Re: debian/upstream/edam on wiki Re: added notion of edam to https://wiki.debian.org/debian/upstream
Hi Jon,
On 10/03/16 15:51, jison@cbs.dtu.dk wrote:
> To get the EDAM annotations, it could be much more straightforward to wait until the SEQwiki tools imported into bio.tools
Hm. Right. Can wait, indeed.
> (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).
Right. I was discussing with Matus yesterday that we should craft some
dh_edam tool to facilitate the creation of those files.
["dh" is a common prefix for "debian helper" tools.]
That tool should get a reference entry from which to retrieve the
annotation.
> Matus will be on-hand in NO and hopefully can help take it forward.
We might need to think for a moment on provenance of annotation in
bio.tools. And I have a few comments on how to adjust your schema to
facilate the merging of data from multiple sources. No idea about how
much you want to hear about it, though :)
Best,
Steffen
>
>> Hi Jon, hi Andreas,
>>
>> On 09/03/16 22:45, jison@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
>>
>>
>
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