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

John Graybeal jbgmeta1 at stanford.edu
Thu Nov 5 17:46:36 PST 2015


Yes, the only way to get ontology sizes for older versions/submissions is to parse them. 

> If yes, I am guessing that the recommended method does not guarantee history for _all_ BioPortal's ontologies?

I may not understand this question. We *have* saved all the ontologies that have been submitted, so you should be able to access them all to my knowledge.

John


> On Nov 5, 2015, at 3:06 PM, Simon Kocbek <simon.kocbek at rmit.edu.au> wrote:
> 
> 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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