession`	Closest reference accession	`string`
`name`	`closest-ref-name`	Closest reference name	`string`
`percentCoverage`	`closest-ref-pct-coverage`	Closest reference percent coverage	`float`
`percentIdentical`	`closest-ref-pct-ident`	Closest reference percent identity	`float`
`alignLength`	`closest-ref-align-len`	Closest reference alignment length	`int32`

Element Structure

Field	Table Field Mnemonic	Table Column Name	Type	Examples
`symbol`	`elem-symbol`	Element symbol	`string`	`vanS-A` `copB`
`name`	`elem-name`	Element name	`string`	`VanA-type vancomycin resistance histidine kinase VanS` `copper/silver-translocating P-type ATPase CopB`
`length`	`elem-length`	Element length	`int32`
`referenceLength`	`elem-ref-length`	Element reference length	`int32`

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.

ReadToAssemblyCoverage Structure

Field	Table Field Mnemonic	Table Column Name	Type
`contig`	`read-assm-coverage-contig`	Read-to-Assembly-Coverage contig	`uint32`
`assembly`	`read-assm-coverage-assembly`	Read-to-Assembly-Coverage assembly	`uint32`
`ratio`	`read-assm-coverage-ratio`	Read-to-Assembly-Coverage ratio	`float`

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

Taxonomy Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`group`	`tax-group`	Taxonomic group	`string`		`Enterococcus faecium`
`scientificName`	`tax-name`	Taxonomic name	`string`		`Enterococcus faecium EnGen0172`

Orientation Enumeration

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

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 April 12, 2024