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[bioontology-support] Status of imports and Bioportal

Trish Whetzel whetzel at stanford.edu
Sun Jul 17 20:38:20 PDT 2011


Can you clarify the feature request? I'm not sure why an additional button is needed to load a new version when the ontology file location is specified by a URL since this process occurs automatically when a file with updated contents is detected. 

Thanks,
Trish 


On Jul 17, 2011, at 4:36 PM, Alan Ruttenberg wrote:

> 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>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> 




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