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A library for the Synthetic Biology Open Language (SBOL) written in TypeScript, for JavaScript/TypeScript applications in the browser or node.js

TypeScript 100.00%

synbio bioinformatics sbol biology

sboljs3's Introduction

sboljs3 is a library for the Synthetic Biology Open Language (SBOL) written in TypeScript, for JavaScript/TypeScript applications in the browser or node.js.

sboljs3 is built on rdfoo, a library for creating object oriented RDF abstractions in TypeScript. It can therefore be used in conjunction with other rdfoo abstractions. For example, the PROV-O abstraction used by sboljs3 is provided by rdfoo-prov.

Implemented so far

Reading and writing SBOL1, SBOL2, and SBOL3
Converting between SBOL1, SBOL2, and SBOL3
Reading (converting) FASTA and GenBank

Not implemented so far

Writing FASTA and GenBank
Validation

Citation

If you use this library in your work, please cite

@article{sboljs,
  author = {McLaughlin, James Alastair and Myers, Chris J. and Zundel, Zach and Wilkinson, Nathan and Atallah, Christian and Wipat, Anil},
  title = {sboljs: Bringing the Synthetic Biology Open Language to the Web Browser},
  journal = {ACS Synthetic Biology},
  volume = {8},
  number = {1},
  pages = {191-193},
  year = {2019},
  doi = {10.1021/acssynbio.8b00338},
  URL = { https://doi.org/10.1021/acssynbio.8b00338 },
  eprint = {  https://doi.org/10.1021/acssynbio.8b00338 }
}

sboljs3's People

Contributors

Stargazers

Watchers

Forkers

wayoffthecoast

sboljs3's Issues

Should decide if we create namespaces by default in 3.0.1

Component points to namespace

sbolgraph cannot handle CombinatorialDerivation objects

Any file with a CombinatorialDerivation currently produces an opaque failure because sbolgraph currently does not know about CombinatorialDerivation objects.

Example failure:

/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:54477
            throw new Error('unknown type: ' + uri + ' a ' + type);
                  ^

Error: unknown type: https://github.com/iGEM-Engineering/iGEM-distribution/Fluorescent%20Reporter%20Proteins/Fluorescent_Proteins_in_vector_ins a http://sbols.org/v3#CombinatorialDerivation
    at SBOL3.uriToFacade (/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:54477:19)
    at SBOL3GraphView.uriToFacade (/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:49132:23)
    at /Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:58779:37
    at Array.map (<anonymous>)
    at S3Collection.get members [as members] (/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:58779:14)
    at Object.convert3to2 [as default] (/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:55973:33)
    at Function.<anonymous> (/Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:54525:36)
    at Generator.next (<anonymous>)
    at /Users/jakebeal/projects/BioTools/iGEM_distribution/scripts/sbol:54504:71
    at new Promise (<anonymous>)

Should not build namespace by default

Also does not match SBOL 3.0.1 use of namespace

Easy wrapped serializations for other types of serializations

Operator from SequenceOntology is missing

SBOl 2->3 conversion errors

Conversion from SBOL2 to SBOL3 creates files with validation errors.
For example, here are the errors from conversion of this short J23101 XML file:

<?xml version="1.0" encoding="UTF-8"?>
<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#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#dateTime/" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/" xmlns:synbiohub="http://synbiohub.org#" xmlns:sbh="http://wiki.synbiohub.org/wiki/Terms/synbiohub#" xmlns:sybio="http://www.sybio.ncl.ac.uk#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:ncbi="http://www.ncbi.nlm.nih.gov#" xmlns:igem="http://wiki.synbiohub.org/wiki/Terms/igem#" xmlns:genbank="http://www.ncbi.nlm.nih.gov/genbank#" xmlns:gbconv="http://sbols.org/genBankConversion#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:obo="http://purl.obolibrary.org/obo/">
  <sbol:ComponentDefinition rdf:about="https://synbiohub.org/public/igem/BBa_J23101/1">
    <sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_J23101"/>
    <sbol:displayId>BBa_J23101</sbol:displayId>
    <sbol:version>1</sbol:version>
    <prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23101"/>
    <prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
    <dcterms:title>BBa_J23101</dcterms:title>
    <dcterms:description>constitutive promoter family member</dcterms:description>
    <dcterms:created>2006-08-03T11:00:00Z</dcterms:created>
    <dcterms:modified>2015-08-31T04:08:40Z</dcterms:modified>
    <sbh:mutableProvenance>later</sbh:mutableProvenance>
    <sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_J23101/1"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
    <igem:partStatus>Released HQ 2013</igem:partStatus>
    <sbh:mutableDescription>later</sbh:mutableDescription>
    <igem:discontinued>false</igem:discontinued>
    <igem:dominant>true</igem:dominant>
    <igem:experience rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#experience/Works"/>
    <igem:group_u_list>_52_</igem:group_u_list>
    <igem:m_user_id>0</igem:m_user_id>
    <igem:owner_id>483</igem:owner_id>
    <igem:owning_group_id>95</igem:owning_group_id>
    <igem:sampleStatus>In stock</igem:sampleStatus>
    <igem:status rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#status/Available"/>
    <sbh:bookmark>true</sbh:bookmark>
    <sbh:mutableNotes>N/A</sbh:mutableNotes>
    <sbh:star>true</sbh:star>
    <dc:creator>John Anderson</dc:creator>
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
    <sbol:role rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#partType/Regulatory"/>
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
    <sbol:sequence rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence/1"/>
  </sbol:ComponentDefinition>
  <sbol:Sequence rdf:about="https://synbiohub.org/public/igem/BBa_J23101_sequence/1">
    <sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence"/>
    <sbol:displayId>BBa_J23101_sequence</sbol:displayId>
    <sbol:version>1</sbol:version>
    <prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23101"/>
    <prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
    <sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence/1"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
    <sbol:elements>tttacagctagctcagtcctaggtattatgctagc</sbol:elements>
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
  </sbol:Sequence>
  <prov:Activity rdf:about="https://synbiohub.org/public/igem/igem2sbol/1">
    <sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/igem2sbol"/>
    <sbol:displayId>igem2sbol</sbol:displayId>
    <sbol:version>1</sbol:version>
    <dcterms:title>iGEM to SBOL conversion</dcterms:title>
    <dcterms:description>Conversion of the iGEM parts registry to SBOL2.1</dcterms:description>
    <sbh:topLevel rdf:resource="https://synbiohub.org/public/igem/igem2sbol/1"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/james"/>
    <sbh:ownedBy rdf:resource="https://synbiohub.org/user/myers"/>
    <dc:creator>Chris J. Myers</dc:creator>
    <dc:creator>James Alastair McLaughlin</dc:creator>
    <prov:endedAtTime rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-03-06T15:00:00.000Z</prov:endedAtTime>
  </prov:Activity>
</rdf:RDF>

https://synbiohub.org/public/igem/BBa_J23101_sequence: Too few values for property namespace. Expected 1, found 0
https://synbiohub.org/public/igem/BBa_J23101: Too few values for property namespace. Expected 1, found 0
https://synbiohub.org/public/igem/BBa_J23101_sequence: Less than 1 values on <https://synbiohub.org/public/igem/BBa_J23101_sequence>->:hasNamespace
https://synbiohub.org/public/igem/igem2sbol/1: Value does not have class :Identified
https://synbiohub.org/public/igem/BBa_J23101: Less than 1 values on <https://synbiohub.org/public/igem/BBa_J23101>->:hasNamespace
https://synbiohub.org/public/igem/BBa_J23101: Less than 1 values on <https://synbiohub.org/public/igem/BBa_J23101>->:hasNamespace
https://synbiohub.org/public/igem/BBa_J23101_sequence: Less than 1 values on <https://synbiohub.org/public/igem/BBa_J23101_sequence>->:hasNamespace
https://synbiohub.org/public/igem/BBa_J23101_sequence sbol3-10505: Sequence encoding is not in the recommended set

npm i
npm test

and this is the result

> [email protected] test
> bash test.sh

📝 Summary
📊 Statistics
       0 succeeded
       0 failed
       0 succeeded but were different

What other steps do I need to do to run the tests?

Remove "Facade" suffixes from class names

They are getting annoying

SBOL 3->2 conversion loses Activities

When I convert from SBOL3 to SBOL2, I lose Activities.

Example: SBOL3:


<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/elements/1.1/creator> "John Anderson" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/terms/created> "2006-08-03T11:00:00Z" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/terms/modified> "2015-08-31T04:08:40Z" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#description> "constitutive promoter family member" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#displayId> "BBa_J23101" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#hasSequence> <https://synbiohub.org/public/igem/BBa_J23101_sequence> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#name> "BBa_J23101" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000167> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://wiki.synbiohub.org/wiki/Terms/igem#partType/Regulatory> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#type> <http://www.biopax.org/release/biopax-level3.owl#DnaRegion> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2version> "1" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#discontinued> "false" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#dominant> "true" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#experience> <http://wiki.synbiohub.org/wiki/Terms/igem#experience/Works> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#group_u_list> "_52_" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#m_user_id> "0" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#owner_id> "483" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#owning_group_id> "95" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#partStatus> "Released HQ 2013" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#sampleStatus> "In stock" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#status> <http://wiki.synbiohub.org/wiki/Terms/igem#status/Available> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#bookmark> "true" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableDescription> "later" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableNotes> "N/A" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableProvenance> "later" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#star> "true" .
<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/BBa_J23101> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/ns/prov#wasDerivedFrom> <http://parts.igem.org/Part:BBa_J23101> .
<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#displayId> "BBa_J23101_sequence" .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#elements> "tttacagctagctcagtcctaggtattatgctagc" .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sboltools.org/backport#sbol2version> "1" .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/BBa_J23101_sequence> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/ns/prov#wasDerivedFrom> <http://parts.igem.org/Part:BBa_J23101> .
<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/elements/1.1/creator> "Chris J. Myers" .
<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/elements/1.1/creator> "James Alastair McLaughlin" .
<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/terms/description> "Conversion of the iGEM parts registry to SBOL2.1" .
<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/terms/title> "iGEM to SBOL conversion" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v2#persistentIdentity> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#displayId> "igem2sbol" .
<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> .
<https://synbiohub.org/public/igem/igem2sbol> <http://sboltools.org/backport#sbol2version> "1" .
<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> .
<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> .
<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/igem2sbol> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> .
<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/ns/prov#endedAtTime> "2017-03-06T15:00:00+00:00" .

SBOL2 output:

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:backport="http://sboltools.org/backport#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:ns0="http://wiki.synbiohub.org/wiki/Terms/synbiohub#" xmlns:ns1="http://wiki.synbiohub.org/wiki/Terms/igem#" xmlns:ns2="http://purl.org/dc/elements/1.1/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#">
  <sbol:Sequence rdf:about="https://synbiohub.org/public/igem/BBa_J23101_sequence">
    <backport:sbol3namespace rdf:resource="https://synbiohub.org" />
    <ns0:ownedBy rdf:resource="https://synbiohub.org/user/james" />
    <ns0:ownedBy rdf:resource="https://synbiohub.org/user/myers" />
    <prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol" />
    <ns0:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence" />
    <prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23101" />
    <sbol:version>1</sbol:version>
    <sbol:displayId>BBa_J23101_sequence</sbol:displayId>
    <sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence" />
    <sbol:elements>tttacagctagctcagtcctaggtattatgctagc</sbol:elements>
    <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html" />
  </sbol:Sequence>
  <sbol:ComponentDefinition rdf:about="https://synbiohub.org/public/igem/BBa_J23101">
    <backport:sbol3namespace rdf:resource="https://synbiohub.org" />
    <ns1:experience rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#experience/Works" />
    <ns0:bookmark>true</ns0:bookmark>
    <ns2:creator>John Anderson</ns2:creator>
    <ns1:owning_group_id>95</ns1:owning_group_id>
    <ns1:m_user_id>0</ns1:m_user_id>
    <dcterms:created>2006-08-03T11:00:00Z</dcterms:created>
    <sbol:version>1</sbol:version>
    <ns0:mutableDescription>later</ns0:mutableDescription>
    <dcterms:title>BBa_J23101</dcterms:title>
    <ns1:sampleStatus>In stock</ns1:sampleStatus>
    <ns1:group_u_list>_52_</ns1:group_u_list>
    <ns0:ownedBy rdf:resource="https://synbiohub.org/user/james" />
    <ns0:ownedBy rdf:resource="https://synbiohub.org/user/myers" />
    <ns1:status rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#status/Available" />
    <dcterms:description>constitutive promoter family member</dcterms:description>
    <ns1:dominant>true</ns1:dominant>
    <ns1:owner_id>483</ns1:owner_id>
    <ns0:mutableNotes>N/A</ns0:mutableNotes>
    <prov:wasGeneratedBy rdf:resource="https://synbiohub.org/public/igem/igem2sbol" />
    <ns0:star>true</ns0:star>
    <ns1:partStatus>Released HQ 2013</ns1:partStatus>
    <ns0:topLevel rdf:resource="https://synbiohub.org/public/igem/BBa_J23101" />
    <ns1:discontinued>false</ns1:discontinued>
    <prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23101" />
    <ns0:mutableProvenance>later</ns0:mutableProvenance>
    <dcterms:modified>2015-08-31T04:08:40Z</dcterms:modified>
    <sbol:persistentIdentity rdf:resource="https://synbiohub.org/public/igem/BBa_J23101" />
    <sbol:displayId>BBa_J23101</sbol:displayId>
    <backport:sbol3identity rdf:resource="https://synbiohub.org/public/igem/BBa_J23101" />
    <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167" />
    <sbol:role rdf:resource="http://wiki.synbiohub.org/wiki/Terms/igem#partType/Regulatory" />
    <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion" />
    <sbol:sequence rdf:resource="https://synbiohub.org/public/igem/BBa_J23101_sequence" />
  </sbol:ComponentDefinition>
</rdf:RDF>

    # remap sequence encodings:
    encoding_remapping = {
        sbol3.IUPAC_DNA_ENCODING: sbol2.SBOL_ENCODING_IUPAC,
        sbol3.IUPAC_PROTEIN_ENCODING: sbol2.SBOL_ENCODING_IUPAC_PROTEIN,
        sbol3.SMILES_ENCODING: sbol3.SMILES_ENCODING
    }
    for s in (o for o in doc3.objects if isinstance(o, sbol3.Sequence)):
        if s.encoding in encoding_remapping:
            s.encoding = encoding_remapping[s.encoding]
    # remap component types:
    type_remapping = {
        sbol3.SBO_DNA: sbol2.BIOPAX_DNA,
        sbol3.SBO_RNA: sbol2.BIOPAX_RNA,
        sbol3.SBO_PROTEIN: sbol2.BIOPAX_PROTEIN,
        sbol3.SBO_SIMPLE_CHEMICAL: sbol2.BIOPAX_SMALL_MOLECULE,
        sbol3.SBO_NON_COVALENT_COMPLEX: sbol2.BIOPAX_COMPLEX
    }
    for c in (o for o in doc3.objects if isinstance(o, sbol3.Component)):
        c.types = [(type_remapping[t] if t in type_remapping else t) for t in c.types]