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  1. IGB
  2. IGBF-3546

Remove excess BioSAmple IDs in PRJNA980666

        Details

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

          Description

          For Mark's study, at one point we have planned to merging multiple projects together with Glorias data.

          They have since been separated into different Bioprojects.

          The SRA samples have been separated.

          However, I see the Biosamples have not yet been removed correctly.
          The the SRA samples, I can edit and make the changes.

          But that is not the case for biosample as far as I can tell.
          So this task is to figure out how to get the extra biosamples removed from this bioproject PRJNA980666.

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              robofjoy Robert Reid added a comment -

              I made the request with NCBI bioprojects and I am waiting to hear back from them.
              I will take a peak at the current status.

              Show
              robofjoy Robert Reid added a comment - I made the request with NCBI bioprojects and I am waiting to hear back from them. I will take a peak at the current status.
              Hide
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              robofjoy Robert Reid added a comment -

              Biosamples-PRJNA980666.txt

              The Biosamples in question are no longer connected to BioProject PRJNA980666 as seen when you download the NCBI file.
              They have not yet updated 2 locations where it shows they still associated.
              However when you click on the sample or SRA, it shows the proper Bioproject ID.

              I am going to hurry up and wait and see if this jusst needs to to correct on their end.

              Show
              robofjoy Robert Reid added a comment - Biosamples-PRJNA980666.txt The Biosamples in question are no longer connected to BioProject PRJNA980666 as seen when you download the NCBI file. They have not yet updated 2 locations where it shows they still associated. However when you click on the sample or SRA, it shows the proper Bioproject ID. I am going to hurry up and wait and see if this jusst needs to to correct on their end.
              Hide
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              robofjoy Robert Reid added a comment -

              I have sent the NCBI a reminder as an entirely new request:
              Sent to: biosamplehelp@ncbi.nlm.nih.gov

              Hi,

              For this Bioproject:
              https://dataview.ncbi.nlm.nih.gov/object/PRJNA980666

              The following samples are listed in this Bioproject but no longer should be.
              Right now they are assigned to 2 bioprojects.

              They belong solely to BioProject: PRJNA1017816.

              I have not found anywhere that I can make these edits.
              (Their SRR counterparts are correct)

              Rob Reid

              Accession
              SAMN36787018
              SAMN36787017
              SAMN36787016
              SAMN36787015
              SAMN36786978
              SAMN36787014
              SAMN36787013
              SAMN36787012
              SAMN36786983
              SAMN36786982
              SAMN36787045
              SAMN36787044
              SAMN36786981
              SAMN36787043
              SAMN36787042
              SAMN36787040
              SAMN36787041
              SAMN36787039
              SAMN36787038
              SAMN36787037
              SAMN36787034
              SAMN36787035
              SAMN36787036
              SAMN36786980
              SAMN36787011
              SAMN36787010
              SAMN36787009
              SAMN36787008
              SAMN36787007
              SAMN36787006
              SAMN36787005
              SAMN36787033
              SAMN36787004
              SAMN36787032
              SAMN36787031
              SAMN36787029
              SAMN36787030
              SAMN36787028
              SAMN36787027
              SAMN36786977
              SAMN36787026
              SAMN36787003
              SAMN36787002
              SAMN36787001
              SAMN36787000
              SAMN36786999
              SAMN36786998
              SAMN36786997
              SAMN36787025
              SAMN36787024
              SAMN36786979
              SAMN36787023
              SAMN36787022
              SAMN36787021
              SAMN36787019
              SAMN36787020
              SAMN36786996
              SAMN36786995
              SAMN36786994
              SAMN36786993
              SAMN36786991
              SAMN36786992
              SAMN36786990
              SAMN36786989
              SAMN36786987
              SAMN36786988
              SAMN36786986
              SAMN36786985
              SAMN36786984
              SAMN36786974
              SAMN36786975
              SAMN36786976

              Show
              robofjoy Robert Reid added a comment - I have sent the NCBI a reminder as an entirely new request: Sent to: biosamplehelp@ncbi.nlm.nih.gov Hi, For this Bioproject: https://dataview.ncbi.nlm.nih.gov/object/PRJNA980666 The following samples are listed in this Bioproject but no longer should be. Right now they are assigned to 2 bioprojects. They belong solely to BioProject: PRJNA1017816. I have not found anywhere that I can make these edits. (Their SRR counterparts are correct) Rob Reid Accession SAMN36787018 SAMN36787017 SAMN36787016 SAMN36787015 SAMN36786978 SAMN36787014 SAMN36787013 SAMN36787012 SAMN36786983 SAMN36786982 SAMN36787045 SAMN36787044 SAMN36786981 SAMN36787043 SAMN36787042 SAMN36787040 SAMN36787041 SAMN36787039 SAMN36787038 SAMN36787037 SAMN36787034 SAMN36787035 SAMN36787036 SAMN36786980 SAMN36787011 SAMN36787010 SAMN36787009 SAMN36787008 SAMN36787007 SAMN36787006 SAMN36787005 SAMN36787033 SAMN36787004 SAMN36787032 SAMN36787031 SAMN36787029 SAMN36787030 SAMN36787028 SAMN36787027 SAMN36786977 SAMN36787026 SAMN36787003 SAMN36787002 SAMN36787001 SAMN36787000 SAMN36786999 SAMN36786998 SAMN36786997 SAMN36787025 SAMN36787024 SAMN36786979 SAMN36787023 SAMN36787022 SAMN36787021 SAMN36787019 SAMN36787020 SAMN36786996 SAMN36786995 SAMN36786994 SAMN36786993 SAMN36786991 SAMN36786992 SAMN36786990 SAMN36786989 SAMN36786987 SAMN36786988 SAMN36786986 SAMN36786985 SAMN36786984 SAMN36786974 SAMN36786975 SAMN36786976
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              robofjoy Robert Reid added a comment - - edited

              Testing Jira.

              I've deleted the links to PRJNA980666 on the BioSamples. I don't see any data links connecting the 15 BioSamples to PRJNA980666, so the incorrect links should disappear. It may take a day or two for the links in the public pages to be reindexed, so please check tomorrow.

              Regards,
              John B. Anderson, PhD
              BioSample curation staff

              Show
              robofjoy Robert Reid added a comment - - edited Testing Jira. I've deleted the links to PRJNA980666 on the BioSamples. I don't see any data links connecting the 15 BioSamples to PRJNA980666, so the incorrect links should disappear. It may take a day or two for the links in the public pages to be reindexed, so please check tomorrow. Regards, John B. Anderson, PhD BioSample curation staff
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              robofjoy Robert Reid added a comment -

              Somehow, there are now 111 there still when I log into the submission portal.

              However, if you go to NCBI (https://www.ncbi.nlm.nih.gov/), and do a search for:

              PRJNA980666

              It will return 1 Bioproject.

              And 54 SRA samples. This is what we want!!!

              I am ready to call this done!

              Show
              robofjoy Robert Reid added a comment - Somehow, there are now 111 there still when I log into the submission portal. However, if you go to NCBI ( https://www.ncbi.nlm.nih.gov/ ), and do a search for: PRJNA980666 It will return 1 Bioproject. And 54 SRA samples. This is what we want!!! I am ready to call this done!

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                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: