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[bioontology-support] [BioPortal] Feedback from davidnarganes

David Narganes (PG Research) d.narganes at dundee.ac.uk
Thu Feb 7 03:08:59 PST 2019


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:
REST: http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2<http://data.bioontology.org/ontologies/SNOMEDCT/classes/64572001/children?page=2&apikey=6963294e-e7e4-44fa-8093-b893b8666dc0>

but I found them here:
http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=271737000

Thanks again.

Best regards,

David


________________________________
From: Michael Dorf <mdorf at stanford.edu>
Sent: 07 February 2019 02:27
To: support at bioontology.org
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?

http://sparql.bioontology.org/

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:
http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/children<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/64572001/children>

All descendants:
http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F64572001/descendants<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/64572001/descendants>

For more info on our REST API, navigate here:

http://data.bioontology.org/documentation

Hope this helps!

Michael


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


Name: davidnarganes

Email: dnarganes at dundee.ac.uk<mailto:dnarganes at dundee.ac.uk>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3D404177007

Feedback:

email: david.narganes95 at gmail.com<mailto:david.narganes95 at gmail.com>
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,
David

SPARQL query:
```
PREFIX rdfs:
PREFIX rdf:
PREFIX snomedct:
PREFIX skos:

SELECT DISTINCT ?x ?label ?syn
FROM
WHERE
{
?x rdfs:subClassOf* snomedct:64572001 .
?x skos:prefLabel ?label .
?x skos:altLabel ?syn
}
ORDER BY ?label
```

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