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I must admit I agree with the meta-review, I think the reviews are fair in that the article reads more like an Application Note or technical report, and would benefit from a stronger evaluation and justification of its novelty.
I don't think details like the flow diagrams are needed, also the pretty publishing mode pictures feel out of place . The technical work seems sound and very promising - this kind of move towards collaborative and distributed easy-to-use semantic publishing is exactly what is needed to revive academic publication for the 21st century.
I would have appreciated a stronger focus on provenance and attribution, e.g. FOAF is mentioned - strong identification of authors should be even more important in a distributed model, so I would have expected some relation to ORCID - which RDF representations provides FOAF and PROV descriptions of people (and currently planning integration with SPAR ontologies).
Similarly versioning is not mentioned, and a dokieli paper that is published online in a distributed manner (possibly even at multiple locations) and subject to collaborative editing would naturally have many different versions (e.g. pav:hasVersion), which could make it hard to cite which version has actually been reviewed, published, updated, etc.
It would also be important to relate these versions to each-other so you could know when to talk about the "same paper" in a more abstract sense, as with prov:specializationOf or SPAR FaBiO's use of FRBR relations between Work/Expression/Manifestation/Entry - this would particularly become relevant when a dokieli paper is accepted by a more traditional publisher which assign it's own DOIs and republishes the text (the Expression) in a slightly different Manifestation (probably breaking most of the RDFa links) at a different Entry (new URL).
One strong argument for semantic scholarly publication is that you have the possibility to break down the strong barrier between the article text and the traditional supplementary material, as you gain the possibility of a closer integration of data and visualizations from within the dokieli article - as the author has previously shown. One big challenge here is that the boundary of the article becomes blurred - some kind of aggregation of resources that constitute the article in the form of a research object or similar would help to mark out what is the scholarly unit that is actually being proposed for review, publication and citation - and also to help attribution-wise as you can break down what authors contributed where.
For example, it is not clear to me that non-SemWeb researchers are interested in adding RDFa annotations. If that is true (and this is just an hypothesis), how can we encourage them
FYI: im a sem web developer, but not researcher, and I used this system to add RDFa before, just a data point ...