Adding missing defs detected in #1159 #1163

pbuttigieg · 2021-05-14T11:49:14Z

Description and progress notes in #1159

pbuttigieg · 2021-05-15T10:55:51Z

Setting status as "ready for review" to preview merge conflict status

…nd hierarchy shuffling

pbuttigieg · 2021-05-18T15:30:37Z

Could you tell me how to get a graphical view of the proposed hierarchy?
I would like to get this reviewed by my local soil/landscape subject-matter-experts.

@dr-shorthair
I sketched one here #1159 (comment) using VUE, but you could also use a Protégé plugin like OntoGraph to generate a less neat overview (reflecting the work in progress state of things)

pbuttigieg · 2021-05-18T15:40:40Z

Prep for some merge conflicts when the new release hits the master branch....

Edit: refreshingly, no merge conflicts reported

pbuttigieg · 2021-06-11T10:51:05Z

A new non-content error emerges...

But one build passed...

pbuttigieg · 2022-02-07T17:18:03Z

There are some stragglers (marine reef bits) that need more thought and may merge in with the CMECS terms

This should fix the build issues with: * #1172. * #1163

wdduncan · 2022-02-11T01:04:56Z

@pbuttigieg @kaiiam @cmungall The PR now passes the travis_test. Are you ready to merge?

smrgeoinfo · 2022-03-07T18:57:01Z

src/envo/envo-edit.owl

@@ -5448,7 +5464,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000054> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000055> (saline evaporation pond)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Salt_evaporation_ponds"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000055> "A shallow man-made pond designed to produce salt from sea water. The seawater is fed into large ponds and water is drawn out through natural evaporation which allows the salt to be subsequently harvested."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Salt_evaporation_ponds"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000055> "A pond which is 1) shallow, 2) man-made, and 3) designed to produce salt from seawater through evaporation."@en)


there are also saline evaporation ponds adjacent to salt lakes in continental areas, e.g. Great Salt Lake, Utah, or to evaporate saline water used to dissolve subsurface salt deposits e.g. around the Luke salt in the Phoenix area, Arizona.

smrgeoinfo · 2022-03-07T18:59:50Z

src/envo/envo-edit.owl

@@ -5390,19 +5406,19 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000050> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000051> (hot spring)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Hot_spring"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000051> "A spring that is produced by the emergence of geothermally-heated groundwater from the Earth's crust."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Hot_spring"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000051> "A spring through which groundwater, heated by geothermal energy, flows."@en)


why complicate with 'groundwater' and 'heated by geothermal energy'. simplify to
'a spring that emits water that is warmer than the ambient ground temperature'.
Is 'warm spring' a concept in ENVO. Generally 'hot' connotes a temperature above something like human body temperature.

smrgeoinfo · 2022-03-07T19:01:51Z

src/envo/envo-edit.owl

@@ -5751,7 +5766,7 @@ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#has
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000116> <http://purl.obolibrary.org/obo/ENVO_00000070> "\"constructed\" should probably be made something like a quality and this class obsoleted or filled only by inference")
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000070> "constructed feature")
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000070> "human construction"^^xsd:string)
-EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_00000070> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_01001813> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002353> <http://purl.obolibrary.org/obo/ENVO_01000996>)))
+SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000070> <http://purl.obolibrary.org/obo/ENVO_01001813>)


ah, the joy of opaque identifiers. Can't evaluate this statement without resolving the URI...

smrgeoinfo · 2022-03-07T19:02:25Z

src/envo/envo-edit.owl

@@ -5926,7 +5941,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000079> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000080> (mountain range)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "USGS:SDTS"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000080> "A series of connected and aligned mountains or mountain ridges."^^xsd:string)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000080> "A range of mounts which is dominated by mountains."^^xsd:string)


circular. a mountain range is a range.

smrgeoinfo · 2022-03-07T19:03:35Z

src/envo/envo-edit.owl

@@ -6119,12 +6128,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000088> ObjectSomeValuesFrom(<

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000089> (inland cliff)

+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000089> "A cliff which is not adjacent to a major water body."@en)


gramatically should use 'that' instead of 'which'
a cliff that is not adjacent....

smrgeoinfo · 2022-03-07T19:05:40Z

src/envo/envo-edit.owl

 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/ENVO_00000304>))
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000091> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_00002007> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> ObjectUnionOf(<http://purl.obolibrary.org/obo/ENVO_00002139> <http://purl.obolibrary.org/obo/ENVO_00002140> <http://purl.obolibrary.org/obo/ENVO_01000017> <http://purl.obolibrary.org/obo/ENVO_01000018> <http://purl.obolibrary.org/obo/UBERON_0006612>)))))

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000092> (sea beach)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Beach"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000092> "A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a sea."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Beach"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000092> "A beach which is part of a sea shore."^^xsd:string)


the original definition is much better. To understand this revised definition, I have to figure out what you mean by 'beach' and what you mean by 'sea shore'....

smrgeoinfo · 2022-03-07T19:05:56Z

src/envo/envo-edit.owl

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000093> "A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a lake."^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_00000093> "ENVO"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_00000093> "ENVO:00000093"^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000093> "A beach which is part of a lake shore."^^xsd:string)


smrgeoinfo · 2022-03-07T19:07:46Z

src/envo/envo-edit.owl

@@ -6392,6 +6396,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000103> ObjectSomeValuesFrom(<

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000104> (undersea feature)

+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000104> "A hydrographic feature which is located below the surface of a marine water body."@en)


hmmm, wouldn't features on the sea floor (sand waves, biogenic mounds, rift valleys, seamounts, reefs) also be considered undersea features? these are not hydrographic.

smrgeoinfo · 2022-03-07T19:09:01Z

src/envo/envo-edit.owl

@@ -6819,13 +6822,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000120> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000121> (artificial channel)

+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000121> "A channel of a watercource which has been constructed by humans or their technologies."@en)


I think 'a channel constructed by humans' is all you need.

smrgeoinfo · 2022-03-07T19:11:03Z

src/envo/envo-edit.owl

@@ -6865,29 +6868,25 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000124> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000125> (mineral spring)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Mineral_spring"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000125> "A spring whose water contains a significant amount of dissolved minerals, that derive from the rocks through which the water flows."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Mineral_spring"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000125> "A spring which  water contains a significant amount of dissolved minerals, that derive from the rocks through which the water flows."^^xsd:string)


don't complicate with stuff that should be in notes.
'A spring that emits water containing a significant amount of dissolved minerals'.
Of course a purist might want to know what you mean by 'minerals'

smrgeoinfo · 2022-03-07T19:12:56Z

src/envo/envo-edit.owl

 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000127> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000086> <http://purl.obolibrary.org/obo/ENVO_01000230>))

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000128> (dry valley)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Dry_valley"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000128> "A valley that no longer has a surface flow of water. Typically found in either Karst (limestone) or chalk terrain."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Dry_valley"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000128> "A valley which no longer has water flowing or accumulating over its surface."^^xsd:string)


why 'no longer'???
A valley that does not contain perennial surface water.

smrgeoinfo · 2022-03-07T19:13:30Z

src/envo/envo-edit.owl

 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000128> "https://en.wikipedia.org/wiki/Dry_valley"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_00000128> "ENVO"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_00000128> "ENVO:00000128"^^xsd:string)
+AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00000128> "Typically found in either Karst (limestone) or chalk terrain."@en)


what about dry valleys in deserts?

smrgeoinfo · 2022-03-07T19:16:55Z

src/envo/envo-edit.owl


 # Class: <http://purl.obolibrary.org/obo/ENVO_00000150> (coral reef)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Coral_reef"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000150> "Aragonite structures produced by living organisms, found in shallow, marine waters with little nutrients in the water."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Coral_reef"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000150> "A marine reef which is composed primarily of aragonite structures produced by living organisms, found in shallow, low-nutrient waters."@en)


I'd suggest 'calcium-rich carbonate minerals'. If its a 'coral' reef, don't the 'living organisms' have to be members of that genus? Is there such a thing as a 'non-marine' reef??

smrgeoinfo · 2022-03-07T19:18:37Z

src/envo/envo-edit.owl


 # Class: <http://purl.obolibrary.org/obo/ENVO_00000175> (karst)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Karst"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000175> "A feature shaped by the dissolution of a soluble layer or layers of bedrock, usually carbonate rock such as limestone or dolomite. These landscapes display distinctive surface features and underground drainages, and in some examples there may be little or no surface drainage."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Karst"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000175> "A surface landform which is formed by the dissolution of a soluble layer or layers of bedrock."^^xsd:string)


simplify
' ... dissolution of soluble bedrock'

smrgeoinfo · 2022-03-07T19:24:16Z

src/envo/envo-edit.owl

@@ -9746,14 +9735,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000324> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000325> (polje)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://wasg.iinet.net.au/terminol.html"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000325> "A large closed depression draining underground, witha flat floor across which there may be an intermittent or perennial stream and which may be liable to flood and become a lake. The floor makes a sharp break with parts of surrounding slopes."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "http://wasg.iinet.net.au/terminol.html"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000325> "A large closed depression draining underground, with a flat floor across which there may be an intermittent or perennial stream and which may be liable to flood and become a lake. The floor makes a sharp break with parts of surrounding slopes."^^xsd:string)


a note indicating the connotation of karst association would be useful.

smrgeoinfo · 2022-03-07T19:27:18Z

src/envo/envo-edit.owl


-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Harbor"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000463> "A place where ships may shelter from the weather or are stored."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Harbor"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000463> "A landform which provides shelter from atmospheric weather and marine currents, waves, and other dynamics."^^xsd:string)


perhaps 'a shoreline landform...' otherwise any cave would meet this definition.

smrgeoinfo · 2022-03-07T19:29:36Z

src/envo/envo-edit.owl

 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000508> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/ENVO_00002000>))

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000509> (marine terrace)

+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000509> "A terrace which is located in a marine water body."@en)


I think marine terraces are located along the shore line of a marine water body; many of them are subaerial, not submerged.

smrgeoinfo · 2022-03-07T19:40:20Z

src/envo/envo-edit.owl

@@ -12617,53 +12592,51 @@ AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/ENVO_00000886

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000887> (large river biome)

-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_00000887> "ENVO"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_00000887> "ENVO:00000887"^^xsd:string)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000887> "A freshwater river biome which is determined by a large river."@en)


i assume 'large river' is defined in ENVO? what does 'determined by a river' mean?

smrgeoinfo · 2022-03-07T19:41:06Z

src/envo/envo-edit.owl

 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_00000887> "wwfBiome")
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00000887> "\"Large\" is ambiguous. For details on \"Large rivers\" (e.g. the Mekong river) see http://worldwildlife.org/biomes/large-river-ecosystems This class will be replaced with a less ambiguous class."^^xsd:string)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000887> "large river biome"^^xsd:string)
 SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000887> <http://purl.obolibrary.org/obo/ENVO_01000253>)

 # Class: <http://purl.obolibrary.org/obo/ENVO_00000888> (large river headwater biome)

-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_00000888> "ENVO"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_00000888> "ENVO:00000888"^^xsd:string)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000888> "A freshwater river biome which is determined by the headwaters of a large river."@en)


since the headwaters of a large river a likely to be small rivers, how is this different from a 'small river biome'?

smrgeoinfo · 2022-03-07T19:42:37Z

src/envo/envo-edit.owl


 # Class: <http://purl.obolibrary.org/obo/ENVO_00000889> (large river delta biome)

-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/ENVO_00000889> "ENVO"^^xsd:string)
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/ENVO_00000889> "ENVO:00000889"^^xsd:string)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000889> "A freshwater river biome which is determined by the delta of a large river."@en)


seem like language like 'a biome hosted by the delta of a river' would be better way to define. Isn't a biome hosted by some environment?

smrgeoinfo · 2022-03-07T19:45:21Z

src/envo/envo-edit.owl

@@ -12800,16 +12771,16 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00001999> ObjectSomeValuesFrom(<

 # Class: <http://purl.obolibrary.org/obo/ENVO_00002000> (slope)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002000> "A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and  relatively flat surrounding land."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002000> "A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land."^^xsd:string)


Isn't the essential feature of a slope the fact that is has a surface elevation gradient greater than something like 5 degrees? This definition would include flat terraces between a peak and a valley as slopes.

smrgeoinfo · 2022-03-07T19:46:27Z

src/envo/envo-edit.owl

@@ -13519,26 +13481,27 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002118> <http://purl.obolibrar

 # Class: <http://purl.obolibrary.org/obo/ENVO_00002119> (alkaline hot spring)

-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002119> "A hot spring whose water has an alkaline pH."^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://orcid.org/0000-0002-4366-3088>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002119> "A alkaline spring through which groundwater, heated by geothermal energy, flows."@en)


original definition is better.

kaiiam · 2022-03-09T21:11:55Z

Still some missing definitions e.g. glaze ENVO_01001849. I'll try to use robot export to see what classes are missing definitions at some point.

addressed the a... terms of #1159

24c64d5

pbuttigieg added the bug label May 14, 2021

pbuttigieg self-assigned this May 14, 2021

pbuttigieg linked an issue May 14, 2021 that may be closed by this pull request

Terms missing definitions #1159

Closed

pbuttigieg added this to In Progress in betterTech May 14, 2021

pbuttigieg marked this pull request as draft May 14, 2021 11:49

pbuttigieg added 3 commits May 14, 2021 15:27

added defs for soil terms in #1159

ad59423

Merge branch 'master' into issue-1159

d9ddede

addressing #1159 with some significant rearrangements to landforms

ebedb20

pbuttigieg marked this pull request as ready for review May 15, 2021 10:55

pbuttigieg added 2 commits May 15, 2021 14:26

more definitions to address #1159, with some resultant relabellings a…

8fc6723

…nd hierarchy shuffling

more defs and hierarchy refinement for #1159

94826df

Further addressing #1159 and adding coherence to spring hierarchy

ea10af9

pbuttigieg added 3 commits June 25, 2021 17:01

biomes defined for #1159

2248804

some updates for 1159

e263a00

clean up merge

cb867fa

kaiiam mentioned this pull request Feb 10, 2022

Issue 1160 #1172

Merged

cmungall added a commit that referenced this pull request Feb 10, 2022

Fix github actions to not build imports

4238f50

This should fix the build issues with: * #1172. * #1163

cmungall mentioned this pull request Feb 10, 2022

Fix github actions to not build imports #1292

Merged

Merge branch 'master' into issue-1159

3302bda

cmungall approved these changes Feb 11, 2022

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pbuttigieg merged commit 504ada3 into master Mar 7, 2022

smrgeoinfo reviewed Mar 7, 2022

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pbuttigieg deleted the issue-1159 branch August 15, 2022 16:22

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Adding missing defs detected in #1159 #1163

Adding missing defs detected in #1159 #1163

pbuttigieg commented May 14, 2021

pbuttigieg commented May 15, 2021

pbuttigieg commented May 18, 2021 •

edited

pbuttigieg commented May 18, 2021 •

edited

pbuttigieg commented Jun 11, 2021 •

edited

pbuttigieg commented Feb 7, 2022

wdduncan commented Feb 11, 2022

smrgeoinfo Mar 7, 2022 •

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kaiiam commented Mar 9, 2022

		@@ -6119,12 +6128,11 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000088> ObjectSomeValuesFrom(<

		# Class: <http://purl.obolibrary.org/obo/ENVO_00000089> (inland cliff)

		AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000089> "A cliff which is not adjacent to a major water body."@en)

		@@ -6392,6 +6396,7 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000103> ObjectSomeValuesFrom(<

		# Class: <http://purl.obolibrary.org/obo/ENVO_00000104> (undersea feature)

		AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000104> "A hydrographic feature which is located below the surface of a marine water body."@en)

		@@ -6819,13 +6822,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000120> <http://purl.obolibrar

		# Class: <http://purl.obolibrary.org/obo/ENVO_00000121> (artificial channel)

		AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000121> "A channel of a watercource which has been constructed by humans or their technologies."@en)


		AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Harbor"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000463> "A place where ships may shelter from the weather or are stored."^^xsd:string)
		AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "https://en.wikipedia.org/wiki/Harbor"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000463> "A landform which provides shelter from atmospheric weather and marine currents, waves, and other dynamics."^^xsd:string)

Adding missing defs detected in #1159 #1163

Adding missing defs detected in #1159 #1163

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pbuttigieg commented May 14, 2021

pbuttigieg commented May 15, 2021

pbuttigieg commented May 18, 2021 • edited

pbuttigieg commented May 18, 2021 • edited

pbuttigieg commented Jun 11, 2021 • edited

pbuttigieg commented Feb 7, 2022

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kaiiam commented Mar 9, 2022

pbuttigieg commented May 18, 2021 •

edited

pbuttigieg commented May 18, 2021 •

edited

pbuttigieg commented Jun 11, 2021 •

edited

smrgeoinfo Mar 7, 2022 •

edited