Add slot to capture long read sequencing DNA extraction method

src/data/valid/Biosample-possibly-exhaustive.yaml

@@ -1580,10 +1580,10 @@ other_treatment: unconstrained text
 start_date_inc: '2023-01-27'
 start_time_inc: 13:42+0000
 project_id: no example from MIxS
-replicate_number: '1'
+replicate_number: 1
 sample_shipped: 15 g
 sample_type: soil - water extract
-technical_reps: '2'
+technical_reps: 2
 analysis_type:
   - metabolomics
   - metagenomics

src/data/valid/Database-interleaved.yaml

@@ -3009,10 +3009,10 @@ biosample_set:
     start_date_inc: '2023-01-27'
     start_time_inc: 13:42+0000
     project_id: no example from MIxS
-    replicate_number: '1'
+    replicate_number: 1
     sample_shipped: 15 g
     sample_type: soil - water extract
-    technical_reps: '2'
+    technical_reps: 2
     analysis_type:
       - metabolomics
       - metagenomics

src/schema/core.yaml

@@ -9,9 +9,7 @@ imports:
   - attribute_values
   - basic_slots
   - basic_classes
-  - portal_emsl
-  - portal_jgi_metagenomics
-  - portal_jgi_metatranscriptomics
+  - portal_user_facility
   - portal_mixs_inspired
   - portal_sample_id
 

src/schema/portal_user_facility.yaml

@@ -0,0 +1,145 @@
+name: user_facility_metadata
+description: This file defines terms that appear in the 'JGI-Metagenomics', `JGI-Metagenomics Long Read`, `JGI-Metatranscriptomics`, `EMSL` sections
+  of the NMDC sample metadata submission portal, which is implemented with DataHarmonizer
+  as of Spring 2022
+title: 'NMDC Schema supplement for Submission Portal: User Facility Metadata'
+id: https://w3id.org/nmdc/portal/jgi_metagenomics
+
+license: https://creativecommons.org/publicdomain/zero/1.0/
+
+imports:
+  - portal_enums
+  - nmdc_types
+
+prefixes:
+  linkml: "https://w3id.org/linkml/"
+  nmdc: "https://w3id.org/nmdc/"
+
+default_prefix: nmdc
+default_range: string
+
+slots:
+  rna_collect_site:
+    description: Provide information on the site your RNA sample was collected from
+    title: RNA collection site
+    examples:
+      - value: untreated pond water
+    rank: 15
+    recommended: true
+    deprecated: true; as of 2025-10-10, NMDC doesn't need to store this JGI metadata slot & it's now captured directly in the submission portal schema to support submissions
+  rna_isolate_meth:
+    description: Describe the method/protocol/kit used to extract DNA/RNA.
+    title: RNA isolation method
+    examples:
+      - value: phenol/chloroform extraction
+    aliases:
+      - Sample Isolation Method
+    rank: 16
+    recommended: true
+  rna_organisms:
+    description: List any organisms known or suspected to grow in co-culture, as well
+      as estimated % of the organism in that culture.
+    title: RNA expected organisms
+    examples:
+      - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
+          (1%)
+    rank: 14
+    recommended: true
+    deprecated: true; as of 2025-10-10, NMDC doesn't need to store this JGI metadata slot & it's now captured directly in the submission portal schema to support submissions
+  dna_lr_isolate_meth:
+    description: Describe the method/protocol/kit used to extract DNA/RNA for long read sequencing.
+    title: DNA isolation method for long read sequencing
+    examples:
+      - value: phenol/chloroform extraction
+    rank: 16
+    recommended: true
+    aliases:
+      - Sample Isolation Method
+  dna_collect_site:
+    description: Provide information on the site your DNA sample was collected from
+    title: DNA collection site
+    examples:
+      - value: untreated pond water
+    rank: 15
+    recommended: true
+    deprecated: true; as of 2025-10-10, NMDC doesn't need to store this JGI metadata slot & it's now captured directly in the submission portal schema to support submissions
+  dna_isolate_meth:
+    description: Describe the method/protocol/kit used to extract DNA/RNA.
+    title: DNA isolation method
+    examples:
+      - value: phenol/chloroform extraction
+    rank: 16
+    recommended: true
+    aliases:
+      - Sample Isolation Method
+  dna_organisms:
+    description: List any organisms known or suspected to grow in co-culture, as well
+      as estimated % of the organism in that culture.
+    title: DNA expected organisms
+    examples:
+      - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles
+          (1%)
+    rank: 14
+    recommended: true
+    deprecated: true; as of 2025-10-10, NMDC doesn't need to store this JGI metadata slot & it's now captured directly in the submission portal schema to support submissions
+  emsl_store_temp:
+    description: The temperature at which the sample should be stored upon delivery
+      to EMSL
+    title: EMSL sample storage temperature, deg. C
+    range: float
+    todos:
+      - add 'see_also's with link to NEXUS info
+    comments:
+      - Enter a temperature in celsius. Numeric portion only.
+    examples:
+      - value: '-80'
+    rank: 4
+    recommended: true
+  project_id:
+    description: Proposal IDs or names associated with dataset
+    title: project ID
+    rank: 1
+    recommended: true
+  sample_shipped:
+    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
+      sample sent to EMSL.
+    title: sample shipped amount
+    comments:
+      - This field is only required when completing metadata for samples being submitted
+        to EMSL for analyses.
+    examples:
+      - value: 15 g
+      - value: 100 uL
+      - value: 5 mL
+    rank: 3
+    recommended: true
+  sample_type:
+    description: Type of sample being submitted
+    title: sample type
+    comments:
+      - This can vary from 'environmental package' if the sample is an extraction.
+    examples:
+      - value: water extracted soil
+    rank: 2
+    range: SampleTypeEnum
+    recommended: true
+  replicate_number:
+    description: If sending biological replicates, indicate the rep number here.
+    title: replicate number
+    range: integer
+    comments:
+      - This will guide staff in ensuring your samples are blocked & randomized correctly
+    rank: 6
+    recommended: true
+  technical_reps:
+    description: If sending technical replicates of the same sample, indicate the
+      replicate count.
+    title: number technical replicate
+    range: integer
+    comments:
+      - This field is only required when completing metadata for samples being submitted
+        to EMSL for analyses.
+    examples:
+      - value: '2'
+    rank: 5
+    recommended: true

src/scripts/check_schema_self_containment.py

@@ -28,10 +28,8 @@
     "src/schema/nmdc_subsets.yaml",
     "src/schema/nmdc_types.yaml",
     "src/schema/nmdc.yaml",
-    "src/schema/portal_emsl.yaml",
     "src/schema/portal_enums.yaml",
-    "src/schema/portal_jgi_metagenomics.yaml",
-    "src/schema/portal_jgi_metatranscriptomics.yaml",
+    "src/schema/portal_user_facility.yaml",
     "src/schema/portal_mixs_inspired.yaml",
     "src/schema/portal_sample_id.yaml"
 }