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ApolloDev / apollo-sv

Repository for Apollo-SV ontology. Versioning Apollo-SV independently of the software was made easiest by having it as a separate repository.
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APOLLO "contamination" doesn't pertain to plant or animal organisms? #234

Open ddooley opened 1 year ago

ddooley commented 1 year ago

The definition and axioms for contamination process (aka biological contamination) forbid it occurring a material entity that is not an organism.

"The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity or the process of reproduction of a pathogen in or on a material entity that is not an organism."

Why limit biological contamination to non-organisms? Contaminated food is what we of course are primarily interested, and that can include e-coli contaminated fenugreek seeds / plants etc. Perhaps there is another word for this behaviour?

Also, what should we call the process after a food item has completed this contamination process, is contaminated, and pathogen reproduction occurs to bring the contaminant up to enough of an amount to potentially cause harm? Food biological spoilage?

We're looking at creating a hierarchy of contamination and decontamination processes and artifacts in FoodOn or wherever people recommend. Our hierarchy is (tentatively) at bottom of https://github.com/FoodOntology/foodon/issues/201

hoganwr commented 5 months ago

Happy to discuss and rework the definitions to accommodate. I don't think we intended to exclude food contamination. Note that we did attempt to cover situations where organisms can be contaminated: "The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity" which of course includes organism. THe latter half of the definition is the only part of the definition that applies to non-organisms.