[IGBF-3546] Remove excess BioSAmple IDs in PRJNA980666 - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
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Story Points:
1
Epic Link:
Support NSF pollen grant
Sprint:
Spring 1, Spring 2, Spring 3

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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Biosamples-PRJNA980666.txt
29 kB
29/Jan/24 3:48 PM

Activity

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Robert Reid created issue - 18/Jan/24 10:07 AM

Robert Reid made changes - 18/Jan/24 10:07 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Robert Reid made changes - 18/Jan/24 10:08 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 20/Jan/24 4:45 PM

Sprint

Spring 1 [ 185 ]

Spring 1, Spring 2 [ 185, 186 ]

Ann Loraine made changes - 20/Jan/24 4:45 PM

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Robert Reid added a comment - 29/Jan/24 8:23 AM

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.

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Robert Reid added a comment - 29/Jan/24 8:23 AM 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.

Robert Reid made changes - 29/Jan/24 3:48 PM

Attachment

Biosamples-PRJNA980666.txt [ 18189 ]

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Robert Reid added a comment - 29/Jan/24 3:51 PM

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.

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Robert Reid added a comment - 29/Jan/24 3:51 PM 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.

Ann Loraine made changes - 02/Feb/24 6:27 PM

Sprint

Spring 1, Spring 2 [ 185, 186 ]

Spring 1, Spring 2, Spring 3 [ 185, 186, 187 ]

Ann Loraine made changes - 02/Feb/24 6:27 PM

Rank

Ranked higher

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Robert Reid added a comment - 05/Feb/24 12:00 PM

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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Robert Reid added a comment - 05/Feb/24 12:00 PM 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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Robert Reid added a comment - 05/Feb/24 1:06 PM - 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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Robert Reid added a comment - 05/Feb/24 1:06 PM - 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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Robert Reid added a comment - 12/Feb/24 9:20 AM

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

Robert Reid added a comment - 12/Feb/24 9:20 AM 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!

Robert Reid made changes - 12/Feb/24 9:20 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]