Notebook

Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in the RDF/XML format. For more details, see Demir E et al. 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9).

http://www.biopax.org/ Specification: http://www.biopax.org/release/biopax-level3-documentation.pdf https://pypi.org/project/pybiopax/ https://github.com/indralab/pybiopax

For the reactions you need probably the BiochemicalReaction and Degradation. For the PhysicalEntities you would use Protein and RNA. For the inhibition you will probably use Modulation. Have a look at the specification and the introduction to BioPax.

Example for fetching information https://github.com/indralab/pybiopax/blob/master/notebooks/tutorial.ipynb

In [1]:

import os
from pathlib import Path

import pybiopax
from pybiopax.api import model_to_owl_str
from pybiopax.biopax import (
    BioSource,
    CellularLocationVocabulary,
    Control,
    PhysicalEntity,
    Rna,
    UnificationXref,
)
from pybiopax.biopax.base import Protein
from pybiopax.biopax.model import (
    BiochemicalReaction,
    BioPaxModel,
    Provenance,
    PublicationXref,
    Stoichiometry,
)

/usr/local/lib/python3.10/dist-packages/tqdm-4.64.1-py3.10.egg/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

In [2]:

def create_repressilator(biopax_path: Path) -> BioPaxModel:
    """Create repressilator using biopax."""
    objects = []

    # <bp:Protein rdf:about="PX">
    #  <bp:xref rdf:resource="http://identifiers.org/uniprot/P03023" />
    #  <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">LacI protein</bp:displayName>
    # </bp:Protein>
    # Protein(LacI protein)
    # {'_controller_of': set(), 'xref': [<pybiopax.biopax.util.UnificationXref object at 0x7fe1eb423160>],
    # 'display_name': 'LacI protein', 'standard_name': None, '_name': [], 'evidence': [], 'uid': 'PX', 'comment': [], 'availability': None, 'data_source': [], '_participant_of': set(), 'feature': [], 'not_feature': [], 'member_physical_entity': [], 'cellular_location': None, '_component_of': set(), '_member_physical_entity_of': {PhysicalEntity(PX), PhysicalEntity(PX), PhysicalEntity(PX)}, 'entity_reference': None}
    #
    # <bp:PhysicalEntity rdf:about="RIGHT_0_conversion_Reaction5_PY">
    #  <bp:cellularLocation rdf:resource="cell" />
    #  <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">PY</bp:displayName>
    #  <bp:memberPhysicalEntity rdf:resource="PY" />
    # </bp:PhysicalEntity>

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction5_PY",
        display_name="PY",
        cellular_location="cell",
        member_physical_entity="PY",
    )
    objects.append(p1)

    # <bp:Stoichiometry rdf:about="LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY">
    #  <bp:physicalEntity rdf:resource="LEFT_0_conversion_Reaction2_Y" />
    #  <bp:stoichiometricCoefficient rdf:datatype = "http://www.w3.org/2001/XMLSchema#float">1.0</bp:stoichiometricCoefficient>
    # </bp:Stoichiometry>
    s1 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction2_Y",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    # '''
    # <bp:Provenance rdf:about="datasource_1">
    #  <bp:xref rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000012" />
    #  <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">BioModels Database</bp:displayName>
    # </bp:Provenance>
    # '''
    p3 = Provenance(
        uid="datasource_1",
        xref="http://identifiers.org/biomodels.db/BIOMD0000000012",
        display_name="BioModels Database",
    )
    objects.append(p3)
    #
    p4 = PublicationXref(
        uid="http://identifiers.org/pubmed/10659856", id="10659856", db="PubMed"
    )
    objects.append(p4)

    p5 = Provenance(
        uid="datasource_2",
        xref="http://identifiers.org/biomodels.db/MODEL6615351360",
        display_name="BioModels Database",
    )
    objects.append(p5)

    u1 = UnificationXref(
        uid="http://identifiers.org/biomodels.db/BIOMD0000000012",
        id="BIOMD0000000012",
        db="BioModels Database",
    )
    objects.append(u1)

    u2 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0006402",
        id="GO:0006402",
        db="Gene Ontology",
    )
    objects.append(u2)

    s2 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction7_PX",
        stoichiometric_coefficient="1",
    )
    objects.append(s2)

    #
    # '''
    # <bp:Control rdf:about="control_Reaction4_X_0">
    #  <bp:controlled rdf:resource="conversion_Reaction4" />
    #  <bp:controlType rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
    #  <bp:controller rdf:resource="PEP0_control_Reaction4X" />
    # </bp:Control>
    # '''
    c1 = Control(
        uid="control_Reaction4_X_0",
        controlled="conversion_Reaction4",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction4X",
    )
    objects.append(c1)

    s2 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction6_PZ",
        stoichiometric_coefficient="1",
    )
    objects.append(s2)

    c2 = PhysicalEntity(
        uid="PEP0_control_Reaction4X",
        cellular_location="cell",
        display_name="X",
        member_physical_entity="X",
    )
    objects.append(c2)

    u3 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0030163",
        id="GO:0030163",
        db="Gene Ontology",
    )
    objects.append(u3)

    s3 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction12_Z",
        stoichiometric_coefficient="1",
    )
    objects.append(s3)

    c3 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction7_PX",
        cellular_location="cell",
        display_name="PX",
        member_physical_entity="PX",
    )
    objects.append(c3)

    s4 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction11_Y",
        stoichiometric_coefficient="1",
    )
    objects.append(s4)

    c4 = CellularLocationVocabulary(
        uid="cell", term="cell", xref="http://identifiers.org/obo.go/GO:0005623"
    )
    objects.append(c4)

    b1 = BiochemicalReaction(
        uid="conversion_Reaction12",
        xref="http://identifiers.org/obo.go/GO:0006351",
        participant_stoichiometry="RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY",
        display_name="transcription of CI",
        right="RIGHT_0_conversion_Reaction12_Z",
    )
    objects.append(b1)

    b1 = BiochemicalReaction(
        uid="conversion_Reaction11",
        xref="http://identifiers.org/obo.go/GO:0006351",
        participant_stoichiometry="RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY",
        display_name="transcription of TetR",
        right="RIGHT_0_conversion_Reaction11_Y",
    )
    objects.append(b1)

    b1 = BiochemicalReaction(
        uid="conversion_Reaction10",
        xref="http://identifiers.org/obo.go/GO:0006351",
        participant_stoichiometry="RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY",
        display_name="transcription of LacI",
        right="RIGHT_0_conversion_Reaction10_X",
    )
    objects.append(b1)

    p1 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction9_PZ",
        cellular_location="cell",
        display_name="PZ",
        member_physical_entity="PZ",
    )
    objects.append(p1)

    u1 = UnificationXref(
        uid="http://identifiers.org/kegg.compound/C00046",
        id="C00046",
        db="KEGG Compound",
    )
    objects.append(u1)

    u1 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0005623",
        id="GO:0005623",
        db="Gene Ontology",
    )
    objects.append(u1)

    p1 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction8_PY",
        cellular_location="cell",
        display_name="PY",
        member_physical_entity="PY",
    )
    objects.append(p1)

    u1 = UnificationXref(
        uid="http://identifiers.org/chebi/CHEBI:33699", id="CHEBI:33699", db="ChEBI"
    )
    objects.append(u1)

    p1 = Protein(
        uid="PX",
        xref="http://identifiers.org/uniprot/P03023",
        display_name="LacI protein",
    )
    objects.append(p1)

    p1 = Protein(
        uid="PY",
        xref="http://identifiers.org/uniprot/P04483",
        display_name="TetR protein",
    )
    objects.append(p1)

    s1 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction10_X",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    p1 = Protein(
        uid="PZ",
        xref="http://identifiers.org/uniprot/P03034",
        display_name="cI protein",
    )
    objects.append(p1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction2",
        xref="http://identifiers.org/obo.go/GO:0006402",
        participant_stoichiometry="LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY",
        left="LEFT_0_conversion_Reaction2_Y",
        display_name="degradation of TetR transcripts",
    )
    objects.append(c1)

    s1 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction4_PX",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    p1 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction3_Z",
        cellular_location="cell",
        display_name="Z",
        member_physical_entity="Z",
    )
    objects.append(p1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction3",
        xref="http://identifiers.org/obo.go/GO:0006402",
        participant_stoichiometry="LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY",
        left="LEFT_0_conversion_Reaction3_Z",
        display_name="degradation of CI transcripts",
    )
    objects.append(c1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction4",
        xref="http://identifiers.org/obo.go/GO:0006412",
        participant_stoichiometry="RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY",
        display_name="translation of LacI",
        right="RIGHT_0_conversion_Reaction4_PX",
    )
    objects.append(c1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction5",
        xref="http://identifiers.org/obo.go/GO:0006412",
        participant_stoichiometry="RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY",
        display_name="translation of TetR",
        right="RIGHT_0_conversion_Reaction5_PY",
    )
    objects.append(c1)

    p1 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction2_Y",
        cellular_location="cell",
        display_name="Y",
        member_physical_entity="Y",
    )
    objects.append(p1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction6",
        xref="http://identifiers.org/obo.go/GO:0006412",
        participant_stoichiometry="RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY",
        display_name="translation of CI",
        right="RIGHT_0_conversion_Reaction6_PZ",
    )
    objects.append(c1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction7",
        xref="http://identifiers.org/obo.go/GO:0030163",
        participant_stoichiometry="LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY",
        display_name="degradation of LacI",
        left="LEFT_0_conversion_Reaction7_PX",
    )
    objects.append(c1)

    s1 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction9_PZ",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction8",
        xref="http://identifiers.org/obo.go/GO:0030163",
        participant_stoichiometry="LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY",
        display_name="degradation of TetR",
        left="LEFT_0_conversion_Reaction8_PY",
    )
    objects.append(c1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction9",
        xref="http://identifiers.org/obo.go/GO:0030163",
        participant_stoichiometry="LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY",
        display_name="degradation of CI",
        left="LEFT_0_conversion_Reaction9_PZ",
    )
    objects.append(c1)

    u1 = UnificationXref(
        uid="http://identifiers.org/taxonomy/562", id="562", db="Taxonomy"
    )
    objects.append(u1)

    s1 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction1_X_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction1_X",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction4_PX",
        cellular_location="cell",
        display_name="PX",
        member_physical_entity="PX",
    )
    objects.append(p1)

    u1 = UnificationXref(
        uid="http://identifiers.org/uniprot/P03034",
        id="P03034",
        db="UniProt Knowledgebase",
    )
    objects.append(u1)

    p1 = PhysicalEntity(
        uid="PEP0_control_Reaction10PZ",
        cellular_location="cell",
        display_name="PZ",
        member_physical_entity="PZ",
    )
    objects.append(p1)

    s1 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction3_Z",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction10_X",
        cellular_location="cell",
        display_name="X",
        member_physical_entity="X",
    )
    objects.append(p1)

    b1 = BioSource(uid="biosource_1", xref="http://identifiers.org/taxonomy/562")
    objects.append(b1)

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction11_Y",
        cellular_location="cell",
        display_name="Y",
        member_physical_entity="Y",
    )
    objects.append(p1)

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction12_Z",
        cellular_location="cell",
        display_name="Z",
        member_physical_entity="Z",
    )
    objects.append(p1)

    s1 = Stoichiometry(
        uid="LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY",
        physical_entity="LEFT_0_conversion_Reaction8_PY",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    p1 = PhysicalEntity(
        uid="RIGHT_0_conversion_Reaction6_PZ",
        cellular_location="cell",
        display_name="PZ",
        member_physical_entity="PZ",
    )
    objects.append(p1)

    p1 = PhysicalEntity(
        uid="PEP0_control_Reaction6Z",
        cellular_location="cell",
        display_name="Z",
        member_physical_entity="Z",
    )
    objects.append(p1)

    p1 = PhysicalEntity(
        uid="PEP0_control_Reaction11PX",
        cellular_location="cell",
        display_name="PX",
        member_physical_entity="PX",
    )
    objects.append(p1)

    r1 = Rna(
        uid="Y",
        xref=[
            "http://identifiers.org/chebi/CHEBI:33699",
            "http://identifiers.org/kegg.compound/C00046",
            "http://identifiers.org/uniprot/P04483",
        ],
        display_name="TetR mRNA",
    )
    objects.append(r1)

    r1 = Rna(
        uid="X",
        xref=[
            "http://identifiers.org/chebi/CHEBI:33699",
            "http://identifiers.org/kegg.compound/C00046",
            "http://identifiers.org/uniprot/P03023",
        ],
        display_name="LacI mRNA",
    )
    objects.append(r1)

    s1 = Stoichiometry(
        uid="RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY",
        physical_entity="RIGHT_0_conversion_Reaction5_PY",
        stoichiometric_coefficient="1",
    )
    objects.append(s1)

    r1 = Rna(
        uid="Z",
        xref=[
            "http://identifiers.org/chebi/CHEBI:33699",
            "http://identifiers.org/kegg.compound/C00046",
            "http://identifiers.org/uniprot/P03034",
        ],
        display_name="cI mRNA",
    )
    objects.append(r1)

    c1 = Control(
        uid="control_Reaction6_Z_0",
        controlled="conversion_Reaction6",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction6Z",
    )
    objects.append(c1)

    c1 = Control(
        uid="control_Reaction12_PY_0",
        controlled="conversion_Reaction12",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction12PY",
    )
    objects.append(c1)

    p1 = PhysicalEntity(
        uid="PEP0_control_Reaction12PY",
        cellular_location="cell",
        display_name="PY",
        member_physical_entity="PY",
    )
    objects.append(p1)

    u1 = UnificationXref(
        uid="http://identifiers.org/biomodels.db/MODEL6615351360",
        id="MODEL6615351360",
        db="BioModels Database",
    )
    objects.append(u1)

    u1 = UnificationXref(
        uid="http://identifiers.org/uniprot/P03023",
        id="P03023",
        db="UniProt Knowledgebase",
    )
    objects.append(u1)

    c1 = Control(
        uid="control_Reaction10_PZ_0",
        controlled="conversion_Reaction10",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction10PZ",
    )
    objects.append(c1)

    u1 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0006412",
        id="GO:0006412",
        db="Gene Ontology",
    )
    objects.append(u1)

    u1 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0040029",
        id="GO:0040029",
        db="Gene Ontology",
    )
    objects.append(u1)

    u1 = UnificationXref(
        uid="http://identifiers.org/obo.go/GO:0006351",
        id="GO:0006351",
        db="Gene Ontology",
    )
    objects.append(u1)

    c1 = Control(
        uid="control_Reaction5_Y_0",
        controlled="conversion_Reaction5",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction5Y",
    )
    objects.append(c1)

    p1 = PhysicalEntity(
        uid="LEFT_0_conversion_Reaction1_X",
        cellular_location="cell",
        display_name="X",
        member_physical_entity="X",
    )
    objects.append(p1)

    p1 = PhysicalEntity(
        uid="PEP0_control_Reaction5Y",
        cellular_location="cell",
        display_name="Y",
        member_physical_entity="Y",
    )
    objects.append(p1)

    c1 = Control(
        uid="control_Reaction11_PX_0",
        controlled="conversion_Reaction11",
        control_type="INHIBITION",
        controller="PEP0_control_Reaction11PX",
    )
    objects.append(c1)

    c1 = BiochemicalReaction(
        uid="conversion_Reaction1",
        xref="http://identifiers.org/obo.go/GO:0006402",
        participant_stoichiometry="LEFT_0_conversion_Reaction1_X_STOICHIOMETRY",
        display_name="degradation of LacI transcripts",
        left="LEFT_0_conversion_Reaction1_X",
    )
    objects.append(c1)

    u1 = UnificationXref(
        uid="http://identifiers.org/uniprot/P04483",
        id="P04483",
        db="UniProt Knowledgebase",
    )
    objects.append(u1)
    # '''
    # <bp:BiochemicalReaction rdf:about="conversion_Reaction12">
    #  <bp:xref rdf:resource="http://identifiers.org/obo.go/GO:0006351" />
    #  <bp:participantStoichiometry rdf:resource="RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY" />
    #  <bp:displayName rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">transcription of CI</bp:displayName>
    #  <bp:right rdf:resource="RIGHT_0_conversion_Reaction12_Z" />
    # </bp:BiochemicalReaction>
    # '''
    # b1=BiochemicalReaction(uid="conversion_Reaction12", displayName="transcription of CI")
    # objects.append(b1)

    model = BioPaxModel(
        objects={o.uid: o for o in objects},
        xml_base="http://www.biopax.org/release/biopax-level3.owl#",
    )
    owl_str: str = model_to_owl_str(model)
    os.makedirs(os.path.dirname(biopax_path), exist_ok=True)

    with open(biopax_path, "w") as f_biopax:
        f_biopax.write(owl_str)

    print("-" * 80)
    print(owl_str)
    print("-" * 80)

    return model

In [3]:

if __name__ == "__main__":
    from combine_notebooks import RESULTS_DIR

    create_repressilator(biopax_path=RESULTS_DIR / "repressilator_biopax.owl")

Serializing OWL elements: 100% 73.0/73.0 [00:00<00:00, 5.10kit/s]

--------------------------------------------------------------------------------
<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base="http://www.biopax.org/release/biopax-level3.owl#">
  <owl:Ontology rdf:about="">
 <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#"/>
  </owl:Ontology>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction5_PY">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction2_Y</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:Provenance rdf:ID="datasource_1">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioModels Database</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/biomodels.db/BIOMD0000000012</bp:xref>
</bp:Provenance>

<bp:PublicationXref rdf:about="http://identifiers.org/pubmed/10659856">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PubMed</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10659856</bp:id>
</bp:PublicationXref>

<bp:Provenance rdf:ID="datasource_2">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioModels Database</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/biomodels.db/MODEL6615351360</bp:xref>
</bp:Provenance>

<bp:UnificationXref rdf:about="http://identifiers.org/biomodels.db/BIOMD0000000012">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioModels Database</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BIOMD0000000012</bp:id>
</bp:UnificationXref>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0006402">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0006402</bp:id>
</bp:UnificationXref>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction7_PX</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:Control rdf:ID="control_Reaction4_X_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction4</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction4X</bp:controller>
</bp:Control>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction6_PZ</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction4X">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0030163">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0030163</bp:id>
</bp:UnificationXref>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction12_Z</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction7_PX">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction11_Y</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:CellularLocationVocabulary rdf:ID="cell">
 <bp:term rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:term>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0005623</bp:xref>
</bp:CellularLocationVocabulary>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction12">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transcription of CI</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction12_Z</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006351</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction11">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transcription of TetR</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction11_Y</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006351</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction10">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">transcription of LacI</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction10_X</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006351</bp:xref>
</bp:BiochemicalReaction>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction9_PZ">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:UnificationXref rdf:about="http://identifiers.org/kegg.compound/C00046">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">KEGG Compound</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">C00046</bp:id>
</bp:UnificationXref>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0005623">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0005623</bp:id>
</bp:UnificationXref>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction8_PY">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:UnificationXref rdf:about="http://identifiers.org/chebi/CHEBI:33699">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ChEBI</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CHEBI:33699</bp:id>
</bp:UnificationXref>

<bp:Protein rdf:ID="PX">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LacI protein</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P03023</bp:xref>
</bp:Protein>

<bp:Protein rdf:ID="PY">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TetR protein</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P04483</bp:xref>
</bp:Protein>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction10_X</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:Protein rdf:ID="PZ">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cI protein</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P03034</bp:xref>
</bp:Protein>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction2">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of TetR transcripts</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction2_Y</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006402</bp:xref>
</bp:BiochemicalReaction>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction4_PX</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction3_Z">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction3">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of CI transcripts</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction3_Z</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006402</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction4">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">translation of LacI</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction4_PX</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006412</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction5">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">translation of TetR</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction5_PY</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006412</bp:xref>
</bp:BiochemicalReaction>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction2_Y">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction6">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">translation of CI</bp:displayName>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:right rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction6_PZ</bp:right>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006412</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction7">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of LacI</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction7_PX</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0030163</bp:xref>
</bp:BiochemicalReaction>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction9_PZ</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction8">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of TetR</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction8_PY</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0030163</bp:xref>
</bp:BiochemicalReaction>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction9">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of CI</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction9_PZ</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0030163</bp:xref>
</bp:BiochemicalReaction>

<bp:UnificationXref rdf:about="http://identifiers.org/taxonomy/562">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Taxonomy</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">562</bp:id>
</bp:UnificationXref>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction1_X_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction1_X</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction4_PX">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:UnificationXref rdf:about="http://identifiers.org/uniprot/P03034">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt Knowledgebase</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P03034</bp:id>
</bp:UnificationXref>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction10PZ">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction3_Z</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction10_X">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:BioSource rdf:ID="biosource_1">
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/taxonomy/562</bp:xref>
</bp:BioSource>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction11_Y">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction12_Z">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Stoichiometry rdf:ID="LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction8_PY</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:PhysicalEntity rdf:ID="RIGHT_0_conversion_Reaction6_PZ">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PZ</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction6Z">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Z</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction11PX">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PX</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Rna rdf:ID="Y">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TetR mRNA</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/chebi/CHEBI:33699</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/kegg.compound/C00046</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P04483</bp:xref>
</bp:Rna>

<bp:Rna rdf:ID="X">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LacI mRNA</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/chebi/CHEBI:33699</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/kegg.compound/C00046</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P03023</bp:xref>
</bp:Rna>

<bp:Stoichiometry rdf:ID="RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY">
 <bp:physicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RIGHT_0_conversion_Reaction5_PY</bp:physicalEntity>
 <bp:stoichiometricCoefficient rdf:datatype="http://www.w3.org/2001/XMLSchema#float">1</bp:stoichiometricCoefficient>
</bp:Stoichiometry>

<bp:Rna rdf:ID="Z">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cI mRNA</bp:displayName>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/chebi/CHEBI:33699</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/kegg.compound/C00046</bp:xref>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/uniprot/P03034</bp:xref>
</bp:Rna>

<bp:Control rdf:ID="control_Reaction6_Z_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction6</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction6Z</bp:controller>
</bp:Control>

<bp:Control rdf:ID="control_Reaction12_PY_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction12</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction12PY</bp:controller>
</bp:Control>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction12PY">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PY</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:UnificationXref rdf:about="http://identifiers.org/biomodels.db/MODEL6615351360">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioModels Database</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">MODEL6615351360</bp:id>
</bp:UnificationXref>

<bp:UnificationXref rdf:about="http://identifiers.org/uniprot/P03023">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt Knowledgebase</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P03023</bp:id>
</bp:UnificationXref>

<bp:Control rdf:ID="control_Reaction10_PZ_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction10</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction10PZ</bp:controller>
</bp:Control>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0006412">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0006412</bp:id>
</bp:UnificationXref>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0040029">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0040029</bp:id>
</bp:UnificationXref>

<bp:UnificationXref rdf:about="http://identifiers.org/obo.go/GO:0006351">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Gene Ontology</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0006351</bp:id>
</bp:UnificationXref>

<bp:Control rdf:ID="control_Reaction5_Y_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction5</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction5Y</bp:controller>
</bp:Control>

<bp:PhysicalEntity rdf:ID="LEFT_0_conversion_Reaction1_X">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">X</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:PhysicalEntity rdf:ID="PEP0_control_Reaction5Y">
 <bp:cellularLocation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</bp:cellularLocation>
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:displayName>
 <bp:memberPhysicalEntity rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Y</bp:memberPhysicalEntity>
</bp:PhysicalEntity>

<bp:Control rdf:ID="control_Reaction11_PX_0">
 <bp:controlType rdf:datatype="http://www.w3.org/2001/XMLSchema#string">INHIBITION</bp:controlType>
 <bp:controlled rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conversion_Reaction11</bp:controlled>
 <bp:controller rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PEP0_control_Reaction11PX</bp:controller>
</bp:Control>

<bp:BiochemicalReaction rdf:ID="conversion_Reaction1">
 <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">degradation of LacI transcripts</bp:displayName>
 <bp:left rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction1_X</bp:left>
 <bp:participantStoichiometry rdf:datatype="http://www.w3.org/2001/XMLSchema#string">LEFT_0_conversion_Reaction1_X_STOICHIOMETRY</bp:participantStoichiometry>
 <bp:xref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://identifiers.org/obo.go/GO:0006402</bp:xref>
</bp:BiochemicalReaction>

<bp:UnificationXref rdf:about="http://identifiers.org/uniprot/P04483">
 <bp:db rdf:datatype="http://www.w3.org/2001/XMLSchema#string">UniProt Knowledgebase</bp:db>
 <bp:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">P04483</bp:id>
</bp:UnificationXref>
</rdf:RDF>

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