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

John Graybeal jgraybeal at
Fri Apr 17 09:57:14 PDT 2020

Hello Andreas,

I think this question is ideally asked of the SNOMED CT organization. We are not lawyers, and our users need to resolve legal and licensing questions directly with the providers who have specified the license. (Also, we have no idea what the legal system says in your non-member territory.)

I would just note, as a lay person, that a literal reading of the cited language would mean that Google could never put up a web page (which relies on record systems, databases, *and* documents) that contain a SNOMED CT identifier. So, no public resource could ever put up a web page with such an identifier. So, there could never be any posted discussion of SNOMED CT identifiers. Which would fairly clearly violate fair use legal standards in the United States, but your situation in a non-member territory would be different.

That may or may not have any implications for your application. As a practical matter, it would inform how I would interpret this kind of narrow use of a secondary provision of the identifier. (If I had to. Which I don't, because, see first paragraph.)

Hope this helps your process. Best wishes for your thesis.


On Apr 16, 2020, at 10:41 AM, Andreas Benndorf <s1anbenn at<mailto:s1anbenn at>> wrote:

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

  1.  Send the document text to the annotator endpoint using the MEDDRA ontology.
  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 information.

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 CT® 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
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

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