MBGD API Documentation

Base URL
All API endpoints start with the following base URL:
https://mbgdapi.nibb.ac.jp/

Shared Query Parameters:
Parameter Type Description
format string Optional. Specifies the format of the response. Can be one of the following:
  • json: Returns data in JSON format. [Default]
  • xml: Returns data in XML format.
  • html: Returns data in HTML format, which displays the data as a table in the web browser.
  • tsv: Returns data in TSV (Tab-separated Values) format. The file will be downloaded mbgdapi.tsv.
  • csv: Returns data in CSV (Comma-separated Values) format. The file will be downloaded name mbgdapi.csv.
  • fasta: Returns data in FASTA format. For /chromseq, /proteinseq or /geneseq ONLY. The file will be downloaded name mbgdapi.fasta.
limit integer Optional. The maximum number of results to return. [Default: none]
offset integer Optional. The number of genomes to skip before beginning to return results. [Default: 0]
order string Optional. The order to sort the results in. Can be one of the following:
  • asc: [Default]
  • desc:
version string Optional. Specify the version of the MBGD dataset. [Default: current]
  • 2015_1:
  • 2016_1:
  • 2018_1:
  • 2022_1:
  • 2024_1: [Default (current)]


Available Endpoints Examples Search for spid, taxid etc.


GET   /genome
  • Returns a list of complete genomes.
Path Prameters:
    None
Response:
  • spid - species ID
  • sp - species code
  • abbrev - Abbreviated name
  • orgname - Organism name
  • strain - Strain name
  • taxid - Taxonomy ID
  • tax_family - Taxonomy family name
  • tax_genus - Taxonomy genus name
  • tax_species - Taxonomy species name
  • source - Source
  • medid -
  • date_release - Release of date
  • date_modify - Modified date
  • seq_status - Sequence status
GET   /genome/:sp
    Returns information about a specific genome.
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • Same as /genome
GET   /chromosome/:sp
  • Returns chromosome information for given spid.
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • spid - species ID
  • sp - species code
  • name - Chromosome name
  • seqno - Number of chromosome
  • type - Chromosome type
  • shape - Chromosome shape
  • accession - NCBI accession No.
  • accession_gbk - GenBank accesson No.
  • seq_length - Chromosome length
  • count_genes - Number of genes
  • source - Source
GET   /chromseq/:sp
  • Returns all chromosome sequcences for given spid. To download a fasta format file, specify "format=fasta"
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • spid - species ID
  • sp - species code
  • name - Chromosome name
  • seqno - Number of chromosome
  • type - Chromosome type
  • shape - Chromosome shape
  • accession - NCBI accession No.
  • accession_gbk - GenBank accesson No.
  • seq_length - Chromosome length
  • count_genes - Number of genes
  • source - Source
GET   /gene/:sp
  • Returns a list of all genes for a given spid.
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • sp - species code
  • name - Gene name
  • gene - Gene symbol
  • from1 -
  • to1 -
  • dir - Gene direction
  • transl_table -
  • codon_start - Codon start
  • protid - NCBI accession No.
  • protid_gbk - GenBank accession No.
  • gi - Gene Identifier (Discontinued by NCBI)
  • geneid - NCBI Gene ID
  • descr - Description
GET   /gene/:sp/:name
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
Response:
  • Same as /gene/:sp
GET   /proteinseq/:sp
  • Returns all protein sequence for given sp. To download a fasta format file, specify "format=fasta"
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • sp - species code
  • name - Chromosome name
  • gene - Gene Symbol
  • descr - Description
  • seq - Sequence
GET   /proteinseq/:sp/:name
  • Returns protein sequence for given sp and gene name. To download a fasta format file, specify "format=fasta"
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
Response:
  • sp - species code
  • name - Chromosome name
  • gene - Gene Symbol
  • descr - Description
  • seq - Sequence
GET   /geneseq/:sp/:name
  • Returns all nucleotide sequence for given sp. To download a fasta format file, specify "format=fasta"
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
Response:
  • Same as /proteinseq/:sp
GET   /geneseq/:sp/:name
  • Returns nucleotide sequence for given sp and gene name. To download a fasta format file, specify "format=fasta"
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
Response:
  • Same as /proteinseq/:sp/:name
GET   /ortholog-group/top/:clustid
  • Returns members of a given orthologous group (default set). (Version > 2022)
Path Parameters:
  • clustid - Cluster ID (Integer e.g. 1001)
Response:
  • clustid - Cluster ID
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
  • dom - domain number
  • from1 -
  • to1 -
GET   /ortholog-group/:taxid/:clustid
  • Returns members of a phylogeny-specific orthologous group. (Version > 2022)
Path Parameters:
  • taxid - Taxonomy ID (e.g. tax1101)
  • clustid - Cluster ID (Integer e.g. 1001)
Response:
  • Same as /ortholog-group/top/:clustid
GET   /ortholog-group/:taxid/:clustid/extend
  • Returns extended members of a phylogeny-specific orthologous group. (Version > 2022)
Path Parameters:
  • taxid - Taxonomy ID (e.g. tax1101)
  • clustid - Cluster ID (Integer e.g. 1001)
Response:
  • Same as /ortholog-group/top/:clustid
GET   /ortholog-group_by_gene/:sp/:name?recursive=[true|false]
  • Returns the ortholog groups that the specified gene is assigned to. (Version > 2022)
Path Parameters:
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
Query Parameters:
  • recursive=[true|false] - Whether to recursively traverse hierarchical ortholog groups [Default: false, in which case only top-level ortholog groups are output]
Response:
  • tabid - phylogeny-specific table ID
  • clustid - Cluster ID
  • sp - species code (3-5 letters e.g. eco)
  • name - Gene name
  • spname - sp + name
  • dom - domain number
  • from1 -
  • to1 -
GET   /taxonomy/:taxid
  • Returns details for a given taxonomy ID.
Path Parameters:
  • taxid - Taxonomy ID (e.g. tax1101)
Response:
  • taxid - Taxonomy ID
  • name - Sciencific name
  • rank - Taxonomic rank


  • Return a list of complete genomes of current version(2024_1) MBGD with detailed information. Default JSON response
    https://mbgdapi.nibb.ac.jp/genome
  • Return a list of complete genomes of 2018_1 version MBGD with detailed information. Default JSON response
    https://mbgdapi.nibb.ac.jp/genome?version=2018_1
  • Display the eco (Escherichia coli K-12 MG1655) information table on a browser.
    https://mbgdapi.nibb.ac.jp/genome/eco?format=html
  • Download the all hsa (Homo sapience)'s chromosomes information as tab-delimited text file.
    https://mbgdapi.nibb.ac.jp/chromosome/hsa?format=tab
  • Download the all hpy (Helicobacter pylori 26695)'s chromosome sequence as FASTA format file.
    https://mbgdapi.nibb.ac.jp/chromseq/hpy?format=fasta
  • Download the all eco (Escherichia coli K-12 MG1655)'s information as CSV format file.
    https://mbgdapi.nibb.ac.jp/gene/eco?format=csv
  • Display the eco (Escherichia coli K-12 MG1655) gene B0001's nucleotide sequence on a browser.
    https://mbgdapi.nibb.ac.jp/geneseq/eco/B0001?format=html
  • Download the all lla (Lactococcus lactis IL1403)'s protein sequences as FASTA format.
    https://mbgdapi.nibb.ac.jp/proteinseq/lla?format=fasta
  • Returns all members of the Cluster ID 1001 orthologous group. Default JSON response
    • Version > 2022
      • https://mbgdapi.nibb.ac.jp/ortholog-group/top/1001
    • Version 2015-2018
      • https://mbgdapi.nibb.ac.jp/ortholog-group/1001?version=2018_1
  • Returns members specific to the taxonomy ID 9 in the Cluster ID 164. Default JSON response (Version > 2022)
    https://mbgdapi.nibb.ac.jp/ortholog-group/tax9/164
  • Returns extended members specific to the taxonomy ID 9 in the Cluster ID 164. Default JSON response (Version > 2022)
    https://mbgdapi.nibb.ac.jp/ortholog-group/tax9/164/extend
  • HTML display all ortholog groups containing the buc's BU030 gene. If "recursive=true" is specified, taxon-specific ortholog groups are also returned. (Version > 2022)
    https://mbgdapi.nibb.ac.jp/ortholog-group_by_gene/buc/BU030?recursive=true&format=html
  • Returns the detail for taxonomy ID 79328. XML response
    https://mbgdapi.nibb.ac.jp/taxonomy/tax79328?format=xml




Input a search term at least 3 characters and press return.
Search for spid, taxid, strain.


Open the list of taxonomy that has specific ortholog groups