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[bioontology-support] Versioning Question

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 16 10:39:38 PDT 2017


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:

http://data.bioontology.org/documentation#nav_usage

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

http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34122?include=all<http://data.bioontology.org/ontologies/NCIT/classes/http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C34122?include=all>

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
Synonyms
Definitions
Obsolete
CUI
Semantic Types
Parents

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.:

[cid:FF910EF6-A29B-42E0-BDAE-F7255DB2364B at stanford.edu]

Hope that helps.

Kind regards,
Jennifer



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

Jennifer,
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:
<image.png>
when i query the term I get:
http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34122

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

Thanks for your help!
Jason


On Thu, May 11, 2017 at 3:31 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> 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:

http://data.bioontology.org/ontologies/NCIT/submissions

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

http://data.bioontology.org/ontologies/NCIT/latest_submission

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

http://data.bioontology.org/ontologies/NCIT/classes

… retrieves class data from the latest submission.

The REST API is documented here:

http://data.bioontology.org/documentation

Kind regards,
Jennifer




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

I see there are multiple versions of the NCIT ontology show by using the following query:
"PREFIX omv: <http://omv.ontoware.org/2005/05/ontology#>

SELECT ?ont ?name ?acr
WHERE {
?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:
"
FROM <http://bioportal.bioontology.org/ontologies/NCIT>
"
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,
Jason
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