Re: Subclass caching has some problems on Fuseki startup

> SNOMED has a conversion to OWL - isn't that OWL functional syntax? Or do you > have another tool that converts RF2 to RDF? I used the SNOMED tool to convert to OWL functional syntax, then used robot to convert that to turtle > what OWL features are you going to use? SNOMED uses more than sub

Re: Subclass caching has some problems on Fuseki startup

On 22/09/2021 17:17, Brandon Sara wrote: We will when we start pulling in realtime data that we want the SNOMED inference rules to help us discover new knowledge with. SNOMED has a conversion to OWL - isn't that OWL functional syntax? Or do you have another tool that converts RF2 to RDF?

Re: Subclass caching has some problems on Fuseki startup

> Which reasoner? IIRC SnomedCT uses various OWL features > The default RDFS reasoner does not include the "rdf4" rule which is a > whole-dataset rule > A ruleset tuned to needs may work better. I tried this to only include subclass and equivalent class using the generic reasoner, but the datase

Re: Subclass caching has some problems on Fuseki startup

(Obviously SNOMED CT is difficult for me to work with as it is licensed and not available directly in RDF, at least last time I looked - you have to produce it locally- It was about 5M triples. On 22/09/2021 03:09, Brandon Sara wrote: We need the inference so that we can know equivalence betwe

Re: Subclass caching has some problems on Fuseki startup

On 21/09/2021 23:42, Ryan Stokes wrote: Thanks for giving this some more thought, Andy. We could consider different ways of doing both inference and updating. I think the basic requirements are that a collection of common medical datasets (ICD-10, RxNorm, and the like) be treated as a high-pe

Re: Subclass caching has some problems on Fuseki startup

We need the inference so that we can know equivalence between classes and subclass relationships (eg "type 2 diabetes" is still "diabetes" because it's is a subclass of diabetes). Another dataset that I've never been able to get to load with any inference enabled is SNOMED CT. Even when removin

Re: Subclass caching has some problems on Fuseki startup

Thanks for giving this some more thought, Andy. We could consider different ways of doing both inference and updating. I think the basic requirements are that a collection of common medical datasets (ICD-10, RxNorm, and the like) be treated as a high-performance ontology - updated at most daily fr

Re: Subclass caching has some problems on Fuseki startup

Hi Ryan, On 17/09/2021 16:22, Ryan Stokes wrote: Hi Andy, By way of introduction I've been exploring ontology solutions with Brandon recently using Jena and Fuseki and come to appreciate your capable stewardship and responsive engagement with this community. Thank you. I was able to replicate

Re: Subclass caching has some problems on Fuseki startup

Hi Andy, By way of introduction I've been exploring ontology solutions with Brandon recently using Jena and Fuseki and come to appreciate your capable stewardship and responsive engagement with this community. Thank you. I was able to replicate Brandon's problem loading the ICD-10 dataset using a

Re: Subclass caching has some problems on Fuseki startup

Hi Brandon, The configuration is quite complex - it's likely due to the inference layer but it would be worth trying without the text index to confirm that especially for the loading. Do you need all that offers or is all you want RDFS subc

Re: Subclass caching has some problems on Fuseki startup

I have been able to create an easily reproducible scenario that others can use to replicate and test the issues that I’m seeing: 1. Start fuseki using the config that I’ve listed below. 2. Attempt to load the latest version of ICD-10 CM as provided freely by BioPortal: https://bioportal.bioontol

Re: Subclass caching has some problems on Fuseki startup

On 27.08.21 22:09, Brandon Sara wrote: I’ve finally tracked down the problem (at least at a high level). When using the Transitive Reasoner, there is a block of code which caches all sub class triples (https://github.com/apache/jena/blob/main/jena-core/src/main/java/org/apache/jena/reasoner/

Re: Subclass caching has some problems on Fuseki startup

On 27/08/2021 21:09, Brandon Sara wrote: I’ve finally tracked down the problem (at least at a high level). When using the Transitive Reasoner, there is a block of code which caches all sub class triples (https://github.com/apache/jena/blob/main/jena-core/src/main/java/org/apache/jena/reasoner/tran

Subclass caching has some problems on Fuseki startup

I’ve finally tracked down the problem (at least at a high level). When using the Transitive Reasoner, there is a block of code which caches all sub class triples (https://github.com/apache/jena/blob/main/jena-core/src/main/java/org/apache/jena/reasoner/transitiveReasoner/TransitiveEngine.java#L3