Krishna to agro prj patterns for #1228 (#1330)

* Added CC pattern classes (desc for issues list)

Addresses issues
#369 #370 #371 #372 #373 #374  #401 #402 #403 #404 #405 #406 #407 #408 #409 #410 #411 #412 #414

* Added CC pattern class per issue #394

Ran dosdp run per previous commit with current class substitution.

* Revert "Added CC pattern class per issue #394"

This reverts commit e74d8aa.

* Revert "Added CC pattern classes (desc for issues list)"

This reverts commit 0064be2.

* Rerun pattern add using make recipe

* Revert "Rerun pattern add using make recipe"

This reverts commit d8e1124.

* Added EAL and CC pattern-based classes

See issues from list for classes added:
Chemical Concentration [CC]
 closes #369
 closes #394
 closes #401
 closes #402
 closes #403
 closes #404
 closes #405
 closes #406
 closes #407
 closes #408
 closes #409
 closes #410
 closes #411
 closes #412
 closes #414

Entity Attribute Location [EAL]
 closes #367
 closes #370
 closes #371
 closes #372
 closes #373
 closes #374
 closes #396
 closes #413
 closes #429

* #368 [EA] Added class 'color of soil'

* #360 Added class 'hours of sunshine'

Corrected previous commit's EAL pattern ids
Imported pato term: duration
Added class 'hours of sunshine' using EA pattern and revised label to correct string

* #366 Add class 'pressure of vapour'

* #361 [EA] Added class 'runoff volume'

closes #361

* #353,#354,#355 [EA] Added 'evaporation', 'evapotranspiration', 'rain' volumes

* Added classes for water infiltration

Added classes:
- water infiltration
- soil water infiltration

* #415 added classes for exchangeable potassium

Added classes:
- exchangeable potassium
- exchangeable ion

* #417 added class 'residual water'

* Added class 'exchangeable calcium'

* Added class 'cation exchange capacity'

* update DL 'exchangeable ion'

relation to 'CEC'

* #422 added class 'percentage base saturation'

* #415 #417 #418 Added CC patterns

Added patterns for classes:
- exchangeable potassium content in soil
- residual water content in soil
- exchangeable calcium content in soil

* Update 'water infiltration' DL

* #395 #398 #420 #432 Added classes in EA pattern

Added classes:
- soil water infiltration speed
- topsoil thickness
- soil drainage speed
- air temperature amplitude

* run robot dosdp patterns for CC & EA

Imported PATO term
corrected EA IRI

* regenerating pato_import.owl

* fixing semantics for manually added classes in #1228

* fixing unsatisfiable axiom https://github.com/EnvironmentOntology/envo/runs/7767526832?check_suite_focus=true#step:4:26

* deleting envo-edit-module-merged.owl

* fixing erroneous EAL patterns, manual reconfig of generated classes, IDs commented out in EAL txt module file

* attempting fix of https://github.com/EnvironmentOntology/envo/runs/7771430536?check_suite_focus=true#step:4:26

* regenerating all modules

Co-authored-by: Krishna Udaiwal <krishna.u@hotmail.com>
Co-authored-by: pier.buttigieg <pier.buttigieg@gitlab.hzdr.de>

src/envo/imports/pato_terms.txt

@@ -272,5 +272,7 @@ http://purl.obolibrary.org/obo/PATO_0001997 # decreased amount
 http://purl.obolibrary.org/obo/pato#decreased_in_magnitude_relative_to
 http://purl.obolibrary.org/obo/pato#increased_in_magnitude_relative_to
 http://purl.obolibrary.org/obo/PATO_0000323 # white
+http://purl.obolibrary.org/obo/PATO_0001309 # duration
 http://purl.obolibrary.org/obo/PATO_0040009 # bowl shaped
 http://purl.obolibrary.org/obo/PATO_0001295 # albedo
+http://purl.obolibrary.org/obo/PATO_0000915 # thickness

src/envo/modules/chemical_concentration.csv

@@ -101,3 +101,20 @@ ENVO:3200056,,CHEBI:27007,tin,ENVO:01000406,snow
 ENVO:3200057,,CHEBI:33341,titanium,ENVO:01000406,snow
 ENVO:3200058,,CHEBI:33331,yttrium,ENVO:01000406,snow
 ENVO:3200059,,CHEBI:16199,urea,ENVO:00002006,liquid water
+ENVO:3200060,,CHEBI:15379,oxygen,ENVO:00001998,soil
+ENVO:3200061,,CHEBI:25154,manganese molecular entity,ENVO:00001998,soil
+ENVO:3200062,,CHEBI:24873,iron molecular entity,ENVO:00001998,soil
+ENVO:3200063,,CHEBI:33620,aluminium molecular entity,ENVO:00001998,soil
+ENVO:3200064,,CHEBI:25108,magnesium molecular entity,ENVO:00001998,soil
+ENVO:3200065,,CHEBI:26712,sodium molecular entity,ENVO:00001998,soil
+ENVO:3200066,,CHEBI:50335,organic nitrogen anion,ENVO:00001998,soil
+ENVO:3200067,,CHEBI:25710,organophosphorus compound,ENVO:00001998,soil
+ENVO:3200068,,CHEBI:26082,phosphorus molecular entity,ENVO:00001998,soil
+ENVO:3200069,,CHEBI:26217,potassium molecular entity,ENVO:00001998,soil
+ENVO:3200070,,CHEBI:3311,calcium carbonate,ENVO:00001998,soil
+ENVO:3200071,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil
+ENVO:3200072,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil
+ENVO:3200073,,CHEBI:16189,sulfate,ENVO:00001998,soil
+ENVO:3200074,,ENVO:06105237,exchangeable potassium,ENVO:00001998,soil
+ENVO:3200075,,ENVO:06105238,residual water,ENVO:00001998,soil
+ENVO:3200076,,ENVO:06105239,exchangeable calcium,ENVO:00001998,soil

src/envo/modules/chemical_concentration.obo

@@ -613,3 +613,105 @@ name: concentration of urea in liquid water
 def: "The concentration of urea when measured in liquid water." []
 synonym: "liquid water urea concentration" EXACT []
 
+[Term]
+id: ENVO:3200060
+name: concentration of oxygen in soil
+def: "The concentration of oxygen when measured in soil." []
+synonym: "soil oxygen concentration" EXACT []
+
+[Term]
+id: ENVO:3200061
+name: concentration of manganese molecular entity in soil
+def: "The concentration of manganese molecular entity when measured in soil." []
+synonym: "soil manganese molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200062
+name: concentration of iron molecular entity in soil
+def: "The concentration of iron molecular entity when measured in soil." []
+synonym: "soil iron molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200063
+name: concentration of aluminium molecular entity in soil
+def: "The concentration of aluminium molecular entity when measured in soil." []
+synonym: "soil aluminium molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200064
+name: concentration of magnesium molecular entity in soil
+def: "The concentration of magnesium molecular entity when measured in soil." []
+synonym: "soil magnesium molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200065
+name: concentration of sodium molecular entity in soil
+def: "The concentration of sodium molecular entity when measured in soil." []
+synonym: "soil sodium molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200066
+name: concentration of organic nitrogen anion in soil
+def: "The concentration of organic nitrogen anion when measured in soil." []
+synonym: "soil organic nitrogen anion concentration" EXACT []
+
+[Term]
+id: ENVO:3200067
+name: concentration of organophosphorus compound in soil
+def: "The concentration of organophosphorus compound when measured in soil." []
+synonym: "soil organophosphorus compound concentration" EXACT []
+
+[Term]
+id: ENVO:3200068
+name: concentration of phosphorus molecular entity in soil
+def: "The concentration of phosphorus molecular entity when measured in soil." []
+synonym: "soil phosphorus molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200069
+name: concentration of potassium molecular entity in soil
+def: "The concentration of potassium molecular entity when measured in soil." []
+synonym: "soil potassium molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200070
+name: concentration of calcium carbonate in soil
+def: "The concentration of calcium carbonate when measured in soil." []
+synonym: "soil calcium carbonate concentration" EXACT []
+
+[Term]
+id: ENVO:3200071
+name: concentration of organic molecular entity in soil
+def: "The concentration of organic molecular entity when measured in soil." []
+synonym: "soil organic molecular entity concentration" EXACT []
+
+[Term]
+id: ENVO:3200072
+name: concentration of tetraphosphorus decaoxide in soil
+def: "The concentration of tetraphosphorus decaoxide when measured in soil." []
+synonym: "soil tetraphosphorus decaoxide concentration" EXACT []
+
+[Term]
+id: ENVO:3200073
+name: concentration of sulfate in soil
+def: "The concentration of sulfate when measured in soil." []
+synonym: "soil sulfate concentration" EXACT []
+
+[Term]
+id: ENVO:3200074
+name: concentration of exchangeable potassium in soil
+def: "The concentration of exchangeable potassium when measured in soil." []
+synonym: "soil exchangeable potassium concentration" EXACT []
+
+[Term]
+id: ENVO:3200075
+name: concentration of residual water in soil
+def: "The concentration of residual water when measured in soil." []
+synonym: "soil residual water concentration" EXACT []
+
+[Term]
+id: ENVO:3200076
+name: concentration of exchangeable calcium in soil
+def: "The concentration of exchangeable calcium when measured in soil." []
+synonym: "soil exchangeable calcium concentration" EXACT []
+