Evening all A few thoughts:
Perhaps something to check the EDAM annotations are valid wrt the latest EDAM ? Something to check package description for export (to bio.tools) has not become out of synch with what's in bio.tools And I wonder about the relationship between the "EDAM metadata files" and the "metainfo XML files" (in /usr/share/appdata/ ?) Cheers Jon > 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" <[email protected]> >> An: "Booth, Timothy G." <[email protected]>, "Debian Med Project List" >> <[email protected]>, "Peter Rice" >> <[email protected]>, "Hervé Ménager" <[email protected]> >> Cc: "Jon Ison" <[email protected]> >> 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 [email protected] >> > with a subject of "unsubscribe". Trouble? Contact >> > [email protected] >> > Archive: >> > https://lists.debian.org/8c33d34d431a974eaea913101dda19440781235...@nerckwmbc.ad.nerc.ac.uk >> > >> > >> >> -- >> http://fam-tille.de >> >> > >
