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

Clement Jonquet jonquet at lirmm.fr
Mon Mar 17 08:01:45 PDT 2014


Hi Ray, all

 

We had that issue a few years ago when using the “filtering by semantic type” option of the Annotator.

This was happening on every ontologies that is in the UMLS but not imported in BP via the UMLS loader. 

 

At that time, we did a patch for each ontology concerned.

One way to fix this would be, when an ontology is uploaded in BP and selected as part of the UMLS group,  to offer a field to select which property is the CUI and which property is the TUI or STY (not the id but the  string for semantic types).

Similar to what we do with label property etc.

Maybe in the future, you will have request to ‘import’ other property from UMLS.

 

When uploading NCIT (from the Owl version), Sherri would just have to select:

CUI_property = P207

STY_property = P106

TUI_property = none

 

Bye

Clement

 

De : bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] De la part de Ray Fergerson
Envoyé : vendredi 14 mars 2014 01:18
À : Lee M Surprenant; support
Cc : De Coronado, Sherri (NIH/NCI) [E]
Objet : Re: [bioontology-support] NCIT concepts missing cui and semantic type via REST API

 

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=all

However, 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 its gotta be getting it from somewhere…

Is it a known issue?

thanks,

Lee Surprenant
IBM Emerging Technologies | jStart Team
lmsurpre at us.ibm.com <mailto:lmsurpre at us.ibm.com>  | (919) 543-8919

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