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design patterns for emission processes #1039

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cmungall opened this issue Nov 18, 2020 · 1 comment
Open

design patterns for emission processes #1039

cmungall opened this issue Nov 18, 2020 · 1 comment

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@cmungall
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http://purl.obolibrary.org/obo/ENVO_01000742 carbon-bearing gas emission process
SubClassOf has quality some quality of a gas and has output some (has part some carbon atom)

this is cryptically incoherent - a process cannot have the quality of a gas

http://purl.obolibrary.org/obo/ENVO_01000769 carbon dioxide emission process

SubClassOf

has output some (
carbon dioxide and
has quality some quality of a gas)

This is dubious - individual chemical entities do not have qualities such as being a gas

In the release of ENVO we have methane and carbon-bearing emission as siblings:

image

by the definition of CB, methane should be a subclass - but the axiomatization is too opaque/inconsistent for the reasoner to determine this

as usual, I suggest a simpler design pattern, with no nesting. emission processes and environmental transfer process in general should avoid complex nested classes with chebi. use either plain chebi classes, or plain environmental materials (e.g subclasses of gas)

E.g. X emission = MTP and results-in-transport-of some X and has-end-location some atmosphere

@pbuttigieg
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pbuttigieg commented Mar 9, 2021

http://purl.obolibrary.org/obo/ENVO_01000742 carbon-bearing gas emission process
SubClassOf has quality some quality of a gas and has output some (has part some carbon atom)

this is cryptically incoherent - a process cannot have the quality of a gas

Yes, very odd - what's your proposed solution?

http://purl.obolibrary.org/obo/ENVO_01000769 carbon dioxide emission process

SubClassOf

has output some (
carbon dioxide and
has quality some quality of a gas)

This is dubious - individual chemical entities do not have qualities such as being a gas

Why not? Would this rather be

'has output' some (('environmental material' and 'composed primarily of' some 'carbon dioxide) and 'has quality' some 'quality of a gas')

I suppose you'd advise breaking that down for simplicity: how would you do that to preserve the semantics expressed?

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