Align Library Minimal Metadata, Library Generation LinkML Schema, and NIMP Terminology List

[puja-trivedi]

Task: Align Library Minimal Metadata, Library Generation LinkML Schema, and NIMP Terminology List

Sources:

1. Library Minimal Metadata
2. LinkML Schema Note: The LinkML model was defined based off a spreadsheet created by Lydia.
3. NIMP Terminology Browser List

Tasks

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Task 1: Create BICAN UUID

• PD-SHSHZS25: BarcodedCellSample.barcoded_cell_sample_preparation_date
• PD-TDTDDF25: BarcodedCellSample.barcoded_cell_sample_technique
• PD-NLNONY46: Tissue.structure
• PD-WKWKFB34: Slab.slab_local_name
• PD-RPRPTM41: ROI.roi_local_name

Task 2: Report Missing BICAN UUID to NIMP

• attributes listed in task 1
• DissociatedCellSample.patched_cell_structure (NIMP:PD-RCRCEV39), BICAN_UUID:7636b4c8-12f6-4b33-bdc6-c2f1a3b1c953
• BarcodedCellSample.barcoded_cell_sample_tag_local_name (NIMP:PD-FOFEUU27), BICAN_UUID:8877f8f0-3939-4062-84c9-414bdcdd04ca
• LibraryAliquot.fastq_file_alignment_status (NIMP:PD-KRKRCT43), BICAN_UUID:834a0e66-fd81-4d9c-b379-146372c3a629

Analysis

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Group 1: Attributes in LinkML and NIMP but NOT in Library Minimal Metadata

1. PD-SHSHZS25: BarcodedCellSample.barcoded_cell_sample_preparation_date
2. PD-TDTDDF25: BarcodedCellSample.barcoded_cell_sample_technique
3. PD-NLNONY46: Tissue.structure
4. PD-WKWKFB34: Slab.slab_local_name
5. PD-RPRPTM41: ROI.roi_local_name

Group 2: Aligned Attributes across Library Minimal Metadata and NIMP but MISSING BICAN UUID in NIMP (also not in LinkML)

NIMP: PD-RCRCEV39
Spreadsheet: 7636b4c8-12f6-4b33-bdc6-c2f1a3b1c953 | patched cell structure | dissociated cell sample |

Group 3: Attributes in Library Minimal Metadata but NOT in NIMP and LinkML

Note: I searched for these attributes by their BICAN UUID in NIMP but there was no match. Additionally, I was also unable to find a match for these attributes when trying to search by their attribute name i.e. PhiX spike in percent or fastq file alignment status

1. b5ab26ad-d523-406e-a85b-e77f2f4b06b5
2. 834a0e66-fd81-4d9c-b379-146372c3a629
3. 76c905d5-ef4a-421a-bd59-b541c5c1d45d
4. f22ac08a-bb81-4524-91f0-0e1e1a032335
5. 8877f8f0-3939-4062-84c9-414bdcdd04ca
6. cf1b7c96-cdc1-4eed-8e76-ac44fbd151f7
7. 184abbaf-baff-4b5f-b51e-dd38de6006af (this is a duplicate entry : 0c8628d0-809b-458c-b4b3-686131dceef8)
8. 5ace37aa-85d6-4493-909e-8fc221ec2609
9. 32f2d02b-7300-4554-aa93-6de6e456eda7
10. 0b9a9cbc-b8dd-42a2-a567-aafd9370db30
11. e7bc38d8-7315-40be-b8b7-923bf770ff38
12. b1b923ac-c218-4db4-a3b1-45a219612567
13. af1a6f3f-aca9-4452-b86e-f3c70c3600b6
14. a61c1d55-b880-499c-ba4a-30311fdca62f
15. 0b94df0d-d96e-4d49-a498-b3eb83afc5f8
16. a1a1b046-549d-4e94-9b3c-5fac2a31fdd6

| BICAN UUID                           | Proposed BICAN Field                   | LinkML Class Name       |
|:-------------------------------------|:---------------------------------------|:------------------------|
| b5ab26ad-d523-406e-a85b-e77f2f4b06b5 | PhiX spike in percent                  | library pool            |
| 76c905d5-ef4a-421a-bd59-b541c5c1d45d | custom primers                         | library pool            |
| f22ac08a-bb81-4524-91f0-0e1e1a032335 | length of Read 1                       | library pool            |
| cf1b7c96-cdc1-4eed-8e76-ac44fbd151f7 | library pool tube avg size bp          | library pool            |
| 32f2d02b-7300-4554-aa93-6de6e456eda7 | library pool tube contents nM          | library pool            |
| 0b9a9cbc-b8dd-42a2-a567-aafd9370db30 | length of Read 2 (for Paired End Runs) | library pool            |
| e7bc38d8-7315-40be-b8b7-923bf770ff38 | embargo date                           | library pool            |
| b1b923ac-c218-4db4-a3b1-45a219612567 | library pool tube volume ul            | library pool            |
| af1a6f3f-aca9-4452-b86e-f3c70c3600b6 | library pool fmol                      | library pool            |
| a61c1d55-b880-499c-ba4a-30311fdca62f | length of Index 2 (i5 Primer)          | library pool            |
| 0b94df0d-d96e-4d49-a498-b3eb83afc5f8 | length of Index 1 (i7 Primer)          | library pool            |
| a1a1b046-549d-4e94-9b3c-5fac2a31fdd6 | loading concentration pM               | library pool            |
| 834a0e66-fd81-4d9c-b379-146372c3a629 | fastq file alignment status            | library aliquot         |
| 184abbaf-baff-4b5f-b51e-dd38de6006af | dissociated cell source barcode name   | dissociated cell sample |
| 8877f8f0-3939-4062-84c9-414bdcdd04ca | study sets                             | barcoded cell sample    |
| 5ace37aa-85d6-4493-909e-8fc221ec2609 | enriched cell sample container name    | enriched cell sample    |

Group 4: Attributes with BICAN UUID in NIMP but NOT in LinkML Model and Library Minimal Metadata

Note: this list is excluding attributes belonging to Donor and IC Form class

1. Resource Type: Tissue, Variable Name: species, NIMP NHASH : PD-CIONCA52, BICAN UUID : 6837cb02-6bd7-4fb8-838c-9062ead96ba4