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BioKIC / NEON-Biorepository

Development base for the NEON Biorepository Data Portal host by BioKIC - Arizona State University (https://biorepo.neonscience.org)
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Small mammal samples requiring physical label and sampleID updates #332

Closed kyule closed 2 weeks ago

kyule commented 3 years ago

Attached is a sheet of small mammal sampleIDs that need to be corrected. This will require, in some cases updates to physical labels, as well as occurrence record and manifest updates.

If samples don't require physical label updates, let me know and I can correct the data for those. biorepoSampleIDNotFoundInNeonData_edited.xlsx

These updates came from Rachel Swanson and Katie Levan via a Service Now ticket.

azhar-h commented 3 years ago

Data edits are batch updated on backend. I'll follow up once I've checked labels and updated them as necessary.

kyule commented 3 years ago

Awesome. Here is a new batch coming from NEON and their ongoing QAQC. Same process will be required. ASU_MAMtrapsamples_missingfromNEON_v2_sampleIDsOnly.xlsx

kyule commented 3 years ago

Here is a third duplicateBiorepoSamples_RSedits.xlsx batch of edits requiring the same process. These are corrected sampleIDs for duplicate records.

kyule commented 3 years ago

These samples also need to be looked at. There was a duplicate issue, and it appears that the fecal sample was included in an ear sample shipment causing some additional confusion.

This is what Rachel Swanson believes to be correct:

sampleID Barcode UNDE.20180711.R4464.F D00000012453 UNDE.20180711.R4464.E D00000012598

azhar-h commented 3 years ago

Awesome. Here is a new batch coming from NEON and their ongoing QAQC. Same process will be required. ASU_MAMtrapsamples_missingfromNEON_v2_sampleIDsOnly.xlsx

This links to a blank spreadsheet.

kyule commented 3 years ago

Strange. I think this should work. ASU_MAMtrapsamples_missingfromNEON_v2_sampleIDsOnly.xlsx .

azhar-h commented 3 years ago

Strange. I think this should work. ASU_MAMtrapsamples_missingfromNEON_v2_sampleIDsOnly.xlsx .

That one worked. It's kind of unclear - what is the actual request for the physical sample? Confirm sampleID, barcode, sample class? Many (most) of these mammal samples, envelope or vial, are only labelled with the barcode.

kyule commented 3 years ago

If only the barcode is associated with the sample, then only the portal data needs to be changed. I can makes those updates if preferred, but I wasn't positive for which sample classes that was the case or if that has always been consistent within sample classes.

The exception is that fecal-ear sample pair I described (UNDE.20180711.R4464.F/E). If the samples do not have sampleIDs on any physical location, only whether the samples are actually feces vs an ear punch needs to be confirmed.

azhar-h commented 3 years ago

If only the barcode is associated with the sample, then only the portal data needs to be changed. I can makes those updates if preferred, but I wasn't positive for which sample classes that was the case or if that has always been consistent within sample classes.

The exception is that fecal-ear sample pair I described (UNDE.20180711.R4464.F/E). If the samples do not have sampleIDs on any physical location, only whether the samples are actually feces vs an ear punch needs to be confirmed.

When available, the barcode (sampleCode) is used. For older samples where barcodes were not used, sampleID is used.

kyule commented 3 years ago

When available, the barcode (sampleCode) is used. For older samples where barcodes were not used, sampleID is used.

So sampleID is never printed for any cryo sample for which a barcode exists?

azhar-h commented 3 years ago

When available, the barcode (sampleCode) is used. For older samples where barcodes were not used, sampleID is used.

So sampleID is never printed for any cryo sample for which a barcode exists?

Both barcode and sampleID on soils, and usually the filter cartridges. On mammal samples, barcode only.

azhar-h commented 1 year ago

From: Kelsey Yule @.> Sent: Thursday, August 24, 2023 2:25 PM To: BioKIC/NEON-Biorepository @.> Cc: Azhar Husain @.>; Assign @.> Subject: [BioKIC/NEON-Biorepository] Small mammal samples requiring physical label and sampleID updates (#332)

Attached is a sheet of small mammal sampleIDs that need to be corrected. This will require, in some cases updates to physical labels, as well as occurrence record and manifest updates.

If samples don't require physical label updates, let me know and I can correct the data for those. biorepoSampleIDNotFoundInNeonData_edited.xlsxhttps://urldefense.com/v3/__https:/github.com/BioKIC/NEON-Biorepository-Data-Docs/files/5732164/biorepoSampleIDNotFoundInNeonData_edited.xlsx__;!!IKRxdwAv5BmarQ!dHpvZt5XCd7JVUEgsfbZUbdTCe_WyEggxAnkcyDZGKTmuYwFqm5SezUD2lERtxM8OxZ4h9wfBgXLrmXZC1I2zge9Zso$

These updates came from Rachel Swanson and Katie Levan via a Service Now ticket.

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/BioKIC/NEON-Biorepository/issues/332__;!!IKRxdwAv5BmarQ!dHpvZt5XCd7JVUEgsfbZUbdTCe_WyEggxAnkcyDZGKTmuYwFqm5SezUD2lERtxM8OxZ4h9wfBgXLrmXZC1I2_19wb-A$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/APXZAQBSESLQXDJUV2Q3A23XW7BBXANCNFSM6AAAAAA35TSMYU__;!!IKRxdwAv5BmarQ!dHpvZt5XCd7JVUEgsfbZUbdTCe_WyEggxAnkcyDZGKTmuYwFqm5SezUD2lERtxM8OxZ4h9wfBgXLrmXZC1I25tzaBUA$. You are receiving this because you were assigned.Message ID: @.**@.>>

kyule commented 2 weeks ago

I believe all but some that can be dealt with via the other seperate ticket have now been dealt with using searchable alternative identifiers, so no need to physically update the sample imo.