How to use sbol3 - 10 common examples

To help you get started, we’ve selected a few sbol3 examples, based on popular ways it is used in public projects.

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SynBioDex / pySBOL / sbol3 / interaction.py View on Github

def __init__(self, rdf_type=SBOL_INTERACTION, uri='example', interaction_type=SBO_INTERACTION):
        super().__init__(rdf_type, uri)
        self.functionalComponents = OwnedObject(self, SBOL_FUNCTIONAL_COMPONENTS, '0', '*', [libsbol_rule_18])
        self._types = URIProperty(self, SBOL_TYPES, '1', '*', [], interaction_type)
        self.participations = OwnedObject(self, SBOL_PARTICIPATIONS, '0', '*', [])
        self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])
        # TODO hidden properties

SynBioDex / pySBOL / sbol3 / component.py View on Github

def __init__(self, rdf_type, uri, definition, access, version):
        super().__init__(rdf_type, uri, version)
        self.definition = ReferencedObject(self, SBOL_DEFINITION, SBOL_COMPONENT_DEFINITION, '1', '1', [], definition)
        self._access = URIProperty(self, SBOL_ACCESS, '0', '1', [], access)
        self.mapsTos = OwnedObject(self, SBOL_MAPS_TOS, '0', '*', [])
        self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])

SynBioDex / pySBOL / sbol3 / document.py View on Github

super().__init__(SBOL_DOCUMENT, URIRef(""), VERSION_STRING)
        if os.path.exists(LOGGING_CONFIG):
            fileConfig(LOGGING_CONFIG)
        else:
            self.logger.setLevel(logging.INFO)
        self.logger = logging.getLogger(__name__)

        # A RDFLib representation of the triples.
        # Initialized when parsing a graph.
        # Updated when writing a graph.
        self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

if os.path.exists(LOGGING_CONFIG):
            fileConfig(LOGGING_CONFIG)
        else:
            self.logger.setLevel(logging.INFO)
        self.logger = logging.getLogger(__name__)

        # A RDFLib representation of the triples.
        # Initialized when parsing a graph.
        # Updated when writing a graph.
        self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

# A RDFLib representation of the triples.
        # Initialized when parsing a graph.
        # Updated when writing a graph.
        self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

# Updated when writing a graph.
        self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

SynBioDex / pySBOL / sbol3 / document.py View on Github

self.logger.setLevel(logging.INFO)
        self.logger = logging.getLogger(__name__)

        # A RDFLib representation of the triples.
        # Initialized when parsing a graph.
        # Updated when writing a graph.
        self.graph = None
        # The Document's register of objects
        self.objectCache = {}  # Needed?
        self.SBOLObjects = {}  # Needed?
        self.resource_namespaces = None
        self.designs = OwnedObject(self, SYSBIO_DESIGN, '0', '*', [libsbol_rule_11])
        self.builds = OwnedObject(self, SYSBIO_BUILD, '0', '*', [libsbol_rule_12])
        self.tests = OwnedObject(self, SYSBIO_TEST, '0', '*', [libsbol_rule_13])
        self.analyses = OwnedObject(self, SYSBIO_ANALYSIS, '0', '*', [libsbol_rule_14])
        self.componentDefinitions = OwnedObject(self, SBOL_COMPONENT_DEFINITION, '0', '*', None)
        self.moduleDefinitions = OwnedObject(self, SBOL_MODULE_DEFINITION, '0', '*', None)
        self.models = OwnedObject(self, SBOL_MODEL, '0', '*', None)
        self.sequences = OwnedObject(self, SBOL_SEQUENCE, '0', '*', None)
        self.collections = OwnedObject(self, SBOL_COLLECTION, '0', '*', None)
        self.activities = OwnedObject(self, PROVO_ACTIVITY, '0', '*', None)
        self.plans = OwnedObject(self, PROVO_PLAN, '0', '*', None)
        self.agents = OwnedObject(self, PROVO_AGENT, '0', '*', None)
        self.attachments = OwnedObject(self, SBOL_ATTACHMENT, '0', '*', None)
        self.combinatorialderivations = OwnedObject(self, SBOL_COMBINATORIAL_DERIVATION, '0', '*', None)
        self.implementations = OwnedObject(self, SBOL_IMPLEMENTATION, '0', '*', None)
        self.sampleRosters = OwnedObject(self, SYSBIO_SAMPLE_ROSTER, '0', '*', [validation.libsbol_rule_16])
        self.experiments = OwnedObject(self, SBOL_EXPERIMENT, '0', '*', None)
        self.experimentalData = OwnedObject(self, SBOL_EXPERIMENTAL_DATA, '0', '*', None)
        self._citations = URIProperty(self, PURL_URI + "bibliographicCitation", '0', '*', None)
        self._keywords = URIProperty(self, PURL_URI + "elements/1.1/subject", '0', '*', None)

How to use sbol3 - 10 common examples

To help you get started, we’ve selected a few sbol3 examples, based on popular ways it is used in public projects.

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