Merge pull request #1572 from HumanCellAtlas/esv-edam-Issue1571

Fixed class from data:0006 to EDAM:0006. Fixes #1571
HumanCellAtlas · Aug 28, 2024 · 417f077 · 417f077
2 parents bb5d805 + e7fd055
commit 417f077
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Showing 7 changed files with 41 additions and 13 deletions.
diff --git a/changelog.md b/changelog.md
@@ -7,6 +7,34 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
 
+### [module/ontology/file_content_ontology.json - v2.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [type/file/analysis_file.json - v8.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [type/file/supplementary_file.json - v3.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [core/file/file_core.json - v7.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [type/file/image_file.json - v3.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [type/file/reference_file.json - v4.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
+### [type/file/sequence_file.json - v10.0.0] - 2024-08-28
+### Fixed
+Fixed class from data:0006 to EDAM:0006. Fixes #1571
+
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [module/biomaterial/medical_tests.json - v1.0.0] - 2024-08-13

diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md
@@ -57,8 +57,8 @@ Location: module/ontology/file_content_ontology.json
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
 text | General description of the contents of the file. | string | yes |  | Content description |  | DNA sequence (raw); Sequence alignment
-ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Content description ontology ID |  | data:3497; data:0863
-ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Content description ontology label |  | DNA sequence (raw); Sequence alignment
+ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Content description ontology ID |  | EDAM:3494; EDAM:0863
+ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Content description ontology label |  | DNA sequence; Sequence alignment
 
 ## Length unit ontology<a name='Length unit ontology'></a>
 _A term that may be associated with a cell type-related ontology term._

diff --git a/infrastructure_testing_files/current/dcp_integration_test_metadata_1_SS2_bundle.xlsx b/infrastructure_testing_files/current/dcp_integration_test_metadata_1_SS2_bundle.xlsx
diff --git a/infrastructure_testing_files/current/dcp_integration_test_metadata_1_optimus_10X_bundle.xlsx b/infrastructure_testing_files/current/dcp_integration_test_metadata_1_optimus_10X_bundle.xlsx
diff --git a/...ure_testing_files/current/not_accessioned_dcp_integration_test_metadata_1_SS2_bundle.xlsx b/...ure_testing_files/current/not_accessioned_dcp_integration_test_metadata_1_SS2_bundle.xlsx
diff --git a/json_schema/module/ontology/file_content_ontology.json b/json_schema/module/ontology/file_content_ontology.json
@@ -31,18 +31,18 @@
             "type": "string",
             "graph_restriction":  {
                 "ontologies" : ["obo:edam", "obo:efo"],
-                "classes": ["data:0006", "IAO:0000030"],
+                "classes": ["EDAM:0006", "IAO:0000030"],
                 "relations": ["rdfs:subClassOf"],
                 "direct": false,
                 "include_self": false
             },
-            "example": "data:3497; data:0863",
+            "example": "EDAM:3494; EDAM:0863",
             "user_friendly": "Content description ontology ID"
         },
         "ontology_label": {
             "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.",
             "type": "string",
-            "example": "DNA sequence (raw); Sequence alignment",
+            "example": "DNA sequence; Sequence alignment",
             "user_friendly": "Content description ontology label"
         }
     }

diff --git a/json_schema/versions.json b/json_schema/versions.json
@@ -1,12 +1,12 @@
 {
-    "last_update_date": "2024-08-13T12:07:03Z",
+    "last_update_date": "2024-08-28T14:24:32Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
                 "biomaterial_core": "8.4.0"
             },
             "file": {
-                "file_core": "6.4.0"
+                "file_core": "7.0.0"
             },
             "process": {
                 "process_core": "10.0.0"
@@ -42,7 +42,7 @@
                 "disease_ontology": "5.4.0",
                 "enrichment_ontology": "1.2.6",
                 "ethnicity_ontology": "5.3.9",
-                "file_content_ontology": "1.1.0",
+                "file_content_ontology": "2.0.0",
                 "file_format_ontology": "1.0.0",
                 "instrument_ontology": "5.3.6",
                 "length_unit_ontology": "5.3.5",
@@ -98,11 +98,11 @@
                 "specimen_from_organism": "10.9.0"
             },
             "file": {
-                "analysis_file": "7.0.0",
-                "image_file": "2.5.0",
-                "reference_file": "3.5.0",
-                "sequence_file": "9.6.0",
-                "supplementary_file": "2.5.0"
+                "analysis_file": "8.0.0",
+                "image_file": "3.0.0",
+                "reference_file": "4.0.0",
+                "sequence_file": "10.0.0",
+                "supplementary_file": "3.0.0"
             },
             "process": {
                 "analysis": {