Software development: rethink display during Knowledge Base Sprint?

[magelm]

Will we be discussing the presentation and information display of the software tools during the Knowledge base Sprint? If yes, a few thoughts to consider and clarify:

• if we want to promote/ encourage these tools, better visibility is needed -- is the knowledge base the right place for this? -- and more metadata is needed > see issue 84 for list of suggested metadata fields
• the title Available Tools of NFDI4Microbiota members suggests that N4M members have developed these tools and the text states that these tools "should be integrated and endorsed by the NFDI4Microbiota umbrella" -- what does integration mean? --- As nextflow/nf-core instance via CloWM (hard integration)? --- As soft integration where the tool exists on it's own? -> I think this is the case for most of the stated tools here.
• update on databases is needed, e.g. Strain Info

[Kobert]

@magelm Discussing this during the Knowledge Base sprint is a good idea. We'll reserve some time for this. @jvddorpe

Also, @magelm Thanks for raising all of these issues.

[cpauvert]

After a discussion, we plan to try to include the tools on bio.tools (see #84). I'm starting with GUNC as a first prototype to showcase today for the sprint.

EDIT GUNC is already there: https://bio.tools/gunc

[cpauvert]

Compiling a list of tools that are already there (tagging also @thoelken and @pmjklemm from the tool survey)

• [x] https://bio.tools/gunc (input, output metadata could be improved)
• [x] https://bio.tools/checkm (input, output, operation metadata could be improved)
• [ ] checkm2
• [x] https://bio.tools/eggnog-mapper-v2 (input, output metadata could be improved)
• [x] https://bio.tools/motus
• [x] https://bio.tools/proteinortho (ok)
• [ ] AMBER is listed but this reference a different software
• [x] https://bio.tools/bacdive (ok)
• [x] https://bio.tools/eggnog the database but the metadata relates to the database construction
• [x] https://bio.tools/mediadive
• [x] https://bio.tools/bioautoml (input, output metadata missing, BSD license missing: on github though)

[cpauvert]

maybe we could simply create a "microbiome" domain on bio.tools following the documentation: https://biotools.readthedocs.io/en/latest/biotools_domains.html to start gathering tools. Would be more inclusive than a "nfdi4microbiota"?

vote for your preference:

• :microbe: ~microbiome.bio.tools~
• :computer: https://nfdi4microbiota.bio.tools

[magelm]

DSMZ's StrainInfo is also accessible and will also be somehow connected to the webportal itself.

• [ ] https://straininfo.dsmz.de/ -> there is a bio.tools entry for the old StrainInfo. How should we update to include the new StrainInfo in a NFDI4Microbiota dedicated collection/ domain on bio.tools? -> metadata suggestions: different primary contacts, free of charge, Open Access (?), credit/ support, documentation pages, Web API, CC BY 4.0 license -> tag suggestions: Database portal, Taxonomy, Microbial collection, Microbiology, Data retrieval

[cpauvert]

Domain is created and the tools can be added there

[magelm]

@konrad : The N4M contact form is currently part of the tool overview page. Can this be deleted from the overview, as we will not include it in bio.tools?

• [ ] None (ZB MED): Utility flask app for contact notification on the NFDI4Microbiota homepage -> line 223 02-toolsurvey.md

[cpauvert]

the collection NFDI4Microbiota now exists (https://bio.tools/t?collectionID=%22NFDI4Microbiota%22) but the tools that are part of the domain are not automatically part of the collection. Authors /editors of the tool description need to add it. We could use it for N4M participants

[cpauvert]

To clarify (thanks @Ka-Markus for the incentive to write it down)

Domain

• We have a domain that lists tools endorsed by the consortium at https://nfdi4microbiota.bio.tools
• For now, I am the only one able to add tools already on bio.tools to this domain (maybe this will change with improved rights)

Collection

• We also have a collection https://bio.tools/t?collectionID=%22NFDI4Microbiota%22, and all tool from this collection will display a small "NFDI4Microbiota" label.
• For now, there are no tools in this collection.

Editing tool notice

• For now, you need rights to edit a notice, and you can request them, we plan to list the changes we want to implement in the https://github.com/bio-tools/biotoolsRegistry/issues

this information should go on the KB as well.

[magelm]

• [x] https://bio.tools/itol (bio.tools says free of charge, but itol currently only offers a paid plan) -> issue opened on github bio.tools

[magelm]

• [ ] https://bio.tools/ipath (can somebody point me to where the license information can be found on iPath webpage?)

[magelm]

[x] https://bio.tools/mpa_portable -> for metaproteomeanalyzer this should be the correct bio.tools entry based on the KB-provided github address @cpauvert