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Unique classification and identification of model elements

Look for other standards: - BioPAX (composition) - CellML (aggregation) - Other SBML L3 extensions (modules - rule-based modeling). Unique classification and identification of model elements. Different types of species: proteins, small molecules, complexes.

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Unique classification and identification of model elements

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  1. Look for other standards: - BioPAX (composition) - CellML (aggregation)- Other SBML L3 extensions (modules - rule-based modeling)

  2. Unique classification and identification of model elements Different types of species: proteins, small molecules, complexes. User-specified grouping: ligand-binding module, Grb2 interactions Different types of reactions: biochemical reaction, complex assembly

  3. Interaction Physical Entity Control Conversion Protein Small Molecule Complex RNA Catalysis Modulation Biochemical Reaction Transport Complex Assembly TransportWith BiochemicalReaction Structure consistent with BioPAX ontology • BioPax stands for Biological PAthway eXchange

  4. <species compartment="R_7660" id="REACT_4932_2" metaid="metaid_0000006" name="REACT_4932_2_Cyclin_A_Cdk2_complex"> <annotation> <rdf:RDF xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"> <rdf:Description rdf:about="#metaid_0000006"> <bqbiol:hasPart> <rdf:Bag> <rdf:li rdf:resource="http://www.uniprot.org/#P24941"/> </rdf:Bag> </bqbiol:hasPart> <bqbiol:isVersionOf> <rdf:Bag> <rdf:li rdf:resource="http://www.reactome.org/#REACT_4932.2"/> </rdf:Bag> </bqbiol:isVersionOf> </rdf:Description> </rdf:RDF> </annotation> </species> • Fictional species. • Relationships, e.g. has a component, isVersionOf

  5. <component name="EGF">       <variable units="nanomolar" public_interface="out" name="EGF“ initial_value="680"/>    <variable units="flux" public_interface="in" name="v1"/>    <variable units="second" public_interface="in" name="time"/>           dEGF/dt = -v1   </component>  <component name="R">       <variable units="nanomolar" public_interface="out" name="R“ initial_value="100"/>    <variable units="flux" public_interface="in" name="v1"/>    <variable units="second" public_interface="in" name="time"/>          dR/dt = -v1     </component>  <component name="Ra">        <variable units="nanomolar" public_interface="out" name="Ra"/>    <variable units="flux" public_interface="in" name="v1"/>    <variable units="second" public_interface="in" name="time"/>          dRa/dt = v1  </component>  <component name="v1">    <variable units="flux" public_interface="out" name="v1"/>      <variable units="nanomolar" public_interface="in" name="R"/>    <variable units="nanomolar" public_interface="in" name="EGF"/>       <variable units="second_order_rate_constant" name="k1“ initial_value="0.003"/>    <variable units="first_order_rate_constant" name="k1“ initial_value="0.06"/>

  6. <connection>    <map_components component_2="v1" component_1="EGF"/>    <map_variables variable_2="EGF" variable_1="EGF"/>    <map_variables variable_2="v1" variable_1="v1"/>  </connection>  <connection>    <map_components component_2="v1" component_1="R"/>    <map_variables variable_2="R" variable_1="R"/>    <map_variables variable_2="v1" variable_1="v1"/>  </connection>  <connection>    <map_components component_2="v1" component_1="Ra"/>    <map_variables variable_2="Ra" variable_1="Ra"/>    <map_variables variable_2="v1" variable_1="v1"/>  </connection> 

  7. reaction rules = modules molecule types = interfaces A begin molecule types A(b, b1, b2, …) B(a, a1, a2, …) end molecule types b b1 B a a1 a + b B A A B begin reaction rules A(b) + B(a) <-> A(b!1).B(a!1) kp1,km1 end reaction rules a bond between two components

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