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[bioontology-support] Status of imports and Bioportal

Alan Ruttenberg alanruttenberg at gmail.com
Mon Jul 18 01:11:24 PDT 2011


On Sun, Jul 17, 2011 at 11:38 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> 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.

The feature request was for a different case - an essentially static
file corresponding (typically) to the version IRI.
There is typically no need to check this every day, and in fact after
some time it would be an error if it changed - so bioportal picking up
the change wouldn't be helpful.

So: 2 cases

1) The one you have - you give a "latest" URI and bioportal picks up
the versions by checking daily.
2) You give a URL which you intend to name a static ontology. But
giving the URL is easier than uploading the ontology.

-Alan

>
> 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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