Recommended schema updates to be included in openMINDS v5.0 release - research product(s) (versions)

[UlrikeS91]

Brain atlas (BA) and Common coordinate space (CS)

• make required:
  • 'howToCite' - to provide some information about e.g. authors or when no PID is stated (which is an optional field)
  • 'usedSpecies' - inconsistency between BA and CS (CS already requires it); also, we haven't encountered a single example where this is not possible to provide, so let's formalize this (NOTE: values will become more flexible allowing other taxonomic groups, see below)
• make optional:
  • 'author' - due to duplication issues and inconsistency between BA and CS (CS does not require it) and other reasons (e.g. GDPR)
• change property and/or value:
  • see Allowing other taxonomic ranks stated for brain atlases (changing property "usedSpecies") #293; specific suggestion:
    • add new schema category (e.g. 'biologicalTaxon') to applicable existing controlledTerm schemas (i.e., 'biologicalOrder' and 'species')
    • change property name 'usedSpecies' to 'usedTaxon'
    • change value of property from "linkedTypes": [ "controlledTerms:Species ] to "_linkedCategories": [ "biologicalTaxon" ]

Brain atlas version (BAV) and Common coordinate space version (CSV)

• make required:
  • 'howToCite' - to provide some information about e.g. authors or when no PID is stated (which is an optional field)
  • ' type' of BAV - not sure why this was optional in the first place
• make optional:
  • 'coordinateSpace' of BAV - due to parcellation models not having one
  • 'license' - inconsistency between BA and CS (CS does not require it) and due to lack of documentation, this is often hard to come by or defined through the copyright
• change instructions:
  • see Update instructions for the axes origin of both coordinate space versions #298 ('axisOrigin' of CSV)

[lzehl]

@UlrikeS91 a couple of comments for these updates:

Properties author and custodian is going to be deleted from BA, BAV, CS, CSV as discussed in openMetadataInitiative/openMINDS_core#513
Instead all of them will receive a contribution (required) and contributorAffiliation (optional) property; for the required contribution we can state any of the PIDs for the owning legal entity of the BA(V)/CS(V) in the role of the provider.

Property license will be deleted for all RP(V)s as discussed in openMetadataInitiative/openMINDS_core#505
Instead property usageCondition will be added as required property with 1-N; linkedTypes [Copyright, License, UsageAgreement]. Copyright is getting a new property rightsReservationClause to allow for more detailed copyright information.

[UlrikeS91]

Based on a discussion between @lzehl and I, I will also update "CommonCoordinateSpace(Version)" to "CommonCoordinateFramework(Version)"

These are the VERY rough definitions for certain elements that we came up with:
A coordinate system provides a numerical description of location by linking each point in a space to a specific set of values. (mathematically inspired definition)
An anatomical space adds biological meaning and structural context to those numerical locations.
Reference data are a representative set of primary anatomical imaging data that provide the foundational spatial information upon which all further anatomical context is built.
A coordinate framework is the structured work that integrates the anatomical space (with its coordinate system) and the reference data into a single, coherent product.

Based on these definitions, our "space" is actually significantly closer to the coordinate framework definitions than the anatomical space definition. Improving these elements in SANDS is a larger update and will not be done now, but we should already update the name of the existing schema to its closest fitting term.

[UlrikeS91]

during offline meeting: rename brain atlas (version) to anatomical atlas (version) or just atlas (version)

@aeidi89 and @tgbugs, what do you think?

[UlrikeS91]

during offline meeting: rename brain atlas (version) to anatomical atlas (version) or just atlas (version)

@aeidi89 and @tgbugs, what do you think?

conclusion with @tgbugs: anatomical atlas