model extraction process

[aclum]

Deliverable this task is associated with

6

RACI

Responsible: @mslarae13 @turbomam @aclum
Accountable: @aclum
Consulted:
Informed:

Describe the task?

Using NEON as an example to model a PlannedProcess for extraction

slots (slot names are placeholders based on neon column headers):
inputs - id from Class Biosample
outputs - id from Class AnalyticalSample
laboratoryName
protocol_name
processedDate
sampleMass
nucleicAcidConcentration
nucleicAcidQuantMethod - enum of instrument names?
nucleicAcidPurity
nucleicAcidRange
qaqcStatus - enum of {Pass, Fail}

Work is being done in this branch of nmdc-schema

Criteria for completion

A Class Extraction exists in a released version of the NMDC schema along with example valid data.

Completion Date (Goal)

June 16
Target Sprint Start & End Dates

Start: May 22
End: June 2

Tag Blocker/Contingent upon issues

[aclum]

@turbomam I've made example the following example data files
https://github.com/microbiomedata/nmdc-schema/blob/issue-906-dna_extraction/src/data/valid/Database-extraction_set-exhaustive.yaml
https://github.com/microbiomedata/nmdc-schema/blob/issue-906-dna_extraction/src/data/valid/Database-extraction_set-minimal.yaml
https://github.com/microbiomedata/nmdc-schema/blob/issue-906-dna_extraction/src/data/valid/Database-analytical_sample-minimal.yaml
https://github.com/microbiomedata/nmdc-schema/blob/issue-906-dna_extraction/src/data/valid/Database-analytical_sample-extract-exhaustive.yaml
I've also updated Class Database to include extraction_set and analytical_sample_set and updated processing_institution_enum.

What I need from you is

• new Class for Extraction
• new slots for Class Extraction
• new slots for ProcessedSample
• new enumeration for the range of slot status for Class Extraction
• new enumeration for the range of slot instrument_name for Class ProcessedSample
• new enumeration for the range of slot extraction_target for Class Extraction

[ssarrafan]

Based on last comment moving to new sprint

[aclum]

enum for instrument_name to be handled in #1033