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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