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