Open Microscopy Environment

Dear All,

Can you please give me information on how to describe PDF using ontologies
for the meta-information in OME-XML (or OME-TIFF) files?

Now, we aim to develop RDF-meta-data services for both numerical data with
our BDML format (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382901/)
extracted microscopy images and the corresponding images with the OME-XML
format in our SSBD database.

I'm looking for examples of such RDF descriptions (especially, about xyz-t dimensions
and their scale units....) and information about relevant Web sites.

Best,
Yukako.

tohsato wrote:Dear All

Hi Yukako,

Can you please give me information on how to describe PDF using ontologies
for the meta-information in OME-XML (or OME-TIFF) files?

I don't know if we have any immediate solutions, but perhaps we can work something out.

Now, we aim to develop RDF-meta-data services for both numerical data with
our BDML format (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382901/)
extracted microscopy images and the corresponding images with the OME-XML
format in our SSBD database.

Interesting! Could you possibly attach or paste a sample of the BDML and the OME-XML files that you already have, so we have something concrete to discuss?

I'm looking for examples of such RDF descriptions (especially, about xyz-t dimensions
and their scale units....) and information about relevant Web sites.

If you really want every piece of OME metadata available as an RDF, then currently there's nothing provided in the standard. There was some work in Australia to take a previous version of the OME-XML specification and turn it into OWL:

http://www.itee.uq.edu.au/eresearch/projects/fusion/ome

I think this or related work was written up in The Semantic Web - ISWC 2004: Third International Semantic Web Conference as "Rules-By-Example - A Novel Approach to Semantic Indexing and Querying of Images", Suzanne Little and Jane Hunter.

If there's interest in that kind of representation, then it would be good to hear it.

However, there's another intermediate step that we could use, and for which a concrete example would be useful. RDF ultimately just consists of URI-URI-(URI|value) triples. If we could provide you useful URIs say for the RDF predicate, then you might be able to write something of the form:

Code: Select all

<?xml version="1.0" encoding="UTF-8"?>
    <!DOCTYPE RDF [
        <!ENTITY ome "https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome_xsd.html#" >
    ]>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
             xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
             xmlns:ome="&ome;" ...>
   
        <rdf:Description
            rdf:about="YOUR-RESOURCE-HERE">
            <ome:Pixels_SizeX>512</ome:Pixels_SizeX>
        </rdf:Description>



Best,
Yukako.

Cheers,
~Josh.

Dear jmoore,

Thank you for your advices.

According to your advice, I constructed RDF structures for metadata of images,
which are managed by OMERO in our SSBD database. I will attach that as pictures.

In the structures, we mapped element in OME.xml to ontology for Media
Resources (http://www.w3.org/ns/ma-ont) as soon as possible.
The strategy aims to integrate images obtained by not only microscopy,
but digital camera as well.

I would appreciate it if I could get your advice in regards to that matter.

Best,
Yukako

Dear Yukako

Thanks for submitting the pictures. Josh Moore is currently on vacations.
We will try, in the meantime, to look at files and see if we can advice
Sorry for not being able to give a more concrete solution.

Thank you for your patience and interest

Regards
Jmarie

Hi Yukako,

sorry for the long wait. (Vacation was good, thanks. )

Are you looking for general feedback about the schema or something in particular? One first thing I noticed was that both your Dataset (which is more like an OME image?) and an Image (which is a an OMERO plane?) have the timeslice and the pixels quantity. Is that intended?

Perhaps more importantly, was there anything that from our side would have helped you to define the schema, like more descriptive URLs etc?

Cheers,
~Josh.