Re: Aw: Re: ELIXIR tools registry participation - richer metadata for our packages
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" <andreas@an3as.eu>
>> An: "Booth, Timothy G." <tbooth@ceh.ac.uk>, "Debian Med Project List" <debian-med@lists.debian.org>, "Peter Rice"
>> <ricepeterm@yahoo.co.uk>, "Hervé Ménager" <herve.menager@gmail.com>
>> Cc: "Jon Ison" <jison@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
>> >
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>> >
>> >
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>> >
>> >
>>
>> --
>> http://fam-tille.de
>>
>>
>
>
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