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In its anatomy browser BioDigital has a feature where the website displays text that it doesn't license under CC BY-SA. At the end of that text the user can click on "Read more". If he does an inline popup appears showing information from Wikipedia mobile. This popup refers at it's end to being licensed CC-BY-SA.

Is it in compliance with the CC BY-SA license to use content this way? Can they show CC BY-SA licensed content from Wikipedia while showing on the same screen content that they don't license under CC BY-SA?

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Usual caveat: IANAL/IANYL, but as far as I can determine, it's fine. Displaying two things side-by-side on a web page no more makes either a derivative work of the other than putting two pieces of content on a DVD, and giving that to you, does. In the latter case, the GPL (v2, in this case) refers to this as mere aggregation, and notes that

mere aggregation of another work [...] with the Program [...] on a volume of a storage or distribution medium does not bring the other work under the scope of this License.

To my mind, as long as all content is clearly labelled with its licence, so you can determine which content is free and which is proprietary to the publisher, no further licensing issues are implicitly engaged.

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