JervenBolleman/FALDO-paper — pull request #29 by peterjc (2014-11-13 02:32:58+00:00)
Title: More on INSDC compound locations

This splits "Complement strand and INSDC compound locations" into two sections, "Complement strand" and "INSDC compound locations", and expands the text about ``join``/``order`` vs ``ListOfRegions``/``BagOfRegions`` which was previously only hinted at in the implementation section:

There are 3 more classes faldo:CollectionOfRegions and its subclasses) that
are only there for backwards compatibility with INSDC join features with uncertain
semantics. i.e. those join regions where a conversion program can only state that
there are some regions and that the order that they are declared in the INSDC
record might have biological significance.

I've also added a *TODO* comment for adding an example using ``ListOfRegions`` which I feel is currently unclear. Has anyone written the RDF for such an example already?

For "best practice" here (avoid ``ListOfRegions`` by making the exons explicit), can we directly mention/cite the DDBJ/EBI joint RDF Summit held in May 2014, Japan? https://github.com/dbcls/rdfsummit/wiki

Should we also add the RDF Summit to the acknowledgements?

CC @ktym @JervenBolleman @joejimbo @helios @micheldumontier @tfuji (which I think is all the FALDO paper co-authors who were at the RDF Summit)