Added spatio-temporal scale #1576

timalamenciak · 2024-12-12T15:04:58Z

Added terms for scale (spatio-temporal) and subclasses micro-scale, meso-scale, macro-scale, mega-scale. Addressing issue #1569

Added terms for scale (spatio-temporal) and subclasses micro-scale, meso-scale, macro-scale, mega-scale. Addressing issue EnvironmentOntology#1569

pbuttigieg

I think we need to find the right superclass for "scale" in PATO, or mint one if there's nothing appropriate present. PATO's 'physical quality' is a fair start.

scale =def. "A physical quality which inheres in a bearer by virtue of its size, extent, or degree relative to other entities."

xref https://www.merriam-webster.com/dictionary/scale

and then we can formulate the others like:

'spatiotemporal scale' =def. "A scale which inheres in a bearer by virtue of its extent in space and time."

'geographic megascale' =def. "A spatiotemporal scale which inheres in a bearer that has a spatial extent of 1,000,000,000,000 m² or greater and temporal a temporal extent of 1,000,000 years or greater."

timalamenciak · 2024-12-13T20:34:50Z

I think we need to find the right superclass for "scale" in PATO, or mint one if there's nothing appropriate present. PATO's 'physical quality' is a fair start.

I'm not sure that a scale is a physical quality. I think that it inheres in a description or observation. An apple doesn't have a scale, but a picture of an apple does. This is the reason why I thought it would fit under qualitative - PATO:0000068:

qualitative=def"A quality of an entity that is descriptive or observational, typically not represented numerically."

pbuttigieg · 2024-12-13T22:25:22Z

I'm not sure that a scale is a physical quality. I think that it inheres in a description or observation. An apple doesn't have a scale, but a picture of an apple does.

An apple does have a scale - mesoscopic scale. Spatiotemporal scale is a relativistic way of expressing an entity's spatiotemporal footprint, its size through time (a fundamentally physical thing). In that sense, it's a relational quality, and the definition specifies what it's being related to (e.g. lengths, areas, volumes, and time ranges).

I don't think a specifically dependent continuant (like a quality) can inhere in a generically dependent continuant (like a description or observation), at least not in a metaphysical way.

This is the reason why I thought it would fit under qualitative - PATO:0000068:

this class is a very odd one in PATO, an ontology of qualities. It's a strange attempt to represent qualitative and quantitative data types or variables as specifically dependent continuants.

pbuttigieg · 2024-12-13T22:54:54Z

An alternative is to create spatiotemporal entities e.g (1D time, and 2D space) for each scale category and figure out a relation that expresses that a given ecosystem occupies these immaterial entities

BFO used to have such relations, but they seem obsolete, and their domains are occurrents.

http://purl.obolibrary.org/obo/BFO_0000083 (BFO):
occupies spatial region at some time

http://purl.obolibrary.org/obo/BFO_0000130 (BFO):
occupies spatiotemporal region

http://purl.obolibrary.org/obo/BFO_0000155 (BFO):
occupies temporal region

Their ghosts are still around in various imports like this one

It's possible that RO tried to absorb these in relations like spatially coextensive with and simultaneous with. They don't seem very clear though.

If we choose this way, we'll mint what we need in ENVO

pbuttigieg · 2024-12-16T02:16:26Z

Another approach would be to create subclasses of PATO's size and duration, although duration is a process quality. Perhaps age is better.

These would be labelled like "geographic megascale age" and "geographic megascale size", and could be applied to material entities via 'has quality' independently, as needed.

pbuttigieg · 2024-12-16T13:50:47Z

Another approach would be to create subclasses of PATO's size and duration, although duration is a process quality. Perhaps age is better.

These would be labelled like "geographic megascale age" and "geographic megascale size", and could be applied to material entities via 'has quality' independently, as needed.

@timalamenciak I think this is the most approachable way for now, that's also reasonably accurate.

Definitions (which would dbxref https://en.wikipedia.org/wiki/Scale_(geography) ) would look like the examples below.

Note that we should use "landscape [...]scale" as a prefix, as geographic scale is one class of such scales (cartographic being another)

Age

For chronological age subclasses:

'landscape megascale age' =def. "Chronological age which inheres in a bearer by virtue of that bearer existing for at least 1,000,000 years."

Area

For area subclasses:

'landscape mesoscale size' =def. "An area quality which inheres in a bearer by virtue of that bearer having an area of between 1,000,000 and 10,000,000,000 square metres"

@pbuttigieg

Per @pbuttigieg review - added classes for "landscape Xscale age" under PATO:0001486 and "landscape Xscale size" under PATO:0001323

pbuttigieg

Some corrections and questions

pbuttigieg · 2024-12-16T15:45:42Z

src/envo/envo-edit.owl

@@ -48903,6 +48998,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000111> "editor preferred term~editor preferred label")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000412> "imported from")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000424> "expand expression to")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0000068> "A quality of an entity that is descriptive or observational, typically not represented numerically.")


Not sure what's happening here in the Named Individuals block - could you clarify?

pbuttigieg · 2024-12-16T15:46:29Z

src/envo/envo-edit.owl

+# Class: <http://purl.obolibrary.org/obo/PATO_0001486> (chronological age)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PATO_0001486> "An age quality that exists by virtue of the time (years and months) that the bearer has existed.")
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PATO_0001486> "chronological age")
+SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001486> <http://purl.obolibrary.org/obo/PATO_0000011>)
+


Was this added manually or via a process like https://github.com/EnvironmentOntology/envo/wiki/Import-terms-from-other-ontologies?

@timalamenciak this process is a bit involved, but it's worth knowing how to set up the docker container that runs all the robot tools etc.

If this is too much right now, don't worry - we can fix it later. Proceed like you are right now and create a new issue to patch up the import of chronological age

This was added manually using Protege. I can look through the process shortly though and take another run at it.

It takes some docker magic, but isn't that hard if you have the memory (around 16 GB for the container is usually enough, processing the CHEBI and NCBITaxon imports hog memory)

Added PATO chronologic age import as issue #1587

pbuttigieg · 2024-12-16T15:52:23Z

src/envo/envo-edit.owl

+
+# Class: <http://purl.obolibrary.org/obo/ENVO_03620015> (landscape macroscale size)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620015> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 10,000,000,000 and 10,000,000,000,000 square metres")


10e10 is 100,000,000,000

I prefer exponential notation, but is it even true that this is an accepted cutoff? Sources would be good

pbuttigieg · 2024-12-16T15:54:00Z

src/envo/envo-edit.owl

+
+# Class: <http://purl.obolibrary.org/obo/ENVO_03620016> (landscape mesoscale size)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620016> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 1,000,000 and 10,000,000,000 square metres.")


10e6 is and 10,000,000 and 10e10 is 100,000,000,000

pbuttigieg · 2024-12-16T15:54:42Z

src/envo/envo-edit.owl

+
+# Class: <http://purl.obolibrary.org/obo/ENVO_03620017> (landscape microscale size)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620017> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 0 and 1,000,000 square metres")


10e6 is and 10,000,000

cmungall · 2024-12-17T00:53:20Z

src/envo/envo-edit.owl

+AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> <http://purl.obolibrary.org/obo/ENVO_03620010> "https://orcid.org/0000-0002-4366-3088")
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_03620010> <https://orcid.org/0000-0002-1296-2528>)
+AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_03620010> "2024-12-16T14:35:15Z"^^xsd:dateTime)
+AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_03620010> "https://en.wikipedia.org/wiki/Scale_(geography)")


I wouldn't use an xref here..

cmungall · 2024-12-17T00:53:37Z

src/envo/envo-edit.owl

+
+# Class: <http://purl.obolibrary.org/obo/ENVO_03620013> (landscape microscale age)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620013> "Chronological age which inheres in a bearer by virtue of that bearer existing for between1 and 500 years.")


Added spatio-temporal scale

5a94173

Added terms for scale (spatio-temporal) and subclasses micro-scale, meso-scale, macro-scale, mega-scale. Addressing issue EnvironmentOntology#1569

timalamenciak requested a review from pbuttigieg December 12, 2024 15:04

timalamenciak mentioned this pull request Dec 12, 2024

Updating to include terms relevant to restoration ecology and conservation #1577

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pbuttigieg assigned pbuttigieg and timalamenciak and unassigned pbuttigieg Dec 16, 2024

pbuttigieg added the enhancement label Dec 16, 2024

pbuttigieg mentioned this pull request Dec 16, 2024

Add micro, meso, macroscopic size qualities #1580

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Removed scale under qualitative and added under PATO age and size

d6df28b

Per @pbuttigieg review - added classes for "landscape Xscale age" under PATO:0001486 and "landscape Xscale size" under PATO:0001323

pbuttigieg reviewed Dec 16, 2024

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cmungall reviewed Dec 17, 2024

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Added spatio-temporal scale #1576

Added spatio-temporal scale #1576

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		# Class: <http://purl.obolibrary.org/obo/ENVO_03620015> (landscape macroscale size)

		AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_03620015> "An area quality which inheres in a bearer by virtue of that bearer having an area of between 10,000,000,000 and 10,000,000,000,000 square metres")

Added spatio-temporal scale #1576

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Added spatio-temporal scale #1576

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Age

Area

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