Hi Steffen To get the EDAM annotations, it could be much more straightforward to wait until the SEQwiki tools imported into bio.tools (this right now is the #1 content priority) and then export to DebianMed of the descriptions from there (using the format/tool that Hervé was leading discussions on at the Sprint).
Matus will be on-hand in NO and hopefully can help take it forward. Cheers Jon > Hi Jon, hi Andreas, > > On 09/03/16 22:45, ji...@cbs.dtu.dk wrote: >> Thanks for this work, folks. >> >> The ELIXIR bods have been swamped since the sprint; March is also >> horrendous: this situation will improve in April! >> Watch >> this space ... :) > It seems like I will make to Trondheim next week. If so then it would be > nice if you could summon someone (or have reserve time locally) to > prepare that we can perform updates of our submissions with Hervé's > upload tool. > > I would also like to start transferring the EDAM annotation from > SeqAnswers. Is there something beyond > https://github.com/bio-tools/biotoolsConnect/blob/master/SEQwiki/ > to start from? My idea was that I just indicate in debian/copyright that > the file debian/upstream/edam has its origins with bio.tools whenever I > take any information from there. > > What I just noticed - while it is easy to have a CC license for a single > file, the upload tool also takes information from debian/control and > debian/copyright, which is typically under the GPL or with whatever the > upstream source license is. This needs some debate, still. We could for > instance introduce a dual license, but this is something the individual > maintainer of the packaging should decide - not allowing the individual > to decide freely would mean a strong opposition. For most uploads there > will be packages already described in bio.tools, just with a different > source, so the information uploaded is already redundant. One would just > like to tag an existing entry with the notion that there is also a > Debian package available. I remember your current API not to be prepared > for that, still, this would come handy, both for a reduction of labour > and concerns on conflicting licenses. > >> Andreas: >>> On Wed, Mar 09, 2016 at 06:55:44PM +0100, Steffen M�ller wrote: >>>> I have now also prepared a more detailed version on >>>> https://wiki.debian.org/debian/upstream/edam >>>> that I hope to help ourselves a bit in organising bits and pieces that >>>> shall help our data flow. >>> Nice. Thanks for this helpful piece of information. I added the -j >>> option of the scriot to this doc. > I had a few pull requests myself. :) >>>> We should possibly also think about preparing an edam Debian package. >>>> This should contain the tools of Andreas >>> Regarding my "tool" I'm not yet convinced that it should be packaged >>> since it is really only an example how to query UDD serving as potential >>> kick-start for writing a tool. Nice that you obviously tried it - I was >>> hoping that our edam partners would take over the ball ... > There are "horses for courses", as I had learned :) It is quite an > impressive query. > > Let them do their homework for the updates of entries and your example > script will find its audience. > > Best, > > Steffen > >