feature/120-uv-vis-fluorescence-examples

examples/README.md

@@ -15,6 +15,10 @@ To generate the output of each DCAT-AP profile into a TTL graph run:
     ````commandline
     uv run linkml-convert -t ttl ../tests/data/valid/NMRAnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C NMRAnalysisDataset
     ````
+  * Convert a single point UV-vis spectroscopy-specific DCAT-AP extension conform example
+    ````commandline
+    uv run linkml-convert -t ttl ../tests/data/valid/Single-UVvis-450nm-AnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C AnalysisDataset
+    ````
   * Convert domain agnostic DCAT-AP extension conform example of a MaterialSample
     ````commandline
     uv run linkml-convert -t ttl ../tests/data/valid/MaterialSample-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C MaterialSample
@@ -37,6 +41,10 @@ To generate the output of each DCAT-AP profile into a JSON file:
     ````commandline
     uv run linkml-convert -t json ../tests/data/valid/NMRAnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C NMRAnalysisDataset
     ````
+  * Convert a single point UV-vis spectroscopy-specific DCAT-AP extension conform example
+    ````commandline
+    uv run linkml-convert -t json ../tests/data/valid/Single-UVvis-450nm-AnalysisDataset-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C AnalysisDataset
+    ````
   * Convert domain agnostic DCAT-AP extension conform example of a MaterialSample
     ````commandline
     uv run linkml-convert -t json ../tests/data/valid/MaterialSample-001.yaml -s src/dcat_4c_ap/schema/dcat_4c_ap.yaml -P "_base=https://search.nfdi4chem.de/dataset/" -C MaterialSample

examples/jupyter/chem_dcat_ap_explorer.ipynb

@@ -0,0 +1,109 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "11d9ab98",
+   "metadata": {},
+   "source": [
+    "# Chem-DCAT-AP Explorer notebook\n",
+    "\n",
+    "This notebook is an interactive tool for exploring the [Chem-DCAT-AP](https://github.com/nfdi4chem/chem-dcat-ap) framework.\n",
+    "It illustrates how to use the Chem-DCAT-AP python data structures to create and manipulate metadata about chemistry related datasets.\n",
+    "\n",
+    "This is useful, if one wants to create metadata for a dataset programmatically (e.g. by retrieving information from a database).\n",
+    "\n",
+    "## Installation\n",
+    "To run this notebook, please ensure you have the necessary dependencies installed. You can install them using uv:\n",
+    "\n",
+    "```bash\n",
+    "# in the root directory of the project, please run:\n",
+    "uv sync \n",
+    "```\n",
+    "\n",
+    "## Running the notebook\n",
+    "\n",
+    "Once you have the dependencies installed, you can run this notebook simply by opening this notebook in vscode and\n",
+    "point to the virtual environment created by uv, or you can run it directly in your terminal (dcat-4c-ap = .venv) or by\n",
+    "using Jupyter:\n",
+    "\n",
+    "```bash\n",
+    "uv run jupyter notebook examples/jupyter/chem_dcat_ap_explorer.ipynb\n",
+    "```\n",
+    "\n",
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b72ca59d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from chem_dcat_ap.datamodel.chem_dcat_ap_pydantic import Catalogue, Dataset, Distribution, DataService"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f300ca1f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chem_dataset = Dataset(\n",
+    "    title=\"Example Dataset\",\n",
+    "    description=\"This is an example dataset for demonstration purposes.\",\n",
+    "    issued=\"2024-01-01\",\n",
+    "    modified=\"2024-01-02\",\n",
+    "    identifier=\"https://example.com/dataset/1\",\n",
+    ")\n",
+    "chem_catalogue = Catalogue(\n",
+    "    title=\"Example Catalogue\",\n",
+    "    description=\"This is an example catalogue for demonstration purposes.\",\n",
+    "    issued=\"2024-01-01\",\n",
+    "    modified=\"2024-01-02\",\n",
+    "    identifier=\"https://example.com/catalogue/1\",\n",
+    "    dataset=[chem_dataset],\n",
+    ")\n",
+    "print(chem_catalogue.model_dump_json(indent=2))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8b4fc28b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b4ec208",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "dcat-4c-ap",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyproject.toml

@@ -29,6 +29,11 @@ dev = [
     "mknotebooks>= 0.8.0",
     "pytest>=8.3.5",
     "coverage>=7.8.0",
+    "ipykernel>=6.31.0",
+    "pre-commit>=4.3.0",
+]
+test = [
+    "pytest>=8.4.2",
 ]
 
 # See https://hatch.pypa.io/latest/config/build/#file-selection for how to

src/chem_dcat_ap/schema/chem_dcat_ap.yaml

@@ -1,6 +1,6 @@
 ---
 id: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry/
-version: "0.1.0rc2.post33.dev0+fb29e03e" # Managed by dynamic-versioning. Don't change this line!
+version: "0.1.0rc2.post34.dev0+cb44dfdb" # Managed by dynamic-versioning. Don't change this line!
 name: chem-dcat-ap
 title: ChemDCAT-AP
 description: |-

tests/data/valid/Kinetics-UVvis-450nm-AnalysisDataset-001.yaml

@@ -0,0 +1,220 @@
+---
+id: handle:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3
+other_identifier:
+  - notation: https://pid4cat.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3
+title:
+  - "Kinetic UV-vis analysis at 450 nm of CRS-50440"
+description:
+  - "Dataset for time-resolved UV-visible spectroscopy (UV-vis) kinetics measurement at 450 nm wavelength"
+theme:
+  - preferred_label:
+      - "Science and technology"
+is_about_entity:
+  - id: handle:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
+    title: "CRS-50440"
+    description: "The analysed chemical substance sample CRS-50440."
+    rdf_type:
+      id: CHEBI:59999
+      title: "chemical substance"
+    has_part:
+      - id: handle:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2#EvaluatedCompound
+        description: "compound assigned to handle:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2"
+        other_identifier:
+          - notation: https://pubchem.ncbi.nlm.nih.gov/compound/26248854
+        rdf_type:
+          id: CHEBI:23367
+          title: molecular entity
+        has_qualitative_attribute:
+          - rdf_type:
+              id: CHEMINF:000059
+              title: "InChiKey"
+            value: KVOIVNBYNQXCNY-BOCHJOTCSA-N
+            title: "assigned InChiKey"
+          - rdf_type:
+              id: CHEMINF:000113
+              title: "InChi"
+            value: "InChI=1S/C11H12N2S/c1-12-7-10-8-14-11(13-10)9-5-3-2-4-6-9/h2-6,8,12H,7H2,1H3"
+            title: "assigned InChi"
+          - rdf_type:
+              id: CHEMINF:000018
+              title: "SMILES descriptor"
+            value: "CNCc1csc(n1)c1ccccc1"
+            title: "assigned SMILES"
+          - rdf_type:
+              id: CHEMINF:000042
+              title: "molecular formula"
+            value: "C11H12N2S"
+            title: "assigned molecular formula"
+          - rdf_type:
+              id: CHEMINF:000107
+              title: "IUPAC name"
+            value: "N-methyl-1-(2-phenyl-1,3-thiazol-4-yl)methanamine"
+            description: Chemotion IUPAC name
+          - rdf_type:
+              id: CHEMINF:000107
+              title: "IUPAC name"
+            value: "Methyl[(2-phenyl-1,3-thiazol-4-yl)methyl]amine"
+            description: PubChem IUPAC name
+        has_quantitative_attribute:
+          - has_quantity_type: http://qudt.org/vocab/quantitykind/MolarMass
+            unit: https://qudt.org/vocab/unit/GM-PER-MOL
+            value: 204.072119
+            description: "Molar mass as specified in the Chemotion repository."
+          - has_quantity_type: http://qudt.org/vocab/quantitykind/MolarMass
+            unit: https://qudt.org/vocab/unit/GM-PER-MOL
+            value: 204.29
+            description: "Molar mass as specified in PubChem"
+was_generated_by:
+  - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvisKineticAnalysis
+    title:
+      - "UV-vis kinetic analysis at 450 nm"
+    description:
+      - "Analysis of the time-resolved UV-visible trace at 450 nm wavelength."
+    rdf_type:
+      id: CHMO:0000596
+      title: "UV-visible spectroscopy"
+    evaluated_entity:
+      - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm
+        title: "UV-vis kinetic trace at 450 nm"
+        description: "Time-resolved UV-vis measurements recorded during the kinetics experiment."
+        rdf_type:
+          id: CHMO:0000596
+          title: "UV-visible spectroscopy"
+        has_qualitative_attribute:
+          - rdf_type:
+              id: CHMO:0000597
+              title: "measurement wavelength"
+            value: "450"
+            title: "Wavelength of measurement"
+        has_quantitative_attribute:
+          - rdf_type:
+              id: CHMO:0000599
+              title: "sample temperature information"
+            title: "sample temperature setting"
+            has_quantity_type: http://qudt.org/vocab/quantitykind/Temperature
+            unit: https://qudt.org/vocab/unit/K
+            value: 293.15
+          - rdf_type:
+              id: CHMO:0000600
+              title: "instrument resolution"
+            value: 1.0
+            has_quantity_type: http://qudt.org/vocab/quantitykind/Wavelength
+            unit: https://qudt.org/vocab/unit/NM
+            title: "Instrument resolution at 450 nm"
+        has_part:
+          - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm_t0s
+            title: "0 s measurement"
+            part_of:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm
+                title: "UV-vis kinetic trace at 450 nm"
+            has_quantitative_attribute:
+              - rdf_type:
+                  id: CHMO:0000602
+                  title: "measurement time"
+                title: "Measurement time"
+                has_quantity_type: http://qudt.org/vocab/quantitykind/Time
+                unit: https://qudt.org/vocab/unit/SEC
+                value: 0
+              - rdf_type:
+                  id: CHMO:0000598
+                  title: "absorbance value"
+                value: 0.85
+                has_quantity_type: http://qudt.org/vocab/quantitykind/DimensionlessRatio
+                unit: https://qudt.org/vocab/unit/ABS
+                title: "Absorbance at 450 nm"
+          - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm_t60s
+            title: "60 s measurement"
+            part_of:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm
+                title: "UV-vis kinetic trace at 450 nm"
+            has_quantitative_attribute:
+              - rdf_type:
+                  id: CHMO:0000602
+                  title: "measurement time"
+                title: "Measurement time"
+                has_quantity_type: http://qudt.org/vocab/quantitykind/Time
+                unit: https://qudt.org/vocab/unit/SEC
+                value: 60
+              - rdf_type:
+                  id: CHMO:0000598
+                  title: "absorbance value"
+                value: 0.78
+                has_quantity_type: http://qudt.org/vocab/quantitykind/DimensionlessRatio
+                unit: https://qudt.org/vocab/unit/ABS
+                title: "Absorbance at 450 nm"
+          - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm_t120s
+            title: "120 s measurement"
+            part_of:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm
+                title: "UV-vis kinetic trace at 450 nm"
+            has_quantitative_attribute:
+              - rdf_type:
+                  id: CHMO:0000602
+                  title: "measurement time"
+                title: "Measurement time"
+                has_quantity_type: http://qudt.org/vocab/quantitykind/Time
+                unit: https://qudt.org/vocab/unit/SEC
+                value: 120
+              - rdf_type:
+                  id: CHMO:0000598
+                  title: "absorbance value"
+                value: 0.70
+                has_quantity_type: http://qudt.org/vocab/quantitykind/DimensionlessRatio
+                unit: https://qudt.org/vocab/unit/ABS
+                title: "Absorbance at 450 nm"
+          - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm_t180s
+            title: "180 s measurement"
+            part_of:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticTrace_450nm
+                title: "UV-vis kinetic trace at 450 nm"
+            has_quantitative_attribute:
+              - rdf_type:
+                  id: CHMO:0000602
+                  title: "measurement time"
+                title: "Measurement time"
+                has_quantity_type: http://qudt.org/vocab/quantitykind/Time
+                unit: https://qudt.org/vocab/unit/SEC
+                value: 180
+              - rdf_type:
+                  id: CHMO:0000598
+                  title: "absorbance value"
+                value: 0.63
+                has_quantity_type: http://qudt.org/vocab/quantitykind/DimensionlessRatio
+                unit: https://qudt.org/vocab/unit/ABS
+                title: "Absorbance at 450 nm"
+        was_generated_by:
+          - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_KineticMeasurement_450nm
+            title:
+              - "UV-vis kinetic measurement at 450 nm"
+            description:
+              - "Time-resolved UV-vis acquisition from 0 to 180 seconds."
+            rdf_type:
+              id: CHMO:0000596
+              title: "UV-visible spectroscopy"
+            evaluated_entity:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N.2
+                title: "CRS-50440"
+            carried_out_by:
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_Spectrometer
+                rdf_type:
+                  id: OBI:0000566
+                  title: "UV-vis instrument"
+                title: "UV-Vis Spectrophotometer Model XYZ"
+                description: 'The UV-Vis spectrophotometer used for the kinetics measurement at 450 nm.'
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_SampleCell
+                description: "Sample cell used for the kinetics measurement"
+                has_part:
+                  - id: https://pubchem.ncbi.nlm.nih.gov/compound/12345
+                    rdf_type:
+                      id: CHEBI:12345
+                      title: "cuvette"
+                    title: "1 cm cuvette"
+              - id: doi:10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_Wavelength
+                title: "measurement wavelength"
+                part_of:
+                  - title: "450 nm"
+                    description: "The wavelength of measurement"
+                    id: https://doi.org/10.14272/UGRXAOUDHZOHPF-UHFFFAOYSA-N/CHMO0000595.3#UVvis_Wavelength_450nm
+                    rdf_type:
+                      id: CHMO:0000601
+                      title: "wavelength"