IRC log of hcls on 2023-11-02

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Meeting: FHIR RDF
14:56:12 [dbooth]
Chair: David Booth
15:00:39 [dbooth]
Present: Avanti Paturkar, Allen Flynn, Erich Bremer, EricP
15:01:14 [dbooth]
ACTION: DBooth to put full zoom info on RDF mtg page, for dial-in
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Present+ Rob Hausam
15:02:58 [dbooth]
Topic: Introductions
15:04:37 [dbooth]
Erich: dep of informatics, working on RDF 15 years, working on software for teachers, bridging to clinical . Stonybrook Univ.
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Present+ Jim Balhoff
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Present+ Gaurav Vaidya
15:09:18 [dbooth]
Topic: Relating imaging data to clinical info
15:09:46 [dbooth]
erich: Tagging onto OMOP group and, diacon group. Trying to integrate spacial info, and make heatmaps.
15:10:00 [dbooth]
... I'm using RDF, but want to walk it to clinical info also.
15:10:26 [dbooth]
... Any work done w diacom or OMOP?
15:10:42 [dbooth]
eric: Some of the same people worked on an OMOP mapping a while ago.
15:11:11 [dbooth]
... Didn't do anything between images and OMOP. Not aware of images to OMOP. Maybe Scott Marshall?
15:11:40 [dbooth]
erich: Imaging and clinical domains seem to be separated. Want to bring them together.
15:11:53 [dbooth]
... OMOP is tyring to use Daicom verbiage.
15:12:13 [dbooth]
... Have annotations by the files are usable, but cannot bring up 3M image iunless there's spacial info.
15:12:27 [dbooth]
... Cannot decode the image and put it on the screen quickly. Need spacial info.
15:12:40 [dbooth]
... Same applies to deep learning pipelines.
15:13:00 [dbooth]
eric: Write-up of baby use case for clinical setting?
15:13:28 [dbooth]
erich: Not aware. Also work w cancer imaging archive. They get a lot of images submitted, and de-ided clincial info. People now want both.
15:13:48 [dbooth]
... Diacom is noce, but unless you set standards of what should be included, you get a lot of empty boxes.
15:14:05 [dbooth]
... Noe of these groups are bridgeing each other.
15:14:41 [dbooth]
dbooth: Need to get folks together to duscuss?
15:15:10 [dbooth]
erich: David Kume said thatere;s some diacom, but no official mapping. Series of XML docs, you need to extract info from them.
15:15:31 [dbooth]
... FHIR is better, OMOP has CSV which is better. Need to convince people that this is needed.
15:15:47 [dbooth]
... Easier to build something to show them the value, to get them hungry to discuss.
15:15:59 [dbooth]
... Otherwise OMOP group has 100 people.
15:16:21 [dbooth]
... Any image could have 1M segmentations, with lots of info associated.
15:16:33 [dbooth]
... Cannot use standard RDF DB -- billions of triples.
15:16:52 [dbooth]
... Need to break into separate storage, then need to get clinical date into it.
15:17:20 [dbooth]
... In semweb, lots of greag components, but nobody knows what it becomes yet.
15:18:37 [dbooth]
tim: little familar w diacom. Thought diacom modalities didn't seem they had depth. Have you looked at relevant FHIR resources? Visionoing more detailed modeling of those modalidties in FHIR?
15:19:32 [dbooth]
erich: Looking for low hanging fruite. Collected a lot of COVID imagery 80-100M radiology images.
15:19:32 [dbooth]
... Wrote software to extract diacom data and RDF-ized it. Loaded into virtuoso to query.
15:19:43 [dbooth]
... Diacom allows linking by accession IDs, dates, etc.
15:20:01 [dbooth]
... Brought into relational data laek, but how to connect them back? Some terms connect, but not all.
15:20:55 [dbooth]
... Stonybrook purchansing scanners to scan. Say we'll need to decide what to collect on patients, etc. Otherwise you just have a big [pile of images.
15:22:03 [dbooth]
dbooth: Maybe show what you have so far?
15:22:45 [dbooth]
erich: Could show soon as use case. ONe odball thing: images range from 300M to 3GB, and my computer gets chewed up.
15:23:12 [dbooth]
... Having the pipeline data from deep learning, in central RDF DB is not scalabl, virtuoso w TB of RAm.
15:23:40 [dbooth]
... With a lot of these files, putting into central store, you're doing spacial indexing, but considering it all part of the same space.
15:24:02 [dbooth]
... I partitioned out the spacial info into separate files. Originally going to use RDF HDT in separate files.
15:24:24 [dbooth]
... But some pieces were missing. Did something similar: Apache jena graph, backed by apache arrow.
15:24:39 [dbooth]
... RDF mapped to chunks. Predicates being loaded separately.
15:24:49 [dbooth]
... That allowed performant viewing.
15:25:05 [dbooth]
... There all in their separate worlds.
15:25:28 [dbooth]
... Could show you in a couple of weeks. Was using W3C opena nnoatations. But recently changes to geoSPARQL.
15:25:49 [dbooth]
... Creating feature collections and specifying other data, heatmaps and segmentation.
15:26:07 [dbooth]
... published a paper in 2019, 7k images of several cancer types.
15:26:17 [dbooth]
... Did a preload to see how it will work.
15:27:18 [dbooth]
allen: https://www.netestate.de/dicom/DICOM_metadata_as_RDF.pdf
15:27:31 [dbooth]
erich: preprint: https://arxiv.org/abs/2304.10612
15:29:00 [dbooth]
Topic: Fixing RDF examples
15:29:51 [dbooth]
tim: Jim and I have PRs open that fix a lot of example. I guess I need to post in zulip.
15:30:16 [dbooth]
eric: Recently working on something that ports between FHIR JSON and FHIR Turtle, to be able to compare the graph and see if they are the same.
15:31:04 [dbooth]
dbooth; Would that be usable in the RDF playground for validation?
15:31:23 [dbooth]
eric: No, different code base. Using it for AMIA tutorial.
15:31:48 [dbooth]
... Wanted to test against official examples and see where we differ.
15:32:04 [dbooth]
... Goal in playground was to not be tied to FHIR resources, to allow us of other logicla models.
15:32:31 [dbooth]
... Current work depends on standard FHIR core.
15:35:13 [dbooth]
https://github.com/w3c/hcls-fhir-rdf/labels/Turtle
15:36:28 [dbooth]
jim: Want to be able to gen one FHIR RDF example at a time
15:36:59 [dbooth]
ACTION: tim to make github issue about gen one FHIR RDF exmape at a time
15:43:09 [dbooth]
Topic: Elment summary
15:43:11 [dbooth]
https://github.com/w3c/hcls-fhir-rdf/issues/133
15:43:33 [dbooth]
tim: Need a way to connect a Patient class to the StructureDefinition for Patient, for example.
15:44:07 [dbooth]
... Suggestion was to put in the class definition in the FHIR RDF ontollgy.
15:45:08 [dbooth]
tim: IN RDF we have the distinction bewteen the class and the StructureDef. Need to tie them together.
15:45:34 [dbooth]
... Then I need to know which properties are included in the resource summary. That info is in the StructureDef but not in the class.
15:45:53 [dbooth]
... That link would them together.
15:46:16 [dbooth]
eric: Sounds like the right way to do it.
15:46:40 [dbooth]
dbooth: What exactly would the URL be?
15:47:04 [dbooth]
eric: We'd need to work on the RDF-ization of the StructreDefs. Algorithm might work out of the box, but not guaranteed.
15:47:27 [dbooth]
... No sure they'd be dereferenceable, but we don't control that.
15:49:04 [dbooth]
eric: Big prob w examples is that an overhaul to make them resolvable would give you a FHIR server. That would be a very helpful.
15:49:24 [dbooth]
.. .Would be a great opportunity to enable follow-your-nose.
15:54:29 [dbooth]
ACTION: Eric to make github issue about making FHIR examples dereferenceable
15:56:13 [dbooth]
tim: This looks like the right URL https://www.hl7.org/fhir/patient.profile.ttl.html So this could go in the Patient class…. Or we could put the Patient class IRI in the profile
15:57:46 [dbooth]
tim: Maybe have prov:isDefinedBy https://www.hl7.org/fhir/patient.profile.ttl.html
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16:01:28 [dbooth]
tim; That's an annotation property.
16:03:47 [dbooth]
ACTION: Tim to show example of linking class to structure def, and also show how an objectProperty could be used instead
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ADOURNED
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