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[bioontology-support] SNOMED CT Properties

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Sep 23 17:47:00 PDT 2020


Hello Daniel,

I’m not aware of a way that you could get triples directly from the REST API.

It’s perhaps worth mentioning though, that it’s a hypermedia style API. For example, when you retrieve the “Dementia” class (http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006), the API returns a set of links that allow you to navigate to related content, e.g., the containing ontology, parent classes, child classes, etc.:


[cid:A3A88E4A-3449-413F-96AA-AEE60D04A828 at stanford.edu]


Furthermore, if you were to retrieve the properties of the “Dementia” class, you can examine the property values to see the sort of Class property Class and Class property somethingElse relationships you mentioned:


[cid:08934458-02B3-4CD6-B1D5-4C3C1F280375 at stanford.edu]
 Kind regards,
Jennifer



On Sep 23, 2020, at 2:34 PM, Daniel Martinez <d.martinez1 at uniandes.edu.co<mailto:d.martinez1 at uniandes.edu.co>> wrote:

Hello Jennifer

Thank you for your response. I have an additional question. Is there some way to retrieve triples via the REST API?

For example, Class property Class or Class property somethingElse?

Thank you again,

Daniel

De: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Enviado el: miércoles, 23 de septiembre de 2020 11:21 a. m.
Para: Daniel Martinez <d.martinez1 at uniandes.edu.co<mailto:d.martinez1 at uniandes.edu.co>>
CC: support at bioontology.org<mailto:support at bioontology.org>
Asunto: Re: [bioontology-support] SNOMED CT Properties

Hello Daniel

We’ve not had the resources to maintain the open SPARQL endpoint, and the data therein is very outdated.

You can use our REST API (which we are actively maintaining) to retrieve the properties for said class. One example of a REST call that retrieves properties is:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006?include=all<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006%3Finclude%3Dall&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854079607&sdata=ENjlRok56QNF4WkDm1Vo6Ri2TP2FxoFebp%2FWhodGPIA%3D&reserved=0>

… or, you could do something pared down / more performant like this:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006?include=prefLabel,properties&display_links=false&display_context=false<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FSNOMEDCT%2Fclasses%2Fhttp%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006%3Finclude%3DprefLabel%2Cproperties%26display_links%3Dfalse%26display_context%3Dfalse&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854089605&sdata=zRpM8ArqanNfwVy6H%2BbPmr%2BNaE6nQIIObIkBhOvKvew%3D&reserved=0>

Our REST API is documented here:

http://data.bioontology.org/documentation#nav_home<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fdocumentation%23nav_home&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854089605&sdata=d73G22B%2B5XgCQBuhYBK3bOvPRYSFT6%2BKrGVsa1e1cgw%3D&reserved=0>

You’ll need an API key to use the API. Instructions for getting one are here:

https://www.bioontology.org/wiki/BioPortal_Help#Getting_an_API_key<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bioontology.org%2Fwiki%2FBioPortal_Help%23Getting_an_API_key&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854099590&sdata=A%2BdfSCa%2Bumncy2W0IH%2FzawI60Zy15tZXtpjP56aBimQ%3D&reserved=0>

Kind regards,
Jennifer



On Sep 22, 2020, at 2:12 PM, Daniel Martinez <d.martinez1 at uniandes.edu.co<mailto:d.martinez1 at uniandes.edu.co>> wrote:

Hello,

I’m doing this query on Bioportal Endpoint, to retrieve the properties of the class http://purl.bioontology.org/ontology/SNOMEDCT/52448006<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854099590&sdata=2Po7XeMccVuLwYtT%2FRwdVIZGmCs2cp2%2BhwXQtA2OekM%3D&reserved=0>

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854109583&sdata=DEv%2B178P4mD4hDGj81kB%2BWNiJXFCDelhWPzH9MGBBnQ%3D&reserved=0>>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C0%7C637364748854109583&sdata=pIjcdg%2BBb6MehXPKbwQCphOojIiiyjMhhJUuJW2QRvc%3D&reserved=0>>

SELECT DISTINCT ?p WHERE {
  GRAPH <http://bioportal.bioontology.org/ontologies/SNOMEDCT<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854119580&sdata=oUP1kKFJwyStfuRLFQS0adJ63x7hLU%2FmNJtOILddlCQ%3D&reserved=0>> {
         <http://purl.bioontology.org/ontology/SNOMEDCT/52448006<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F52448006&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854119580&sdata=u%2B9jdCsnsD04lpNddpJyuES0NoCAjV2jVVApzO%2FOioQ%3D&reserved=0>> ?p ?o .
  }
}

In the results I get, I can see some of the properties, but not all of them. For example, in the class Webpage there is the property
Cause of
Epilepsy co-occurrent and due to dementia<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FSNOMEDCT%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org%252Fontology%252FSNOMEDCT%252F724992007&data=02%7C01%7C%7Cd8314475d44c4f458af008d85fdcb66a%7Cfabd047cff48492a8bbb8f98b9fb9cca%7C1%7C1%7C637364748854129578&sdata=d5ZSWuUN6UoKNWxLJyzU1QRsTXFvPw%2FHwB8iW5NOHH8%3D&reserved=0>

But in the query results this property doesn’t appear.

Can you please tell why is this? Or am I writing and incorrect query?

Thank you very much

Daniel
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