Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Versioning Question

Jennifer Leigh Vendetti vendetti at stanford.edu
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 stanford.edu]


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

http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34055?display_links=false&display_context=false&include=prefLabel<http://data.bioontology.org/ontologies/NCIT/classes/http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C34055?display_links=false&display_context=false&include=prefLabel>

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

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


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

Quick Question, Why is the following giving me an internal server error?
http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34055?include=id

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

On May 16, 2017 1:39 PM, "Jennifer Leigh Vendetti" <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> 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:

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.:

<Screenshot 2017-05-16 10.24.49.png>

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
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170524/311be486/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2017-05-23 17.53.30.png
Type: image/png
Size: 326519 bytes
Desc: Screenshot 2017-05-23 17.53.30.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170524/311be486/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2017-05-23 17.55.53.png
Type: image/png
Size: 22696 bytes
Desc: Screenshot 2017-05-23 17.55.53.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20170524/311be486/attachment-0003.png>


More information about the bioontology-support mailing list