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Aw: Re: Lets talk about debian/upstream/edam (Was: r18733 - in trunk/packages/bowtie/tags: . 1.1.1-2/debian 1.1.1-2/debian/upstream)

Hi Andreas,

> On Tue, Feb 03, 2015 at 03:32:12PM +0100, Hervé Ménager wrote:
> > >Charles had removed the file which was recently added at the sprint - I
> > >guess because he was not aware about its nature.  I think before those
> > >files will be added we should talk about it and send a short
> > >introduction to the list.
> > 
> > I completely agree with you, and I am sorry if any of my actions
> > actually disturbed the work of debian team members.
> As Charles meanwhile confirmed it was no real problem.

That was my fault. If I recall correctly, I had stored that 
playground-work of Tim and mine in that folder rather keeping it
separate while things are still evolving. Sorry, Charles.

> > >Hervé, Steffen, would you be so kind to do this?
> > 
> > I would suggest that I write a draft for such an introduction, then
> > validate it with Andreas, Steffen and Jon Ison before to send it.
> > What about it?
> Either this or discussing it right on the mailing list.  IMHO it is the
> right forum.

That is much appreciated. It is not that the Debian Med community was
left uninformed before, e.g. there was a report of Tim and mine while
still in Copenhagen, and we had a report from the 2014 Stonehaven Sprint
on it, if I am not erroneous. We just did not yet initiate any joint
annotation spree that would yield many debian/upstream/edam files,
yet. It is just all still work in progress and the EDAM ontology will need
to develop along our annotations and, which makes the involvement of
Debian so tantalising, to match all our diverse domain knowledge.
Those emerging EDAM annotations in my mind pave an acceptance of a
community-run Linux distribution as a regular means to share scientific
infrastructure, so I am really excited about this development.
> > >which is completely available in UDD you most probably are suffering
> > >from an unfortunate design for the problem you want to solve.  I admit
> > >I'm coming up a bit late with this since the Sprint is over but I have
> > >realised this right now.  We should have definitely talked about the
> > >usage of UDD which contains *all* machine readable metadate about our
> > >packages in a very easily accessible form.
> > 
> > If UDD contains all the metadata, then yes, I'm all in favor of
> > this! I really like parsing files, but if there is already a unified
> > source for this, I'll have a look into it.
> The different sources of information are just parsed and assembled in
> UDD.  Any additional parsing is IMHO duplicated work and error prone.

You have more of an overview on what the UDD can do, so just guide us,
please. From what I have grasped so far, we should not attempt to bring
the EDAM annotation into the UDD since any ontological description of
Debian packages should be agnostic to the ontology used. I am exceptionally
happy about the debian/upstream/[packagename.]edam solution so far and
would leave any integration of that information in a database to the
ELIXIR effort. That said, I am also completely for a normalised effort
and there should be no redundancy between  debian/upstream/metadata and
debian/upstream/edam. Any parsing code for debian/upstream/metadata that
was created for the UDD may possibly be shared with the code needed to
fill the ELIXIR catalog - I would just prefer working with the files in
the repository more. The parsing of the edam YAML file is, thanks to
Hervé, a non-issue.



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