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[bioontology-support] Status of imports and Bioportal

Trish Whetzel whetzel at stanford.edu
Sun Jul 17 06:43:20 PDT 2011


BioPortal handles imports the same as Protege 3.x, therefore the imports will be loaded by loading the single IAO file.   

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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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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