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[bioontology-support] Usage of Semantic Types via BioPortal REST-API

Andreas Benndorf s1anbenn at
Thu Apr 16 10:41:21 PDT 2020

Dear Sir or Madam,


in my master's thesis I am developing a Named Entity Recognition system that
can retrieve, inter alia, health care activities and diseases in text

For the recognition I will use the BioPortal REST-API as follows:

1.	Send the document text to the annotator endpoint using the MEDDRA
2.	For every found term in the text, look up the semantic type in the
returned JSON file and distinguish with the aid of several semantic types
whether the term is a health care activity or a disease. For this, some
constants are used in my program for several semantic types like "Sign or
Symptom (T184)".
3.	Then the term is saved as an annotation without the semantic type


I don't have a UMLS license and I live in a non-member territory. Is the
described procedure compliant to the Terms of Use of BioPortal?

In particular, I am referring to the following passage of the Terms of Use:


"The sub-licensee is only permitted to access SNOMED CTR using this software
(or service) for the purpose of exploring and evaluating the terminology. 2,
The sub-licensee is not permitted the use of this software as part of a
system that constitutes a SNOMED CT "Data Creation System" or "Data Analysis
System", as defined in the IHTSDO Affiliate License. This means that the
sub-licensee must not use NCBO BioPortal to add or copy SNOMED CT
identifiers into any type of record system, database or document."


MEDDRA allows the usage without a license for a research project. So, this
shouldn't be a problem.

But is the extraction and the distinction of the semantic type from the
response of MEDDRA adding or copying "SNOMED CT identifiers into any type of
record system, database or document" - especially regarding the fact that I
am not saving the semantic type anywhere permanently?


Thank you very much in advance for your response.


Kind regards,

Andreas Benndorf

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