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  1. IGB
  2. IGBF-3129

Enable IGB to directly consume data from UCSC JSON API

        Details

        • Type: Epic
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • 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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              relates to

              Epic - Created by JIRA Software - do not edit or delete. Issue type for a big user story that needs to be broken down. IGBF-3555 Add Ensembl REST API to IGB

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-3601 Investigate microbe genome availability from UCSC

              • Major - Major loss of function.
              • To-Do

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
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                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2869 [ IGBF-2869 ]
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                nfreese Nowlan Freese made changes -
                Issue Type Task [ 3 ] Epic [ 10000 ]
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                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Epic Child IGBF-2869 [ 21022 ]
                nfreese Nowlan Freese made changes -
                Epic Name Add UCSC REST API to IGB
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2869 [ IGBF-2869 ]
                nfreese Nowlan Freese made changes -
                Epic Child IGBF-3501 [ 22720 ]
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                Epic Child IGBF-3502 [ 22721 ]
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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 - - edited Documentation DAS: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download23 API: https://genome.ucsc.edu/goldenPath/help/api.html
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                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

                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
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                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 -

                Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn
                Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes

                Show
                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
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3555 [ IGBF-3555 ]
                nfreese Nowlan Freese made changes -
                Epic Child IGBF-3584 [ 22803 ]
                nfreese Nowlan Freese made changes -
                Epic Child IGBF-3599 [ 22818 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3601 [ IGBF-3601 ]
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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
                nfreese Nowlan Freese made changes -
                Epic Child IGBF-3574 [ 22793 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-02-15 at 2.24.48 PM.png [ 18213 ]
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                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.
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                nfreese Nowlan Freese made changes -
                Comment [ Tested Sravani's branch on my Mac.

                Available files appear in their respective folders. Able to load data from each folder. No issues in log when building or running.

                Ready for pull request. ]
                jsirigin Jaya Sravani Sirigineedi made changes -
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                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
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                Status To-Do [ 10305 ] In Progress [ 3 ]
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                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
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                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
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                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
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                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
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                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
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                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: