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[bioontology-support] Question about "synonyms" in LOINC

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Apr 14 14:29:52 PDT 2017


Hi Jessie,


On Apr 13, 2017, at 8:33 AM, Jessie Tenenbaum, Ph.D. <jessie.tenenbaum at duke.edu<mailto:jessie.tenenbaum at duke.edu>> wrote:

Hello-

Can you help me understand these 3 different terms from LOINC for “Blood Pressure”? They all map to the same CUI (is that the UMLS ID?) but seem to have 3 unique LOINC IDs

http://purl.bioontology.org/ontology/LNC/LP90874-6

http://purl.bioontology.org/ontology/LNC/LP40259-1
 http://purl.bioontology.org/ontology/LNC/MTHU008342


LOINC is imported into BioPortal from the UMLS.  Each time the UMLS is released, we have a program that converts data from the UMLS database into RDF that can be consumed by BioPortal.  The code for that program is open source and available via our GitHub repository:

https://github.com/ncbo/umls2rdf

I took a look at the ontology source file for LOINC that was generated by the above program.  All 3 of these terms are declared as classes:

Snippet of LP90874-6 declaration:

<http://purl.bioontology.org/ontology/LNC/LP90874-6> a owl:Class ;
skos:prefLabel """Blood pressure"""@eng ;
skos:notation """LP90874-6"""^^xsd:string ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/8357-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/9855-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/8358-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/9856-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/9857-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/9858-2> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/18684-1> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/18685-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/28139-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/34538-9> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/34553-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/35094-2> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/43152-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/41902-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/41904-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/41901-0> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/41903-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/45372-0> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/50402-7> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/50403-5> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/55284-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/55417-0> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58294-0> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58296-5> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58297-3> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58298-1> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58300-5> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58301-3> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/58295-7> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/62392-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/62393-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/64206-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/64496-3> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/66238-7> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/71789-2> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/71895-7> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/71896-5> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/72075-5> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/72076-3> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/72165-4> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/72164-7> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/76539-6> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/76538-8> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/76537-0> ;
<http://purl.bioontology.org/ontology/LNC/fragments_for_synonyms_of> <http://purl.bioontology.org/ontology/LNC/76532-1> ;
umls:cui """C0005823"""^^xsd:string ;
umls:tui """T040"""^^xsd:string ;
umls:hasSTY <http://purl.bioontology.org/ontology/STY/T040> ;

Snippet of LP40259-1 declaration:

<http://purl.bioontology.org/ontology/LNC/LP40259-1> a owl:Class ;
skos:prefLabel """Blood pressure"""@eng ;
skos:notation """LP40259-1"""^^xsd:string ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/8357-6> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/9855-8> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/18684-1> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/18685-8> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/28139-4> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/34538-9> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/34553-8> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/35094-2> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/43152-8> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/41904-4> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/45372-0> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/50402-7> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/50403-5> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/55284-4> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/55417-0> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58294-0> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58296-5> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58297-3> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58298-1> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58300-5> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58301-3> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/58295-7> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/62392-6> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/62393-4> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/64206-6> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/64496-3> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/66238-7> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/71789-2> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/71895-7> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/71896-5> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/72075-5> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/72076-3> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/72165-4> ;
<http://purl.bioontology.org/ontology/LNC/component_of> <http://purl.bioontology.org/ontology/LNC/72164-7> ;
umls:cui """C0005823"""^^xsd:string ;
umls:tui """T040"""^^xsd:string ;
umls:hasSTY <http://purl.bioontology.org/ontology/STY/T040> ;

Snippet of MTHU008342 declaration:

<http://purl.bioontology.org/ontology/LNC/MTHU008342> a owl:Class ;
skos:prefLabel """Blood pressure"""@eng ;
skos:notation """MTHU008342"""^^xsd:string ;
<http://purl.bioontology.org/ontology/LNC/associated_with> <http://purl.bioontology.org/ontology/LNC/18684-1> ;
umls:cui """C0005823"""^^xsd:string ;
umls:tui """T040"""^^xsd:string ;
umls:hasSTY <http://purl.bioontology.org/ontology/STY/T040> ;


Yes - the CUI is the UMLS CUI.




I’m wondering why they differ, where they come from, and why they do not render within the hierarchy of LOINC- selecting them after searching shows them as a sibling of top level concepts. (see below)


With regard to the rendering, none of these classes have rdfs:subClassOf declarations.  It appears that the classes are indexed by our system and show up in search results, but don’t appear initially in the tree hierarchy due to the lack of subClassOf declarations.  The decision to insert the class at the top-level of the tree (making it appear as a sibling) after being selected in the “Jump To:” box is code that predates my arrival in the group.  So, not sure I have anything enlightening to say here, other than we probably needed a place to put it when someone selects it.

In terms of where these terms come from and why they differ, I’m not sure.  What I usually do in these cases is go to the UMLS Metathesaurus Browser to see if the terms are listed there, but I tried logging in and it looks like our license has expired.  So, I’ll need to get that renewed before I can double-check their content.



While I’m asking, can you also tell me how “Associated with” is populated? It too differs between the 3.


I looked at all 3 of the blood pressure terms in BioPortal, and I can only see one with an associated_with property.  Are you seeing something different?

Jennifer


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