xas schema and dataset

Dataset/p65_example_data.yaml

-owner: "Kermit the Frog"
-type: raw
-principalInvestigator: "Dr. Bunsen Honeydew"
-scientificMetadata:
-#   special_p65_parameter: "something"
+experimentID: EXP-001
+sample:
+      sampleID: SAMPLE-001
+      material: Platinum on Alumina
+      preparationMethod: Impregnation
+      catalyst: Platinum (1 wt%)
+      reactionConditions: 
+        temperature:
+            unit: degC
+            value: 300
+        pressure:
+            unit: atm
+            value: 1
+        gas: H2
+      description: A sample of platinum nanoparticles dispersed on gamma-alumina support.
+      dSpacing: 3.54  # in angstroms
+      crystalType: Cubic
+instrument:
+      instrumentID: INSTR-001
+      name: Synchrotron Beamline Instrument
+      facility: DESY
+      beamline: P65
+      energyRange:
+        minEnergy: 
+            value: 5000
+            unit: eV
+        maxEnergy:
+            value: 25000
+            unit: eV  # in eV
+technique:
+      techniqueType: EXAFS
+      edge: K-edge
+      detector: Fluorescence
+      monochromator: Si111
+dataProcessing:
+      software: Athena
+      version: 0.9.26
+      method: Background subtraction and Fourier transform
+metadata:
+      project: "Catalysis Study for Platinum-Based Catalysts"
+      experimenter: "Dr. John Doe"
+startTime: "2024-08-01T09:00:00"
+endTime: "2024-08-01T12:00:00"
 
-  rockit_data:
-   #  DiffractionMetadata:
-   sample_environment:
-      GasComposition: "CO2"
-      GasSystem:
-         GasSys_Instrument_type: massflow_meter
-         GasSys_Instrument_type: flow_calibrator
-         # Instruments:  
-         #   Instrument_id: [25,35] 
-      motors: 
-         motor1:
-            value: 5
-            unit: mm
-         motor2:
-            value: 5
-            unit: mm
-         motor3:
-            value: 5
-            unit: mm
-        
-       
 
-  sample:
-    temperature:
-       value: 15
-       unit: K
-   #   layer_structure: "Si/SiO/DIP"
-    chemical_composition: "Si/SiO/DIP"
\ No newline at end of file

schema/base_sample.yaml

@@ -13,18 +13,35 @@ classes:
     abstract: true
     description: generic sample description
     attributes:
+      sampleID:
+        description: Unique identifier for the sample
+        required: true
+      material:
+        description: Material of the sample
+      preparationMethod:
+        description: Method used to prepare the sample
+      catalyst:
+        description: Catalyst used in the experiment
+      reactionConditions:
+        description: Reaction conditions (e.g., temperature, pressure)
+        range: ReactionConditions
+      description:
+        description: Detailed description of the sample
+      dSpacing:
+        description: Interplanar spacing (d-spacing) of the sample in angstroms
+        range: float
       chemical_composition:
         range: string
-      temperature:
-        range: TemperatureMeasurment
-      pressure:
-        range: PressureMeasurement
       environment:
         description: indentifier of specific sample environment
         range: string
         # Todo: see if this is feasable ... maybe sample envirenment should be split from sample completely
   SolidStateSample:
     is_a: Sample
+    attributes:
+      crystalType:
+        description: Crystal structure type of the sample (e.g., cubic, hexagonal)
+        range: CrystalTypeEnum
   LiquidSurfaceSammple:
     is_a: Sample
     attributes:
@@ -36,3 +53,27 @@ classes:
       layer_structure:
         range: string
         # Todo: see if feasable: use ORSO SampleModel String
+  ReactionConditions:
+    description: Reaction conditions (e.g., temperature, pressure)
+    attributes: 
+      temperature: 
+        range: TemperatureMeasurment
+      pressure: 
+        range: PressureMeasurement 
+      gas: 
+        range: string
+enums:
+  CrystalTypeEnum:
+    permissible_values:
+      Cubic:
+        description: Cubic crystal structure
+      Hexagonal:
+        description: Hexagonal crystal structure
+      Tetragonal:
+        description: Tetragonal crystal structure
+      Orthorhombic:
+        description: Orthorhombic crystal structure
+      Monoclinic:
+        description: Monoclinic crystal structure
+      Triclinic:
+        description: Triclinic crystal structure
\ No newline at end of file

schema/technique_xas_catalysis.yaml

 id: https://public-data.desy.de/metadata/xas-catalysis
-name: XAS Catalysis
+name: xas-catalysis
 description: Schema for X-ray Absorption Spectroscopy (XAS) technique in catalysis experiments at the DESY P65 beamline
 prefixes:
   schema: http://schema.org/
@@ -7,12 +7,14 @@ prefixes:
 default_range: string
 
 imports:
-  - [linkml:types, base_sample, sample_environment]
+  - linkml:types
+  - base_types
+  - base_sample
 
 default_prefix: xas_catalysis
 
 types:
-  float:  
+  float:
     base: float
   datetime:
     base: datetime
@@ -26,7 +28,7 @@ classes:
         required: true
       sample:
         description: Information about the sample used in the experiment
-        range: Sample
+        range: SolidStateSample
       instrument:
         description: Information about the instrument used for the experiment
         range: Instrument
@@ -46,23 +48,6 @@ classes:
         description: End time of the experiment
         range: datetime
 
-  Sample:
-    description: Information about the sample used in the XAS catalysis experiment
-    attributes:
-      sampleID:
-        description: Unique identifier for the sample
-        required: true
-      material:
-        description: Material of the sample
-      preparationMethod:
-        description: Method used to prepare the sample
-      catalyst:
-        description: Catalyst used in the experiment
-      reactionConditions:
-        description: Reaction conditions (e.g., temperature, pressure)
-      description:
-        description: Detailed description of the sample
-
   Instrument:
     description: Information about the instrument used for the XAS catalysis experiment
     attributes:
@@ -73,10 +58,10 @@ classes:
         description: Name of the instrument
       facility:
         description: Facility where the instrument is located
-        default: DESY
+        range: string
       beamline:
         description: Beamline used for the experiment
-        default: P64
+        range: string
       energyRange:
         description: Energy range used in the experiment
         range: EnergyRange
@@ -100,11 +85,11 @@ classes:
     attributes:
       minEnergy:
         description: Minimum energy in electron volts (eV)
-        range: float
+        range: EnergyMeasurement
         required: true
       maxEnergy:
         description: Maximum energy in electron volts (eV)
-        range: float
+        range: EnergyMeasurement
         required: true
 
   Technique:
@@ -158,3 +143,5 @@ enums:
         description: Silicon (311) monochromator
       Ge111:
         description: Germanium (111) monochromator
+
+  

scripts/validate_p65_data.sh

+# linkml-validate -s ./schema/beamline_p08.yaml -C P08Dataset  ./Dataset/p08_example_data.yaml   
+linkml-validate -s ../schema/technique_xas_catalysis.yaml -C CatalysisExperiment ../Dataset/p65_example_data.yaml 
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