Re: Requested reminder for Andreas: Put EDAM version into udd
Hi Steffen,
On Thu, Mar 21, 2019 at 04:52:58PM +0100, Steffen Möller wrote:
> Hi Andreas,
>
> On 10.03.19 18:13, Steffen Möller wrote:
> > Many greetings from the Debian Med Sprint - Andreas sits next to me
> > and asked for this reminder. This is also an opportunity to remind you
> > all about the package annotation with the edamontology we are
> > (optionally) doing as described on
> > https://wiki.debian.org/debian/upstream/edam . This annotation is
> > mean to help with the linearisation of tools to form workflows.
> > Eventually.
>
> This is not the email I wanted to have quoted, but, anyway - it is
> pretty close :o)
>
> Do you see a chance to find the reason why the edam_topic
> (https://salsa.debian.org/blends-team/website/blob/fad26b67e7a1f9787d7c3a8d03ead001f96e8c94/webtools/blendstasktools.py#L364)
> is not presented on the Debian task pages? You recall that patch-attempt
> of mine.
>
> The edam.sh script of yours has it as
>
> bibdoi.value as doi,
> edam.topics as topics,
> edam.scopes as edam_scopes,
> biotools.entry as "bio.tools",
> omictools.entry as "OMICtools",
> seqwiki as "SEQwiki",
> scicrunch as "SciCrunch",
>
> and it shows a series of entries with topics, which to me indicates that
> the data is in the udd. Once working I'll then add a link the EDAM
> ontology browser of Hervé. The issue of that will be that term names are
> (theoretically) ambiguous unless accompanied by a version of the
> ontology. At the time, to keep everything human-readable, we had decided
> to store the names of the entries, not their identifier.
The problem is not that the data are missing in UDD. The query that is
fetching the data from UDD to build the task pages is just querying what
is needed (and topic was not needed before).
Please ping me again if you see no activity from me until Monday
Andreas.
--
http://fam-tille.de
Reply to: