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WU-BIMAC / NBOMicroscopyMetadataSpecs

The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.
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Schema URL and other header information #19

Open joshmoore opened 4 years ago

joshmoore commented 4 years ago

After a recent ping from Caterina, I was working through the current proposal. Something occurred to me that I should have raised sooner:

https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines/blob/master/Model/in%20progress/v02-00/4DN-BINA-OME-Microscopy%20Metadata_CORE%2BBASIC.xsd#L44-L48

<xsd:schema xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
  targetNamespace="http://www.openmicroscopy.org/Schemas/OME/2016-06"
  xmlns:xsd="http://www.w3.org/2001/XMLSchema"
  xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2016-06" version="3"
  elementFormDefault="qualified">

identify this file as being the official 2016-06 schema and could lead to confusion in the community. We will need a way to make it clear that the XSD files in this repository extend rather than replace the OME Schema.

cc: @sbesson @jburel @jrswedlow

strambc commented 4 years ago

Thank you @joshmoore for bringing this to our attention.

Would the following changes in the header address the concern?

Proposed change version 1 <xsd:schema xmlns="http://www.NamespaceTest.org/Schemas/NBO/2020-11" targetNamespace="http://www.NamespaceTest.org/Schemas/NBO/2020-11" xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:OME="http://www.openmicroscopy.org/Schemas/OME/2016-06" version="3" elementFormDefault="qualified">

or do we also have to remove any reference to the :OME suffix as in version 2?

Proposed change version 2 <xsd:schema xmlns="http://www.NamespaceTest.org/Schemas/NBO/2020-11" targetNamespace="http://www.NamespaceTest.org/Schemas/NBO/2020-11" xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:NBO="http://www.NamespaceTest.org/Schemas/NBO/2020-11" version="02.00" elementFormDefault="qualified">

NOTE NBO stands for 4dNulceome Bina Ome extension

sbesson commented 4 years ago

@strambc thanks for the two proposals. Looking at it briefly, I do not see any fundamental issue with the version 1. It mostly declares a new 4DN schema under a new namespace but imports the 2016-06 OME schema using the OME: prefix. This matches my understanding of the 4DN extension.

This layout is the closest to the one described in this section of the ome-model developer documentation. There are a few additional suggestions on this page that might be required including importing the OME schema using xs:import.

strambc commented 4 years ago

Thank you @sbesson I will take another look at the development guide to make sure we are aligned with the recommendations therein. cc: @Akramhar