diff --git a/database-example/README.md b/database-example/README.md
index c0e96ca..2cc3c86 100644
--- a/database-example/README.md
+++ b/database-example/README.md
@@ -24,7 +24,7 @@ _Output_
```bash
๐ Connected
-๐ Creating tables for data model ../specifications/STRENDADB_light_20240208.md
+๐ Creating tables for data model ../specifications/STRENDADB_light_20240904_fix.md
โ
โโโ Table __model_meta__ not existing. Adding to DB!
โโโ Added table model 'DATA_MODEL' to __model_meta__ table
@@ -33,16 +33,17 @@ _Output_
โโโ Added table model 'Experiment' to __model_meta__ table
โโโ Added table model 'ProteinDescription' to __model_meta__ table
โโโ Added table model 'ProteinSource' to __model_meta__ table
-โโโ Added table model 'Modifications' to __model_meta__ table
+โโโ Added table model 'SequenceModifications' to __model_meta__ table
+โโโ Added table model 'PosttranslationalModifications' to __model_meta__ table
โโโ Added table model 'ProteinReaction' to __model_meta__ table
โโโ Added table model 'Dataset' to __model_meta__ table
โโโ Added table model 'AssayConditions' to __model_meta__ table
โโโ Added table model 'SmallAssayComponents' to __model_meta__ table
โโโ Added table model 'MacromolecularComponents' to __model_meta__ table
โโโ Added table model 'RoleOfComponent' to __model_meta__ table
+โโโ Added table model 'CompoundClassification' to __model_meta__ table
โโโ Added table model 'ResultsSet' to __model_meta__ table
-โโโ Added table model 'InitialKinetics' to __model_meta__ table
-โโโ Added table model 'Parameter' to __model_meta__ table
+โโโ Added table model 'InitialKineticsParameters' to __model_meta__ table
โโโ Added table model 'Activation' to __model_meta__ table
โโโ Added table model 'Inhibition' to __model_meta__ table
โโโ Created table 'Publication'
@@ -50,16 +51,17 @@ _Output_
โโโ Created table 'Experiment'
โโโ Created table 'ProteinDescription'
โโโ Created table 'ProteinSource'
-โโโ Created table 'Modifications'
+โโโ Created table 'SequenceModifications'
+โโโ Created table 'PosttranslationalModifications'
โโโ Created table 'ProteinReaction'
โโโ Created table 'Dataset'
โโโ Created table 'AssayConditions'
โโโ Created table 'SmallAssayComponents'
โโโ Created table 'MacromolecularComponents'
โโโ Created table 'RoleOfComponent'
+โโโ Created table 'CompoundClassification'
โโโ Created table 'ResultsSet'
-โโโ Created table 'InitialKinetics'
-โโโ Created table 'Parameter'
+โโโ Created table 'InitialKineticsParameters'
โโโ Created table 'Activation'
โโโ Created table 'Inhibition'
โโโ Added primary key 'id' to table Publication
@@ -67,37 +69,37 @@ _Output_
โโโ Added primary key 'id' to table Experiment
โโโ Added primary key 'id' to table ProteinDescription
โโโ Added primary key 'id' to table ProteinSource
-โโโ Added primary key 'id' to table Modifications
+โโโ Added primary key 'id' to table SequenceModifications
+โโโ Added primary key 'id' to table PosttranslationalModifications
โโโ Added primary key 'id' to table ProteinReaction
โโโ Added primary key 'id' to table Dataset
โโโ Added primary key 'id' to table AssayConditions
โโโ Added primary key 'id' to table SmallAssayComponents
โโโ Added primary key 'id' to table MacromolecularComponents
โโโ Added primary key 'id' to table RoleOfComponent
+โโโ Added primary key 'id' to table CompoundClassification
โโโ Added primary key 'id' to table ResultsSet
-โโโ Added primary key 'id' to table InitialKinetics
-โโโ Added primary key 'id' to table Parameter
+โโโ Added primary key 'id' to table InitialKineticsParameters
โโโ Added primary key 'id' to table Activation
โโโ Added primary key 'id' to table Inhibition
โโโ Added join table 'Publication_author_Author'
โโโ Added join table 'Publication_experiment_Experiment'
โโโ Added foreign key 'protein_assay__fk' to table 'Experiment'
-โโโ Added foreign key 'modifications__fk' to table 'ProteinDescription'
-โโโ Added foreign key 'source__fk' to table 'ProteinDescription'
+โโโ Added foreign key 'protein_sequence__fk' to table 'ProteinDescription'
+โโโ Added foreign key 'posttranslational_modifications__fk' to table 'ProteinDescription'
+โโโ Added foreign key 'protein_source__fk' to table 'ProteinDescription'
โโโ Added foreign key 'reaction__fk' to table 'ProteinDescription'
-โโโ Added join table 'ProteinDescription_characteristics_Dataset'
+โโโ Added join table 'ProteinDescription_protein_characterization_Dataset'
โโโ Added join table 'Dataset_assay_conditions_AssayConditions'
-โโโ Added join table 'Dataset_result_set_ResultsSet'
-โโโ Added foreign key 'initial_kinetics__fk' to table 'ResultsSet'
+โโโ Added join table 'Dataset_results_set_ResultsSet'
+โโโ Added foreign key 'small_assay_components__fk' to table 'AssayConditions'
+โโโ Added foreign key 'macromolecular_components__fk' to table 'AssayConditions'
+โโโ Added foreign key 'role__fk' to table 'MacromolecularComponents'
+โโโ Added foreign key 'initial_kinetic_parameters__fk' to table 'ResultsSet'
โโโ Added foreign key 'activation__fk' to table 'ResultsSet'
โโโ Added foreign key 'inhibition__fk' to table 'ResultsSet'
-โโโ Added foreign key 'km__fk' to table 'InitialKinetics'
-โโโ Added foreign key 'kcat__fk' to table 'InitialKinetics'
-โโโ Added foreign key 'v__fk' to table 'InitialKinetics'
-โโโ Added foreign key 'kcat_over_km__fk' to table 'InitialKinetics'
-โโโ Added foreign key 'v_over_km__fk' to table 'InitialKinetics'
โ
-โฐโโ ๐ Created all tables for data model ../specifications/STRENDADB_light_20240208.md
+โฐโโ ๐ Created all tables for data model ../specifications/STRENDADB_light_20240904_fix.md
```
## Working with the database
diff --git a/database-example/UseDatabase.ipynb b/database-example/UseDatabase.ipynb
index 6216d67..47830d3 100644
--- a/database-example/UseDatabase.ipynb
+++ b/database-example/UseDatabase.ipynb
@@ -2,7 +2,20 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": null,
+ "id": "a11cc25d-8c46-4f11-adee-b7bccba862b3",
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [],
+ "source": [
+ "!pip install rich\n",
+ "!pip install git+https://github.com/JR-1991/sdrdm-database.git"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
"id": "1c534e43-b832-4d0c-954d-9d6d7440814a",
"metadata": {},
"outputs": [
@@ -15,6 +28,8 @@
}
],
"source": [
+ "import rich\n",
+ "\n",
"from sdRDM import DataModel\n",
"from sdrdm_database import DBConnector\n",
"from sdrdm_database.dbconnector import SupportedBackends\n",
@@ -32,18 +47,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
- "id": "fcc59938-9f63-43d6-b34e-4d67acf5151f",
- "metadata": {},
- "outputs": [],
- "source": [
- "# Build Python classes\n",
- "libStrenda = DataModel.from_markdown(\"../specifications/STRENDADB_light_20240208.md\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
+ "execution_count": 3,
"id": "f225b616-690c-4575-a1a8-d5f9fa5fc49e",
"metadata": {},
"outputs": [
@@ -53,17 +57,17 @@
"['Activation',\n",
" 'AssayConditions',\n",
" 'Author',\n",
+ " 'CompoundClassification',\n",
" 'Dataset',\n",
" 'Dataset_assay_conditions_AssayConditions',\n",
- " 'Dataset_result_set_ResultsSet',\n",
+ " 'Dataset_results_set_ResultsSet',\n",
" 'Experiment',\n",
" 'Inhibition',\n",
- " 'InitialKinetics',\n",
+ " 'InitialKineticsParameters',\n",
" 'MacromolecularComponents',\n",
- " 'Modifications',\n",
- " 'Parameter',\n",
+ " 'PosttranslationalModifications',\n",
" 'ProteinDescription',\n",
- " 'ProteinDescription_characteristics_Dataset',\n",
+ " 'ProteinDescription_protein_characterization_Dataset',\n",
" 'ProteinReaction',\n",
" 'ProteinSource',\n",
" 'Publication',\n",
@@ -71,23 +75,24 @@
" 'Publication_experiment_Experiment',\n",
" 'ResultsSet',\n",
" 'RoleOfComponent',\n",
+ " 'SequenceModifications',\n",
" 'SmallAssayComponents',\n",
" '__model_meta__']"
]
},
- "execution_count": 4,
+ "execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "# Check tables\n",
+ "# Check, if the tables have been created!\n",
"db.connection.list_tables()"
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 14,
"id": "bb2c49e7-2f97-4c33-86c8-16b60c683808",
"metadata": {},
"outputs": [
@@ -96,37 +101,214 @@
"output_type": "stream",
"text": [
"Publication\n",
- "โโโ id [value=daf3d60d-de35-401a-99a8-8216f5116b4e]\n",
+ "โโโ id [value=4c63272b-e99e-4e05-aa09-cf751fa4d62b]\n",
+ "โโโ title [value=Test]\n",
"โโโ doi [value=SomeDOI]\n",
"โโโ pmid [value=SomePMID]\n",
- "โโโ author [value=None]\n",
- "โ โโโ 0\n",
- "โ โโโ Author\n",
- "โ โโโ id [value=8fc97783-978f-497b-8c83-662e0fcd8799]\n",
- "โ โโโ name [value=StrendaMan]\n",
- "โ โโโ affiliation [value=Strenda]\n",
- "โโโ experiment [value=None]\n",
+ "โโโ author [value=None]\n",
" โโโ 0\n",
- " โโโ Experiment\n",
- " โโโ id [value=f45cf9d6-8662-4f45-b649-b5e323b3e5d5]\n",
- " โโโ name [value=Experiment]\n",
- " โโโ assay_type [value=Type]\n",
+ " โโโ Author\n",
+ " โโโ id [value=02e113da-37b1-486f-8dfa-231ffcf11940]\n",
+ " โโโ name [value=StrendaMan]\n",
+ " โโโ affiliation [value=Strenda]\n",
"ClassNode(/Publication, class_name=None, constants={}, id=None, module=None, outer_type=None)\n"
]
}
],
"source": [
- "# Build dataset to insert later\n",
- "dataset = libStrenda.Publication(doi=\"SomeDOI\", pmid=\"SomePMID\")\n",
- "dataset.add_to_author(name=\"StrendaMan\", affiliation=\"Strenda\")\n",
+ "# Grab the \"Publication\" model from the Database\n",
+ "Publication = db.get_table_api(\"Publication\")\n",
"\n",
- "experiment = dataset.add_to_experiment(\n",
- " name=\"Experiment\",\n",
- " assay_type=\"Type\",\n",
- ")\n",
+ "# Build dataset to insert later!\n",
+ "dataset = Publication(title=\"Test\", doi=\"SomeDOI\", pmid=\"SomePMID\")\n",
+ "dataset.add_to_author(name=\"StrendaMan\", affiliation=\"Strenda\")\n",
"\n",
"print(dataset.tree())"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "daa29c3d-17b5-41e5-a48b-b81da377eb46",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "โ
Inserted 1 rows into the database.\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "โ
Inserted \u001b[1;36m1\u001b[0m rows into the database.\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Insert the row into the database\n",
+ "db.insert(dataset)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "80aaf8db-2b7a-415d-8c33-b9748fc3e07a",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "โ
Inserted 20 rows into the database.\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "โ
Inserted \u001b[1;36m20\u001b[0m rows into the database.\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Let's create more random datasets\n",
+ "import random\n",
+ "\n",
+ "options = [\"Strenda\", \"Biocatalysis\", \"EnzymeML\", \"Workshop\"] \n",
+ "datasets = []\n",
+ "\n",
+ "for _ in range(20):\n",
+ " dataset = libStrenda.Publication(\n",
+ " title=random.choice(options),\n",
+ " doi=random.choice(options),\n",
+ " pmid=random.choice(options),\n",
+ " )\n",
+ " \n",
+ " dataset.add_to_author(name=\"StrendaMan\", affiliation=\"Strenda\")\n",
+ "\n",
+ " datasets.append(dataset)\n",
+ "\n",
+ "# Add all of them at once!\n",
+ "db.insert(*datasets)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "id": "a14bcacf-8998-4552-a94c-68af22b0f307",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "21 entries found!\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "\u001b[1;36m21\u001b[0m entries found!\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Publication\n",
+ "โโโ id [value=00c65cff-21d0-493f-81aa-5d32d8992474]\n",
+ "โโโ title [value=Test]\n",
+ "โโโ doi [value=SomeDOI]\n",
+ "โโโ pmid [value=SomePMID]\n",
+ "โโโ author [value=None]\n",
+ " โโโ 0\n",
+ " โโโ Author\n",
+ " โโโ id [value=6bf4f0db-82eb-431e-9eef-139a83149bca]\n",
+ " โโโ name [value=StrendaMan]\n",
+ " โโโ affiliation [value=Strenda]\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "ClassNode(/Publication, class_name=None, constants={}, id=None, module=None, outer_type=None)\n",
+ "\n"
+ ],
+ "text/plain": [
+ "\u001b[1;35mClassNode\u001b[0m\u001b[1m(\u001b[0m\u001b[35m/\u001b[0m\u001b[95mPublication\u001b[0m, \u001b[33mclass_name\u001b[0m=\u001b[3;35mNone\u001b[0m, \u001b[33mconstants\u001b[0m=\u001b[1m{\u001b[0m\u001b[1m}\u001b[0m, \u001b[33mid\u001b[0m=\u001b[3;35mNone\u001b[0m, \u001b[33mmodule\u001b[0m=\u001b[3;35mNone\u001b[0m, \u001b[33mouter_type\u001b[0m=\u001b[3;35mNone\u001b[0m\u001b[1m)\u001b[0m\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Lets fetch them from the database!\n",
+ "result = db.get(db.get_table_api(\"Publication\"))\n",
+ "\n",
+ "# Should be 21! Lets inspect the amount and the first entry\n",
+ "rich.print(f\"{len(result)} entries found!\")\n",
+ "rich.print(result[0].tree())"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "id": "931a7297-ca7a-4551-abaf-02bab72351d7",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "โโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ\n",
+ "โ title โ doi โ pmid โ id โ\n",
+ "โกโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฉ\n",
+ "โ !string โ string โ string โ !string โ\n",
+ "โโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค\n",
+ "โ Test โ SomeDOI โ SomePMID โ 00c65cff-21d0-493f-81aa-5d32d8992474 โ\n",
+ "โ Workshop โ Biocatalysis โ Biocatalysis โ 0b345fa6-7b82-4544-ac66-f08f3e91cfee โ\n",
+ "โ Workshop โ Biocatalysis โ Workshop โ 0f25b517-1a5e-4da8-8dc9-7b5a87658832 โ\n",
+ "โ EnzymeML โ Workshop โ Strenda โ 20ac6092-8697-4714-a120-9e476d3a613f โ\n",
+ "โ Workshop โ Strenda โ Workshop โ 267b9093-0252-47b8-96f2-5fae11398c44 โ\n",
+ "โ Workshop โ Strenda โ Strenda โ 289c4ab5-1677-4c7b-886a-d84b88b164a3 โ\n",
+ "โ Workshop โ EnzymeML โ EnzymeML โ 3b63d1dc-a6bd-4fb1-a65a-ae6af97712cc โ\n",
+ "โ Biocatalysis โ Biocatalysis โ EnzymeML โ 3da1b160-5e29-47bb-9912-3d32193b2486 โ\n",
+ "โ Strenda โ Biocatalysis โ Workshop โ 44f9a8af-c387-4a65-9761-de63ffbc75e0 โ\n",
+ "โ Strenda โ Strenda โ Biocatalysis โ 4d108d69-4f02-4ada-a506-52198f7e64c7 โ\n",
+ "โ โฆ โ โฆ โ โฆ โ โฆ โ\n",
+ "โโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "โโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโณโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ\n",
+ "โ\u001b[1m \u001b[0m\u001b[1mtitle\u001b[0m\u001b[1m \u001b[0m\u001b[1m \u001b[0mโ\u001b[1m \u001b[0m\u001b[1mdoi\u001b[0m\u001b[1m \u001b[0m\u001b[1m \u001b[0mโ\u001b[1m \u001b[0m\u001b[1mpmid\u001b[0m\u001b[1m \u001b[0m\u001b[1m \u001b[0mโ\u001b[1m \u001b[0m\u001b[1mid\u001b[0m\u001b[1m \u001b[0m\u001b[1m \u001b[0mโ\n",
+ "โกโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโฉ\n",
+ "โ \u001b[2m!string\u001b[0m โ \u001b[2mstring\u001b[0m โ \u001b[2mstring\u001b[0m โ \u001b[2m!string\u001b[0m โ\n",
+ "โโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโผโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโค\n",
+ "โ \u001b[32mTest \u001b[0m โ \u001b[32mSomeDOI \u001b[0m โ \u001b[32mSomePMID \u001b[0m โ \u001b[32m00c65cff-21d0-493f-81aa-5d32d8992474\u001b[0m โ\n",
+ "โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32m0b345fa6-7b82-4544-ac66-f08f3e91cfee\u001b[0m โ\n",
+ "โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32mWorkshop \u001b[0m โ \u001b[32m0f25b517-1a5e-4da8-8dc9-7b5a87658832\u001b[0m โ\n",
+ "โ \u001b[32mEnzymeML \u001b[0m โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mStrenda \u001b[0m โ \u001b[32m20ac6092-8697-4714-a120-9e476d3a613f\u001b[0m โ\n",
+ "โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mStrenda \u001b[0m โ \u001b[32mWorkshop \u001b[0m โ \u001b[32m267b9093-0252-47b8-96f2-5fae11398c44\u001b[0m โ\n",
+ "โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mStrenda \u001b[0m โ \u001b[32mStrenda \u001b[0m โ \u001b[32m289c4ab5-1677-4c7b-886a-d84b88b164a3\u001b[0m โ\n",
+ "โ \u001b[32mWorkshop \u001b[0m โ \u001b[32mEnzymeML \u001b[0m โ \u001b[32mEnzymeML \u001b[0m โ \u001b[32m3b63d1dc-a6bd-4fb1-a65a-ae6af97712cc\u001b[0m โ\n",
+ "โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32mEnzymeML \u001b[0m โ \u001b[32m3da1b160-5e29-47bb-9912-3d32193b2486\u001b[0m โ\n",
+ "โ \u001b[32mStrenda \u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32mWorkshop \u001b[0m โ \u001b[32m44f9a8af-c387-4a65-9761-de63ffbc75e0\u001b[0m โ\n",
+ "โ \u001b[32mStrenda \u001b[0m โ \u001b[32mStrenda \u001b[0m โ \u001b[32mBiocatalysis\u001b[0m โ \u001b[32m4d108d69-4f02-4ada-a506-52198f7e64c7\u001b[0m โ\n",
+ "โ \u001b[2mโฆ\u001b[0m โ \u001b[2mโฆ\u001b[0m โ \u001b[2mโฆ\u001b[0m โ \u001b[2mโฆ\u001b[0m โ\n",
+ "โโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโดโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# You can also view individual tables\n",
+ "db.connection.table(\"Publication\")"
+ ]
}
],
"metadata": {
diff --git a/database-example/create_tables.py b/database-example/create_tables.py
index c6b351b..6a08c82 100644
--- a/database-example/create_tables.py
+++ b/database-example/create_tables.py
@@ -12,4 +12,4 @@
)
# Create the tables in the database
-db.create_tables("../specifications/STRENDADB_light_20240208.md")
+db.create_tables("../specifications/STRENDADB_light_20240904_fix.md")
diff --git a/gen.toml b/gen.toml
index f25045e..679b648 100644
--- a/gen.toml
+++ b/gen.toml
@@ -1,7 +1,7 @@
[meta]
name = "STRENDA-DB"
description = "This is a code and schema generator for Strenda Biocatalysis."
-paths = ["specifications/STRENDADB_light_20240208.md"]
+paths = ["specifications/STRENDADB_light_20240904_fix.md"]
[generate]
xml-schema = { out = "schemes/strenda.xsd" }
diff --git a/specifications/STRENDADB_light_20240904_fix.md b/specifications/STRENDADB_light_20240904_fix.md
new file mode 100644
index 0000000..1917e9b
--- /dev/null
+++ b/specifications/STRENDADB_light_20240904_fix.md
@@ -0,0 +1,315 @@
+# STRENDA DB
+
+## Administration
+
+## Data
+
+### Publication
+
+This is the publication that includes the experimental results of an enzyme kinetics characterization.
+
+- **title**
+ - Type: string
+ - Description: title of the publication
+- doi
+ - Type: string
+ - Description: identifier of the publication
+- pmid
+ - Type: string
+ - Description: identifier of the publication as indexed in PubMed
+- author
+ - Type: Author[]
+- experiment
+ - Type: Experiment[]
+
+### Author
+
+- **name**
+ - Type: string
+ - Description: name of the author. Nomenclature: Family name initials first name
+- affiliation
+ - Type: string
+ - Description: name of organizaton, department, city, country
+- email
+ - Type: string
+ - Description: email address
+- orcid
+ - Type: string
+ - Description: ORCID idenfier
+
+### Experiment
+
+- name_of_experiment
+ - Type: string
+ - Description: name of the experiment, just for internal purposes
+- type_of_assay
+ - Type: string
+ - Description: name of the assay
+- direction_of_the_assay
+ - Type: string
+- definition_of_the_compound_monitored
+ - Type: string
+ - Description:
+- continuously_monitored
+ - Type: string
+ - Description: selection of the stopping procedure
+- directly_monitored
+ - Type: string
+- protein_assay
+ - Type: ProteinDescription
+
+### ProteinDescription
+
+- uniprotkb_ac
+ - Type: string
+ - Description: identifier obtained from UniProtKB
+- protein_name
+ - Type: string
+ - Description: name of the protein as of UniProtKB
+- protein_sequence
+ - Type: SequenceModifications
+ - Description: amino acid sequence as from UniProtKB
+- posttranslational_modifications
+ - Type: PosttranslationalModifications
+- protein_source
+ - Type: ProteinSource
+- reaction
+ - Type: ProteinReaction
+- protein_characterization
+ - Type: Dataset[]
+
+### ProteinSource
+
+- expression_system
+ - Type: string
+ - Description: Description of expression system if heterologously expressed
+- organism
+ - Type: string
+ - Description: as in UniProtKB provided, name of organism
+- taxon_id
+ - Type: string
+ - Description: ID as obtained from NCBI Taxonomy
+- strain
+ - Type: string
+ - Description: name or identifier of the strain
+- cell_type
+ - Type: string
+ - Description: determination of the cell in which the protein is expressed
+- tissue
+ - Type: string
+ - Description: determination of the tissue, ideally BTO is used
+- localization
+ - Type: string
+ - Description: determination of the localization (membran, cytosol, etc.)
+
+### SequenceModifications
+
+- sequence_modification
+ - Type: string
+ - Description: modified amino acid sequence
+- specification_of_the_type_of_modification
+ - Type: string
+ - Description: Description of the types of modifications
+
+### PosttranslationalModifications
+
+- determination_of_ptm
+ - Type: string
+ - Description: Phosphorylation, Glycosylation, Acetylation, Hydroxylation, Methylation, Other
+
+### ProteinReaction
+
+- ec_number
+ - Type: string
+ - Description: EC number obtained from ExplorEnz
+- reaction_as_in_explorenz
+ - Type: string
+ - Description: reaction as described in ExplorEnz
+- comment
+ - Type: string
+ - Description: comment on the protein reaction if not properly described in ExplorEnz
+
+### Dataset
+
+- name
+ - Type: string
+ - Description: name of the dataset
+- assay_conditions
+ - Type: AssayConditions[]
+- results_set
+ - Type: ResultsSet[]
+- doi
+ - Type: string
+ - Description: DOI of the dataset
+
+### AssayConditions
+
+- small_assay_components
+ - Type: SmallAssayComponents
+ - Description: Description of the compound used in the assay
+- macromolecular_components
+ - Type: MacromolecularComponents
+ - Description: Description of the macromolecular components
+- concentration_of_the_assayed_protein
+ - Type: string
+ - Description: value with unit
+- description_of_concentration_measurement
+ - Type: string
+ - Description: free text field
+- ph
+ - Type: string
+ - Description: value and unit
+- pd
+ - Type: string
+ - Description: value and unit
+- temperature
+ - Type: string
+ - Description: value and unit, K and Celsius
+
+### SmallAssayComponents
+
+- role
+ - Type: string
+ - Description: role in the assay, i.e. substrate, product, etc.
+- initial_concentration_fixed
+ - Type: string
+ - Description: unit, value
+- initial_concentration_varied
+ - Type: string
+ - Description: concentration range, value, unit
+- compound_name
+ - Type: string
+ - Description: name as obtained from PubChem
+- inchi
+ - Type: string
+ - Description: InChi string
+- iupac
+ - Type: string
+ - Description: IUPAC name
+- chebi_id
+ - Type: string
+ - Description: identifier
+- pubchem_cid
+ - Type: string
+ - Description: identifier
+
+### MacromolecularComponents
+
+- role
+ - Type: RoleOfComponent
+ - Description: role in the assay, i.e. substrate, product, etc.
+- initial_concentration_fixed
+ - Type: string
+ - Description: unit, value
+- initial_concentration_varied
+ - Type: string
+ - Description: concentration range, value, unit
+- classification
+ - Type: string
+ - Description: protein, carbohydrate, DNA, RNA, etc.
+- compound_name
+ - Type: string
+ - Description: name as obtained from PubChem
+- inchi
+ - Type: string
+ - Description: InChi string
+- iupac
+ - Type: string
+ - Description: IUPAC name
+- database_used
+ - Type: string
+ - Description: name of the database
+- identifier
+ - Type: string
+ - Description: identifier
+
+### RoleOfComponent
+
+- substrate
+ - Type: string
+ - Description: substrate of chemical reaction
+- product
+ - Type: string
+ - Description: production of chemical reaction
+- inhibitor
+ - Type: string
+ - Description: component that inhibits the chemical reaction
+- activator
+ - Type: string
+ - Description: component that activates/enhances the chemical reaction
+
+### CompoundClassification
+
+- protein
+ - Type: string
+- carbohydrate
+ - Type: string
+- dna
+ - Type: string
+- rna
+ - Type: string
+- lipid
+ - Type: string
+- other
+ - Type: string
+
+### ResultsSet
+
+- name
+ - Type: string
+ - Description: Name of the results set
+- initial_kinetic_parameters
+ - Type: InitialKineticsParameters
+ - Description: Km, kcat, V, kcat/Km, V/Km
+- activation
+ - Type: Activation
+- inhibition
+ - Type: Inhibition
+
+### InitialKineticsParameters
+
+- km
+ - Type: string
+ - descriptor: value, SE, unit
+- kcat
+ - Type: string
+ - descriptor: value, SE, unit
+- v
+ - Type: string
+ - descriptor: value, SE, unit
+- kcat_over_km
+ - Type: string
+ - descriptor: value, SE, unit
+- v_over_km
+ - Type: string
+ - descriptor: value, SE, unit
+
+### Activation
+
+- affinity_constant
+ - Type: string
+ - descriptor: value, SE, unit, true or apparent
+- velocity_no_activator
+ - Type: string
+ - Description: velocity without activator
+- velocity_at_max_concentration
+ - Type: string
+ - Description: velocity at maximum concentration of activator
+- saturation
+ - Type: string
+ - Description: statement whether the concentration was saturating or not
+- incluence_no_activator
+ - Type: string
+ - Description: Influence on MM kinetics. Schema: Value, SE, Unit, true/apparent
+- influence_at_maxconcentration
+ - Type: string
+ - Description: Influence on MM kinetics. Schema: Value, SE, Unit, true/apparent
+
+### Inhibition
+
+- reversibility_yes
+ - Type: string
+ - Description: inhbition type - competitive, uncompetitive, mixed, kic, SE, Unit, Math function
+- reversibility_no
+ - Type: string
+ - Description: ki, SE, Unit, Comment