Re: debian/upstream/edam on wiki Re: added notion of edam to https://wiki.debian.org/debian/upstream
Excellent. We have a bio.tools issue for this, and I've assigned it to you to lead, Matus (forgive my rude presumption :)
https://biotools.sifterapp.com/issues/32
As for schema - please fire away! But that's a discussion probably for registry-core list (do you want in, by the way
Steffen? See bio.tools/governance. You don't have to sell your soul :)
Cheers
Jon
> 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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