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[bioontology-support] BioPortal: Questions

Samson Tu swt at
Wed Jul 11 23:53:54 PDT 2018

Hi Jennifer,

For me, the question is not whether the Metathesaurus browser display semantic type information of an UMLS concept derived from a terminology. The question is why Bioportal should model semantic type information as part of a terminology’s representation as an ontology, and therefore include STY as part of the ontology. First, when NCBO makes a UMLS-derived terminology available on Bioportal, is the expectation that it has UMLS-augmented relations or that it has only relations that are in the original terminology? Until today I didn’t realize that UMSL-derived terminologies I download from Bioportal have extra concepts that are not in the original terminology. Second, why isn’t it sufficient to encode the semantic types as string annotations (as it does already)? Doing so would avoid the problem of unexpected concepts turning up in search results.

I suspect that there are good reasons for the design choices made in the UMLS-terminology-extraction code. In any case, we probably have to live with the constraints imposed by these choices. It is better that we clarify that UMLS-derived terminologies on Bioportal, by design, have STY included so that semantic type information is explicitly modeled. Those who need a “clean” version probably can adapt the UMLS-terminology-extraction code to get different versions of the terminologies. (Or they need to filter out STY concepts in search results obtained from Bioportal. Or Bioportal search API can do the filtering.)

With best regards,

On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hi Samson,

On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at<mailto:swt at>> wrote:

When I searched NLM’s Metathesaurus browser for “Antibiotic” with ATC as the source terminology, I didn't get STY’s Antibiotic in the results. In that respect Bioportal’s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal’s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?

Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can’t speak with complete authority on this topic. I’ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an “MRSTY” table with an “STY” column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label “RESPIRATORY SYSTEM DRUGS”), and see that they provide semantic type data in the result:

<Screenshot 2018-07-11 16.58.22.png>

It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:

<Screenshot 2018-07-11 17.21.29.png>



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