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  1. IGB
  2. IGBF-1793

Investigate web link-outs for personal genome visualization

    Details

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

      Description

      Situation: There are multiple websites that provide additional information regarding the SNPs from personal genomics data, such as SNPedia or dbSNP .

      Task: Create a list of useful websites to link out to from IGB.

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            ann.loraine Ann Loraine added a comment - - edited

            This could be very useful for showing summary information about variants:
            https://myvariant.info/
            It is a REST service that returns JSON with summary information about SNPs and other variants.
            The Web site above has examples showing how to use it.
            It is one of the "biothings" APIs which brings together a lot of information about genomic entities into computer-friendly formats.
            So for example, IGB could use the information directly, or IGB could link to a Web page (hosted on Bioviz or some other site) that shows data from the REST service. There are a lot of possibilities.
            Attached is a sample output in json - the same example from the Web site, which is: https://myvariant.info/v1/variant/chr6%3Ag.152708291G%3EA?dotfield=true&callback=%20

            Show
            ann.loraine Ann Loraine added a comment - - edited This could be very useful for showing summary information about variants: https://myvariant.info/ It is a REST service that returns JSON with summary information about SNPs and other variants. The Web site above has examples showing how to use it. It is one of the "biothings" APIs which brings together a lot of information about genomic entities into computer-friendly formats. So for example, IGB could use the information directly, or IGB could link to a Web page (hosted on Bioviz or some other site) that shows data from the REST service. There are a lot of possibilities. Attached is a sample output in json - the same example from the Web site, which is: https://myvariant.info/v1/variant/chr6%3Ag.152708291G%3EA?dotfield=true&callback=%20
            Hide
            sameer Sameer Shanbhag (Inactive) added a comment -

            I have attached the list of links that SNPeida has on their website if that is what we are looking at.

            Show
            sameer Sameer Shanbhag (Inactive) added a comment - I have attached the list of links that SNPeida has on their website if that is what we are looking at.
            Show
            stiwari8 Srishti Tiwari (Inactive) added a comment - http://www.hgmd.cf.ac.uk/ac/index.php
            Hide
            stiwari8 Srishti Tiwari (Inactive) added a comment - - edited

            The above service is in Beta Testing stage and the website advises that we should restrict the request to 1 request per second (as of now). It can fetch important information that can be helpful for the end user.
            To solve this problem we can lazy load data as the user browses the genome. We will also need to look at how we visualize the data if we intend to use this service.

            Show
            stiwari8 Srishti Tiwari (Inactive) added a comment - - edited The above service is in Beta Testing stage and the website advises that we should restrict the request to 1 request per second (as of now). It can fetch important information that can be helpful for the end user. To solve this problem we can lazy load data as the user browses the genome. We will also need to look at how we visualize the data if we intend to use this service.
            Show
            nfreese Nowlan Freese added a comment - https://api.ncbi.nlm.nih.gov/variation/v0/#/SPDI/get_spdi__spdi__rsids
            Hide
            nfreese Nowlan Freese added a comment -

            Please also look to see if APIs are available from services such as dbSNP.

            Show
            nfreese Nowlan Freese added a comment - Please also look to see if APIs are available from services such as dbSNP.

              People

              • Assignee:
                stiwari8 Srishti Tiwari (Inactive)
                Reporter:
                nfreese Nowlan Freese
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                Dates

                • Created:
                  Updated:
                  Resolved: