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  1. IGB
  2. IGBF-3129

Enable IGB to directly consume data from UCSC JSON API

    Details

    • Type: Epic
    • Status: To-Do (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Epic Name:
      Add UCSC REST API to IGB
    • Story Points:
      5

      Description

      See linked tickets.

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            nfreese Nowlan Freese added a comment - - edited Documentation DAS: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 API: https://genome.ucsc.edu/goldenPath/help/api.html
            Show
            nfreese Nowlan Freese added a comment - The queries below should produce equivalent output DAS: https://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=M:1,16569 API: https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM
            Hide
            nfreese Nowlan Freese added a comment -

            Using the hg38 human genome as an example:
            DAS Types (available files for that genome): https://genome.ucsc.edu/cgi-bin/das/hg38/types
            DAS Entry Points (chromosomes for that genome): https://genome.ucsc.edu/cgi-bin/das/hg38/entry_points

            Show
            nfreese Nowlan Freese added a comment - Using the hg38 human genome as an example: DAS Types (available files for that genome): https://genome.ucsc.edu/cgi-bin/das/hg38/types DAS Entry Points (chromosomes for that genome): https://genome.ucsc.edu/cgi-bin/das/hg38/entry_points
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            nfreese Nowlan Freese added a comment -
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            nfreese Nowlan Freese added a comment - Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes
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            nfreese Nowlan Freese added a comment - - edited

            Additional API examples:

            • List all of the tracks available for the mm39 mouse genome:
              https://api.genome.ucsc.edu/list/tracks?genome=mm39;trackLeavesOnly=1
            • Get the all_mrna track data for the mm39 mouse genome on chromosome 1 from 60380220 to 60429457:
              https://api.genome.ucsc.edu/getData/track?genome=mm39;track=all_mrna;chrom=chr1;start=60380220;end=60429457
            • Get the genomic sequence for the specified region on chromosome 1 for the mm39 mouse genome:
              https://api.genome.ucsc.edu/getData/sequence?genome=mm39;chrom=chr1;start=60380220;end=60429457
            Show
            nfreese Nowlan Freese added a comment - - edited Additional API examples: List all of the tracks available for the mm39 mouse genome: https: //api.genome.ucsc.edu/list/tracks?genome=mm39;trackLeavesOnly=1 Get the all_mrna track data for the mm39 mouse genome on chromosome 1 from 60380220 to 60429457: https: //api.genome.ucsc.edu/getData/track?genome=mm39;track=all_mrna;chrom=chr1;start=60380220;end=60429457 Get the genomic sequence for the specified region on chromosome 1 for the mm39 mouse genome: https: //api.genome.ucsc.edu/getData/sequence?genome=mm39;chrom=chr1;start=60380220;end=60429457
            Hide
            jsirigin Jaya Sravani Sirigineedi added a comment -

            The response for the https://api.genome.ucsc.edu/list/tracks?genome=galGal6 without any additional filter has few parent and children tracks in it, and the parent tracks doesn't have any data in the https://api.genome.ucsc.edu//getData/track?genome=galGal6&track=cons77wayViewelements&chrom=chr1&start=1&end=248956 API, it says in the response to query only for the children and the parent container doesn't have data. Attached a screenshot below. To avoid these tracks to show up in the available tracks list we can use this URL instead https://api.genome.ucsc.edu/list/tracks?genome=galGal6;trackLeavesOnly=1 which has the trackLeavesOnly=1 parameter added to it which filters out the parents and gives us only the children in the response.

            Show
            jsirigin Jaya Sravani Sirigineedi added a comment - The response for the https://api.genome.ucsc.edu/list/tracks?genome=galGal6 without any additional filter has few parent and children tracks in it, and the parent tracks doesn't have any data in the https://api.genome.ucsc.edu//getData/track?genome=galGal6&track=cons77wayViewelements&chrom=chr1&start=1&end=248956 API, it says in the response to query only for the children and the parent container doesn't have data. Attached a screenshot below. To avoid these tracks to show up in the available tracks list we can use this URL instead https://api.genome.ucsc.edu/list/tracks?genome=galGal6;trackLeavesOnly=1 which has the trackLeavesOnly=1 parameter added to it which filters out the parents and gives us only the children in the response.

              People

              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                • Created:
                  Updated: