Semantic Types with new OME-XML release

[mmoulis]

Hi !

I am currently using the new release of OME XML (2011-06) and i would like to make new types. So I would like to make my own types in a <SemanticTypeDefinitions> section but it seems to be invalid. When I try to validate my xml file with the bio format command tools xmlvalid, i get :

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Validating C:\***\test2.xml
cvc-complex-type.2.4.a: Invalid content was found starting with element 'SemanticTypeDefinitions'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2011-06": Project, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Dataset, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Experiment, "http://www.openmicroscopy.org/Schemas/SPW/2011-06":Plate, "http://www.openmicroscopy.org/Schemas/SPW/2011-06":Screen, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Experimenter, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Group, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Instrument, "http://www.openmicroscopy.org/Schemas/OME/2011-06":Image, "http://www.openmicroscopy.org/Schemas/SA/2011-06":StructuredAnnotations, "http://www.openmicroscopy.org/Schemas/ROI/2011-06":ROI, "http://www.openmicroscopy.org/Schemas/OME/2011-06":BinaryOnly}' is expected.
Error validating document: 1 errors found


It seems that the STD namespace is not recognized.

The header of my file XML file is :

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<?xml version="1.0" encoding="UTF-8"?>
<!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://ome-xml.org/wiki/OmeTiff. -->
<OME
    xmlns="http://www.openmicroscopy.org/Schemas/OME/2011-06"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:STD="http://www.openmicroscopy.org/Schemas/STD/2009-09"
    xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06
                        http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd
                        http://www.openmicroscopy.org/Schemas/STD/2009-09
                        http://www.openmicroscopy.org/Schemas/STD/2009-09/STD.xsd">


So where is the problem ?

Thanks for your help,

Kind regards;

Marius

[ajpatterson]

Hi Marius,

Semantic Types were a carry over from the old OME server (which stopped active development in 2005).

They were removed completely from the schema in 2010. The modern way of adding user customisable values to the schema is using Structured Annotations (introduced in 2008).

See:
http://www.ome-xml.org/wiki/StructuredAnnotations
http://trac.openmicroscopy.org.uk/ome/w ... nnotations
http://trac.openmicroscopy.org.uk/ome/w ... nnotations

The namespace for structured annotations is

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http://www.openmicroscopy.org/Schemas/SA/2011-06/SA.xsd

A list of the Active and Legacy Schemas is always available at:
http://www.openmicroscopy.org/Schemas/
along with a history of the versions.

To see the changes between versions see the pages under:
http://www.ome-xml.org/wiki/ChangesFor

As a general rule all the namespaces you use in any single document need to be from the same schema version.

If you have any further questions just ask.

Hope this helps,

Andrew

[mmoulis]

Thanks a lot!

I'll check these informations.

Kind regards,

Marius

[mmoulis]

Hi again!

I tried to use Structured Annotations and everything is fine with Comment Annotation. When I add something like :

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<StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2011-06">
        <CommentAnnotation ID="Annotation:2" Namespace="">
            <Value>Some comments here</Value>
        </CommentAnnotation>
</StructuredAnnotations>


Everything is fine since I get back this comment in OMERO.insight after importation into OMERO.

But, when I try :

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<StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2011-06">
        <DoubleAnnotation ID="Annotation:4">
            <Description>DoubleAnnotation test</Description>
            <Value>3.012</Value>
        </DoubleAnnotation>
</StructuredAnnotations>


or :

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<StructuredAnnotations xmlns="http://www.openmicroscopy.org/Schemas/SA/2011-06">
        <XMLAnnotation ID="Annotation:1" Namespace="">
            <Description> XML ANNOTATION TEST</Description>
            <Value>
                <test>TEST</test>
            </Value>
        </XMLAnnotation>
</StructuredAnnotations>


I don't get back information from OMERO.insight or I don't find them.

So how can I retrieve my XML Annotations or Double Annotation or the other ones into OMERO.insight ?

Plus, how the field <Description>Description</Description> put into an annotation works ?

Thanks in advance,

Marius

[wmoore]

If you have the web client set up, you should see XML annotations displayed in the image metadata panel beside the other annotations.

This is not supported in Insight yet, but will be in future. See http://trac.openmicroscopy.org.uk/ome/ticket/6287

Will.

[mmoulis]

I've just checked, and my XML Annotations are well displayed in OMERO.web.

I will wait the last version of OMERO clients to see them into insight.

Thanks a lot!

Marius

[ajpatterson]

Hello Marius,

Not all of the Annotation types will be visible in OMERO.insight but you should be able to see them in OMERO.web as well as retrieve them pragmatically from the OMERO server using the API.

We are working on adding display of the other types to Insights and have an open story for these tasks.
http://trac.openmicroscopy.org.uk/ome/ticket/3541

I have added a link to this post from one of the the tasks.

Description is purely a text description of what the annotation value is. It is an optional attribute. Some clients may choose to display it, others might not. It should not be relied on to contain any important information. The unique identifier what any user code should use to locate annotations is the namespace. If you are writing Structured Annotations you should declare the namespace otherwise you could not recover your annotations at a later date.

For samples I normaly use:

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sample:ome:...

e.g.

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sample:ome:omero:render:cut-off-max

You probably want something like:

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your:company:url:yourapplication:...

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your:company:url:yourapplication:this:annotation:identifier

Hope this helps,

Andrew

[mmoulis]

I really appreciate this quick but great support ! Thanks for all !

If I can make some suggestion :
* It might be very interesting that the external SAs be visible in "Acquisition" Tab in OMERO.insight and OMERO.web at the bottom of the sections Microscope, Image and so on. So, when a user check the acquisition metadatas using insight, he could see the OMERO's data model sections (microscope, Image, Channel1...) and the other metadatas sections such as "MyMetadataGroup1", "MyMetadatGroup2" and so on... I don't know if i am enough clear

* When I discover the OME-XML data model, I have to admit that i was quite lost. For example, the fact that STD and CA are deprecated is not obvious and should be underline in your website (http://www.ome-xml.org). To conclude, I suggest that the OME-XML documentation be more visible and more accessible

That said, I want to say that this forum and OMERO support in general is perfect.