microbiomedata · brynnz22 · Dec 12, 2023 · Dec 12, 2023 · Dec 12, 2023 · Dec 12, 2023
diff --git a/date_placeholder.txt b/date_placeholder.txt
@@ -0,0 +1 @@
+Tue Dec 12 12:47:32 EST 2023
diff --git a/...d/OmicsProcessing-invalid-omics-type.yaml → ...id/DataGeneration-invalid-omics-type.yaml b/...d/OmicsProcessing-invalid-omics-type.yaml → ...id/DataGeneration-invalid-omics-type.yaml
@@ -1,4 +1,4 @@
-id: nmdc:omprc-99-zUCd5N
+id: nmdc:datgen-99-zUCd5N
 alternative_identifiers:
   - gold:Gp0108335
 name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/src/data/invalid/OmicsProcessing-no-id.yaml → src/data/invalid/DataGeneration-no-id.yaml b/src/data/invalid/OmicsProcessing-no-id.yaml → src/data/invalid/DataGeneration-no-id.yaml
diff --git a/src/data/invalid/Database-invalid-omics-processing.yaml b/src/data/invalid/Database-invalid-omics-processing.yaml
@@ -1,5 +1,5 @@
-omics_processing_set:
-  - id: nmdc:omprc-99-zUCd5N
+data_generation_set:
+  - id: nmdc:datgen-99-zUCd5N
     alternative_identifiers:
       - gold:Gp0108335
     name: Thawing permafrost microbial communities from the Arctic, studying carbon
@@ -18,7 +18,7 @@ omics_processing_set:
       - nmdc:sty-00-555xxx
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-gKlQlF
+  - id: nmdc:datgen-99-gKlQlF
     alternative_identifiers:
       - gold:Gp0108340
     name: Thawing permafrost microbial communities from the Arctic, studying carbon
@@ -37,7 +37,7 @@ omics_processing_set:
       - nmdc:sty-00-555xxx
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-5kgIJR
+  - id: nmdc:datgen-99-5kgIJR
     alternative_identifiers:
       - gold:Gp0108341
     name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/src/data/valid/OmicsProcessing-1.yaml → src/data/valid/DataGeneration-1.yaml b/src/data/valid/OmicsProcessing-1.yaml → src/data/valid/DataGeneration-1.yaml
@@ -1,4 +1,4 @@
-id: nmdc:omprc-99-zUCd5N
+id: nmdc:datgen-99-zUCd5N
 alternative_identifiers:
   - gold:Gp0108335
 name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/...ta/valid/OmicsProcessing-ndsdc-bioproject → ...ata/valid/DataGeneration-ndsdc-bioproject b/...ta/valid/OmicsProcessing-ndsdc-bioproject → ...ata/valid/DataGeneration-ndsdc-bioproject
@@ -1,4 +1,4 @@
-id: nmdc:omprc-11-pf500b03
+id: nmdc:datgen-11-pf500b03
 gold_sequencing_project_identifiers:
   - gold:Gp0704888
 name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/...icsProcessing-processing-institution.yaml → ...ataGeneration-processing-institution.yaml b/...icsProcessing-processing-institution.yaml → ...ataGeneration-processing-institution.yaml
@@ -1,4 +1,4 @@
-id: nmdc:omprc-99-zUCd5N
+id: nmdc:datgen-99-zUCd5N
 alternative_identifiers:
   - gold:Gp0108335
 name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/src/data/valid/DataObject-mass_spec.yaml b/src/data/valid/DataObject-mass_spec.yaml
@@ -1,6 +1,6 @@
 id: nmdc:dobj-12-bxzqgh77
 name: SpruceW_P19_15_22Jun17_Pippin_17-04-06
-description: raw instrument file for nmdc:omprc-11-bn8jcq58
+description: raw instrument file for nmdc:datgen-11-bn8jcq58
 file_size_bytes: 1150434379
 url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/SpruceW_P19_15_22Jun17_Pippin_17-04-06.raw
 md5_checksum: 3EFB4966125DFA9329ADE5B18EADDA8E

diff --git a/src/data/valid/DataObject-my_emsl_prefix.yaml b/src/data/valid/DataObject-my_emsl_prefix.yaml
@@ -1,6 +1,6 @@
 id: nmdc:dobj-11-mzxj8743
 name: Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw
-description: raw instrument file for nmdc:omprc-11-7nfk8n58
+description: raw instrument file for nmdc:datgen-11-7nfk8n58
 file_size_bytes: 448727423
 url: https://nmdcdemo.emsl.pnnl.gov/proteomics/raw/Froze_Core_2015_S1_30_40_3_QE_26May16_Pippin_16-03-39.raw
 md5_checksum: ED2BA6CD95CE5D86D8D29A8DD548F48F

diff --git a/...ata/valid/Database-omics-processings.yaml → ...data/valid/Database-data-generations.yaml b/...ata/valid/Database-omics-processings.yaml → ...data/valid/Database-data-generations.yaml
@@ -1,5 +1,5 @@
-omics_processing_set:
-  - id: nmdc:omprc-99-zUCd5N
+data_generation_set:
+  - id: nmdc:datgen-99-zUCd5N
     alternative_identifiers:
       - gold:Gp0108335
     name: Thawing permafrost microbial communities from the Arctic, studying carbon
@@ -18,7 +18,7 @@ omics_processing_set:
       - nmdc:sty-00-555xxx
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-gKlQlF
+  - id: nmdc:datgen-99-gKlQlF
     alternative_identifiers:
       - gold:Gp0108340
     name: Thawing permafrost microbial communities from the Arctic, studying carbon
@@ -37,7 +37,7 @@ omics_processing_set:
       - nmdc:sty-00-555xxx
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-5kgIJR
+  - id: nmdc:datgen-99-5kgIJR
     alternative_identifiers:
       - gold:Gp0108341
     name: Thawing permafrost microbial communities from the Arctic, studying carbon

diff --git a/src/data/valid/Database-multiple-paths.yaml b/src/data/valid/Database-multiple-paths.yaml
@@ -31,8 +31,8 @@ biosample_set:
       has_raw_value: ENVO:00005792
       term:
         id: ENVO:00005792
-omics_processing_set:
-  - id: nmdc:omprc-99-zUCd5N
+data_generation_set:
+  - id: nmdc:datgen-99-zUCd5N
     alternative_identifiers:
       - gold:Gp0108335
     name: a process in which a biosample was sequenced?

diff --git a/src/data/valid/Database-neon_Biosample_to_DataObject_NEON.json b/src/data/valid/Database-neon_Biosample_to_DataObject_NEON.json
@@ -143,9 +143,9 @@
       "type": "nmdc:DataObject"
     }
   ],
-  "omics_processing_set": [
+  "data_generation_set": [
     {
-      "id": "nmdc:omprc-11-s9xj2r24",
+      "id": "nmdc:datgen-11-s9xj2r24",
       "name": "Test NEON data",
       "has_input": [
         "nmdc:procsm-99-xyz3"
@@ -171,7 +171,7 @@
       "name": "TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 ",
       "started_at_time": "2023-03-23T17:17:05.111689+00:00",
       "ended_at_time": "2023-03-23T17:17:05.111725+00:00",
-      "was_informed_by": "nmdc:omprc-11-s9xj2r24",
+      "was_informed_by": "nmdc:datgen-11-s9xj2r24",
       "execution_resource": "NERSC-Cori",
       "git_url": "https://github.com/microbiomedata/ReadsQC",
       "has_input": [

diff --git a/src/data/valid/Database-neon_Biosample_to_DataObject_NEON.yaml b/src/data/valid/Database-neon_Biosample_to_DataObject_NEON.yaml
@@ -90,8 +90,8 @@ data_object_set:
   data_object_type: Filtered Sequencing Reads
   url: https://data.microbiomedata.org/data/1472_51293/qa/1472_51293.filtered.fastq.gz
   type: nmdc:DataObject
-omics_processing_set:
-- id: nmdc:omprc-11-s9xj2r24
+data_generation_set:
+- id: nmdc:datgen-11-s9xj2r24
   name: Test NEON data
   has_input:
   - nmdc:procsm-99-xyz3
@@ -110,7 +110,7 @@ read_qc_analysis_activity_set:
   name: 'TEST Read QC Activity for nmdc:wfrqc-12-63da5n74 '
   started_at_time: '2023-03-23T17:17:05.111689+00:00'
   ended_at_time: '2023-03-23T17:17:05.111725+00:00'
-  was_informed_by: nmdc:omprc-11-s9xj2r24
+  was_informed_by: nmdc:datgen-11-s9xj2r24
   execution_resource: NERSC-Cori
   git_url: https://github.com/microbiomedata/ReadsQC
   has_input:

diff --git a/src/data/valid/Database-nmdc-example.yaml b/src/data/valid/Database-nmdc-example.yaml
@@ -61,8 +61,8 @@ study_set:
         doi_provider: osti
     type: nmdc:Study
     study_category: research_study
-omics_processing_set:
-  - id: nmdc:omprc-99-9XUVVF
+data_generation_set:
+  - id: nmdc:datgen-99-9XUVVF
     alternative_identifiers:
       - gold:Gp0225767
     name: Forest soil microbial communities from Barre Woods Harvard Forest LTER site,
@@ -84,7 +84,7 @@ omics_processing_set:
       - nmdc:sty-00-31415
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-dk9vgI
+  - id: nmdc:datgen-99-dk9vgI
     alternative_identifiers:
       - gold:Gp0208560
     name: Permafrost microbial communities from Stordalen Mire, Sweden - 611E1M metaG
@@ -103,7 +103,7 @@ omics_processing_set:
       - nmdc:sty-00-8675309
     processing_institution: JGI
     type: nmdc:OmicsProcessing
-  - id: nmdc:omprc-99-MVW1FV
+  - id: nmdc:datgen-99-MVW1FV
     alternative_identifiers:
       - gold:Gp0306221
     name: Rhizosphere microbial communities from Carex aquatilis grown in University

diff --git a/src/schema/external_identifiers.yaml b/src/schema/external_identifiers.yaml
@@ -277,14 +277,14 @@ slots:
     mixins:
       - igsn_identifiers
 
-  ## OmicsProcessing
+  ## DataGeneration
 
   omics_processing_identifiers:
     abstract: true
     is_a: external_database_identifiers
 
   gold_sequencing_project_identifiers:
-    domain: OmicsProcessing
+    domain: DataGeneration
     is_a: omics_processing_identifiers
     mixins:
       - gold_identifiers
@@ -295,7 +295,7 @@ slots:
 
   insdc_experiment_identifiers:
     is_a: external_database_identifiers
-    domain: OmicsProcessing
+    domain: DataGeneration
     pattern: "^insdc.sra:(E|D|S)RX[0-9]{6,}$"
     mixins:
       - insdc_identifiers