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[bioontology-support] [BioPortal] Feedback from davidnarganes

David Narganes (PG Research) d.narganes at
Fri Feb 8 01:54:02 PST 2019

Hi Michael,

Yes, thanks. It is what I wanted. Nevertheless, I receive an internal server error when querying for all "descendants" of disease AND their "properties":


but it's fine with "descendants" but not "properties":


Don't worry, I got all the altLabels with a webcrawler with the URIs of the descendants.

Many thanks Michael,


From: Michael Dorf <mdorf at>
Sent: 07 February 2019 21:36
To: David Narganes (PG Research)
Cc: support at
Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes

Hi David,

The properties that we don’t store directly in our ontology model are placed in the “properties” collection. You can get these values by adding a few extra parameters to the REST call:,synonym,definition,cui,semanticType,obsolete,properties

Let me know if this is what you wanted.


On Feb 7, 2019, at 3:08 AM, David Narganes (PG Research) <d.narganes at<mailto:d.narganes at>> wrote:

Hi Michael,

Many thanks, I have what I wanted now.

One last thing, the REST services do not contain all "synonyms/altLabels".

E.g. Anemia:

but I found them here:

Thanks again.

Best regards,


From: Michael Dorf <mdorf at<mailto:mdorf at>>
Sent: 07 February 2019 02:27
To: support at<mailto:support at>
Cc: David Narganes (PG Research)
Subject: Re: [bioontology-support] [BioPortal] Feedback from davidnarganes

Hi David,

Thank you for contacting us. Just to clarify, are you attempting to use our publicly available SPARQL endpoint?

If that’s the case, please note that we haven’t been maintaining it consistent with our latest code releases and ontology repository. The data contained in that endpoint is at least five-to-six years old. We have a very small engineering team, and we try to focus our efforts on a path of providing new services with an up-to-date content. Unfortunately, the SPARQL endpoint (at least at present) isn’t on that list.

That said, if you are trying to retrieve subclasses of the term “disease” in SNOMEDCT, the two REST services below are available to assist you. They both return a paginated list that you can iterate over programmatically.

Direct children:<>

All descendants:<>

For more info on our REST API, navigate here:

Hope this helps!


On Feb 6, 2019, at 11:06 AM, support at<mailto:support at> wrote:

Name: davidnarganes
Email: dnarganes at<mailto:dnarganes at>

email: david.narganes95 at<mailto:david.narganes95 at>
Dear Sir/Madame,
I can't use the property path expressions in SPARQL 1.1. Please see ```rdfs:subClassOf*``` in the SPARQL query below. I cannot get all the direct and indirect subclasses of the concept "disease".
Could you please actualise it?
Many thanks,
SPARQL query:
PREFIX rdfs:
PREFIX snomedct:
PREFIX skos:

SELECT DISTINCT ?x ?label ?syn
?x rdfs:subClassOf* snomedct:64572001 .
?x skos:prefLabel ?label .
?x skos:altLabel ?syn
ORDER BY ?label

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The University of Dundee is a registered Scottish Charity, No: SC015096

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