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SynBioDex / sboljs3

A library for the Synthetic Biology Open Language (SBOL) written in TypeScript, for JavaScript/TypeScript applications in the browser or node.js
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SBOL 3->2 conversion loses Activities #15

Open jakebeal opened 2 years ago

jakebeal commented 2 years ago

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>