the synthetic biology open language (sbol) data...

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


SBOL 2.0 Data Model


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.


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).


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).


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>


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〉".


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.


TopLevel

ModuleDefinitionModelComponentDefinitionSequence GenericTopLevel

Identified

Collection

TopLevel


Collection

members 0..*

Collection

TopLevel


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>


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


http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html

http://www.chem.qmul.ac.uk/iupac/AminoAcid/

http://www.opensmiles.org/opensmiles.html

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>


ComponentDefinition

SequenceConstraint

TopLevel

sequences 0..*

Sequence

components 0..*

sequenceAnnotations0..*

sequenceConstraints

0..*

ComponentDefinition-types[1..*] : URI-roles[0..*] : URI

Component

SequenceAnnotation


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


http://www.biopax.org/release/biopax-level3.owl#DnaRegion

http://www.biopax.org/release/biopax-level3.owl#RnaRegion

http://www.biopax.org/release/biopax-level3.owl#Protein

http://www.biopax.org/release/biopax-level3.owl#SmallMolecule

http://www.biopax.org/release/biopax-level3.owl#Complex

http://identifiers.org/so/SO:0000167








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"/>



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.


http://sbols.org/v2#public

http://sbols.org/v2#private

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.


http://sbols.org/v2#useRemote

http://sbols.org/v2#useLocal

http://sbols.org/v2#verifyIdentical

http://sbols.org/v2#merge

MapsTo (Example)


SequenceAnnotation (Child of ComponentDefinition)

component 0..1

Component

Identified

Locationlocations

1..*

SequenceAnnotation


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.


http://sbols.org/v2#inline

http://sbols.org/v2#reverseComplement

LacI Inverter


LacI Inverter (SBOL)


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.


http://sbols.org/v2#precedes

http://sbols.org/v2#sameOrientationAs

http://sbols.org/v2#oppositeOrientationAs

SequenceConstraint (Question)

QUESTION: Redrew the UML diagram below using SequenceConstraintsrather than SequenceAnnotations.


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


http://identifiers.org/edam/format_2585



http://identifiers.org/biomodels.sbo/SBO:0000062


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>


ModuleDefinition

TopLevel

models0..* Model

Module

modules 0..*

Interaction

interactions 0..*

FunctionalComponent

functionalComponents0..*

ModuleDefinition-roles[0..*] : URI


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.


http://sbols.org/v2#in

http://sbols.org/v2#out

http://sbols.org/v2#inout

http://sbols.org/v2#none

Module (Child of ModuleDefinition)

ModuleDefinition

definition 1 MapsTo

mapsTos0..*

Identified

Module


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








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








LacI Inverter


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]


Genetic Toggle Switch


Genetic Toggle Switch (SBOL)

MapsTo...-refinement : Verify Identical


Module...-displayId : "TetR_Inverter"



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



local

local

local

local

Module...-displayId : "LacI_Inverter"

participant

participant

participant

Participation...-roles : [Reactant]


Interaction...-displayId : "IPTG_Binding"-types : [Non-Covalent Binding]


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




Interaction...-displayId : "aTc_Binding"-types : [Non-Covalent Binding]


FunctionalComponent...-displayId : "aTc"-access : Public-direction : Input


ModuleDefinition...-displayId : "LacI_TetR_Toggle"


Genetic Toggle Switch


Genetic Toggle Switch (SBOL)



Module...-displayId : "TetR_Inverter"



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


ModuleDefinition...-displayId : "TetR_Inverter"

remote FunctionalComponent

...-displayId : "TetR"-access : Public-direction : Output



local

local

local

local

Module...-displayId : "LacI_Inverter"

participant

participant

participant



Interaction...-displayId : "IPTG_Binding"-types : [Non-Covalent Binding]


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




Interaction...-displayId : "aTc_Binding"-types : [Non-Covalent Binding]


FunctionalComponent...-displayId : "aTc"-access : Public-direction : Input


ModuleDefinition...-displayId : "LacI_TetR_Toggle"


Annotations (Child of Identified)

annotations 0..*

NestedAnnotations-nestedQName[1] : QName-nestedURI[1] : URI

value1

annotations 0..*

AnnotationValue

Literal URI

Annotation-qName[1] : QName

Identified


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"/>



GenericTopLevel

GenericTopLevel-rdfType[1] : QName

TopLevel


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>


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.


https://github.com/SynBioDex/SBOLTestSuite

http://www.async.ece.utah.edu/sbol-validator/

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