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[bioontology-support] Versioning Question

Jennifer Leigh Vendetti vendetti at
Tue May 23 17:58:54 PDT 2017

Hi Jason,

ID is a bit of a special case in the API.  The ID of the entity is always returned, and does not need to be passed as an include parameter.  If you make the call you reference below w/out the "include=id”, the call will return successfully:

[cid:274634DA-EC2B-414C-B52F-3C2573BD894C at]

If what you are trying to do is limit what is returned, you could modify the call to be as follows:<>

… which would return only a small subset of information about the class:

[cid:18A7836A-119A-4FBD-A377-499190D31947 at]
Kind regards,

On May 23, 2017, at 8:07 AM, jason marr <jmarr1990 at<mailto:jmarr1990 at>> wrote:

Quick Question, Why is the following giving me an internal server error?

On Tue, May 16, 2017 at 1:55 PM, jason marr <jmarr1990 at<mailto:jmarr1990 at>> wrote:
It does thank you!

On May 16, 2017 1:39 PM, "Jennifer Leigh Vendetti" <vendetti at<mailto:vendetti at>> wrote:
Hi Jason,

By default, the REST API only shows a subset of properties for a given object.  If you want to see all properties, you need to override this behavior with the include=all parameter.  This is documented in the “General Usage” section of the API documentation:

In your example from below, you would adjust the URL to the following:<>

For every ontology class in BioPortal, we try to populate and display a set of what we refer to as “standard BioPortal properties”, which includes:

Class ID
Preferred Label
Semantic Types

You will see these as top-level entries in the JSON results.  Any other properties, which we refer to as “user defined”, will appear in the nested “properties", i.e.:

<Screenshot 2017-05-16 10.24.49.png>

Hope that helps.

Kind regards,

On May 16, 2017, at 6:56 AM, jason marr <jmarr1990 at<mailto:jmarr1990 at>> wrote:

Thanks so much! Was able to switch over to the REST api instead of the sparql endpoint. One question, when I pull a class I was expecting the properties of that class, this does not seem to be the case. I'm currently searching for the children of a top level term, and parsing the results. I tried the term search as well, still the same result. Where exactly is the following data stored:
when i query the term I get:

I'm not seeing those terms in the picture in the result, maybe in the mapping?

Thanks for your help!

On Thu, May 11, 2017 at 3:31 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:
Hi Jason,

I assume you’re referring to the BioPortal SPARQL endpoint?  We published that as a beta service several years ago, but haven’t had the resources to keep the data up-to-date.

Alternatively, we actively maintain a REST API for accessing the most recent BioPortal data.  You can find information about the various submissions of NCIT using this call:

The highest ID is the latest submission.  Or, you can see information about the latest submission using this call:

Any other calls you make to retrieve NCIT content are executed against data from the latest submission, e.g.:

… retrieves class data from the latest submission.

The REST API is documented here:

Kind regards,

On May 11, 2017, at 6:32 AM, jason marr <jmarr1990 at<mailto:jmarr1990 at>> wrote:

I see there are multiple versions of the NCIT ontology show by using the following query:
"PREFIX omv: <>

SELECT ?ont ?name ?acr
?ont a omv:Ontology .
?ont omv:acronym ?acr .
?ont omv:name ?name .
  FILTER regex(?name,  "NCI")

I'm assuming the results returned by that are simply the versioned ontologies highest number being the newest. But when to query the NCIT ontology I use:
So my question is does that ^^ route to the latest revision of NCIT? or are the versions returned in first query outdated and NCIT resolves to the latest? I don't see anything in the doc about this.

Thanks for the clarification,
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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