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

John Graybeal jbgmeta1 at stanford.edu
Thu Nov 5 11:58:30 PST 2015


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





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