sbol2.document

Module Contents

Classes

Document

The Document is a container for all SBOL data objects.

Functions

_make_validation_request(options: Mapping[str, Union[bool, str]])

validate(doc: Document, options: Mapping[str, Any])

rtype

Dict[str, Any]

IGEM_STANDARD_ASSEMBLY(parts_list)

Attributes

SBOL_DATA_MODEL_REGISTER

igem_assembly_scars

sbol2.document.SBOL_DATA_MODEL_REGISTER
class sbol2.document.Document(filename=None)

Bases: sbol2.identified.Identified

The Document is a container for all SBOL data objects.

In a previous era, engineers might sit at a drafting board and draft a design by hand. The engineer’s drafting sheet in LibSBOL is called a Document. The Document serves as a container, initially empty, for SBOL data objects. All file I/O operations are performed on the Document to populate it with SBOL objects representing design elements.

compare(self, other)
addCitation(self, new_citation)
removeCitation(self, index=0)
addKeyword(self, new_keyword)
removeKeyword(self, index=0)
add(self, sbol_obj)

Register an object in the Document.

Parameters

sbol_obj – The SBOL object(s) you want to serialize. Either a single object or a list of objects.

Returns

None

add_list(self, sbol_objs)
addNamespace(self, namespace, prefix)

Add a new namespace to the Document.

Parameters

  • namespace – The namespace, eg. http://sbols.org/v2#

  • prefix – The namespace prefix, eg. sbol

Returns

addComponentDefinition(self, sbol_obj)

Convenience method for adding a component definition.

Parameters

sbol_obj – component definition

Returns

None

addModuleDefinition(self, sbol_obj)

Convenience method for adding a module definition.

Parameters

sbol_obj – module definition

Returns

None

addCollection(self, sbol_obj)

Convenience method for adding a collection.

Parameters

sbol_obj – a Collection

Returns

None

addSequence(self, sbol_obj)

Convenience method for adding a sequence.

Parameters

sbol_obj – sequence

Returns

None

addModel(self, sbol_obj)

Convenience method for adding a model.

Parameters

sbol_obj – model

Returns

None

addImplementation(self, implementation)

Convenience method for adding an implementation.

addAttachment(self, attachment)

Add an attachment to this document.

abstract create(self, uri)

Creates another SBOL object derived from TopLevel and adds it to the Document. NOTE: originally from ReferencedObject :param uri: In “open world” mode, this is a full URI and the same as the returned URI. If the default namespace for libSBOL has been configured, then this argument should simply be a local identifier. If SBOL-compliance is enabled, this argument should be the intended displayId of the new object. A full URI is automatically generated and returned. :return: The full URI of the created object

get(self, uri)

Finds the SBOL object with the given URI.

Parameters

uri (str) – URI of the extension object

Returns

The matching SBOLObject

Return type

SBOLObject

Raises

SBOLError if the given uri is not found

abstract getAll(self)

Retrieve a list of objects from the Document.

Returns

A list of objects from the Document.

getComponentDefinition(self, uri)
getModuleDefinition(self, uri)
getSequence(self, uri)
getModel(self, uri)
getImplementation(self, uri)
getCollection(self, uri: str) → sbol2.collection.Collection
write(self, filename)

Serialize all objects in this Document to an RDF/XML file.

Parameters

filename – The full name of the file you want to write

(including file extension). :return: A string with the validation results, or empty string if validation is disabled.

read(self, filename)

Read an RDF/XML file and attach the SBOL objects to this Document.

Existing contents of the Document will be wiped. :param filename: The full name of the file you want to read (including file extension). :return: None

readString(self, sbol_str)

Read an RDF/XML string and attach the SBOL objects to this Document.

Existing contents of the Document will be wiped.

Parameters

sbol_str – A string formatted in SBOL.

Returns

None

writeString(self)

Convert data objects in this Document into textual SBOL.

Returns

A string representation of the objects in this Document.

append(self, filename, overwrite: bool = False)

Read an RDF/XML file and attach the SBOL objects to this Document.

New objects will be added to the existing contents of the Document. :param filename: The full name of the file you want to read (including file extension). :param overwrite: Boolean indicating whether to overwrite existing objects :return: None

appendString(self, sbol_str: str, overwrite: bool = False)

Read an RDF/XML document from a string and attach the SBOL objects to this Document.

New objects will be added to the existing contents of the Document. :param sbol_str: A string of RDF/XML :param overwrite: Boolean indicating whether to overwrite existing objects :return: None

_append_graph(self, new_graph: rdflib.Graph, overwrite: bool)
parse_all(self)
parse_objects_inner(self, subject, obj)
parse_properties_inner(self, subject, predicate, obj)
find_reference(self, uri)

Find objects that reference the given URI. Returns a list of objects. The list will be empty if no references were found.

parse_annotation_objects(self)

Parse leftover objects from reading and link them up where they belong. These are usually extension-type objects.

infer_resource_namespaces(self)
dress_document(self)
convert_ntriples_encoding_to_ascii(self, s)
abstract request_comparison(self, diff_file)

Perform comparison on Documents using the online validation tool.

This is for cross-validation of SBOL documents with libSBOLj. Document comparison can also be performed using the built-in compare method. :param diff_file: :return: The comparison results

clear(self, clear_graph=True)

Delete all properties and objects in the Document.

Returns

None

abstract query_repository(self, command)
Parameters

command –

Returns

str

abstract search_metadata(self, role, type, name, collection)
Parameters

  • role –

  • type –

  • name –

  • collection –

Returns

str

doc_serialize_rdf2xml(self, outfile)

Serialize RDF XML. :param outfile: output file :return: None

update_graph(self)

Update the RDF triples representation of data. :return:

validate(self)

Run validation on this Document via the validation tool (locally or online, depending on configuration)

Returns

A string containing a message with the validation results

Return type

str

size(self)

Get the total number of objects in the Document, including SBOL core object and custom annotation objects.

Returns

The total number of objects in the Document.

__len__(self)

Get the total number of objects in the Document, including SBOL core object and custom annotation objects.

(Returns the same thing as size())

Returns

The total number of objects in the Document.

__bool__(self)
__str__(self)

Produce a string representation of the Document.

Returns

A string representation of the Document.

__iter__(self)
__next__(self)
abstract cacheObjectsDocument(self)
referenceNamespace(self, uri)

Replaces the namespace with a reference and removes the default namespace, shortening the URI. :param uri: :return: str

summary(self)

Produce a string representation of the Document.

Returns

A string representation of the Document.

find(self, uri)

Search recursively for an SBOLObject in this Document that matches the uri.

Parameters

uri – The identity of the object to search for.

Returns

A pointer to the SBOLObject,

or NULL if an object with this identity doesn’t exist.

getTypeURI(self)
getTopLevel(self, uri)
copy(self, target_namespace=None, target_doc=None, version=None)
exportToFormat(self, language: str, output_path: str)
convert(self, language, output_path)
importFromFormat(self, input_path: str, overwrite=False)

Import the specified file into this document.

getExtensionObject(self, uri: str) → sbol2.object.SBOLObject

Deprecated. Use Document.get instead.

Parameters

uri (str) – URI of the extension object

Returns

The matching SBOLObject

Return type

SBOLObject

Raises

SBOLError if the given uri is not found

addExtensionObject(self, obj: sbol2.object.SBOLObject) → None

Deprecated. Use Document.add instead.

Parameters

obj (SBOLObject) – An SBOLObject to add to this document

Returns

None

sbol2.document._make_validation_request(options: Mapping[str, Union[bool, str]])
sbol2.document.validate(doc: Document, options: Mapping[str, Any])
Return type

Dict[str, Any]

sbol2.document.igem_assembly_scars = Multiline-String
Show Value
  1<?xml version="1.0" encoding="utf-8"?>
  2<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/"
  3xmlns:dcterms="http://purl.org/dc/terms/"
  4xmlns:gbconv="http://sbols.org/genBankConversion#"
  5xmlns:genbank="http://www.ncbi.nlm.nih.gov/genbank#"
  6xmlns:igem="http://wiki.synbiohub.org/wiki/Terms/igem#"
  7xmlns:ncbi="http://www.ncbi.nlm.nih.gov#"
  8xmlns:obo="http://purl.obolibrary.org/obo/"
  9xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
 10xmlns:prov="http://www.w3.org/ns/prov#"
 11xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
 12xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
 13xmlns:sbh="http://wiki.synbiohub.org/wiki/Terms/synbiohub#"
 14xmlns:sbol="http://sbols.org/v2#"
 15xmlns:sybio="http://www.sybio.ncl.ac.uk#"
 16xmlns:synbiohub="http://synbiohub.org#"
 17xmlns:xsd="http://www.w3.org/2001/XMLSchema#dateTime/">
 18<sbol:ComponentDefinition rdf:about="https://synbiohub.org/public/igem/BBa_G0000/1">
 19<dc:creator>Reshma Shetty</dc:creator>
 20<dcterms:created>2007-07-22T11:00:00Z</dcterms:created>
 21<dcterms:description>SpeI/XbaI scar for RBS-CDS junctions</dcterms:description>
 22<dcterms:modified>2015-08-31T04:07:27Z</dcterms:modified>
 23<dcterms:title>scar</dcterms:title>
 24<sbol:displayId>BBa_G0000</sbol:displayId>
 25<sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_G0000"/>
 26<sbol:role rdf:resource="http://identifiers.org/so/SO:0000110"/>
 27<sbol:role rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#partType/DNA"/>
 28<sbol:sequence
 29        rdf:resource="https://synbiohub.org/public/igem/BBa_G0000_sequence/1"/>
 30<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
 31<sbol:version>1</sbol:version>
 32<igem:discontinued>false</igem:discontinued>
 33<igem:dominant>true</igem:dominant>
 34<igem:experience
 35        rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#experience/None"/>
 36<igem:group_u_list>_41_</igem:group_u_list>
 37<igem:m_user_id>0</igem:m_user_id>
 38<igem:owner_id>126</igem:owner_id>
 39<igem:owning_group_id>162</igem:owning_group_id>
 40<igem:sampleStatus>Not in stock</igem:sampleStatus>
 41<igem:status
 42        rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#status/Unavailable"/>
 43<sbh:bookmark>false</sbh:bookmark>
 44<sbh:mutableDescription>
 45    This is the sequence of the SpeI/XbaI scar for RBS-CDS junctions in
 46    BioBricks standard assembly.
 47</sbh:mutableDescription>
 48<sbh:mutableNotes>
 49    This is a shorter scar to ensure proper spacing between the RBS and CDS.
 50</sbh:mutableNotes>
 51<sbh:mutableProvenance>SpeI/XbaI scar</sbh:mutableProvenance>
 52<sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
 53<sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
 54<sbh:star>false</sbh:star>
 55<sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_G0000/1"/>
 56<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_G0000"/>
 57<prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
 58</sbol:ComponentDefinition>
 59<sbol:Sequence rdf:about="https://synbiohub.org/public/igem/BBa_G0000_sequence/1">
 60<sbol:displayId>BBa_G0000_sequence</sbol:displayId>
 61<sbol:elements>tactag</sbol:elements>
 62<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
 63<sbol:persistentIdentity
 64        rdf:resource="https://synbiohub.org/public/igem/BBa_G0000_sequence"/>
 65<sbol:version>1</sbol:version>
 66<sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
 67<sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
 68<sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_G0000_sequence/1"/>
 69<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_G0000"/>
 70<prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
 71</sbol:Sequence>
 72<sbol:ComponentDefinition rdf:about="https://synbiohub.org/public/igem/BBa_G0002/1">
 73<dc:creator>Reshma Shetty</dc:creator>
 74<dcterms:created>2007-02-26T12:00:00Z</dcterms:created>
 75<dcterms:description>SpeI/XbaI mixed site</dcterms:description>
 76<dcterms:modified>2015-08-31T04:07:27Z</dcterms:modified>
 77<dcterms:title>SX scar</dcterms:title>
 78<sbol:displayId>BBa_G0002</sbol:displayId>
 79<sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_G0002"/>
 80<sbol:role rdf:resource="http://identifiers.org/so/SO:0000110"/>
 81<sbol:role rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#partType/DNA"/>
 82<sbol:sequence rdf:resource="https://synbiohub.org/public/igem/BBa_G0002_sequence/1"/>
 83<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
 84<sbol:version>1</sbol:version>
 85<igem:discontinued>false</igem:discontinued>
 86<igem:dominant>true</igem:dominant>
 87<igem:experience
 88        rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#experience/None"/>
 89<igem:group_u_list>_41_</igem:group_u_list>
 90<igem:m_user_id>0</igem:m_user_id>
 91<igem:owner_id>126</igem:owner_id>
 92<igem:owning_group_id>70</igem:owning_group_id>
 93<igem:sampleStatus>Not in stock</igem:sampleStatus>
 94<igem:status
 95        rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#status/Unavailable"/>
 96<sbh:bookmark>false</sbh:bookmark>
 97<sbh:mutableDescription>
 98    XbaI/SpeI mixed site.  Simply used to aid in entry of parts into the registry.
 99</sbh:mutableDescription>
100<sbh:mutableNotes>None.</sbh:mutableNotes>
101<sbh:mutableProvenance>XbaI and SpeI sites</sbh:mutableProvenance>
102<sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
103<sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
104<sbh:star>false</sbh:star>
105<sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_G0002/1"/>
106<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_G0002"/>
107<prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
108</sbol:ComponentDefinition>
109<sbol:Sequence rdf:about="https://synbiohub.org/public/igem/BBa_G0002_sequence/1">
110<sbol:displayId>BBa_G0002_sequence</sbol:displayId>
111<sbol:elements>tactagag</sbol:elements>
112<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
113<sbol:persistentIdentity
114        rdf:resource="https://synbiohub.org/public/igem/BBa_G0002_sequence"/>
115<sbol:version>1</sbol:version>
116<sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
117<sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
118<sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_G0002_sequence/1"/>
119<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_G0002"/>
120<prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
121</sbol:Sequence>
122<prov:Activity rdf:about="https://synbiohub.org/public/igem/igem2sbol/1">
123<dc:creator>Chris J. Myers</dc:creator>
124<dc:creator>James Alastair McLaughlin</dc:creator>
125<dcterms:description>Conversion of the iGEM parts registry to SBOL2.1
126</dcterms:description>
127<dcterms:title>iGEM to SBOL conversion</dcterms:title>
128<sbol:displayId>igem2sbol</sbol:displayId>
129<sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/igem2sbol"/>
130<sbol:version>1</sbol:version>
131<sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
132<sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
133<sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
134<prov:endedAtTime>2017-03-06T15:00:00.000Z</prov:endedAtTime>
135</prov:Activity>
136</rdf:RDF>
sbol2.document.IGEM_STANDARD_ASSEMBLY(parts_list)