Re: Import of debian med packages metadata to Tools Platform Ecosystem
This is great news, thank you for this, Hervé.
For now I think the most important bit is to have anything that is
automated in some reasonable way. And then let's extend that over time.
This should give edam annotation a particular boost, I tend to think.
You may be aware of an earlier email in which I described the Google
Spreadsheet
https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?usp=sharing
to provide an overview on what packages (rows) are important for which
workflows (columns).
Now imagine what EDAM could do for us along those lines. @Jon,Matúš,
should we possibly do some bulk EDAM annotation just for the packages on
this "virus" tab? I suggest several iterations, like Topics first to
provide the summary scope and I/O+File formats second for the individual
executables once we know more about it all.
Best,
Steffen
On 25.07.20 16:33, Andreas Tille wrote:
> Hi Hervé
>
> On Sat, Jul 25, 2020 at 12:43:08AM +0200, Hervé Ménager wrote:
>> Hello Steffen, everyone,
>> This is to let you know I am currently attending the BCC virtual hackathon (
>> https://bcc2020.github.io/cofest/). With a couple of other people, I have
>> been working on the Tools Platform Ecosystem (
>> https://github.com/bio-tools/content/), continuing among other things the
>> work we have been doing with you and others over the years to integrate
>> metadata from Debian Med packages and bio.tools (among others).
>> I have finalized a first working version of this work, but I took the
>> liberty to modify the biotoolsConnect repository, esp. the script you have
>> created Steffen, to correct a few things. I did so on github (
>> https://github.com/bio-tools/biotoolsConnect) but I know this is a mirror
>> to a repository on Salsa.
> I do not think there is a mirror on Salsa. I've just developed edam.sh
> there as a *simple example*. I admit I'm a bit astonished that
> edamJson2biotools.py is parsing the output of this *example* script
> instead of using the query directly inside the Python script.
>
>> If you need me to do something to synchronize
>> with this other repository, please tell me (and tell me how).
> I think there is no need to syncronise. Its not used there.
>
>> Thanks a lot for your hard work on this subject.
> You are welcome and thanks for your support
>
> Andreas.
>
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