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[bioontology-support] NCIT concepts missing cui and semantic type via REST API

Ray Fergerson ray.fergerson at stanford.edu
Thu Mar 13 17:18:18 PDT 2014


This is confusing. Fortunately the problem is limited to NCIT and one or two 
other ontologies. The story is more than you want to hear.



The UMLS folks assign CUI’s and Semantic Types to terms in UMLS ontologies 
before they become part of the UMLS distribution. We however do not get our 
version of NCIT from the UMLS distribution. By agreement with NCI, we get 
the latest version directly from NCI. NCI adds in CUI and Semantic type 
information into their ontology before we get it. Unfortunately, the 
information is added in a way that is different than the way that UMLS adds 
it. We only recognize CUI’s in the property that UMLS provides. Thus they do 
not show up as a CUI.



However… the field that NCIT uses is available in the “properties” section 
of the returned data. The Semantic type property is #P106 in the NCI 
Thesaurus and looking there we indeed find the semantic type.



Semantic Type:



"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P106": [

·         "Neoplastic Process"

],



Likewise for CUI:



"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P207": [

·         "C0025202"

],



Thus you can get what you want, but it is not straightforward. I will get 
with the NCI folks, copied on this message, to see if we can do better than 
this, but for now, you will have to work around it.



Ray







From: bioontology-support 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Lee M 
Surprenant
Sent: Thursday, March 13, 2014 2:20 PM
To: support
Subject: [bioontology-support] NCIT concepts missing cui and semantic type 
via REST API



How do I retrieve the UMLS_CUI and Semantic Type from an NCI Thesaurus 
concept?
I thought that the following would work:
 <http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224?include=all>http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224?include=allHowever, the result appears as follows:  "prefLabel": "Melanoma",  "obsolete": false,  "children": [ … ],  "parents": [ … ],  "synonym": [ … ],  "definition": [ … ],  "label": [ … ],  "prefixIRI": "C3224",  "notation": null,  "semanticType": [ ],  "cui": null,  "xref": null,Note that this same information is being displayed on the Web UI, so itsgotta be getting it from somewhere…Is it a known issue?thanks,Lee SurprenantIBM Emerging Technologies | jStart Teamlmsurpre at us.ibm.com | (919) 543-8919
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