Metadata

[Helmut Koester]

We are looking into using FAIRDOM Seek around a media-break free DBTL cycle. This would require tight control over custom metadata (also from ontologies). After experimenting around a bit, the solution with Rightfield is not really easy and not user-friendly - and Rightfield does not seem to be supported any longer. 

I saw that with version 1.14 there seems to be better tools for handling custom metadata. Would it be possible to get a better idea how that would look like? Would it be possible to define templates, so when items are uploaded, a template is used for metadata annotation?

Best regards

Helmut

[Stuart Owen]

Hi Helmut,

 

We’d be interested in more details about what you are trying to do, but it sounds like the Sample Types may be more along the lines of what you need. Despite the name, they can apply to any metadata and has the ability to generate templates which can then be upload and extracted. They can include ontology based controlled vocabularies. More details can be found at https://docs.seek4science.org/help/user-guide/create-sample-type.html and https://docs.seek4science.org/help/user-guide/create-sample.html

 

Custom, or what we now more accurately call Extended Metadata is based on very similar to Sample Types, but gets embedded within another type (in particular Investigation, Study Assay) to extend it’s metadata based on certain standards. Currently it is used to support MIAPPE, and there is work going on to support ENA. These are currently only definable programmatically via the database. Although there are future plans to make them user definable (probably via a template) in the future, there are issues to do with mutability, visibility and scope that need solving first – for example once defined they would be very difficult to change afterwards. I’ve attached a picture at the end that clarifies the relationship between Sample Type and Extended Metadata as they are both related and overlap.

 

Regarding RightField, although there hasn’t been a new release for a while it is certainly still supported. Most users won’t see RightField, but only the templates it generates.

 

Regards,

Stuart

 

 

From: seek-de...@googlegroups.com <seek-de...@googlegroups.com> On Behalf Of Helmut Koester
Sent: Tuesday, July 18, 2023 11:36 AM
To: SEEK Developers <seek-de...@googlegroups.com>
Subject: Metadata

 

We are looking into using FAIRDOM Seek around a media-break free DBTL cycle. This would require tight control over custom metadata (also from ontologies). After experimenting around a bit, the solution with Rightfield is not really easy and

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[Helmut Koester]

Thank you for the in-depth response Stuart, we have a better understanding now.

Best regards

Helmut