Metadata for OME Next Generation File Format (NGFF)

Happy Fall Everyone!

I am starting this thread as a follow up to a recent post by @joshmoore on #ome-ngff.

Specifically, with this post, I would like to propose the formation of a community working group to discuss the METADATA CAPTURE and REPRESENTATION aspects of #ome-ngff.

As you know considerable effort has been recently dedicated by different initiatives (i.e., 4DN, BINA, and QUAREP-LiMi, etc.) for the definition of OME-derived COMMUNITY MICROSCOPY METADATA GUIDELINES and MODEL EXTENSIONS (i.e., 4DN-BINA-OME extension).

A KEY RELATED TOPIC is how microscopy metadata (and any other relevant metadata) should be represented in the NGFF.

Currently, the model (https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines ) we are working on is represented as:

  • XSD
  • xls spreadsheet
  • an Entity Relationship graphical representation of the schema (using .graphml)

In addition, @norio.kobayashi at RIKEN and @joshmoore have proposed using RDF/OWL and JSON-LD as the recommended format.

The problem is that all of these formats have to be kept in alignment and there is for example the need for shared converters.

Is there any interest in discussing these topics and working together to find a solution and develop BEST PRACTICES?

Thanks for your attention.

Caterina

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@Thomas_Pengo @heeler @norio.kobayashi @sonami @dsudar @joshmoore

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Hi Caterina,
I’m definitely interested! I’m not sure scheduling wise when makes the most sense but it would be a useful conversation to have even if just to gain insight on the different perspectives.
Thanks,
~Jamie

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I am interested as well.

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@sebi06 and @heeler thank you for your response. Let’s see what other people say and we can organize a Zoom meeting to see where everyone stands on the matter.
TTU soon
Caterina

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I don’t think I can make time for any more zoom meetings, and I would not bring the domain expertise you are looking for, but I would appreciate if I could be kept in the loop somehow to passively monitor the progress - if you set up the list, or have some kind of a forum/repo/community for discussing this.

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Hi @fedorov, sure we will keep you updated :slight_smile:

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@UlrikeBoehm I thought you might be interested!

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Thank you for initiating it! For sure, I am interested. Please could me in! :slight_smile:
And also please let me know how else I could help.

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@federov, this discourse is certainly available for that purpose. I tend to tag with #ome-ngff when necessary. For everyone, there’s info on following specific tags under Following a tag on image.sc (or any Discourse)

All the best,
~Josh

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I would be interested in joining as well

Thanks for the initiative and for including the community!

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Hi @akramhar I think you should be in on this as well!

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Thank you, yes I am very interested!

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Hi Caterina,

I am interested in the topic as well.
Although I don’t think I would be able to deliver values to your initiatives, but I would like to attend your Zoom meeting if that’s alright.

Thanks!

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I would be interested as well to participate in any discussions.

Hi All
thank you for the interest. I will organize a Zoom call and send an invite

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Dear All
thank you for your interest.
Please save the date on November 20th for a Community Zoom Call.
If you have major problem with that date let me know.
Registration information coming soon.
Caterina

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Hi @Caterina 20th is good except the noon-1pm ET time slot.
Thanks,
Damir

Thanks for organising this! I may have missed the information: at which time is it (preferentially in CET units :-)?

Hi All
Just to clarify, for now I am just asking people if they have major problems with the date of November 20th.
Time will have to be compatible with a global set of participants so the meeting willl probably will happen in the US morning.
Thanks
C

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