Duplicate bold samples requiring physical check and subsequent data updates

[kyule]

Attached are samples that need to be physically checked. All but one are ear samples that are duplicated in the DNA samples. They should be checked to see if they are existing samples, empty, or actually fecal samples. If they are ear samples or empty they should be discarded, as their actual originating individual cannot be determined.

The remaining sample is a mosquito dna sample with a duplicate barcode in the manifest.

Sample_DNA_duplicates.xlsx

Making this a Github issue rather than just reporting in Slack because results of the physical check will influence necessary edits to determinations and associations tables.

• Physical sample check @azhar-h
• Update manifests, delete samples as necessary (either @azhar-h or @kyule - whichever preferred)
• Report to NEON via Service Now (@kyule)
• Identify and update sample associations in omoccurassociations (@kyule)
• Reevaluate BOLD determinations and update omoccurdeterminations (@kyule)

[azhar-h]

Hi Kelsey, Trying to figure this out. Can we Zoom at 1:15pm today.

…

________________________________ From: Kelsey Yule ***@***.***> Sent: Tuesday, December 10, 2024 11:41 AM To: BioKIC/NEON-Biorepository ***@***.***> Cc: Azhar Husain ***@***.***>; Mention ***@***.***> Subject: [BioKIC/NEON-Biorepository] Duplicate bold samples requiring physical check and subsequent data updates (Issue #642) Attached are samples that need to be physically checked. All but one are ear samples that are duplicated in the DNA samples. They should be checked to see if they are existing samples, empty, or actually fecal samples. If they are ear samples or empty they should be discarded, as their actual originating individual cannot be determined. The remaining sample is a mosquito dna sample with a duplicate barcode in the manifest. Sample_DNA_duplicates.xlsx<https://urldefense.com/v3/__https://github.com/user-attachments/files/17823169/Sample_DNA_duplicates.xlsx__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcNACaWUw$> Making this a Github issue rather than just reporting in Slack because results of the physical check will influence necessary edits to determinations and associations tables. * Physical sample check @azhar-h<https://urldefense.com/v3/__https://github.com/azhar-h__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcKvYRP94$> * Update manifests, delete samples as necessary (either @azhar-h<https://urldefense.com/v3/__https://github.com/azhar-h__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcKvYRP94$> or @kyule<https://urldefense.com/v3/__https://github.com/kyule__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcJygW2ac$> - whichever preferred) * Report to NEON via Service Now ***@***.***<https://urldefense.com/v3/__https://github.com/kyule__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcJygW2ac$>) * Identify and update sample associations in omoccurassociations ***@***.***<https://urldefense.com/v3/__https://github.com/kyule__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcJygW2ac$>) * Reevaluate BOLD determinations and update omoccurdeterminations ***@***.***<https://urldefense.com/v3/__https://github.com/kyule__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcJygW2ac$>) — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/BioKIC/NEON-Biorepository/issues/642__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIcpEvqQEI$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/APXZAQBX2WHMIGPYVV3O6HL2E4YW3AVCNFSM6AAAAABSDNDVG2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGY3TIMBRG44TSNI__;!!IKRxdwAv5BmarQ!exrZYXG8ypVYqvtrB6KcLQn4rlxQ2567VPWwAkIgMfXlaAlHGxwJivUfCR8uP6hehuIoQ4Xx-fU42anWTfbDVKIczL4RqMY$>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[kyule]

Azhar has checked all of the samples and I've reported the results via ServiceNow, awaiting feedback regarding what should be done with the CCDB plate and any other followups.

[kyule]

@azhar-h After a bunch of back and forth on ServiceNow NEON has agreed that it is best to deaccession that whole mosquito DNA plate that contains sample M30000007654 since we can't be sure that the relationships between the sampleIDs and barcodes are accurate. They asked also for a couple of photos of these plate created by CCDB as they have not seen these samples before and aren't sure what the barcodes, etc, look like.

Thanks!

[azhar-h]

Ok, will do, thanks - will follow up with those pics tomorrow or 06-Jan.

[azhar-h]

CCDB_LVL_plate_06Jan2025.pdf

Images attached.

[kyule]

Awesome. I've sent those images along and will close out the rest now!