[NeXus-committee] NeXus Ontology v2.0

Tue Dec 20 10:51:52 GMT 2022

HI Steve,

v1.1, 2.0, 2.1, 3.0 etc are referring to the ontology and how things are modelled. After settling, I would change them rarely.
The definitions’ short hash on the other hand refers to the different versions of the NeXus standard, so the compatibility here is depending on how much the standard changes. Most of the time it is also changing slowly (like something becomes deprecated, etc.).
So by default, I would say that ALL http://purl.org/nexusformat/*/definitions/*/Field/NXsample/temperature <http://purl.org/nexusformat/*/definitions/*/Field/NXsample/temperature> are compatible. More precise relationships can be added when a new release is coming out and we know what has actually been changed…
Note that v2.0 is already uses owl:deprecated (where a NeXus concept is marked), and owl:priorVersion, owl:backwardCompatibleWith, owl:incompatibleWith etc. can also be of use.

Note that version info is added also for the case if something goes wrong in an application, so one can dig down and find the root cause and then make a proper fix. Note that this cannot be avoided and without the version info such fixes would become even more cumbersome.

Examples from other ontologies: 
https://obofoundry.org/principles/fp-004-versioning.html <https://obofoundry.org/principles/fp-004-versioning.html> 
https://www.w3.org/2007/OWL/wiki/Ontology_Versions <https://www.w3.org/2007/OWL/wiki/Ontology_Versions> 

Bests,
Sandor

> On 20. Dec 2022, at 09:39, Collins, Steve (DLSLtd,RAL,SCI) <steve.collins at diamond.ac.uk> wrote:
> 
> Thanks Sandor,
> This looks fine in principle but may be complicated to implement. Is there a mechanism for determining the relationship between different versions of the same concept?
> Regards,
> Steve
>  
> From: Sandor Brockhauser <sandor.brockhauser at physik.hu-berlin.de <mailto:sandor.brockhauser at physik.hu-berlin.de>> 
> Sent: 19 December 2022 21:47
> To: Collins, Steve (DLSLtd,RAL,SCI) <steve.collins at diamond.ac.uk <mailto:steve.collins at diamond.ac.uk>>
> Cc: heike.goerzig <heike.goerzig at helmholtz-berlin.de <mailto:heike.goerzig at helmholtz-berlin.de>>; NeXus-committee at nexusformat.org <mailto:NeXus-committee at nexusformat.org>
> Subject: Re: [NeXus-committee] NeXus Ontology v2.0
>  
> Hi Steve and Heike,
>  
> Indeed, we could keep them. Please note that in V2, 
> - we use versioning,
> - model all elements of the Vocabulary (definitions/groups/fields/attributes) as concepts/classes, and 
> - tried to find a compromise between the naming conventions of v1 and the actual Vocabulary. In the given example v1:NXsample-temperature, and vocab:NXsample/temperature-field we propose:
> http://purl.org/nexusformat/v2.0/definitions/7ca0338/Field/NXsample/temperature <http://purl.org/nexusformat/v2.0/definitions/7ca0338/Field/NXsample/temperature>
>  
> Looking forward discussing the details and the next steps with you.
>  
> Bests,
> Sandor
>  
> On 19. Dec 2022, at 18:26, Collins, Steve (DLSLtd,RAL,SCI) <steve.collins at diamond.ac.uk <mailto:steve.collins at diamond.ac.uk>> wrote:
>  
> Me too!
> This looks very interesting but I have not had time to look at it.
> Can I ask: do you plan to keep the PIDs for NeXus fields as they are in V1? We would like to start to think about using the PIDs in ICAT tables for some parameters (http://purl.org/nexusformat/definitions/NXsample-temperature <http://purl.org/nexusformat/definitions/NXsample-temperature>, for example) so it would be useful to know if these are likely to change.
> Cheers!
> Steve
>  
> From: Görzig, Heike <heike.goerzig at helmholtz-berlin.de <mailto:heike.goerzig at helmholtz-berlin.de>> 
> Sent: 19 December 2022 16:07
> To: Sandor Brockhauser <sandor.brockhauser at physik.hu-berlin.de <mailto:sandor.brockhauser at physik.hu-berlin.de>>;NeXus-committee at nexusformat.org <mailto:NeXus-committee at nexusformat.org>
> Cc: Collins, Steve (DLSLtd,RAL,SCI) <steve.collins at diamond.ac.uk <mailto:steve.collins at diamond.ac.uk>>
> Subject: AW: [NeXus-committee] NeXus Ontology v2.0
>  
> Hi Sandor,
> Thanks for working on that! Sorry, I could not attend the meeting.
> I have quite a lot of questions. Maybe it would be better to have a meeting next year.
>  
> Best wishes,
> Heike
>  
> Von: NeXus-committee <nexus-committee-bounces at shadow.nd.rl.ac.uk <mailto:nexus-committee-bounces at shadow.nd.rl.ac.uk>> Im Auftrag von Sandor Brockhauser via NeXus-committee
> Gesendet: Freitag, 16. Dezember 2022 22:15
> An: NeXus-committee at nexusformat.org <mailto:NeXus-committee at nexusformat.org>
> Cc: steve.collins at diamond.ac.uk <mailto:steve.collins at diamond.ac.uk>
> Betreff: [NeXus-committee] NeXus Ontology v2.0
>  
> Dear All,
>  
> As discussed on previous NIAC meetings, we have started discussions with Heike and Steve on making a new version of the NeXus Ontology which would cover the full NeXus Vocabulary (https://manual.nexusformat.org/classes/index.html?highlight=vocabulary <https://manual.nexusformat.org/classes/index.html?highlight=vocabulary>) made available during the June Code Camp. With the same effort, we also wanted to address the proper description of the NeXus concepts with their detailed informations, like defined enumerations, deprecations, etc. 
> Last Friday, we had a Sprint Planning Meeting, and I am happy to announce that our FAIRmat development team has implemented a firs proposal for the new version. Please go (https://github.com/nexusformat/NeXusOntology/pull/4 <https://github.com/nexusformat/NeXusOntology/pull/4>) and have a look provide feedback, so we can all work together and make it even better.
> For those using ontology reasoners, I recommend FaCT++.
>  
> Quick summary:
> contains all the concepts for the full NeXus Vocabulary (definitions, groups, fields, attributes)
> defines and handles separately DataTypes and UnitCategories
> supports enumerations and also cardinality (minOccurs/maxOccurs/optional/required/recommended)
> checks and marks if a referenced concept (definition, group, field, attribute) has been specialised (e.g. docstring added, enumeration modified, new concept added or a cardinality of a referenced concept has been changed)
> added support for versioning (Ontology major: 2.0, minor: short hash of the NeXus Definitions used; conversion hash)
> NeXus Definitions are referenced via git submodules for easier access
>  
> Bests,
> Sandor
>  
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