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[bioontology-support] Status of imports and Bioportal

Alan Ruttenberg alanruttenberg at gmail.com
Sun Jul 17 07:36:10 PDT 2011


On Sun, Jul 17, 2011 at 9:43 AM, Trish Whetzel <whetzel at stanford.edu> wrote:
> BioPortal handles imports the same as Protege 3.x, therefore the imports will be loaded by loading the single IAO file.

Thanks, I will try that.

Do you plan to respond to the feature request I made?

-Alan

>
> Ontologies loaded from a URL are refreshed, i.e. are re-loaded when new versions are detected. This "detection" process is run daily.
>
> Trish
>
>
> On Jul 11, 2011, at 7:03 PM, Alan Ruttenberg wrote:
>
>> How does bioportal handle imports in OWL ontologies. The standard
>> distribution of IAO is a small file that imports components (see
>> below). How should this be uploaded to BioPortal? If a URL to this is
>> given, will the imported ontologies also be loaded?
>>
>> Can we have another option for uploading a new ontology:
>> Load from URL (this version will be loaded once)  <refresh>
>>
>> Where the refresh button will cause the URL to be loaded again and
>> replace the current version?
>>
>> OBO Foundry and other ontologies developed according to the OWL 2 spec
>> will have version IRIs that are stable for specific versions and it
>> would be appropriate to be able to load a single version from one of
>> those URIs.
>>
>> Thanks,
>> Alan
>>
>>
>>
>>
>> <?xml version="1.0"?>
>> <rdf:RDF
>>    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>>    xmlns:owl="http://www.w3.org/2002/07/owl#"
>>    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>    xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
>>    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>>  xml:base="http://purl.obolibrary.org/obo/">
>>  <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/iao.owl">
>>    <rdfs:seeAlso>
>>      <owl:Thing
>> rdf:about="http://code.google.com/p/information-artifact-ontology/"/>
>>    </rdfs:seeAlso>
>>    <owl:versionInfo xml:lang="en">2011-05-09</owl:versionInfo>
>>    <owl:versionIRI
>> xml:lang="en">http://purl.obolibrary.org/obo/iao/2011-05-09/iao.owl</owl:versionIRI>
>>    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>>> An information artifact is, loosely, a dependent continuant or
>> its bearer that is created as the result of one or more intentional
>> processes. Examples: uniprot, the english language, the contents of
>> this document or a printout of it, the temperature measurements from a
>> weather balloon. For more information, see the project home page at
>> http://code.google.com/p/information-artifact-ontology/</rdfs:comment>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/obsolete.owl"/>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/iao-main.owl"/>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/externalDerived.owl"/>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/external.owl"/>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/externalByHand.owl"/>
>>    <owl:imports><owl:Ontology
>> rdf:about="http://www.obofoundry.org/ro/ro.owl"/></owl:imports>
>>    <owl:imports
>> rdf:resource="http://purl.obolibrary.org/obo/iao/2011-05-09/ontology-metadata.owl"/>
>>    <owl:imports
>> rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
>>    <owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
>>    <protege:defaultLanguage
>> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
>>  </owl:Ontology>
>> </rdf:RDF>
>> _______________________________________________
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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>



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