Re: use case clarification - cross format annotations

Hi Frederick,
comments in line

On Wed, Dec 3, 2014 at 6:52 AM, Frederick HIrsch <>

> Paolo
> Thanks for providing a use case on the wiki -
> I think what you are saying is that the same document can be provided in
> different formats (e.g. HTML or PDF) at different portals (e.g. PubMed
> Central vs authors personal web site etc) - I guess different portals could
> also offer the same format with different URLs as well.

Correct. This is a very common scenario for scientific papers, one of the
main resources I annotate.

> The use case also says that sometimes these various targets should be
> treated as the same despite having different URLs and sometimes should be
> treated as different, depending on user choice.

Correct. For instance if I annotate with Domeo an HTML version, I want to
see the same annotations on my PDF version through the Utopia client. This
is in fact already implemented through the Annotopia server:

> Thus I have  questions
> - how can a system know that two documents are different representations
> of the same document when they have different URLs?

When tools like Domeo and Annotopia see a document, the first thing they do
is capture available IDs. Domeo looks up for DOIs, PMIDs, PMCIDs, PIIs and
so on. When sanding the annotation to Annotopia, the bibliographic data are
sent as description of the target document. This is done by reusing
existing vocabularies/ontologies.

> - why would a end-user want only to provide annotations for a specific
> representation of the same target and not have it apply to all versions?

It depends what is the task. If the task is to compare output formats you
might want to do that. Also different formats might be different in layout
and the annotation might be related to that.
In general, it is important to know exactly which variant motivated the
annotation so that the process can be fully understood.

> - should we simplify the use case to how to share annotations for a target
> that has multiple instances with different URLs.

I guess so. Keeping in mind that one URL can refer to HTML and one to PDF?

> It seems the big issue here is that different URLs might refer to the same
> target, and how to handle that.

Yup. In my case I incorporate bibliographic data in the annotation. In
alternative something else need to do that job of finding that out.

> I know I’m jumping ahead, but thought I’d ask now.

Good you asked :)

> regards, Frederick
> Frederick Hirsch
> @fjhirsch

Dr. Paolo Ciccarese
Assistant Professor of Neurology, Harvard Medical School
Assistant in Neuroscience, Massachusetts General Hospital
Senior Information Scientist, MGH Biomedical Informatics Core

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Received on Wednesday, 3 December 2014 13:27:37 UTC