Meeting minutes
DICOM
erich: Running DCM to RDF converter on Stoneybrook's largets DICOM repo.
Representation of DICOM "arrays" #149
erich: I've been putting in array handling as part of CDT.
… including multidimensional array access
… Also asked if CDT slicing could be added, supported by Apache Arrow
… Want to extend to multidimensional case.
… Olaf saw the value, but doesn't want to change the spec yet.
detlef: There's implementation in Apache Jena, but no SPARQL support except Jena.
… Virtuoso said "when it's a standard we'll implement it"
dbooth: How much of a show stopper is it for you, to not (yet) have those mulit-dim access functions?
erich: Not much, because I'll implement myself.
… CDT is a possible future solution.
… Another suggestion is what detlef does, to represeent it as JSON.
… which is similar to CDT, but you don't have the SPARQL functions to connect it with other data
erich: Still want DICOM to take this on, but we're doing a starting point.
Using the entity-relationship model of the real world of DICOM #159
dbooth: To gen a DICOM ont, is there a machine readable rep of the ER def?
detlef: Yes, the authoritatieve version is in a set of XML files of the ER model.
… We did it using XSLT, but I cannot give you the code.
… And we use it to factor the DICOM metadata.
erich: I'm trying to express the DICOM std in SHACL. It would be interesting if we produce the same result.
ACTION: Erich to try generating an OWL ont from DICOM ER model, in addition to SHACL
Linking FHIR RDF with DICOM RDF #161
erich: IDK how existing DICOM fits into FHIR
detlef: HL7 v2 is connected with DICOM, so FHIR must have at least that same connection to DICOM.
… There's a workflow for our hospital info sys, to create a study instance ID, and used by all images.
… And for reporting, from DICOM perspective, they can put HL7 v2 as a document, so maybe there is also a way for it to ref FHIR doc.
ACTION: Detlef to look into linking FHIR with DICOM
detlef: You can rely on the pt ID in DICOM, and can link that way to FHIR graph.
… That's already possible.
… Might want more workflow support.
… with RDF support.
dbooth: Also suggest figuring out who in the FHIR community is closest to this.
Relationship of FHIR and DICOM RDF to Linked Web Storage #162
erich: Every POD has its own metadata to expose the data it holds. How do we advertise what's available in a particular POD?
… Maybe advertise the SHACL shapes for the POD.
… Do we need to put anything into FHIRDF RDF to make LWS people happy?
erich: EricP is one of the LWS chairs, and I'm in the WG.
HDT code
detlef: The libraries and code are actually licensed under the lessor GPL license.
erich: Greg Williams is also int w HDT, but some of the docs don't align w the implementation.
… I'm reimplementing HDT, with a slight variaion. I'm using the spiritual design into a HDF5 file. That makes it easier to put the guts of HDT into it, but in an HDF5 file.
… I'm debugging the writing, then will build the reader.
… If that works well, I'll weave it into Jena to do SPARQL queries, and extend to support quads.
… Want to park the HDT into other kinds of file formats. Could even park it into DICOM itself. Blocks, super blocks, etc. all end up being vectors in the end. Could park them in the DICOM and then have software that knows how to interpret them.
… I'm using the HDF viewer as a debugger.
… I think the world needs a binary RDF to deal with the volume of medical data.
erich: HDT gives you index-sorted memory structures.
… Very compact, and doesn't require deserializatoin. But it's read only. Great for bulk data.
ADJOURNED