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Merged
haeussma merged 2 commits into from
Oct 11, 2026
Merged

Move to md-models 0.3.0 and mdmodels 0.4.0 #105

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3bdd9f1
Move to md-models 0.3.0 and mdmodels 0.4.0
haeussma Oct 11, 2026
8a8a906
Write EnzymeML version 2.1 in new documents
haeussma Oct 11, 2026
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1,259 changes: 888 additions & 371 deletions pyenzyme/versions/v2.py
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -17,7 +17,7 @@ dependencies = [
"sympy>=1.12.1,<2",
"pymetadata>=0.5.3,<0.6",
"httpx>=0.27",
"mdmodels>=0.2.4,<0.3",
"mdmodels>=0.4.0,<0.5",
"joblib>=1.5.0,<2",
"bokeh>=3.7.3,<4",
"matplotlib>=3.10,<4",
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2 changes: 1 addition & 1 deletion specs
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Submodule specs updated 10 files
+1 −0 diagrams/v2.md
+4 −2 docs/publications.md
+8 −2 docs/versions/v2.md
+7 −4 schemes/v2/enzymeml-v2-linkml.yaml
+2 −0 schemes/v2/enzymeml-v2.graphql
+11 −1 schemes/v2/enzymeml-v2.json
+5 −2 schemes/v2/enzymeml-v2.proto
+643 −90 schemes/v2/enzymeml-v2.ttl
+60 −53 schemes/v2/enzymeml-v2.xsd
+2 −5 specifications/v2.md
2 changes: 1 addition & 1 deletion tests/fixtures/compose/expected_compose.json
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Expand Up @@ -17,7 +17,7 @@
"enzml:EnzymeMLDocument"
],
"name": "test",
"version": "2",
"version": "2.1",
"creators": [],
"vessels": [
{
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2 changes: 1 addition & 1 deletion tests/fixtures/compose/expected_compose_no_vessel.json
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Expand Up @@ -17,7 +17,7 @@
"enzml:EnzymeMLDocument"
],
"name": "test",
"version": "2",
"version": "2.1",
"creators": [],
"vessels": [],
"proteins": [
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100 changes: 82 additions & 18 deletions tests/fixtures/petab/abts_measurement_model.xml
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Expand Up @@ -200,23 +200,41 @@
<listOfCompartments>
<compartment id="vessel0" name="vessel0" spatialDimensions="3" size="1" units="u4" constant="true">
<annotation>
<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Vessel/79b926ec-6278-43ec-b135-d3a0e30ec5ba">
<rdf:RDF xmlns:OBO="http://purl.obolibrary.org/obo/" xmlns:enzml="http://www.enzymeml.org/v2/" xmlns:ns1="http://www.enzymeml.org/v2/Vessel/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:nodeID="N0a079c57e02a40d5acf6e5652d5759bc">
<schema:identifier>u4</schema:identifier>
<schema:name>l</schema:name>
<enzml:base_units rdf:nodeID="Naf6bc56e87f944179f26bf1409a7f477"/>
</rdf:Description>
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Vessel/3afdb104-63fa-4cf8-94f5-747537d1f378">
<schema:identifier>vessel0</schema:identifier>
<schema:name>vessel0</schema:name>
<OBO:OBI_0002139 rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</OBO:OBI_0002139>
<ns1:unit rdf:nodeID="N0a079c57e02a40d5acf6e5652d5759bc"/>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:constant>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Vessel"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/OBI_0400081"/>
</rdf:Description>
<rdf:Description rdf:nodeID="Naf6bc56e87f944179f26bf1409a7f477">
<enzml:kind>litre</enzml:kind>
<enzml:exponent rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</enzml:exponent>
<enzml:multiplier rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.0</enzml:multiplier>
<enzml:scale rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.0</enzml:scale>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species sboTerm="SBO:0000252" id="slac" name="slac" compartment="vessel0" initialConcentration="0.079037949" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Protein/8fc838cc-55c5-4ee0-ba13-7011a6fae094">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/Protein/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Protein/c3e2e25c-3f58-42c3-844e-a4c62704985c">
<schema:identifier>slac</schema:identifier>
<schema:name>slac</schema:name>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns1:constant>
<ns1:vessel_id>vessel0</ns1:vessel_id>
<schema:citation rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Protein"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/PR_000000001"/>
</rdf:Description>
Expand All @@ -225,9 +243,13 @@
</species>
<species sboTerm="SBO:0000252" id="slac_inactive" name="slac_inactive" compartment="vessel0" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Protein/8c94097f-f06a-4ba1-89f5-17d67bebe4a6">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/Protein/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Protein/728c9e48-d508-46fa-a2bd-e1d0311063f3">
<schema:identifier>slac_inactive</schema:identifier>
<schema:name>slac_inactive</schema:name>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns1:constant>
<ns1:vessel_id>vessel0</ns1:vessel_id>
<schema:citation rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Protein"/>
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/PR_000000001"/>
</rdf:Description>
Expand All @@ -236,29 +258,44 @@
</species>
<species sboTerm="SBO:0000247" id="abts" name="abts" compartment="vessel0" initialConcentration="4.37288121844535" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/f790a43b-4bcd-4c5e-b272-4dba3a995e11">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/SmallMolecule/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/d3c9ec94-b3ca-4d47-9e5f-f132133bd775">
<schema:identifier>abts</schema:identifier>
<schema:name>abts</schema:name>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns1:constant>
<ns1:vessel_id>vessel0</ns1:vessel_id>
<ns1:synonymous_names rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<schema:citation rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species sboTerm="SBO:0000247" id="buffer" name="buffer" compartment="vessel0" initialConcentration="100" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/a04b7c7e-292b-4096-857a-f65df5d93c0a">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/SmallMolecule/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/d2ac8e17-5c14-4d75-a459-00d6d1a954ad">
<schema:identifier>buffer</schema:identifier>
<schema:name>buffer</schema:name>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns1:constant>
<ns1:vessel_id>vessel0</ns1:vessel_id>
<ns1:synonymous_names rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<schema:citation rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species sboTerm="SBO:0000247" id="abts_radical" name="abts_radical" compartment="vessel0" initialConcentration="0" substanceUnits="mole" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/7b4d0da7-bba9-4854-831b-0be4ed1906b0">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/SmallMolecule/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/SmallMolecule/f329753b-59e7-466a-a5e3-99fe6c635d87">
<schema:identifier>abts_radical</schema:identifier>
<schema:name>abts_radical</schema:name>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ns1:constant>
<ns1:vessel_id>vessel0</ns1:vessel_id>
<ns1:synonymous_names rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<schema:citation rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/SmallMolecule"/>
</rdf:Description>
</rdf:RDF>
Expand All @@ -268,8 +305,17 @@
<listOfParameters>
<parameter id="k_cat" name="k_cat" value="1.85" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/d0cb729a-b5cf-42e8-a837-f423ebc56676">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/Parameter/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/90e772b6-582c-4968-978c-e080f46fb95f">
<schema:identifier>k_cat</schema:identifier>
<ns1:name>k_cat</ns1:name>
<ns1:symbol>k_cat</ns1:symbol>
<ns1:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1.85</ns1:value>
<ns1:initial_value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.01</ns1:initial_value>
<ns1:upper_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">2.0</ns1:upper_bound>
<ns1:lower_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1e-06</ns1:lower_bound>
<ns1:fit rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:fit>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:constant>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
Expand All @@ -282,8 +328,17 @@
</parameter>
<parameter id="K_M" name="K_M" value="20" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/6e85535c-c19f-4555-ab47-19c8f7a40a04">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/Parameter/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/c07ea5b3-2c14-497c-9e11-0d868d838e68">
<schema:identifier>K_M</schema:identifier>
<ns1:name>K_M</ns1:name>
<ns1:symbol>K_M</ns1:symbol>
<ns1:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">20.0</ns1:value>
<ns1:initial_value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">120.0</ns1:initial_value>
<ns1:upper_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">150.0</ns1:upper_bound>
<ns1:lower_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1e-06</ns1:lower_bound>
<ns1:fit rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:fit>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:constant>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
Expand All @@ -296,8 +351,17 @@
</parameter>
<parameter id="k_ie" name="k_ie" value="0.001" constant="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/0ca6e0f7-b51b-4815-be14-a0f5860d612c">
<rdf:RDF xmlns:ns1="http://www.enzymeml.org/v2/Parameter/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:schema="https://schema.org/">
<rdf:Description rdf:about="http://www.enzymeml.org/v2/Parameter/de29d237-ed76-4618-8a42-24c755cf91ca">
<schema:identifier>k_ie</schema:identifier>
<ns1:name>k_ie</ns1:name>
<ns1:symbol>k_ie</ns1:symbol>
<ns1:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.001</ns1:value>
<ns1:initial_value rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.01</ns1:initial_value>
<ns1:upper_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">0.05</ns1:upper_bound>
<ns1:lower_bound rdf:datatype="http://www.w3.org/2001/XMLSchema#double">1e-06</ns1:lower_bound>
<ns1:fit rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:fit>
<ns1:constant rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</ns1:constant>
<rdf:type rdf:resource="http://www.enzymeml.org/v2/Parameter"/>
</rdf:Description>
</rdf:RDF>
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8 changes: 6 additions & 2 deletions tests/integration/test_petab.py
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Expand Up @@ -48,15 +48,19 @@ def test_to_petab(self):
"tests/fixtures/petab/abts_measurement_parameters.tsv"
).read()

assert expected_sbml == self._remove_uuid(sbml_path.read_text())
# rdflib writes blank-node annotations in random order.
assert sorted(expected_sbml.splitlines()) == sorted(
self._remove_uuid(sbml_path.read_text()).splitlines()
)
assert expected_condition == condition_path.read_text()
assert expected_observable == observable_path.read_text()
assert expected_measurement == measurement_path.read_text()
assert expected_parameter == parameter_path.read_text()

def _remove_uuid(self, s: str) -> str:
# UUIDs and rdflib's random blank-node IDs differ on every run.
return re.sub(
r"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}",
r"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}|N[0-9a-f]{32}",
"",
s,
)
Expand Down
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