Ddbj Tools#

Configuration File: ddbj_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ddbj_tools.json configuration file.

Available Tools#

DDBJ_get_cross_references (Type: DDBJTool)#

List the DDBJ records linked to an accession, so you can walk a study to its experiments, runs, a…

DDBJ_get_cross_references tool specification

Tool Information:

  • Name: DDBJ_get_cross_references

  • Type: DDBJTool

  • Description: List the DDBJ records linked to an accession, so you can walk a study to its experiments, runs, and samples, or back to its BioProject. Returns linked accessions with their type and URL, plus a count of links per type. Filter with reference_type, e.g. ‘sra-run’. Studies can link thousands of runs, so results are capped by limit.

Parameters:

  • accession (string) (required) DDBJ accession, e.g. ‘DRP000001’.

  • entry_type ([‘string’, ‘null’]) (optional) Override the inferred entry type. One of: bioproject, biosample, sra-study, sra-experiment, sra-run, sra-sample, jga-study.

  • reference_type ([‘string’, ‘null’]) (optional) Only return links of this type, e.g. ‘sra-run’, ‘bioproject’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum links to return (default 25, max 200).

Example Usage:

query = {
    "name": "DDBJ_get_cross_references",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

DDBJ_get_entry (Type: DDBJTool)#

Retrieve a DNA Data Bank of Japan record by accession. DDBJ is the third INSDC member alongside N…

DDBJ_get_entry tool specification

Tool Information:

  • Name: DDBJ_get_entry

  • Type: DDBJTool

  • Description: Retrieve a DNA Data Bank of Japan record by accession. DDBJ is the third INSDC member alongside NCBI/GenBank and EMBL-EBI/ENA, and also hosts JGA (Japan’s controlled-access human archive), GEA (expression), and MetaboBank (metabolomics). The entry type is inferred from the accession prefix (PRJD*=bioproject, SAMD*=biosample, DRP*=sra-study, DRX*=sra-experiment, DRR*=sra-run, DRS*=sra-sample, JGAS*=jga-study, E-GEAD*=gea, MTBKS*=metabobank) unless you pass entry_type. Example: accession=’DRP000001’.

Parameters:

  • accession (string) (required) DDBJ accession, e.g. ‘DRP000001’, ‘PRJDB3490’, ‘JGAS000001’, ‘E-GEAD-1000’, ‘MTBKS102’.

  • entry_type ([‘string’, ‘null’]) (optional) Override the inferred entry type. One of: bioproject, biosample, sra-study, sra-experiment, sra-run, sra-sample, jga-study, gea, metabobank.

Example Usage:

query = {
    "name": "DDBJ_get_entry",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

DDBJ_search_entries (Type: DDBJTool)#

Keyword search one DDBJ entry type (bioproject, biosample, sra-study, sra-experiment, sra-run, sr…

DDBJ_search_entries tool specification

Tool Information:

  • Name: DDBJ_search_entries

  • Type: DDBJTool

  • Description: Keyword search one DDBJ entry type (bioproject, biosample, sra-study, sra-experiment, sra-run, sra-sample, jga-study, gea, metabobank), optionally filtered by organism NCBI taxonomy ID. Example: entry_type=’gea’, keywords=’daptomycin resistance’ finds gene-expression studies on antibiotic resistance. Returns each match’s identifier for use with DDBJ_get_entry or DDBJ_get_cross_references.

Parameters:

  • entry_type (string) (required) Which DDBJ record type to search.

  • keywords (string) (required) Free-text search terms, e.g. ‘daptomycin resistance’.

  • organism_taxid ([‘string’, ‘integer’, ‘null’]) (optional) Optional NCBI taxonomy ID filter, e.g. 9606 (human).

  • limit ([‘integer’, ‘null’]) (optional) Max entries to return, 1-100. Default 25.

Example Usage:

query = {
    "name": "DDBJ_search_entries",
    "arguments": {
        "entry_type": "example_value",
        "keywords": "example_value"
    }
}
result = tu.run(query)