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[bioontology-support] [BioPortal] Ontology metrics - Feedback from Simon K

Simon Kocbek simon.kocbek at rmit.edu.au
Thu Nov 5 15:06:53 PST 2015


Hi John,

thank you for your reply. Referring to first Ray's email below, is
parsing older ontology files the only way to get ontology sizes for
older versions/submissions? If yes, I am guessing that the recommended
method does not guarantee history for _all_ BioPortal's ontologies?

Kind regards,
Simon

On 6 November 2015 at 06:58, John Graybeal <jbgmeta1 at stanford.edu> wrote:
> Hi Simon,
>
> This is a documentation bug; we only calculate metrics for the most recent submission.
>
> The documentation bug is in the response to a REST API call like http://data.bioontology.org/ontologies/BRO/submissions, which includes in the response for example:
>
>>     • "@id": "http://data.bioontology.org/ontologies/BRO/submissions/12",
>>     • "@type": "http://data.bioontology.org/metadata/OntologySubmission",
>>     • -"links": {
>>         • "metrics": "http://data.bioontology.org/ontologies/BRO/submissions/12/metrics",
>>         • -"@context": {
>>             • "metrics": "http://data.bioontology.org/metadata/OntologySubmission"
>>         }
>>     },
>
> The value for metrics in the links field clearly suggests your model should work, but it is not supported and fails in odd ways.
>
> Sorry for your trouble,
>
> john
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
>
>> On Nov 4, 2015, at 9:43 PM, Simon Kocbek <simon.kocbek at rmit.edu.au> wrote:
>>
>> Hi Ray,
>>
>> thank you for your reply. I need information at different time points
>> for many ontologies, so I am trying to solve the problem through
>> BioPortal's RESTful API. However, I am having some troubles.
>>
>> For example, to get information about the first and the last (i.e.,
>> 11th) SNOMEDCT submission I call:
>>   - first submission:
>> http://data.bioontology.org/ontologies/SNOMEDCT/submissions/1/metrics
>>   - last submission:
>> http://data.bioontology.org/ontologies/SNOMEDCT/submissions/11/metrics
>>
>> but I always get the same result:
>> "id": "http://data.bioontology.org/ontologies/SNOMEDCT/submissions/11/metrics",
>> "created": "2015-08-13T13:37:23-07:00",
>> ...
>>
>> Calls for other ontologies act the same way.
>>
>> Bug or am I doing something wrong?
>>
>> Thanks
>> Simon
>>
>>
>>
>> On 17 October 2015 at 05:05, Ray Fergerson <rayferg at stanford.edu> wrote:
>>> You can download the source files from us for many ontologies. Depending on
>>> how the ontology is set up, there may be a lot of older files. You will need
>>> to parse these yourself, presumably using the OWL API. What we have is all
>>> available on our site.
>>>
>>>
>>>
>>> Ray
>>>
>>>
>>>
>>> From: bioontology-support
>>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
>>> support at bioontology.org
>>> Sent: Thursday, October 15, 2015 9:33 PM
>>> To: support at bioontology.org; simon.kocbek at rmit.edu.au
>>> Subject: [bioontology-support] [BioPortal] Feedback from Simon K
>>>
>>>
>>>
>>> Name: Simon K
>>>
>>> Email: simon.kocbek at rmit.edu.au
>>>
>>> Location: https://bioportal.bioontology.org/
>>>
>>>
>>> Feedback:
>>>
>>> Hi,
>>>
>>> Is there a way to get historical data for ontologies? Specifically, I am
>>> interested in ontology sizes (i.e., number of concepts) on specific date.
>>>
>>> Thanks!
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>


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