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ncbo / bioportal-project

Serves to consolidate (in Zenhub) all public issues in BioPortal
BSD 2-Clause "Simplified" License
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process and load UMLS 2021AB release #228

Closed alexskr closed 2 years ago

alexskr commented 2 years ago

NCBITAXON ontology hasn't been updated since 2020AB and needs to be fixed

alexskr commented 2 years ago

owlapi-wrapper run out of java heap space. Hardcoded -Xmx10240M is not enough to process NCBITAXON

jonquet commented 2 years ago

Hi @alexskr @syphax-bouazzouni has created a PR to address the setting of the heap-size: https://github.com/ncbo/ontologies_linked_data/pull/130

We have another out of memory issue showing up (at 4store level) after significantly increasing the heap size at the owl-api level (10>20Gb). We would be interested to know if you run into this too with NCBITAXON. https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/15#issuecomment-1055388402

alexskr commented 2 years ago

@syphax-bouazzouni PR looks great! Thank you!

@jonquet we are not running into this particular problem with 4store when processing NCBITAXON but our environment might be different from what you have. We use separate/dedicated VMs for parsing/ncbo_corn and for 4store so we don't have a memory contention issue you might be running into. Also, we use a secondary 4store instance when processing UMLS ontologies so that it doesn't have to serve life bioportal traffic.