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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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              Issue Links

              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-2246 Create new App to show results from personal genotyping platforms

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1788 [ 17878 ]
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                nfreese Nowlan Freese added a comment -

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

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

                https://api.ncbi.nlm.nih.gov/variation/v0/#/SPDI/get_spdi__spdi__rsids

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                nfreese Nowlan Freese added a comment - https://api.ncbi.nlm.nih.gov/variation/v0/#/SPDI/get_spdi__spdi__rsids
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                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.
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                http://www.hgmd.cf.ac.uk/ac/index.php

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - http://www.hgmd.cf.ac.uk/ac/index.php
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                sameer Sameer Shanbhag (Inactive) made changes -
                Attachment Important Links.PNG [ 14366 ]
                sameer Sameer Shanbhag (Inactive) made changes -
                Comment [ SNPedia Api : https://www.snpedia.com/index.php/Bulk

                I have also attached the Snip from Snpedia Website which links to different websites related to the search. ]
                sameer Sameer Shanbhag (Inactive) made changes -
                Attachment Important Links.PNG [ 14366 ]
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                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.
                sameer Sameer Shanbhag (Inactive) made changes -
                Attachment Important Links.PNG [ 14367 ]
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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
                ann.loraine Ann Loraine made changes -
                Attachment response_1562219666454.json [ 14368 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18515 ] Fall 2019 Workflow Update [ 19073 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19073 ] Revised Fall 2019 Workflow Update [ 21190 ]
                ann.loraine Ann Loraine made changes -
                Summary Investigate Applicable Web Links Investigate web link-outs for personal genome visualization
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1788 [ 17878 ] IGBF-1908 [ 17998 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2246 [ IGBF-2246 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: