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Fwd: [registry-core] heads-up! : bio.tools API / serialisation format changing

As bio.tools now has both full length URIs https://bio.tools/signalp and compact URIs (CURIES) bio.tools/signalp via https://identifiers.org/biotools/signalp I think the https://wiki.debian.org/UpstreamMetadata Registry should stick to URIs.

---------- Forwarded message ----------
From: Jon Ison <jison@bioinformatics.dtu.dk>
Date: 2017-11-17 12:18 GMT+02:00
Subject: [registry-core] heads-up! : bio.tools API / serialisation format changing
To: "Registry mailing list (registry@elixir-dk.org)" <registry@elixir-dk.org>, "registry-core@elixir-dk.org" <registry-core@elixir-dk.org>, "tools@elixir-europe.org" <tools@elixir-europe.org>


Dear folks

 

A revision to biotoolsSchema (https://github.com/bio-tools/biotoolsschema) - the software description model used by bio.tools (https://bio.tools ) - is underway.  It captures requirements gathered over the last year.  biotoolsSchema 3.0.0 will include changes to the API and data serialisation formats which are potentially breaking to software dependencies.  This is just a heads-up that if you think you’ll be affected, then please write to me directly.  I’ll then arrange a group skype where I can walk everyone through the changes.  We’re aiming to release the changes by the end of this month.

 

I apologise in advance for any inconvenience this will cause, but I hope you’ll appreciate the need for improvements, and how we minimise the pain by restricting such breaking changes to once per year.

 

Take care all

 

Jon

 

 

Highlights of planned changes include:

  • Constraints on which tool attributes must be specified are adjusted to match the emerging tool information standard (https://github.com/bio-tools/biotoolsSchemaDocs/blob/master/information_requirement.rst), which specifies what attributes must be specified to achieve a certain level of bio.tools entry completeness from “SPARSE” to “COMPREHENSIVE”.
  • Better support for version information.  Version information can still be attached to the main entry as before, but also at the levels of specific downloads of the tool, publications and identifiers.
  • Support for bio.tools CURIES (compact URIs) - basically the tool identifier with a prefix e.g. “biotools:signalp” trivially resolvable to https://bio.tools/signalp. 
  • Support for various type of identifier (e.g. RRIDs), other than just the bio.tools tool ID, in case these are available / needed.  See also bio.tools via Identifiers.org, e.g. https://identifiers.org/biotools/signalp.
  • Consolidation of credit & contact model, making this more convenient, and in preparation for bio.tools “Contributor Cards” coming next year.

 

 

Jon Ison

Senior Researcher

High Performance Computing

DTU Bioinformatics

 

Technical University of Denmark

Department of Bio and Health Informatics

Kemitorvet

Building 208, Room 013

2800 Kgs. Lyngby

Direct +45 45252477

jison@bioinformatics.dtu.dk

www.dtu.dk/english

http://www.dtu.dk/~/media/DTU_Generelt/Andet/DTU_email_logo_01.gif

 

 


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