Nice! I was thinking about collecting material for an edam-utils package. This script of Andreas would be part of it, an extension for getData to maintain a local copy of the EDAM ontology, Hervé's upload tool to http://bio.tools, .... please ping me about what you consider missing.
Best, Steffen > Gesendet: Samstag, 13. Februar 2016 um 08:47 Uhr > Von: "Andreas Tille" <andr...@an3as.eu> > An: "Booth, Timothy G." <tbo...@ceh.ac.uk>, "Debian Med Project List" > <debian-med@lists.debian.org>, "Peter Rice" <ricepet...@yahoo.co.uk>, "Hervé > Ménager" <herve.mena...@gmail.com> > Cc: "Jon Ison" <ji...@cbs.dtu.dk> > Betreff: Re: ELIXIR tools registry participation - richer metadata for our > packages > > Hi, > > I'd like to add to this old thread some results of a later meeting in > Copenhagen - our Debian Med sprint last week kindly sponsored by DTU. > > I confirm that I took over edam data files in Debian Med packages into > UDD. You can easily query all these data by a script I provided on > Github: > > https://github.com/bio-tools/biotoolsConnect/blob/master/DebianMed/edam.sh > > Feel free to run this script on any Linux machine with a psql client. > > In case you are lacking any such machine but you are a member of the > Debian Med team you can do > > rsync edam.sh alioth.debian.org: > ssh alioth.debian.org > ./edam.sh > > I'd be happy if some of the EDAM people could confirm that this works > for them. > > Kind regards > > Andreas. > > On Thu, Nov 20, 2014 at 05:37:10PM +0000, Booth, Timothy G. wrote: > > Dear all, > > > > This is Steffen and Tim sharing a desk at the Copenhagen Hackathon > > of the ELIXIR-DK Catalog of resources in computational biology. > > There is a general excitement of the collection of tools that > > are associated with Debian Med and its derivatives and we are > > here to > > > > * help the ELIXIR folks to fill their database > > - avoid redundancies > > - render the catalog immediately functional to see Debian packages > > * help ourselves > > - gain extra expressiveness in our own descriptions > > o by adopting the EDAM ontology [1] > > o to have separate annotations for the packages as a whole > > and individual tools (selected binaries in /usr/bin) > > - have some extra visibility > > - find additional users (bare metal and virtualised) > > - explain to the world how inviting Debian is to have one's > > software redistributed > > > > Catalog entries are meant to be provided by the maintainers of > > the software tools in the ELIXIR network. For resources (binaries) > > provided through the Linux distros, we could certainly just fall > > back to the information we already have, but we would like you > > (this list) to comment on the extension of the > > debian/upstream/metadata > > file to accommodate also structured references to semantical > > catalogs like the EDAM ontology. There is a related effort by > > Matus to annotate the DebTags. The format we think about is like > > > > Ontology: http://prefix.of.ontology.org > > feature_name: ontological_description_of_that_feature > > another_feature: id<blank>human_readable > > scope: <list of binaries> | summary > > feature_name: ... > > another_feature: ... > > > > The features may differ between ontologies. We had a look at bowtie to see > > how it goes and we ended up with: > > > > Ontology: http://edamontology.org > > topic: topic_0622 Genomics > > scope: summary > > function: operation_3212 Genome indexing (Burrows-Wheeler) > > function: operation_0292 Sequence alignment generation > > input: data_2975 Nucleic acid sequence (raw) > > input: format_1929 FASTA > > input: format_1930 FASTQ > > output: data_1383 Sequence alignment (nucleic acid) > > output: format_2573 SAM > > scope: bowtie-build > > function: operation_3212 Genome indexing (Burrows-Wheeler) > > input: data_2975 Nucleic acid sequence (raw) > > input: format_1929 FASTA > > output: data_3210 Genome index > > output: ??? Bowtie index format EBWT > > output: ??? Bowtie long index format EBTWL > > scope: bowtie-inspect > > function: operation_1813 Sequence retrieval > > function: operation_0304 Metadata retrieval > > function: operation_0228 Data index analysis > > input: data_3210 Genome index > > input: ??? Bowtie index format EBWT > > input: ??? Bowtie long index format EBTWL > > output: data_2975 Nucleic acid sequence (raw) > > output: format_1929 FASTA > > output: format_1964 plain text format (unformatted) > > scope: bowtie > > function: operation_0350 Sequence database search (by sequence using > > word-based methods) > > function: operation_0292 Sequence alignment generation > > input: data_3210 Genome index > > input: data_2975 Nucleic acid sequence (raw) > > input: format_1964 plain text format (unformatted) > > input: format_1929 FASTA > > input: format_1930 FASTQ > > output: data_1383 Sequence alignment (nucleic acid) > > output: data_0867 Sequence alignment report > > output: format_2573 SAM > > output: ??? Bowtie alignment report format > > > > or if we want to reduce the level of detail to just the summary this could > > be compressed to: > > > > Ontology: http://edamontology.org > > topic: topic_0622 Genomics > > function: operation_3212 Genome indexing (Burrows-Wheeler) > > function: operation_0292 Sequence alignment generation > > input: data_2975 Nucleic acid sequence (raw) > > input: format_1929 FASTA > > input: format_1930 FASTQ > > output: data_1383 Sequence alignment (nucleic acid) > > output: format_2573 SAM > > > > If the list likes this approach, then we can continue annotating a bit more > > and amend our task pages for it all. > > Some tools and suites (eg. EMBOSS) have existing annotations from other > > projects that we can inherit. > > We are not yet confident about what this effectively means e.g. for the > > Ultimate Debian Database. @Charles, can you > > direct us, please? > > > > Best regards from Copenhagen > > > > Steffen and Tim > > > > [1] EDAM ontology - http://bioportal.bioontology.org/ontologies/EDAM > > > > This message (and any attachments) is for the recipient only. NERC is > > subject to the Freedom of Information Act 2000 and the contents of this > > email and any reply you make may be disclosed by NERC unless it is exempt > > from release under the Act. Any material supplied to NERC may be stored in > > an electronic records management system. > > > > > > -- > > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > > with a subject of "unsubscribe". Trouble? Contact > > listmas...@lists.debian.org > > Archive: > > https://lists.debian.org/8c33d34d431a974eaea913101dda19440781235...@nerckwmbc.ad.nerc.ac.uk > > > > > > -- > http://fam-tille.de > >
