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[bioontology-support] Commercial License for Annotations needed or not

John Graybeal jgraybeal at
Mon Jun 24 08:56:04 PDT 2019


Several things must be considered in determining whether you can use BioPortal and its ontologies. The existing BioPortal Terms of Use are at; if you haven't read them already, please do so. We are about to update these Terms of Use, so members of the community are encouraged to contact us with any requests and concerns.

First, the existing BioPortal Terms of Use do not permit commercial or clinical use of the service. There are several reasons for this:
 1) Our service at Stanford University is not capable of sustaining the level of requests required to satisfy regular commercial users.
 2) It is expensive for us to provide this service, and we can not afford to make it freely available to all those who might want to use it in their commercial pipelines.
 3) We have neither governmental approval in the US, nor the necessary investment in the software and its operations, to make it appropriate to use in clinical settings.

If you have a use case which is commercial but not clinical (in the US regulatory sense of 'clinical'), we encourage you to contact us directly about service licensing terms that we can offer, whether for a service we operate, or for downloading and using our Virtual Appliance.

Note that if you download the Virtual Appliance that addresses issue (1) above, but not issues (2) and (3). It would also give you a way to easily manage which ontologies are used in your service, so you could exclude ones for which you don't have licenses (or don't have a need).

Regarding ontologies, additional information about their use can be read in the Terms of Use agreement. To summarize the key point, if there is no "License Information" field in the Summary page of the ontology, or the License Information field is empty, the ontology is made freely available to the public, and you do not have to worry about 'getting a license'. If there is licensing information provided, you have to look up and follow the terms of that are described or referenced. (Most of the terms refer to the UMLS licensing agreement, which is extremely difficult to parse, but we can't give you advice about that.

Finally, I can not offer legal advice anyway, but I note the interpretation of these terms for users who are not in the United States may require special knowledge. (For one example, the SNOMED licensing is country-based.) So you may want to contact a lawyer to discuss your specific situation.

I am sorry that this is so complicated; I hope that some of it may become less complicated with our new Terms of Use. But for commercial use in a clinical setting, I imagine this will always be complicated (at best), at least in the United States.


On Jun 24, 2019, at 2:27 AM, Rayyan Aziz Ansari <r.ansari at<mailto:r.ansari at>> wrote:

I plan to use the Annotator plus to get clinical annotations on doctors notes. I plan to filter/tag using UMLS semantic groups. If i am using this commercially, I am confused about licensing.
Do I have to get a license for ALL possible ontologies that might show up?! that would be unlikely since there are so many.
P.S. I just plan on getting annotations / clinical term recognition and that's all.
Thanks for the information,
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

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