Document validation with linkml-validate and navigating the schema with schemaview

mkdocs.yml

@@ -33,6 +33,8 @@ nav:
   - Schema element deprecation guide: schema_element_deprecation_guide.md
   - v10 vs v11 (Berkeley schema) retrospective: v10-vs-v11-retrospective.md
   - Visualizations: visualizations.md
+  - Data Validation: validation.md
+  - SchemaView: schemaview.md
 
 
 site_url: https://microbiomedata.github.io/nmdc-schema

src/docs/schemaview.md

@@ -0,0 +1,18 @@
+# Using LinkML SchemaView in NMDC
+
+## Introduction
+
+Please see LinkML SchemaView documentation for general information.
+It has several good examples of how to use this module in a python script or from the command line.
+https://linkml.io/linkml/developers/schemaview.html#schemaview
+
+There are also several notebooks that demonstrate SchemaView usage in the LinkML-runtime repository:
+https://github.com/linkml/linkml-runtime/tree/main/notebooks
+
+Finally, the Biolink Model Toolkit is a helper wrapper around SchemaView for use with the Biolink Model and it
+has many examples of customizing SchemaView output for Biolink Model specific use cases.  Similar customizations
+may be helpful for NMDC.
+https://biolink.github.io/biolink-model-toolkit/
+https://github.com/biolink/biolink-model-toolkit/blob/master/examples/bmt-tutorial.ipynb
+
+

src/docs/validation.md

@@ -0,0 +1,50 @@
+# Validating nmdc-schema data against the schema
+
+## Introduction
+
+Please see LinkML Validation documentation for general information on validation with LinkML.
+It has several good examples of how to use linkml-validate in a python script or from the command line.
+https://linkml.io/linkml/data/validating-data.html
+
+
+Using the examples in src/docs/examples, we can validate the data against the schema in python:
+
+```python
+from linkml.validator import validate
+
+instance = {
+    "id": "nmdc:bsm-99-dtTMNb",
+    "associated_studies": ["nmdc:study-00-abc123"],
+    "env_broad_scale": {
+        "has_raw_value": "ENVO:00002030",
+        "term": {
+            "id": "ENVO:00002030"
+        }
+    },
+    "env_local_scale": {
+        "has_raw_value": "ENVO:00002169",
+        "term": {
+            "id": "ENVO:00002169"
+        }
+    },
+    "env_medium": {
+        "has_raw_value": "ENVO:00005792",
+        "term": {
+            "id": "ENVO:00005792"
+        }
+    },
+    "type": "nmdc:Biosample",
+    "analysis_type": [
+        "amplicon sequencing assay",
+        "metagenomics"
+    ]
+}
+
+report = validate(instance, "nmdc.yaml", "Biosample")
+
+if not report.results:
+    print('The instance is valid!')
+else:
+    for result in report.results:
+        print(result.message)
+```