the synthetic biology open language (sbol) data...
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The Synthetic Biology Open Language (SBOL)Data Model
Chris J. Myerson behalf of the SBOL community
University of Utah
SBOL WorkshopAugust 15, 2016
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Sequence Data Standards
SBOL 2.0 TetR GFP
pTet
aTc
GFPTetR
ACTGTGCCGTTAAACGTGATTAAATCCGTACTGATAT…FASTA
TetR GFP
pTetGenBank
TetR
TetR GFP
pTetSBOL 1.1
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SBOL 2.0 Data Model
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SBOL 2.0 Data Model
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SBOL 2.0 Data Model
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Understanding UML Diagrams
Classes represented as boxes labeled with their member variables withtypes and cardinalities.
Arrows with cardinality indicate associations between classes.
A hollow diamond at the origin of an arrow represents shared aggregation(i.e., object is referenced and not owned).
A solid diamond at the origin of an arrow represents compositeaggregation (i.e., child object is owned by its parent object).
Hollow arrows are used to represent inheritance.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Identified (Base Class for All SBOL Objects)
Annotationannotations
0..*
Identified-identity[1] : URI-persistentIdentity[0..1] : URI-displayId[0..1] : String-version[0..1] : String-wasDerivedFrom[0..1] : URI-name[0..1] : String-description[0..1] : String
identity - globally unique URI to identify this object (required).persistentIdentity - identity shared by multiple versions of the same object(optional).displayId - human-readable id composed of alphanumeric andunderscore characters (optional).version - uses semantic versioning to identify multiple versions of thesame object (optional).
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Identified (Base Class for All SBOL Objects)
Annotationannotations
0..*
Identified-identity[1] : URI-persistentIdentity[0..1] : URI-displayId[0..1] : String-version[0..1] : String-wasDerivedFrom[0..1] : URI-name[0..1] : String-description[0..1] : String
wasDerivedFrom - identity of object that this is derived from (optional).
name - human-readable String of arbitrary characters (optional).
description - thorough text description of the object (optional).
annotations - additional data about this object (more later).
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Identified (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_J23119/2">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J23119"/><sbol:displayId> BBa_J23119 </sbol:displayId><sbol:version> 2 </sbol:version><prov:wasDerivedFrom rdf:resource="http://www.partsregistry.org/BBa_J23119/1"/><dcterms:title> J23119 promoter </dcterms:title><dcterms:description> Constitutive promoter </dcterms:description>
</sbol:ComponentDefinition></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Compliant Top-Level URIs
〈URI prefix〉/〈displayId〉/〈version〉
1 The identity MUST begin with a URI prefix that maps to a domain overwhich the user has control.
2 The persistentIdentity and displayId properties are REQUIRED.3 The persistentIdentity MUST end with a delimiter (’/’, ’#’, or ’:’) followed by
the displayId of the object.4 If an object is not given a version, then its identity and persistentIdentity
properties MUST contain the same URI.5 If an object has a version, then its identity property MUST contain a URI
of the form 〈persistentIdentity〉/〈version〉".
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Compliant Child URIs
〈parent persistentIdentity〉/〈displayId〉/〈parent version〉
1 The persistentIdentity MUST begin with the persistentIdentity of its parentobject and be immediately followed by a delimiter (’/’, ’#’, or ’:’) and thedisplayId of the object.
2 The version MUST contain the same String as the version property of theobject’s parent object.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
TopLevel
ModuleDefinitionModelComponentDefinitionSequence GenericTopLevel
Identified
Collection
TopLevel
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Collection
members 0..*
Collection
TopLevel
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Collection (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:Collection rdf:about="http://parts.igem.org/Promoters/Catalog/Anderson">
<sbol:persistentIdentity rdf:resource="http://parts.igem.org/Promoters/Catalog/Anderson"/><sbol:displayId> Anderson </sbol:displayId><dcterms:title> Anderson promoters </dcterms:title><dcterms:description> The Anderson promoter collection </dcterms:description><sbol:member rdf:resource="http://partsregistry.org/Part:BBa_J23119"/>...<sbol:member rdf:resource="http://partsregistry.org/Part:BBa_J23118"/>
</sbol:Collection></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Sequence
TopLevel
Sequence-elements[1] : String-encoding[1] : URI
elements - String of characters representing constituents of a biologicalor chemical molecule.
encoding - URI indicating how elements are to be interpreted.Encoding URI CD TypeIUPAC DNA, RNA http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html DNA, RNAIUPAC Protein http://www.chem.qmul.ac.uk/iupac/AminoAcid/ ProteinSMILES http://www.opensmiles.org/opensmiles.html SmallMolecule
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Sequence (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_J23119"><sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_J23119"/><sbol:displayId> BBa_J23119 </sbol:displayId><prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23119:Design"/><sbol:elements> ttgacagctagctcagtcctaggtataatgctagc </sbol:elements><sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
ComponentDefinition
SequenceConstraint
TopLevel
sequences 0..*
Sequence
components 0..*
sequenceAnnotations0..*
sequenceConstraints
0..*
ComponentDefinition-types[1..*] : URI-roles[0..*] : URI
Component
SequenceAnnotation
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
ComponentDefinition (Types/Roles)
CD Type URI for BioPAX TermDNA http://www.biopax.org/release/biopax-level3.owl#DnaRegionRNA http://www.biopax.org/release/biopax-level3.owl#RnaRegionProtein http://www.biopax.org/release/biopax-level3.owl#ProteinSmall Molecule http://www.biopax.org/release/biopax-level3.owl#SmallMoleculeComplex http://www.biopax.org/release/biopax-level3.owl#Complex
CD Role URI for SequenceOntology Term CD TypePromoter http://identifiers.org/so/SO:0000167 DNARBS http://identifiers.org/so/SO:0000139 DNACDS http://identifiers.org/so/SO:0000316 DNATerminator http://identifiers.org/so/SO:0000141 DNAGene http://identifiers.org/so/SO:0000704 DNAOperator http://identifiers.org/so/SO:0000057 DNAEngineered Gene http://identifiers.org/so/SO:0000280 DNAmRNA http://identifiers.org/so/SO:0000234 RNA
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
ComponentDefinition (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119"/><sbol:displayId> BBa_J23119 </sbol:displayId><dcterms:title> J23119 promoter </dcterms:title><dcterms:description> Constitutive promoter </dcterms:description><sbol:type rdf:resource="http://www.biopax.org/release/biopax -level3.owl#DnaRegion"/><sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/><sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
</sbol:ComponentDefinition></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Component (Child of ComponentDefinition)
ComponentDefinition
definition 1
mapsTos0..* MapsTo
Identified
ComponentInstance-access[1] : URI
Component FunctionalComponent-direction[1] : URI
Access URI Descriptionhttp://sbols.org/v2#public MAY be referred to by remote MapsTo objects.http://sbols.org/v2#private MUST NOT be referred to by remote MapsTo objects.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
MapsTo (Child of ComponentInstance)
Identified
ComponentInstance
MapsTo-refinement[1] : URI
remote 1
local 1
Refinement URI Descriptionhttp://sbols.org/v2#useRemote All references MUST dereference to the remote CI.http://sbols.org/v2#useLocal All references MUST dereference to the local CI.http://sbols.org/v2#verifyIdentical The definition of the local and remote MUST be same CD.http://sbols.org/v2#merge All references MUST dereference to both objects.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
MapsTo (Example)
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SequenceAnnotation (Child of ComponentDefinition)
component 0..1
Component
Identified
Locationlocations
1..*
SequenceAnnotation
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Location (Child of SequenceAnnotation)
GenericLocation
Identified
Range-start[1] : Integer > 0-end[1] : Integer > 0
Cut-at[1] : Integer >= 0
Location-orientation[0..1] : URI
Orientation URI Descriptionhttp://sbols.org/v2#inline The region is inline with the sequence.http://sbols.org/v2#reverseComplement The region is on the reverse-complement translation.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
LacI Inverter (SBOL)
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SequenceConstraint (Child of ComponentDefinition)
Component
Identified
object 1
subject 1
SequenceConstraint-restriction[1] : URI
Restriction URI Descriptionhttp://sbols.org/v2#precedes subject MUST precede object Component.http://sbols.org/v2#sameOrientationAs subject & object MUST have same orientation.http://sbols.org/v2#oppositeOrientationAs subject & object MUST have opposite orientations.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
SequenceConstraint (Question)
QUESTION: Redrew the UML diagram below using SequenceConstraintsrather than SequenceAnnotations.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Model
Model-source[1] : URI-language[1] : URI-framework[1] : URI
TopLevel
source - URI reference to the source file for the model.language - URI that species language in which the model is implemented.
Model Language URI for EDAM TermSBML http://identifiers.org/edam/format_2585CellML http://identifiers.org/edam/format_3240BioPAX http://identifiers.org/edam/format_3156
framework - URI that species modeling framework used.Framework URI for SBO TermContinuous http://identifiers.org/biomodels.sbo/SBO:0000062Discrete http://identifiers.org/biomodels.sbo/SBO:0000063
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Model (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:Model rdf:about="http://www.sbolstandard.org/examples/pIKE_Toggle_1">
<sbol:persistentIdentity rdf:resource="http://www.sbolstandard.org/examples/pIKE_Toggle_1"/><sbol:displayId> pIKE_Toggle_1 </sbol:displayId><dcterms:title> pIKE_Toggle_1 toggle switch </dcterms:title><sbol:source rdf:resource="http://virtualparts.org/part/pIKE_Toggle_1"/><sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/><sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
</sbol:Model></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
ModuleDefinition
TopLevel
models0..* Model
Module
modules 0..*
Interaction
interactions 0..*
FunctionalComponent
functionalComponents0..*
ModuleDefinition-roles[0..*] : URI
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
FunctionalComponent (Child of ModuleDefinition)
ComponentDefinition
definition 1
mapsTos0..* MapsTo
Identified
ComponentInstance-access[1] : URI
Component FunctionalComponent-direction[1] : URI
Direction URI Descriptionhttp://sbols.org/v2#in Indicates that it is an input.http://sbols.org/v2#out Indicates that it is an output.http://sbols.org/v2#inout Indicates that it is both an input and outputhttp://sbols.org/v2#none Indicates that it is neither an input nor output.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Module (Child of ModuleDefinition)
ModuleDefinition
definition 1 MapsTo
mapsTos0..*
Identified
Module
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Interaction (Child of ModuleDefinition)
Participation
Identified
participations0..*
Interaction-types[1..*] : URI
Interaction Type URI for SystemsBiologyOntology TermInhibition http://identifiers.org/biomodels.sbo/SBO:0000169Stimulation http://identifiers.org/biomodels.sbo/SBO:0000170Biochemical Reaction http://identifiers.org/biomodels.sbo/SBO:0000176Non-Covalent Binding http://identifiers.org/biomodels.sbo/SBO:0000177Degradation http://identifiers.org/biomodels.sbo/SBO:0000179Genetic Production http://identifiers.org/biomodels.sbo/SBO:0000589
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Participation (Child of Interaction)
participant 1
FunctionalComponent
Identified
Participation-roles[1..*] : URI
Part. Role URI for SBO Term Interaction TypesInhibitor http://identifiers.org/biomodels.sbo/SBO:0000020 InhibitionStimulator http://identifiers.org/biomodels.sbo/SBO:0000459 StimulationReactant http://identifiers.org/biomodels.sbo/SBO:0000010 Non-Covalent Binding,
DegradationBiochemical Reaction
Product http://identifiers.org/biomodels.sbo/SBO:0000011 Non-Covalent Binding,Genetic Production,Biochemical Reaction
Promoter http://identifiers.org/biomodels.sbo/SBO:0000598 Inhibition, Stimulation,Genetic Production
Modifier http://identifiers.org/biomodels.sbo/SBO:0000019 Biochemical Reaction
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
LacI Inverter (SBOL)
definition definition definition
ComponentDefinition...-displayId : "TetR_Gene"
ComponentDefinition...-displayId : "LacI"
ComponentDefinition...-displayId : "TetR"
FunctionalComponent...-displayId : "TetR"-access : Public-direction : Output
FunctionalComponent...-displayId : "TetR_Gene"-access : Private-direction : None
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Input
model
Model-source : LacI_Inverter.xml-language : SBML-framework : Continuous
participant
Participation...-roles : [Promoter]
Interaction...-displayId : "TetR_Production"-type : [Genetic Production]
participant
Participation...-roles : [Product]
ModuleDefinition...-displayId : "LacI_Inverter"
participant participant
Participation...-roles : [ ]
Participation...-roles : [Inhibitor]
Interaction...-displayId : "LacI_Repression"-types : [Inhibition]
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Genetic Toggle Switch
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Genetic Toggle Switch (SBOL)
MapsTo...-refinement : Verify Identical
MapsTo...-refinement : Verify Identical
Module...-displayId : "TetR_Inverter"
MapsTo...-refinement : Verify Identical
MapsTo...-refinement : Verify Identical
FunctionalComponent...-displayId : "pTet"-access : Private-direction : None
FunctionalComponent...-displayId : "cLacI"-access : Private-direction : None
FunctionalComponent...-displayId : "cTetR"-access : Private-direction : None
FunctionalComponent...-displayId : "pLac"-access : Private-direction : None
remote
remote remote
FunctionalComponent...-displayId : "TetR"-access : Public-direction : Input
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Output
ModuleDefinition...-displayId : "TetR_Inverter"
remote FunctionalComponent
...-displayId : "TetR"-access : Public-direction : Output
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Input
ModuleDefinition...-displayId : "LacI_Inverter"
local
local
local
local
Module...-displayId : "LacI_Inverter"
participant
participant
participant
Participation...-roles : [Reactant]
Participation...-roles : [Product]
Interaction...-displayId : "IPTG_Binding"-types : [Non-Covalent Binding]
Participation...-roles : [Reactant]
FunctionalComponent...-displayId : "IPTG_LacI_Complex"-access : Private-direction : None
FunctionalComponent...-displayId : "aTc_TetR_Complex"-access : Private-direction : None
FunctionalComponent...-displayId : "IPTG"-access : Public-direction : Input
participant
participant
participant
Participation...-roles : [Reactant]
Participation...-roles : [Reactant]
Participation...-roles : [Product]
Interaction...-displayId : "aTc_Binding"-types : [Non-Covalent Binding]
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Output
FunctionalComponent...-displayId : "aTc"-access : Public-direction : Input
FunctionalComponent...-displayId : "TetR"-access : Public-direction : Output
ModuleDefinition...-displayId : "LacI_TetR_Toggle"
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Genetic Toggle Switch
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Genetic Toggle Switch (SBOL)
MapsTo...-refinement : Verify Identical
MapsTo...-refinement : Verify Identical
Module...-displayId : "TetR_Inverter"
MapsTo...-refinement : Verify Identical
MapsTo...-refinement : Verify Identical
FunctionalComponent...-displayId : "pTet"-access : Private-direction : None
FunctionalComponent...-displayId : "cLacI"-access : Private-direction : None
FunctionalComponent...-displayId : "cTetR"-access : Private-direction : None
FunctionalComponent...-displayId : "pLac"-access : Private-direction : None
remote
remote remote
FunctionalComponent...-displayId : "TetR"-access : Public-direction : Input
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Output
ModuleDefinition...-displayId : "TetR_Inverter"
remote FunctionalComponent
...-displayId : "TetR"-access : Public-direction : Output
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Input
ModuleDefinition...-displayId : "LacI_Inverter"
local
local
local
local
Module...-displayId : "LacI_Inverter"
participant
participant
participant
Participation...-roles : [Reactant]
Participation...-roles : [Product]
Interaction...-displayId : "IPTG_Binding"-types : [Non-Covalent Binding]
Participation...-roles : [Reactant]
FunctionalComponent...-displayId : "IPTG_LacI_Complex"-access : Private-direction : None
FunctionalComponent...-displayId : "aTc_TetR_Complex"-access : Private-direction : None
FunctionalComponent...-displayId : "IPTG"-access : Public-direction : Input
participant
participant
participant
Participation...-roles : [Reactant]
Participation...-roles : [Reactant]
Participation...-roles : [Product]
Interaction...-displayId : "aTc_Binding"-types : [Non-Covalent Binding]
FunctionalComponent...-displayId : "LacI"-access : Public-direction : Output
FunctionalComponent...-displayId : "aTc"-access : Public-direction : Input
FunctionalComponent...-displayId : "TetR"-access : Public-direction : Output
ModuleDefinition...-displayId : "LacI_TetR_Toggle"
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Annotations (Child of Identified)
annotations 0..*
NestedAnnotations-nestedQName[1] : QName-nestedURI[1] : URI
value1
annotations 0..*
AnnotationValue
Literal URI
Annotation-qName[1] : QName
Identified
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Annotations (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:pr="http://partsregistry.org"xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119"/><sbol:displayId> BBa_J23119 </sbol:displayId><pr:group> iGEM2006_Berkeley </pr:group><pr:experience rdf:resource="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"/><pr:information>
<pr:Information rdf:about="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"><pr:sigmafactor> //rnap/prokaryote/ecoli/sigma70 </pr:sigmafactor><pr:regulation> //regulation/constitutive </pr:regulation>
</pr:Information></pr:information><dcterms:title> J23119 </dcterms:title><dcterms:description> Constitutive promoter </dcterms:description><sbol:type rdf:resource="http://www.biopax.org/release/biopax -level3.owl#DnaRegion"/><sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
</sbol:ComponentDefinition></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
GenericTopLevel
GenericTopLevel-rdfType[1] : QName
TopLevel
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
GenericTopLevel (Example)
<?xml version ="1.0" ?><rdf:RDF xmlns:myapp="http://www.myapp.org/"xmlns:rdf="http://www.w3.org/1999/02/22 -rdf-syntax -ns#"xmlns:dcterms="http://purl.org/dc/terms/"xmlns:prov="http://www.w3.org/ns/prov#"xmlns:sbol="http://sbols.org/v2#"><sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/cd/BBa_J23119"/><sbol:displayId> BBa_J23119 </sbol:displayId><prov:wasDerivedFrom rdf:resource="http://www.partsregistry.org/Part:BBa_J23119"/><myapp:datasheet rdf:resource="http://www.partsregistry.org/gen/datasheet1"/><dcterms:title> J23119 </dcterms:title><dcterms:description> Constitutive promoter </dcterms:description><sbol:type rdf:resource="http://www.biopax.org/release/biopax -level3.owl#DnaRegion"/><sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
</sbol:ComponentDefinition><myapp:Datasheet rdf:about="http://www.partsregistry.org/gen/datasheet1">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/gen/datasheet1"/><sbol:displayId> datasheet1 </sbol:displayId><myapp:characterizationData rdf:resource="http://www.myapp.org/measurement/1"/><myapp:transcriptionRate> 1 </myapp:transcriptionRate><dcterms:title> Datasheet 1 </dcterms:title>
</myapp:Datasheet></rdf:RDF>
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016
Conclusion (SBOL Compliant Software)
Can either support all classes or only its structural subset.
Can support import of SBOL, export of SBOL, or both (lossy/lossless).
SBOL Test Suite is currently under development here:https://github.com/SynBioDex/SBOLTestSuite
Validate SBOL files generated using the SBOL Validator found here:http://www.async.ece.utah.edu/sbol-validator/
Report SBOL-compliant software to the SBOL editors([email protected]), so it can be listed on the SBOL website.
Chris J. Myers (University of Utah) SBOL Data Model SBOL Workshop / August 15, 2016