Hi Steffen, Andreas, - Thanks for the clarification regarding the mirror. I thought there was a mirror because I read this in the edam.sh comment: " This script lives on https://salsa.debian.org/blends-team/website/commits/master/misc/sql/edam.sh and a redundant copy is held on https://github.com/bio-tools/biotoolsConnect.git/DebianMed/edam.sh "
- regarding the fact of reusing the output of edam.sh rather than a single python script, I wholeheartedly agree. I just focused at first on a minimal working workflow, but time permitting, I'd like to clean up a bit and have a single python tool - regarding EDAM annotations, one source you could possibly use is bio.tools, for the packages which are already cross-linked between debian and bio.tools. Anyway, thanks a lot for your help, I am so very happy this is now up and running! We should set up a plan to continue this work! Best, Hervé On Sat, Jul 25, 2020 at 5:15 PM Steffen Möller <[email protected]> wrote: > 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. > > >
