second link fix to retain elements/ in root

Author: mkapur

README.md

@@ -6,7 +6,7 @@
 [![LinkML](https://img.shields.io/badge/LinkML-schema-blueviolet.svg)](https://linkml.io)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org)
 [![License: CC0-1.0](https://img.shields.io/badge/license-CC0%201.0-lightgrey.svg)](LICENSE)
-[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-informational.svg)](https://EMSL-Computing.github.io/BASALT-Schema)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-informational.svg)](https://emsl-computing.github.io/BASALT-Schema)
 [![DOI](https://zenodo.org/badge/1330063141.svg)](https://doi.org/10.5281/zenodo.21893601)
 
 LinkML schema for MONet/EMSL scientific data across **biogeochemical**, **biological**, and **environmental** domains. Canonical source of truth for samples, provenance, laboratory activities, and analytical products used by the Analysis API and database models.
@@ -17,9 +17,9 @@ Formerly `analysis-api-schema`.
 | --- | --- |
 | **Schema version** | `0.1.0` (see `version` in [`basalt_schema.yaml`](src/basalt_schema/schema/basalt_schema.yaml)) |
 | **Package** | `basalt_schema` (Python package version follows git tags via uv-dynamic-versioning) |
-| **Docs** | https://EMSL-Computing.github.io/BASALT-Schema |
+| **Docs** | https://emsl-computing.github.io/BASALT-Schema |
 | **Repository** | https://github.com/EMSL-Computing/BASALT-Schema |
-| **Canonical URI** | https://EMSL-Computing.github.io/BASALT-Schema |
+| **Canonical URI** | https://emsl-computing.github.io/BASALT-Schema |
 
 ## Repository Structure
 

docs/about.md

@@ -8,8 +8,8 @@ The BASALT schema is a [LinkML](https://linkml.io)-based data model for MONet/EM
 | --- | --- |
 | **Schema version** | `0.1.0` |
 | **Repository** | https://github.com/EMSL-Computing/BASALT-Schema |
-| **Docs** | https://EMSL-Computing.github.io/BASALT-Schema |
-| **Canonical URI** | https://EMSL-Computing.github.io/BASALT-Schema |
+| **Docs** | https://emsl-computing.github.io/BASALT-Schema |
+| **Canonical URI** | https://emsl-computing.github.io/BASALT-Schema |
 | **License** | [CC0 1.0 Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/) |
 
 Schema version is declared in the root LinkML file (`src/basalt_schema/schema/basalt_schema.yaml`) and follows semantic versioning. See the repository README for the release process.

docs/elements/AMP2DataGenerationActivity.md

@@ -21,7 +21,7 @@ _v1 origin: plate-general.yaml AMP2DataGenerationActivity_
 
 
 
-URI: [basalt_schema:AMP2DataGenerationActivity](https://EMSL-Computing.github.io/BASALT-Schema/AMP2DataGenerationActivity)
+URI: [basalt_schema:AMP2DataGenerationActivity](https://emsl-computing.github.io/BASALT-Schema/elements/AMP2DataGenerationActivity)
 
 
 
@@ -144,7 +144,7 @@ URI: [basalt_schema:AMP2DataGenerationActivity](https://EMSL-Computing.github.io
 ### Schema Source
 
 
-* from schema: https://EMSL-Computing.github.io/BASALT-Schema
+* from schema: https://emsl-computing.github.io/BASALT-Schema
 
 
 
@@ -181,7 +181,7 @@ description: 'AMP2 plate measurement (OD, fluorescence, flow cytometry).
 
 
   v1 origin: plate-general.yaml AMP2DataGenerationActivity'
-from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+from_schema: https://emsl-computing.github.io/BASALT-Schema
 is_a: PlateDataGenerationActivity
 slots:
 - measurement_type
@@ -206,13 +206,13 @@ description: 'AMP2 plate measurement (OD, fluorescence, flow cytometry).
 
 
   v1 origin: plate-general.yaml AMP2DataGenerationActivity'
-from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+from_schema: https://emsl-computing.github.io/BASALT-Schema
 is_a: PlateDataGenerationActivity
 attributes:
   measurement_type:
     name: measurement_type
     description: Type of plate measurement (optical_density, fluorescence, flow_cytometry)
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: measurement_type
     owner: AMP2DataGenerationActivity
@@ -223,7 +223,7 @@ attributes:
     name: wavelength_nm
     description: Measurement wavelength in nanometres (e.g. 590 Ecoplate, 610 AMP2
       OD)
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: wavelength_nm
     owner: AMP2DataGenerationActivity
@@ -240,7 +240,7 @@ attributes:
       Examples: "t=0", "t=24h", "t=48h".
 
       Lives on concrete analysis/product subclasses, NOT on base DataGenerationActivity'
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: timepoint_label
     owner: AMP2DataGenerationActivity
@@ -255,7 +255,7 @@ attributes:
       Lower = earlier in series. Use when acquisition_time alone is insufficient.\n\
       \nDDL: ALTER TABLE \"DataGenerationActivity\"\n       ADD COLUMN sequence_order\
       \ INTEGER;"
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: sequence_order
     owner: AMP2DataGenerationActivity
@@ -266,7 +266,7 @@ attributes:
   name:
     name: name
     description: Human-readable name for the entity or activity.
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: name
     owner: AMP2DataGenerationActivity
@@ -296,7 +296,7 @@ attributes:
     name: description
     description: Human-readable description for the entity or activity
     title: description
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: description
     owner: AMP2DataGenerationActivity
@@ -328,7 +328,7 @@ attributes:
   protocol_url:
     name: protocol_url
     description: URL pointing to the protocol used in the activity, if applicable.
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: protocol_url
     owner: AMP2DataGenerationActivity
@@ -339,7 +339,7 @@ attributes:
   protocol_version:
     name: protocol_version
     description: Version of the protocol used in the activity, if applicable.
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: protocol_version
     owner: AMP2DataGenerationActivity
@@ -349,7 +349,7 @@ attributes:
     range: string
   id:
     name: id
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     identifier: true
     alias: id
     owner: AMP2DataGenerationActivity
@@ -429,7 +429,7 @@ attributes:
     required: true
   analyte_id:
     name: analyte_id
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: analyte_id
     owner: AMP2DataGenerationActivity
@@ -438,7 +438,7 @@ attributes:
     range: ProcessedSample
   acquisition_start_time:
     name: acquisition_start_time
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: acquisition_start_time
     owner: AMP2DataGenerationActivity
@@ -448,7 +448,7 @@ attributes:
     required: true
   acquisition_end_time:
     name: acquisition_end_time
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: acquisition_end_time
     owner: AMP2DataGenerationActivity
@@ -458,7 +458,7 @@ attributes:
     required: true
   instrument_used:
     name: instrument_used
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: instrument_used
     owner: AMP2DataGenerationActivity
@@ -467,7 +467,7 @@ attributes:
     range: Instrument
   instrument_operator_id:
     name: instrument_operator_id
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: instrument_operator_id
     owner: AMP2DataGenerationActivity

docs/elements/AMP2ODProduct.md

@@ -17,7 +17,7 @@ _v1 origin: plate-general.yaml AMP2ODProduct_
 
 
 
-URI: [basalt_schema:AMP2ODProduct](https://EMSL-Computing.github.io/BASALT-Schema/AMP2ODProduct)
+URI: [basalt_schema:AMP2ODProduct](https://emsl-computing.github.io/BASALT-Schema/elements/AMP2ODProduct)
 
 
 
@@ -100,7 +100,7 @@ URI: [basalt_schema:AMP2ODProduct](https://EMSL-Computing.github.io/BASALT-Schem
 ### Schema Source
 
 
-* from schema: https://EMSL-Computing.github.io/BASALT-Schema
+* from schema: https://emsl-computing.github.io/BASALT-Schema
 
 
 
@@ -134,7 +134,7 @@ description: 'AMP2 optical density measurement product.
 
 
   v1 origin: plate-general.yaml AMP2ODProduct'
-from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+from_schema: https://emsl-computing.github.io/BASALT-Schema
 is_a: PlateProduct
 slots:
 - plate_reader_model
@@ -155,15 +155,15 @@ description: 'AMP2 optical density measurement product.
 
 
   v1 origin: plate-general.yaml AMP2ODProduct'
-from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+from_schema: https://emsl-computing.github.io/BASALT-Schema
 is_a: PlateProduct
 attributes:
   plate_reader_model:
     name: plate_reader_model
     description: Instrument model used for reading (e.g. "BioTek Epoch2")
     todos:
     - harmonize with existing Instrument modelling
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: plate_reader_model
     owner: AMP2ODProduct
@@ -174,7 +174,7 @@ attributes:
     name: wavelength_nm
     description: Measurement wavelength in nanometres (e.g. 590 Ecoplate, 610 AMP2
       OD)
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: wavelength_nm
     owner: AMP2ODProduct
@@ -191,7 +191,7 @@ attributes:
       Examples: "t=0", "t=24h", "t=48h".
 
       Lives on concrete analysis/product subclasses, NOT on base DataGenerationActivity'
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: timepoint_label
     owner: AMP2ODProduct
@@ -205,7 +205,7 @@ attributes:
     description: Mean measurement across all sample wells (excludes blanks)
     todos:
     - units
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: plate_average
     owner: AMP2ODProduct
@@ -217,7 +217,7 @@ attributes:
     description: Mean measurement of uninoculated control wells
     todos:
     - units
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: blank_mean
     owner: AMP2ODProduct
@@ -227,7 +227,7 @@ attributes:
   cv_percent:
     name: cv_percent
     description: Coefficient of variation across technical replicates
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: cv_percent
     owner: AMP2ODProduct
@@ -246,7 +246,7 @@ attributes:
     todos:
     - decide how to represent in backend (normalized child table with FK to PlateSetupActivity,
       array column, or other)
-    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
+    from_schema: https://emsl-computing.github.io/BASALT-Schema
     rank: 1000
     alias: well_readings
     owner: AMP2ODProduct