Re: DICOM RDF representation

Hi Detle,

On the delay in your response, you are completely forgiven. :-)

Thanks for the links!  I've read your paper and I have a few questions if I
may ask:

1) Is your ontology generated automatically from the normative DICOM XML?
2) If so, is this process open-source?
3) You mentioned in the paper that you convert everything to strings, (not
taking advantage of the value representations).  I take it that an
all-string approach is a big performance hit. Have you (since then)
converted the strings to something more analytically efficient?
4) Can you share any samples of your dicom2RDF conversions?

I've done my own conversion of DICOM to RDF (dcm2rdf) using (like you) the
dcm4che library and scaled this to handle large sets of dcm files.  The
code will generate either a long form conversion keeping VR typing:

<urn:md5:44c5f855d4ee27141c926b2084b461a4> dcm:00080060  [ dcm:Value "XA";
dcm:vr "CS" ] .

or a compact form dropping the VR typing and converting the actual values
to an optimal form.

<urn:md5:44c5f855d4ee27141c926b2084b461a4> dcm:00080060 "XA" .

I tend to use the latter form as it cuts down on the number of triples and
makes for better query performance in the Virtuoso triple store.

All of this is done without a corresponding defined ontology and I would
like to rectify this.  My preference is to see an official DICOM conversion
but I don't know if I am alone in this endeavour.  OWL is good, but it
would also be helpful to have a SHACL equivalent for RDF data validation.

   - Erich
==========================================================
Erich Bremer, M.Sc.
Director, Applied Informatics
Department of Biomedical Informatics
Stony Brook Medicine
Tel. : 1-631-444-3560
Fax  : 1-631-444-8873
Cell : 1-631-681-6228
erich.bremer@stonybrook.edu
Office Location/Mailing Address
HSC, L3: Room 119
Stony Brook, NY 11794-8330



On Mon, Jan 8, 2024 at 10:20 AM Detlef Grittner <detlef.grittner@sohard.de>
wrote:

> Hi Eric,
>
> first let me apologize for the late answer due to all the holidays at the
> end and beginning of the year.
>
> Actually there has been a publication of a project where that DICOM RDF
> has been used: https://pubmed.ncbi.nlm.nih.gov/25160167/
>
> This DICOM RDF is described in an OWL ontology, but the published version
> on BioPortal (https://bioportal.bioontology.org/ontologies/SEDI) is
> completely outdated. I will clarify, if I can provide the current version
> of the ontology on that portal and will let you know.
>
> At the moment there is no lobbying, but I think it would be an interesting
> idea to take that DICOM ontology as a basis for such an effort.
>
> Detlef
>
> Detlef Grittner
> MSc ISM, M.A.
> Software-Entwicklung
>
> SOHARD Software GmbH
> Würzburger Str. 197
> 90766 Fürth
>
> Phone: +49 (0) 911 97341-54
> Fax:   +49 (0) 911 97341-10
> E-Mail: detlef.grittner@sohard.de
>
> Geschäftsführer: Peter Feltens, Sebastian Schnitzenbaumer
> Sitz der Gesellschaft: Fürth
> Registergericht: Amtsgericht Fürth; HRB 11478
> On 14.12.23 16:53, Erich Bremer wrote:
>
> Hi Detlef,
>
> Is there anywhere I can read about your DICOM RDF work?  I think it would
> be helpful if there was an officially sanctioned RDF representation of
> DICOM.  Is anyone lobbying them with the idea?  - Erich
> ==========================================================
> Erich Bremer, M.Sc.
> Director, Applied Informatics
> Department of Biomedical Informatics
> Stony Brook Medicine
> Tel. : 1-631-444-3560
> Fax  : 1-631-444-8873
> Cell : 1-631-681-6228
> erich.bremer@stonybrook.edu
> Office Location/Mailing Address
> HSC, L3: Room 119
> Stony Brook, NY 11794-8330
>
>
>
> On Mon, Dec 4, 2023 at 1:25 PM Detlef Grittner <detlef.grittner@sohard.de>
> wrote:
>
>> Hi all,
>>
>> we've been working together with Scott on projects with DICOM to RDF
>> conversion. But it is not sanctioned in the sense that any organization
>> like w3c or nema has published it as a recommendation or standard.
>>
>> Anyhow, if you're interested we could explore whether our idea of DICOM
>> RDF fits your purpose.
>>
>> Kind Regards,
>>
>>
>> Detlef Grittner
>> MSc ISM, M.A.
>> Software-Entwicklung
>>
>> SOHARD Software GmbH
>> Würzburger Str. 197
>> 90766 Fürth
>>
>> Phone: +49 (0) 911 97341-54
>> Fax:   +49 (0) 911 97341-10
>> E-Mail: detlef.grittner@sohard.de
>>
>> Geschäftsführer: Peter Feltens, Sebastian Schnitzenbaumer
>> Sitz der Gesellschaft: Fürth
>> Registergericht: Amtsgericht Fürth; HRB 11478
>> On 30.11.23 18:29, Eric Prud'hommeaux wrote:
>>
>> Hi Scott, Erich Bremer (Cc'd) is working on a use case that intersects FHIR/RDF and some detail-y bits of DICOM. I'd assumed there was a sanctioned RDF for (all of) DICOM but Erich said there A. wasn't a sanctioned RDF representation for DICOM or B, it didn't include the parts of DICOM that cover his use case. Any leads?
>>
>>
>>