update model and example

database-example/README.md

@@ -24,7 +24,7 @@ _Output_
 ```bash
 🎉 Connected
 
-🚀 Creating tables for data model ../specifications/STRENDADB_light_20240208.md
+🚀 Creating tables for data model ../specifications/STRENDADB_light_20240904_fix.md
 │
 ├── Table __model_meta__ not existing. Adding to DB!
 ├── Added table model 'DATA_MODEL' to __model_meta__ table
@@ -33,71 +33,73 @@ _Output_
 ├── Added table model 'Experiment' to __model_meta__ table
 ├── Added table model 'ProteinDescription' to __model_meta__ table
 ├── Added table model 'ProteinSource' to __model_meta__ table
-├── Added table model 'Modifications' to __model_meta__ table
+├── Added table model 'SequenceModifications' to __model_meta__ table
+├── Added table model 'PosttranslationalModifications' to __model_meta__ table
 ├── Added table model 'ProteinReaction' to __model_meta__ table
 ├── Added table model 'Dataset' to __model_meta__ table
 ├── Added table model 'AssayConditions' to __model_meta__ table
 ├── Added table model 'SmallAssayComponents' to __model_meta__ table
 ├── Added table model 'MacromolecularComponents' to __model_meta__ table
 ├── Added table model 'RoleOfComponent' to __model_meta__ table
+├── Added table model 'CompoundClassification' to __model_meta__ table
 ├── Added table model 'ResultsSet' to __model_meta__ table
-├── Added table model 'InitialKinetics' to __model_meta__ table
-├── Added table model 'Parameter' to __model_meta__ table
+├── Added table model 'InitialKineticsParameters' to __model_meta__ table
 ├── Added table model 'Activation' to __model_meta__ table
 ├── Added table model 'Inhibition' to __model_meta__ table
 ├── Created table 'Publication'
 ├── Created table 'Author'
 ├── Created table 'Experiment'
 ├── Created table 'ProteinDescription'
 ├── Created table 'ProteinSource'
-├── Created table 'Modifications'
+├── Created table 'SequenceModifications'
+├── Created table 'PosttranslationalModifications'
 ├── Created table 'ProteinReaction'
 ├── Created table 'Dataset'
 ├── Created table 'AssayConditions'
 ├── Created table 'SmallAssayComponents'
 ├── Created table 'MacromolecularComponents'
 ├── Created table 'RoleOfComponent'
+├── Created table 'CompoundClassification'
 ├── Created table 'ResultsSet'
-├── Created table 'InitialKinetics'
-├── Created table 'Parameter'
+├── Created table 'InitialKineticsParameters'
 ├── Created table 'Activation'
 ├── Created table 'Inhibition'
 ├── Added primary key 'id' to table Publication
 ├── Added primary key 'id' to table Author
 ├── Added primary key 'id' to table Experiment
 ├── Added primary key 'id' to table ProteinDescription
 ├── Added primary key 'id' to table ProteinSource
-├── Added primary key 'id' to table Modifications
+├── Added primary key 'id' to table SequenceModifications
+├── Added primary key 'id' to table PosttranslationalModifications
 ├── Added primary key 'id' to table ProteinReaction
 ├── Added primary key 'id' to table Dataset
 ├── Added primary key 'id' to table AssayConditions
 ├── Added primary key 'id' to table SmallAssayComponents
 ├── Added primary key 'id' to table MacromolecularComponents
 ├── Added primary key 'id' to table RoleOfComponent
+├── Added primary key 'id' to table CompoundClassification
 ├── Added primary key 'id' to table ResultsSet
-├── Added primary key 'id' to table InitialKinetics
-├── Added primary key 'id' to table Parameter
+├── Added primary key 'id' to table InitialKineticsParameters
 ├── Added primary key 'id' to table Activation
 ├── Added primary key 'id' to table Inhibition
 ├── Added join table 'Publication_author_Author'
 ├── Added join table 'Publication_experiment_Experiment'
 ├── Added foreign key 'protein_assay__fk' to table 'Experiment'
-├── Added foreign key 'modifications__fk' to table 'ProteinDescription'
-├── Added foreign key 'source__fk' to table 'ProteinDescription'
+├── Added foreign key 'protein_sequence__fk' to table 'ProteinDescription'
+├── Added foreign key 'posttranslational_modifications__fk' to table 'ProteinDescription'
+├── Added foreign key 'protein_source__fk' to table 'ProteinDescription'
 ├── Added foreign key 'reaction__fk' to table 'ProteinDescription'
-├── Added join table 'ProteinDescription_characteristics_Dataset'
+├── Added join table 'ProteinDescription_protein_characterization_Dataset'
 ├── Added join table 'Dataset_assay_conditions_AssayConditions'
-├── Added join table 'Dataset_result_set_ResultsSet'
-├── Added foreign key 'initial_kinetics__fk' to table 'ResultsSet'
+├── Added join table 'Dataset_results_set_ResultsSet'
+├── Added foreign key 'small_assay_components__fk' to table 'AssayConditions'
+├── Added foreign key 'macromolecular_components__fk' to table 'AssayConditions'
+├── Added foreign key 'role__fk' to table 'MacromolecularComponents'
+├── Added foreign key 'initial_kinetic_parameters__fk' to table 'ResultsSet'
 ├── Added foreign key 'activation__fk' to table 'ResultsSet'
 ├── Added foreign key 'inhibition__fk' to table 'ResultsSet'
-├── Added foreign key 'km__fk' to table 'InitialKinetics'
-├── Added foreign key 'kcat__fk' to table 'InitialKinetics'
-├── Added foreign key 'v__fk' to table 'InitialKinetics'
-├── Added foreign key 'kcat_over_km__fk' to table 'InitialKinetics'
-├── Added foreign key 'v_over_km__fk' to table 'InitialKinetics'
 │
-╰── 🎉 Created all tables for data model ../specifications/STRENDADB_light_20240208.md
+╰── 🎉 Created all tables for data model ../specifications/STRENDADB_light_20240904_fix.md
 ```
 
 ## Working with the database