You are in REST API » v15.1 || Go to



Genome


Get all organism available on remote server that have genome data available

  • URL: /genomics/taxonomies/
  • Method: GET
  • Parameters: NONE
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/
    

Get all genome types (remote databases) that support given organism. Right now there is only one available: UCSC

  • URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/
  • Method: GET
  • Parameters:
    • taxonomyId - organism taxonomy
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/
    

Get all available genome versions for specified organism and genome type

  • URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions
  • Method: GET
  • Parameters:
    • taxonomyId - organism taxonomy
    • genomeType - remote database where we want to check versions (for now, only UCSC is supported)
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions/
    

Get remote url for specified genome, version, and remote database

  • URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/{version}:getAvailableRemoteUrls
  • Method: GET
  • Parameters:
    • taxonomyId - organism taxonomy
    • genomeType - remote database where we want to check versions (for now, only UCSC is supported)
    • version - version of the genome that we are interested in
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38:getAvailableRemoteUrls
    

Start downloading genome data from remote database to minerva

  • URL: /genomics/
  • Method: POST
  • Parameters:
    • organismId - organism taxonomy
    • type - remote database where we want to check versions (for now, only UCSC is supported)
    • version - version of the genome that we are interested in
    • sourceUrl - url to 2bit file with genome
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
     --data "organismId=9606&type=UCSC&version=hg38&sourceUrl=ftp%3A%2F%2Fhgdownload.cse.ucsc.edu%2FgoldenPath%2Fhg38%2FbigZips%2Fhg38.2bit"
     https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/
    

Get information about specific downloaded genome

  • URL: /genomics/taxonomies/{taxonomyId}/genomeTypes/{genomeType}/versions/{version}/
  • Method: GET
  • Parameters:
    • organismId - organism taxonomy
    • type - remote database where we want to check versions (for now, only UCSC is supported)
    • version - version of the genome that we are interested in
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/taxonomies/9606/genomeTypes/UCSC/versions/hg38/
    

Get information about all downloaded genomes

  • URL: /genomics/
  • Method: GET
  • Parameters: NONE
  • Example:
    curl -X GET https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/
    

Delete downloaded genome

  • URL: /genomics/{genomeId}/
  • Method: DELETE
  • Parameters:
    • genomeId - id of the downloaded genome
  • Example:
    curl -X DELETE --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
    https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/
    

Gene mapping

Add gene mapping

  • URL: /genomics/{genomeId}/geneMapping/
  • Method: POST
  • Parameters:
    • genomeId - id of the downloaded genome
    • name - name of the mapping
    • url - url to big bed file with gene mapping
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
    --data "name=mappingName&url=https%3A%2F%2Fminerva-dev.lcsb.uni.lu%2Ftmp%2FrefGene.bb"
    https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/
    

Delete gene mapping

  • URL: /genomics/{genomeId}/geneMapping/{geneMappingId}
  • Method: DELETE
  • Parameters:
    • genomeId - id of the downloaded genome
    • geneMappingId - id of the gene mapping
  • Example:
    curl -X POST --cookie "MINERVA_AUTH_TOKEN=xxxxxx"  \
    https://minerva-dev.lcsb.uni.lu/minerva/api/genomics/12345/geneMapping/32/
    


Back to top