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  1. IGB
  2. IGBF-3502

Investigate UCSC REST API

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          Situation: Investigate the UCSC REST API to understand what data are available and how they are organized

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              jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

              DasSymloader is used to get segment region specific feature information, to implement this we have to use the https://api.genome.ucsc.edu/getData/track?genome=hg16;track=refGene;chrom=chr1;start=1;end=100000 api for the rest module.

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              jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - DasSymloader is used to get segment region specific feature information, to implement this we have to use the https://api.genome.ucsc.edu/getData/track?genome=hg16;track=refGene;chrom=chr1;start=1;end=100000 api for the rest module.
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              jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment -

              To get the UCSC available genomes use this https://api.genome.ucsc.edu/list/ucscGenomes API and create a similar method like initialize() available in the DasDataProvider in the new UCSC API module. To get the available datasets for a genome use https://api.genome.ucsc.edu/list/tracks?genome=hg38 this api and implement a method similar to getAvailableDataSets(). Also, implement methods that connect to https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 to get the chromosomes for a selected genome, similar to getAssemblyInfo() in DasDataProvider and https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678 api to get the sequence for a particular region, similar to method getSequence().

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              jsirigin Jaya Sravani Sirigineedi (Inactive) added a comment - To get the UCSC available genomes use this https://api.genome.ucsc.edu/list/ucscGenomes API and create a similar method like initialize() available in the DasDataProvider in the new UCSC API module. To get the available datasets for a genome use https://api.genome.ucsc.edu/list/tracks?genome=hg38 this api and implement a method similar to getAvailableDataSets(). Also, implement methods that connect to https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 to get the chromosomes for a selected genome, similar to getAssemblyInfo() in DasDataProvider and https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678 api to get the sequence for a particular region, similar to method getSequence().

                People

                • Assignee:
                  jsirigin Jaya Sravani Sirigineedi (Inactive)
                  Reporter:
                  nfreese Nowlan Freese
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                    Updated:
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