diff --git a/.github/workflows/automated-testing.yml b/.github/workflows/automated-testing.yml
index 75ecc48bd..1ad9fdaf3 100644
--- a/.github/workflows/automated-testing.yml
+++ b/.github/workflows/automated-testing.yml
@@ -12,6 +12,50 @@ jobs:
       - name: make
         run: |
           make
+      - name: validate-profile
+        run: |
+          echo "java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt"
+          java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt
+      - name: verify
+        run: |
+          java -jar build/robot.jar verify --input build/oeo/$(cat VERSION)/oeo-full.owl --queries tests/verify/*
+      - uses: actions/upload-artifact@master
+        with:
+          name: build-artifacts
+          path: build/oeo
+  test:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.7'
+          architecture: x64
+      - uses: actions/setup-java@v2
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+      - uses: actions/download-artifact@master
+        with:
+          name: build-artifacts
+          path: build/oeo
+      - name: install python dependencies
+        run: pip install -r src/scripts/requirements.txt
+      - name: setup robot 1.9.0
+        run: |
+          wget https://github.com/ontodev/robot/releases/download/v1.9.0/robot.jar -O build/robot19.jar
+      - name: Build ETD xlsx
+        run: |
+          java -jar build/robot19.jar merge --input build/oeo/$(cat VERSION)/oeo-full.omn \
+            --include-annotations true \
+          export  --header "ID|LABEL|definition" \
+                  --prefix "OEO: http://openenergy-platform.org/ontology/oeo/OEO_" \
+                  --sort "LABEL" \
+                  --export $(pwd)/build/oeo/$(cat VERSION)/etd.xlsx
+      - name: Build ETD csv
+        run: |
+          python $(pwd)/src/scripts/etd/etd.py $(pwd)/build/oeo/$(cat VERSION)
       - name: consistency
         run: |
           wget https://github.com/owlcs/releases/raw/master/HermiT/org.semanticweb.hermit-packaged-1.4.6.519-SNAPSHOT.jar -O build/hermit.jar
@@ -22,21 +66,39 @@ jobs:
           fi
           echo "Ontology is inconsistent: $OUT"
           exit 1
-      - name: validate-profile
-        run: | 
-          echo "java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt"
-          java -jar build/robot.jar validate-profile --input build/oeo/$(cat VERSION)/oeo-full.owl --profile Full -vvv --output merged-validation.txt
-      - name: verify
-        run: |
-          java -jar build/robot.jar verify --input build/oeo/$(cat VERSION)/oeo-full.owl --queries tests/verify/*
-      - name: competency
-        run: |
-          bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl true
-          bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl false
-      - name: Upload Artifacts
+      - name: Upload Ontology
+        if: always()
         uses: actions/upload-artifact@v3
         with:
           name: build-files
           path: |
             build/**/*
-            !build/**/*.jar
\ No newline at end of file
+            !build/**/*.jar
+      - name: competency
+        continue-on-error: true
+        run: |
+          pytest -s -v
+          # bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl true
+          # bash tests/competency_questions/run_questions.sh "java -jar build/hermit.jar" $(pwd)/build/oeo/$(cat VERSION)/oeo-full.owl false
+      - name: Upload Artifacts
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: test-report
+          path: build/report.json
+      - name: Get Coverage for badge
+        run : |
+          echo "COVERAGE=$(head build/report.json | grep -o '"coverage": "[^"]*"' | grep -o '[^"]*\%')" >> $GITHUB_ENV
+          REF=${{ github.ref }}
+          IFS='/' read -ra PATHS <<< "$REF"
+          BRANCH_NAME="${PATHS[1]}_${PATHS[2]}"
+          echo "BRANCH=$(echo ${BRANCH_NAME})" >> $GITHUB_ENV
+      - name: Coverage Badge
+        uses: schneegans/dynamic-badges-action@v1.0.0
+        with:
+          auth: ${{ secrets.GIST_SECRET }}
+          gistID: 6d00affa9fbc89c79684d62091d96551
+          filename: open_energy_ontology__${{ env.BRANCH }}.json
+          label: CQ Coverage
+          message: ${{ env.COVERAGE }}
+          color: green
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 567609b12..d120bfc65 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 build/
+*/__pycache__/*
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 68bd908df..bfe17e139 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,9 +26,12 @@ and the versioning aims to respect [Semantic Versioning](http://semver.org/spec/
 - secondary energy production (#1619)
 - hydro energy, solar energy, wind energy (#1620)
 - gross domestic product (#1623)
-
+- reimplemented competency question tests in pytest (#1420)
+- added commands to filter competency questions from the command line (#1420)
+- added descriptive names to competency questions. and organized them in directories (#1420)
 
 ### Removed
+- old compteency question bash script (#1420)
 
 ## [1.15.0] - 2023-05-31
 
diff --git a/README.md b/README.md
index e35df8d0b..ef5725a04 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,7 @@
 
 [![License: CC0-1.0](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](http://creativecommons.org/publicdomain/zero/1.0/)
 ![GitHub release (latest by date)](https://img.shields.io/github/v/release/OpenEnergyPlatform/ontology)
+![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/areleu/6d00affa9fbc89c79684d62091d96551/raw/open_energy_ontology__heads_feature-1419-competency-question-coverage-report.json)
 
 # Open Energy Family - Open Energy Ontology (OEO)
 
diff --git a/src/scripts/etd/etd.py b/src/scripts/etd/etd.py
index e2e766d2d..f3a90dfac 100644
--- a/src/scripts/etd/etd.py
+++ b/src/scripts/etd/etd.py
@@ -25,9 +25,7 @@
     df = df.replace('\n', '<br>', regex=True)
     df = df.sort_values("LABEL", key=lambda col: col.str.strip().str.lower())
     # Create one table per letter:
-
-    pathlib.Path(cwd + "/src/scripts/etd/glossary/").mkdir(parents=True, exist_ok=True) 
-
+    pathlib.Path(target_path).joinpath("glossary").mkdir(parents=True, exist_ok=True) 
     # header = GLOSSARY_HEADER + " ".join([f"[{letter}]({BASE_LINK_WIKI}{letter})" for letter in string.ascii_uppercase]) + "\n"
 
     # with open(cwd + "/src/scripts/etd/glossary/glossary.md", "w") as fil:
@@ -55,4 +53,4 @@
     df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-physical/", "")
     df_csv["ID"] = df_csv["ID"].str.replace("http://openenergy-platform.org/ontology/oeo/oeo-model/", "")
     df_csv["ID"] = df_csv["ID"].str.replace(":", "_")
-    df_csv.to_csv(pathlib.Path(target_path).joinpath("glossary/glossary.csv").as_posix(), index=False)
\ No newline at end of file
+    df_csv.to_csv(pathlib.Path(target_path).joinpath("glossary/glossary.csv").as_posix(), index=False)
diff --git a/src/scripts/requirements.txt b/src/scripts/requirements.txt
index d2a0c938b..541c177d3 100644
--- a/src/scripts/requirements.txt
+++ b/src/scripts/requirements.txt
@@ -1,3 +1,5 @@
 pandas
 tabulate
-openpyxl
\ No newline at end of file
+openpyxl
+pytest
+pytest_harvest
\ No newline at end of file
diff --git a/tests/competency_questions/q1.omn b/tests/competency_questions/deprecated/001_biofuel_is_renewable_fuel.omn
similarity index 98%
rename from tests/competency_questions/q1.omn
rename to tests/competency_questions/deprecated/001_biofuel_is_renewable_fuel.omn
index 79d799367..224607e53 100644
--- a/tests/competency_questions/q1.omn
+++ b/tests/competency_questions/deprecated/001_biofuel_is_renewable_fuel.omn
@@ -3,11 +3,11 @@ Prefix: : <http://openenergy-platform.org/ontology/oeo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 # Competency Question: Is  biofuel renewable fuel?
- 
+
 Class: OEO_00000033
 Class: OEO_00000072
 
 Class: OEO_00000072
   SubClassOf: OEO_00000033
-    
+
 # This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409
\ No newline at end of file
diff --git a/tests/competency_questions/q29.omn b/tests/competency_questions/deprecated/029_biofuel_is_classified_as_renewable_fuel.omn
similarity index 85%
rename from tests/competency_questions/q29.omn
rename to tests/competency_questions/deprecated/029_biofuel_is_classified_as_renewable_fuel.omn
index fe6cb326c..9b482e7ba 100644
--- a/tests/competency_questions/q29.omn
+++ b/tests/competency_questions/deprecated/029_biofuel_is_classified_as_renewable_fuel.omn
@@ -12,4 +12,4 @@ Class: OEO_00000033
 Class: OEO_00000072
     SubClassOf: OEO_00000033
 
-# This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409
\ No newline at end of file
+# This competency question gets deprecated with this pull request: https://github.com/OpenEnergyPlatform/ontology/pull/1409
diff --git a/tests/competency_questions/q43.omn b/tests/competency_questions/implementing/043_thermal_energy_bearers_carry_energy.omn
similarity index 88%
rename from tests/competency_questions/q43.omn
rename to tests/competency_questions/implementing/043_thermal_energy_bearers_carry_energy.omn
index dc24c6117..9f021915b 100644
--- a/tests/competency_questions/q43.omn
+++ b/tests/competency_questions/implementing/043_thermal_energy_bearers_carry_energy.omn
@@ -5,15 +5,14 @@ Prefix: obo: <http://purl.obolibrary.org/obo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 
-# Do all hot things carry energy? 
+# Do all hot things carry energy?
 
 Class: owl:Nothing
 
-ObjectProperty: obo:RO_0000053 #bearer_of 
+ObjectProperty: obo:RO_0000053 #bearer_of
 Class: OEO_00000207      #Thermal energy
 ObjectProperty: obo:RO_0000091 #has_disposition
 Class: OEO_00000151 #energy carrier disposition
 
 EquivalentClasses: ((obo:RO_0000053 some OEO_00000207) and not (obo:RO_0000091 some OEO_00000151)), owl:Nothing
 # All bearers of thermal energy have the disposition of being energy carriers
- 
\ No newline at end of file
diff --git a/tests/competency_questions/q44.omn b/tests/competency_questions/implementing/044_renewable_energy_do_not_use_fossil_fuel.omn
similarity index 100%
rename from tests/competency_questions/q44.omn
rename to tests/competency_questions/implementing/044_renewable_energy_do_not_use_fossil_fuel.omn
diff --git a/tests/competency_questions/q48.omn b/tests/competency_questions/implementing/048_energy_from_pv_cell_is_renewable.omn
similarity index 100%
rename from tests/competency_questions/q48.omn
rename to tests/competency_questions/implementing/048_energy_from_pv_cell_is_renewable.omn
diff --git a/tests/competency_questions/q49.omn b/tests/competency_questions/implementing/049_natural_gas_not_anthropogenic.omn
similarity index 100%
rename from tests/competency_questions/q49.omn
rename to tests/competency_questions/implementing/049_natural_gas_not_anthropogenic.omn
diff --git a/tests/competency_questions/q50.omn b/tests/competency_questions/implementing/050_energy_from_coal_powerplant_not_renewable.omn
similarity index 100%
rename from tests/competency_questions/q50.omn
rename to tests/competency_questions/implementing/050_energy_from_coal_powerplant_not_renewable.omn
diff --git a/tests/competency_questions/q45.omn b/tests/competency_questions/model/soundness/045_scenario_realizes_at_most_one_model_calculation_.omn
similarity index 100%
rename from tests/competency_questions/q45.omn
rename to tests/competency_questions/model/soundness/045_scenario_realizes_at_most_one_model_calculation_.omn
diff --git a/tests/competency_questions/q2.omn b/tests/competency_questions/physical/completeness/002_carbon_monoxide_is_air_pollutant.omn
similarity index 100%
rename from tests/competency_questions/q2.omn
rename to tests/competency_questions/physical/completeness/002_carbon_monoxide_is_air_pollutant.omn
diff --git a/tests/competency_questions/q3.omn b/tests/competency_questions/physical/completeness/003_nitrous_oxide_is_greenhouse_gas.omn
similarity index 100%
rename from tests/competency_questions/q3.omn
rename to tests/competency_questions/physical/completeness/003_nitrous_oxide_is_greenhouse_gas.omn
diff --git a/tests/competency_questions/q4.omn b/tests/competency_questions/physical/completeness/004_equivalences_to_flourinated_greenhouse_gases.omn
similarity index 95%
rename from tests/competency_questions/q4.omn
rename to tests/competency_questions/physical/completeness/004_equivalences_to_flourinated_greenhouse_gases.omn
index 63d708f9a..b44195eda 100644
--- a/tests/competency_questions/q4.omn
+++ b/tests/competency_questions/physical/completeness/004_equivalences_to_flourinated_greenhouse_gases.omn
@@ -9,7 +9,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 Class: OEO_00000026
 Class: OEO_00000038
 Class: OEO_00000219
-Class: OEO_00000321
+Class: OEO_00000322
 
 Class: OEO_00000013
     EquivalentTo: OEO_00000026 or OEO_00000038 or OEO_00000219 or OEO_00000322
\ No newline at end of file
diff --git a/tests/competency_questions/q5.omn b/tests/competency_questions/physical/completeness/005_methane_has_normal_state_of_matter_gaseous.omn
similarity index 93%
rename from tests/competency_questions/q5.omn
rename to tests/competency_questions/physical/completeness/005_methane_has_normal_state_of_matter_gaseous.omn
index fb2403d11..14eddf8fc 100644
--- a/tests/competency_questions/q5.omn
+++ b/tests/competency_questions/physical/completeness/005_methane_has_normal_state_of_matter_gaseous.omn
@@ -8,7 +8,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 
 Class: OEO_00000025
 ObjectProperty: OEO_00000529
-Class: OEO_00000182
+Individual: OEO_00000182
 
 Class: OEO_00000025
     SubClassOf: OEO_00000529 value OEO_00000182
\ No newline at end of file
diff --git a/tests/competency_questions/q6.omn b/tests/competency_questions/physical/completeness/006_synthetic_hydrogen_is_synthetic_fuel.omn
similarity index 100%
rename from tests/competency_questions/q6.omn
rename to tests/competency_questions/physical/completeness/006_synthetic_hydrogen_is_synthetic_fuel.omn
diff --git a/tests/competency_questions/q7.omn b/tests/competency_questions/physical/completeness/007_biodisel_is_liquid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q7.omn
rename to tests/competency_questions/physical/completeness/007_biodisel_is_liquid_biofuel.omn
diff --git a/tests/competency_questions/q8.omn b/tests/competency_questions/physical/completeness/008_charcoal_is_energy_carrier_and_has_normal_state_of_matter_solid.omn
similarity index 100%
rename from tests/competency_questions/q8.omn
rename to tests/competency_questions/physical/completeness/008_charcoal_is_energy_carrier_and_has_normal_state_of_matter_solid.omn
diff --git a/tests/competency_questions/q9.omn b/tests/competency_questions/physical/completeness/009_power_line_is_grid_component.omn
similarity index 100%
rename from tests/competency_questions/q9.omn
rename to tests/competency_questions/physical/completeness/009_power_line_is_grid_component.omn
diff --git a/tests/competency_questions/q10.omn b/tests/competency_questions/physical/completeness/010_switchyard_is_grid_component.omn
similarity index 100%
rename from tests/competency_questions/q10.omn
rename to tests/competency_questions/physical/completeness/010_switchyard_is_grid_component.omn
diff --git a/tests/competency_questions/q11.omn b/tests/competency_questions/physical/completeness/011_transformer_is_grid_component.omn
similarity index 100%
rename from tests/competency_questions/q11.omn
rename to tests/competency_questions/physical/completeness/011_transformer_is_grid_component.omn
diff --git a/tests/competency_questions/q12.omn b/tests/competency_questions/physical/completeness/012_gas_fired_power_unit_is_fueled_power_unit.omn
similarity index 83%
rename from tests/competency_questions/q12.omn
rename to tests/competency_questions/physical/completeness/012_gas_fired_power_unit_is_fueled_power_unit.omn
index f570b4309..aba63f3f8 100644
--- a/tests/competency_questions/q12.omn
+++ b/tests/competency_questions/physical/completeness/012_gas_fired_power_unit_is_fueled_power_unit.omn
@@ -4,7 +4,7 @@ Prefix: : <http://openenergy-platform.org/ontology/oeo/>
 Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platform.org/ontology/cc/>
 
 
-#Is a gas fired power unit a fuelled power unit?
+#Is a gas fired power unit a fueled power unit?
 
 Class: OEO_00000017
 Class: OEO_00000175
diff --git a/tests/competency_questions/q13.omn b/tests/competency_questions/physical/completeness/013_hydrogen_power_unit_is_fueled_power_unit.omn
similarity index 100%
rename from tests/competency_questions/q13.omn
rename to tests/competency_questions/physical/completeness/013_hydrogen_power_unit_is_fueled_power_unit.omn
diff --git a/tests/competency_questions/q14.omn b/tests/competency_questions/physical/completeness/014_nuclear_power_unit_is_fueled_power_unit.omn
similarity index 100%
rename from tests/competency_questions/q14.omn
rename to tests/competency_questions/physical/completeness/014_nuclear_power_unit_is_fueled_power_unit.omn
diff --git a/tests/competency_questions/q15.omn b/tests/competency_questions/physical/completeness/015_oil_power_unit_is_fueled_power_unit.omn
similarity index 100%
rename from tests/competency_questions/q15.omn
rename to tests/competency_questions/physical/completeness/015_oil_power_unit_is_fueled_power_unit.omn
diff --git a/tests/competency_questions/q16.omn b/tests/competency_questions/physical/completeness/016_waste_power_unit_is_fueled_power_unit.omn
similarity index 100%
rename from tests/competency_questions/q16.omn
rename to tests/competency_questions/physical/completeness/016_waste_power_unit_is_fueled_power_unit.omn
diff --git a/tests/competency_questions/q17.omn b/tests/competency_questions/physical/completeness/017_biofuel_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q17.omn
rename to tests/competency_questions/physical/completeness/017_biofuel_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q18.omn b/tests/competency_questions/physical/completeness/018_coal_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q18.omn
rename to tests/competency_questions/physical/completeness/018_coal_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q19.omn b/tests/competency_questions/physical/completeness/019_gas_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q19.omn
rename to tests/competency_questions/physical/completeness/019_gas_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q20.omn b/tests/competency_questions/physical/completeness/020_hydrogen_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q20.omn
rename to tests/competency_questions/physical/completeness/020_hydrogen_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q21.omn b/tests/competency_questions/physical/completeness/021_oil_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q21.omn
rename to tests/competency_questions/physical/completeness/021_oil_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q22.omn b/tests/competency_questions/physical/completeness/022_waste_power_plant_is_fueled_power_plant.omn
similarity index 100%
rename from tests/competency_questions/q22.omn
rename to tests/competency_questions/physical/completeness/022_waste_power_plant_is_fueled_power_plant.omn
diff --git a/tests/competency_questions/q23.omn b/tests/competency_questions/physical/completeness/023_amonia_is_air_pollutant.omn
similarity index 100%
rename from tests/competency_questions/q23.omn
rename to tests/competency_questions/physical/completeness/023_amonia_is_air_pollutant.omn
diff --git a/tests/competency_questions/q24.omn b/tests/competency_questions/physical/completeness/024_biodisel_is_liquid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q24.omn
rename to tests/competency_questions/physical/completeness/024_biodisel_is_liquid_biofuel.omn
diff --git a/tests/competency_questions/q25.omn b/tests/competency_questions/physical/completeness/025_biogasoline_is_liquid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q25.omn
rename to tests/competency_questions/physical/completeness/025_biogasoline_is_liquid_biofuel.omn
diff --git a/tests/competency_questions/q26.omn b/tests/competency_questions/physical/completeness/026_carbon_dioxide_is_greenhouse_gas.omn
similarity index 100%
rename from tests/competency_questions/q26.omn
rename to tests/competency_questions/physical/completeness/026_carbon_dioxide_is_greenhouse_gas.omn
diff --git a/tests/competency_questions/q27.omn b/tests/competency_questions/physical/completeness/027_charcoal_is_solid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q27.omn
rename to tests/competency_questions/physical/completeness/027_charcoal_is_solid_biofuel.omn
diff --git a/tests/competency_questions/q28.omn b/tests/competency_questions/physical/completeness/028_coal_is_solid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q28.omn
rename to tests/competency_questions/physical/completeness/028_coal_is_solid_biofuel.omn
diff --git a/tests/competency_questions/q30.omn b/tests/competency_questions/physical/completeness/030_synthetic_fuel_is_combustion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q30.omn
rename to tests/competency_questions/physical/completeness/030_synthetic_fuel_is_combustion_fuel.omn
diff --git a/tests/competency_questions/q31.omn b/tests/competency_questions/physical/completeness/031_renewable_fuel_is_combustion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q31.omn
rename to tests/competency_questions/physical/completeness/031_renewable_fuel_is_combustion_fuel.omn
diff --git a/tests/competency_questions/q32.omn b/tests/competency_questions/physical/completeness/032_waste_fuel_is_combustion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q32.omn
rename to tests/competency_questions/physical/completeness/032_waste_fuel_is_combustion_fuel.omn
diff --git a/tests/competency_questions/q33.omn b/tests/competency_questions/physical/completeness/033_renewable_municipal_waste_is_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q33.omn
rename to tests/competency_questions/physical/completeness/033_renewable_municipal_waste_is_biofuel.omn
diff --git a/tests/competency_questions/q34.omn b/tests/competency_questions/physical/completeness/034_hydrogen_is_combusion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q34.omn
rename to tests/competency_questions/physical/completeness/034_hydrogen_is_combusion_fuel.omn
diff --git a/tests/competency_questions/q35.omn b/tests/competency_questions/physical/completeness/035_methane_is_greenhouse_gas.omn
similarity index 100%
rename from tests/competency_questions/q35.omn
rename to tests/competency_questions/physical/completeness/035_methane_is_greenhouse_gas.omn
diff --git a/tests/competency_questions/q36.omn b/tests/competency_questions/physical/completeness/036_methane_is_combusion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q36.omn
rename to tests/competency_questions/physical/completeness/036_methane_is_combusion_fuel.omn
diff --git a/tests/competency_questions/q37.omn b/tests/competency_questions/physical/completeness/037_natural_gas_is_fossil_combusion_fuel.omn
similarity index 100%
rename from tests/competency_questions/q37.omn
rename to tests/competency_questions/physical/completeness/037_natural_gas_is_fossil_combusion_fuel.omn
diff --git a/tests/competency_questions/q38.omn b/tests/competency_questions/physical/completeness/038_nitrogen_oxide_is_air_pollutant.omn
similarity index 100%
rename from tests/competency_questions/q38.omn
rename to tests/competency_questions/physical/completeness/038_nitrogen_oxide_is_air_pollutant.omn
diff --git a/tests/competency_questions/q39.omn b/tests/competency_questions/physical/completeness/039_particulate_matter_is_air_pollutant.omn
similarity index 100%
rename from tests/competency_questions/q39.omn
rename to tests/competency_questions/physical/completeness/039_particulate_matter_is_air_pollutant.omn
diff --git a/tests/competency_questions/q40.omn b/tests/competency_questions/physical/completeness/040_peat_is_solid_fossil_fuel.omn
similarity index 100%
rename from tests/competency_questions/q40.omn
rename to tests/competency_questions/physical/completeness/040_peat_is_solid_fossil_fuel.omn
diff --git a/tests/competency_questions/q41.omn b/tests/competency_questions/physical/completeness/041_sulphur_dioxide_is_air_pollutant.omn
similarity index 100%
rename from tests/competency_questions/q41.omn
rename to tests/competency_questions/physical/completeness/041_sulphur_dioxide_is_air_pollutant.omn
diff --git a/tests/competency_questions/q47.omn b/tests/competency_questions/physical/completeness/047_portion_of_hydrogen_is_energy_carrier.omn
similarity index 79%
rename from tests/competency_questions/q47.omn
rename to tests/competency_questions/physical/completeness/047_portion_of_hydrogen_is_energy_carrier.omn
index 63174dcd6..1ed407962 100644
--- a/tests/competency_questions/q47.omn
+++ b/tests/competency_questions/physical/completeness/047_portion_of_hydrogen_is_energy_carrier.omn
@@ -8,7 +8,7 @@ Ontology: <http://openenergy-platform.org/ontology/cc/> <http://openenergy-platf
 # Every portion of hydrogen is an energy carrier
 
 ObjectProperty: obo:RO_0000091 # has disposion
-Class: OEO_00000028 # energy carrier disposition
+Class: OEO_00000151 # energy carrier disposition
 
 Class: OEO_00000220 # hydrogen
-    SubClassOf: obo:RO_0000091 some OEO_00000028
+    SubClassOf: obo:RO_0000091 some OEO_00000151
diff --git a/tests/competency_questions/q51.omn b/tests/competency_questions/physical/completeness/051_charcoal_is_solid_biofuel.omn
similarity index 100%
rename from tests/competency_questions/q51.omn
rename to tests/competency_questions/physical/completeness/051_charcoal_is_solid_biofuel.omn
diff --git a/tests/competency_questions/q42.omn b/tests/competency_questions/physical/soundness/042_wind_turbines_not_powered_by_coal.omn
similarity index 100%
rename from tests/competency_questions/q42.omn
rename to tests/competency_questions/physical/soundness/042_wind_turbines_not_powered_by_coal.omn
diff --git a/tests/competency_questions/run_questions.sh b/tests/competency_questions/run_questions.sh
deleted file mode 100755
index de7fc87fe..000000000
--- a/tests/competency_questions/run_questions.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/bash
-
-COMMAND=$1
-MERGED=$2
-EXPECTED_RESULT=$3
-
-INFER="q2.omn q3.omn q4.omn q5.omn q6.omn q7.omn q8.omn q9.omn q10.omn q11.omn q12.omn q13.omn q14.omn q15.omn q16.omn q17.omn q18.omn q19.omn q20.omn q21.omn q22.omn q23.omn q24.omn q25.omn q26.omn q27.omn q28.omn q30.omn q31.omn q32.omn q33.omn q34.omn q35.omn q36.omn q37.omn q38.omn q39.omn q40.omn q41.omn q51.omn "
-NON_INFERABLE_BUT_SHOULD="q42.omn q43.omn q44.omn q46.omn q47.omn q48.omn q49.omn q50.omn"
-DONT_INFER="q1.omn q29.omn q45.omn"
-
-if [ "$EXPECTED_RESULT" = "true" ]
-then
-    LIST=$INFER
-else
-    LIST=$DONT_INFER
-fi
-
-PWD=$(pwd)
-
-for file in $LIST
-do
-    echo "Infer $file"
-    FULLCOMMAND="$COMMAND --premise=file:$MERGED --conclusion=file:$PWD/tests/competency_questions/$file -E"
-    echo "$FULLCOMMAND"
-    RESULT=$($FULLCOMMAND)
-    if [ "$RESULT" != "$EXPECTED_RESULT" ]
-    then
-        echo "Inference failed for $file"
-        echo "Output: $RESULT"
-        exit 1
-    fi
-done
\ No newline at end of file
diff --git a/tests/competency_questions/q46.omn b/tests/competency_questions/social/completeness/046_agent_not_a_person.omn
similarity index 100%
rename from tests/competency_questions/q46.omn
rename to tests/competency_questions/social/completeness/046_agent_not_a_person.omn
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 000000000..2c2bfaa5e
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,8 @@
+
+
+def pytest_addoption(parser):
+    parser.addoption("--selected", action="store", default="")
+    parser.addoption("--report", action="store", default="report.json")
+    parser.addoption("--implementation", action="store_true", default=False, help="Run in development tests")
+    parser.addoption("--deprecated", action="store_true", default=False, help="Run deprecated tests")
+
diff --git a/tests/test_competency_questions.py b/tests/test_competency_questions.py
new file mode 100644
index 000000000..2810e2eb3
--- /dev/null
+++ b/tests/test_competency_questions.py
@@ -0,0 +1,180 @@
+from glob import glob
+import pandas as pd
+from subprocess import Popen, PIPE
+from pathlib import Path
+import json
+import re
+from pytest_harvest import saved_fixture
+import pytest
+import os
+import shutil
+
+CWD = os.getcwd()
+with open(Path(CWD).joinpath("VERSION").as_posix()) as version_file:
+    __version__ = version_file.readlines()[0].strip()
+
+HERMIT_JAR = Path(CWD).joinpath("build/hermit.jar").as_posix()
+JAVA_PATH = shutil.which("java")
+ONTOLOGY_PATH = (
+    Path(CWD)
+    .joinpath("build/oeo")
+    .joinpath(f"{__version__}")
+    .joinpath("oeo-full.omn")
+    .as_posix()
+)
+EXISTING_TERMS_AND_DEFINITONS = (
+    Path(CWD).joinpath("build/oeo").joinpath(f"{__version__}").joinpath("glossary/glossary.csv")
+)
+COMPETENCY_QUESTION_DIRECTORY = Path(CWD).joinpath("tests/competency_questions")
+
+
+@pytest.fixture
+@saved_fixture
+def existing_terms_and_definitons():
+    """
+    Fixture containing the final report
+    """
+    terms_and_definitions = pd.read_csv(EXISTING_TERMS_AND_DEFINITONS)
+    return list(terms_and_definitions["ID"])
+
+@pytest.fixture
+def implementation(request):
+    return request.config.getoption("--implementation")
+
+def pytest_generate_tests(metafunc):
+    if "competency_question_path" in metafunc.fixturenames:
+        competency_question_list = [
+            p for p in glob(COMPETENCY_QUESTION_DIRECTORY.as_posix() + "/**/*.omn", recursive=True)
+        ]
+        selected_filer = metafunc.config.getoption("--selected")
+        run_deprecated = metafunc.config.getoption("--deprecated")
+        competency_question_list = [
+            cq for cq in competency_question_list if selected_filer in cq
+        ]
+        if not run_deprecated:
+            competency_question_list = [cq for cq in competency_question_list if not "deprecated" in cq]
+        metafunc.parametrize("competency_question_path", competency_question_list)
+
+
+def check_competency_question(conclusion, premise):
+    """Check competency question against the given ontology
+
+    Args:
+        conclusion (str): A filepath to the competency question.
+        premise (str): A filepath to the reference ontology.
+
+    Raises:
+        RuntimeError: If calling HermiT raises an error this will be raised as a RuntimeError.
+
+    Returns:
+        (boolean): Returns True if the competency question was sucessfully checked against the ontology.
+    """
+    conclusion = Path(conclusion).resolve().as_posix()
+    p = Popen(
+        [
+            f"{JAVA_PATH}",
+            "-jar",
+            f"{HERMIT_JAR}",
+            f"--premise=file:///{premise}",
+            f"--conclusion=file:///{conclusion}",
+            "-E",
+        ],
+        stdin=PIPE,
+        stdout=PIPE,
+        stderr=PIPE,
+    )
+    output, err = p.communicate(b"input data that is passed to subprocess' stdin")
+    if len(err) == 0:
+        return eval(output.strip().capitalize())
+    else:
+        raise RuntimeError(f"{err}")
+
+
+def search_term_in_question_file(question, pattern=r"\w+_\d{8}"):
+    """Search all the Ontology terms in a specific competency question file
+
+    Args:
+        question (sts): Filepath to the competency question file
+        pattern (regexp, optional): Regular expression of the terms to be searched. Defaults to r"\w+_\d{8}".
+
+    Returns:
+        list: List of all the terms covered by the CQ.
+    """
+    terms = []
+    with open(question, "r") as question_file:
+        for line in question_file.readlines():
+            terms.extend(re.findall(pattern, line))
+    return terms
+
+
+def test_competency_question(
+    competency_question_path, existing_terms_and_definitons, results_bag, implementation
+):
+    """Metatest to produce competency question tests."""
+    implementing = ("implementing" in competency_question_path) and implementation
+    results_bag.questions = {}
+    results_bag.terms = {}
+    name = Path(competency_question_path).stem
+    is_soundness = True if "soundness" in competency_question_path else False
+    failure = ""
+    query_result = False
+    if not name in results_bag.questions:
+        results_bag.questions[name] = {"passed": False, "covers": []}
+    try:
+        query_result = check_competency_question(
+            competency_question_path, ONTOLOGY_PATH
+        )
+        if is_soundness:
+            query_result = not query_result
+        results_bag.questions[name]["passed"] = query_result
+    except RuntimeError as e:
+        results_bag.questions[name]["passed"] = False
+        results_bag.questions[name]["error"] = str(e)
+        failure = str(e)
+
+    terms = search_term_in_question_file(competency_question_path)
+    results_bag.questions[name]["covers"].extend(terms)
+    results_bag.questions[name]["covers"] = list(
+        set(results_bag.questions[name]["covers"])
+    )
+    for term in terms:
+        if term in existing_terms_and_definitons:
+            if not term in results_bag.terms:
+                results_bag.terms[term] = {"covered": False, "by": []}
+            results_bag.terms[term]["covered"] = True
+            results_bag.terms[term]["by"].append(name)
+    if len(failure) > 0 and implementing:
+        raise RuntimeError(failure)
+    if implementing:
+        assert query_result, f"{name} failed"
+
+
+def test_synthesis(fixture_store, existing_terms_and_definitons):
+    """This test should run at the end. Produces the final report.
+
+    Args:
+        fixture_store (fixture): These are all the availible fixtures.
+        existing_terms_and_definitons (fixture): Fixture with existing terms and definitions.
+    """
+    initial_terms = {t : {"covered": False, "by": []} for t in existing_terms_and_definitons if "OEO_" in t}
+    report = {"coverage": "0%", "questions": {}, "terms": initial_terms}
+    for v in fixture_store["results_bag"].values():
+        report["questions"].update(v["questions"])
+        for term in v["terms"].keys():
+            if term in report["terms"]:
+                report["terms"][term] ["covered"] = True
+                report["terms"][term]["by"].extend(v["terms"][term]["by"])
+                report["terms"][term]["by"] = list(set(report["terms"][term]["by"]))
+                report["terms"][term]["by"] = list(set(report["terms"][term]["by"]))
+            else:
+                report["terms"][term] = {
+                    "covered": True,
+                    "by": list(set(report["terms"][term]["by"])),
+                }
+
+    coverage = sum([1 for c in report.get("terms", {}).values() if c["covered"]]) / len(
+        [term for term in existing_terms_and_definitons if "OEO_" in term]
+    )
+    report["coverage"] = "{:.0%}".format(coverage)
+    with open(Path(CWD).joinpath("build/report.json"), "w") as f:
+        json.dump(report, f, indent=4)