Please add Debian Med annotations to the "Community usage"

[matuskalas]

From UDD. @tillea made a script that pulls all the EDAM annotations from there.

Please contact the debian-med mailing list or @tillea if help needed.

[bryan-brancotte]

Hi @matuskalas
Do you have any link where the usage are displayed ?

[tillea]

On Mon, Jul 02, 2018 at 08:31:18AM +0000, bryan brancotte wrote: Do you have any link where the usage are displayed ?

$ edam.sh -h Usage: ./edam.sh [option] -h print this help screen -j JSON export -m forcing public mirror over local one Description: Query local or public UDD for information that could be useful for EDAM.

[bryan-brancotte]

Hi @tillea
I think the attachment was lost during the conversion email->issue.
Note that the "Community usage" rely on webservice in order to display up-to-date informations, which was the reason for me asking for a website with software associated with edam terms

[tillea]

On Mon, Jul 02, 2018 at 08:47:52AM +0000, bryan brancotte wrote: I think the attachment was lost during the conversion email->issue.

There was no attachment. Matus was refering to https://github.com/bio-tools/biotoolsConnect/blob/master/DebianMed/edam.sh and I just "explained" the usage.

[bryan-brancotte]

Hi, thanks for the link. For now we only rely on REST webservice, and web crawling. If you are aware of the existence of one of them for Debian Med feel free to post it here and re-open the ticket.

[tillea]

On Thu, Jul 05, 2018 at 01:06:21AM -0700, bryan brancotte wrote: Hi, thanks for the link. For now we only rely on REST webservice, and web crawling. If you are aware of the existence of one of them for Debian Med feel free to post it here and re-open the ticket.

May be that's a misunderstanding. My script is by NO means a SERVICE. I just gave an EXAMPLE who you can query UDD for relevant data. I assumed Matus had propagated the message that it is NO ready TOOL. You should rather adapt the SQL code and adapt it to some REST service. But that's not my field of work - I simply wanted to help out with UDD internals by this query. Hope this clarifies things - your decision whether you reopen the issue or not. Kind regards, Andreas.

[matuskalas]

This is still something we definitely want, although I'm fully aware that it will be untrivial. However:

• the Tools Ecosystem (https://github.com/bio-tools/content) may help
• and/or Debian (Med/Sci) may want to have a search API that enables a UX-friendly & application-friendly way of searching for packages, including search by EDAM (CC @smoe)