From 0064be2fe7a39bf4defe479160ae716de9067720 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Thu, 28 Oct 2021 21:09:26 -0400 Subject: [PATCH 01/23] 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 --- src/envo/envo-edit.owl | 180 ++ src/envo/modules/chemical_concentration.csv | 20 + src/envo/modules/chemical_concentration.owl | 3146 ++----------------- 3 files changed, 376 insertions(+), 2970 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 12140e92..60da1957 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -40,14 +40,24 @@ Annotation( "https://github.com/Envir Annotation( "ENVO"^^xsd:string) Annotation( "http://environmentontology.org/"^^xsd:anyURI) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -55,10 +65,15 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3722,11 +3737,34 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3739,6 +3777,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -3747,6 +3786,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -41757,6 +41797,146 @@ AnnotationAssertion( "ionizing radiation") SubClassOf( ) +# Class: (concentration of oxygen in soil) + +AnnotationAssertion( "The concentration of oxygen when measured in soil."^^xsd:string) +AnnotationAssertion( "soil oxygen concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of oxygen in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of clay in soil) + +AnnotationAssertion( "The concentration of clay when measured in soil."^^xsd:string) +AnnotationAssertion( "soil clay concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of clay in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of slit in soil) + +AnnotationAssertion( "The concentration of slit when measured in soil."^^xsd:string) +AnnotationAssertion( "soil slit concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of slit in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of sand in soil) + +AnnotationAssertion( "The concentration of sand when measured in soil."^^xsd:string) +AnnotationAssertion( "soil sand concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of sand in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of gravel in soil) + +AnnotationAssertion( "The concentration of gravel when measured in soil."^^xsd:string) +AnnotationAssertion( "soil gravel concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of gravel in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of liquid water in soil) + +AnnotationAssertion( "The concentration of liquid water when measured in soil."^^xsd:string) +AnnotationAssertion( "soil liquid water concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of liquid water in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of manganese molecular entity in soil) + +AnnotationAssertion( "The concentration of manganese molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil manganese molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of manganese molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of iron molecular entity in soil) + +AnnotationAssertion( "The concentration of iron molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil iron molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of iron molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of aluminium molecular entity in soil) + +AnnotationAssertion( "The concentration of aluminium molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil aluminium molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of aluminium molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of magnesium molecular entity in soil) + +AnnotationAssertion( "The concentration of magnesium molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil magnesium molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of magnesium molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of sodium molecular entity in soil) + +AnnotationAssertion( "The concentration of sodium molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil sodium molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of sodium molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of organic nitrogen anion in soil) + +AnnotationAssertion( "The concentration of organic nitrogen anion when measured in soil."^^xsd:string) +AnnotationAssertion( "soil organic nitrogen anion concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of organic nitrogen anion in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of organophosphorus compound in soil) + +AnnotationAssertion( "The concentration of organophosphorus compound when measured in soil."^^xsd:string) +AnnotationAssertion( "soil organophosphorus compound concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of organophosphorus compound in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of phosphorus molecular entity in soil) + +AnnotationAssertion( "The concentration of phosphorus molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil phosphorus molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of phosphorus molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of potassium molecular entity in soil) + +AnnotationAssertion( "The concentration of potassium molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil potassium molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of potassium molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of calcium carbonate in soil) + +AnnotationAssertion( "The concentration of calcium carbonate when measured in soil."^^xsd:string) +AnnotationAssertion( "soil calcium carbonate concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of calcium carbonate in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of organic molecular entity in soil) + +AnnotationAssertion( "The concentration of organic molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil organic molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of organic molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of tetraphosphorus decaoxide in soil) + +AnnotationAssertion( "The concentration of tetraphosphorus decaoxide when measured in soil."^^xsd:string) +AnnotationAssertion( "soil tetraphosphorus decaoxide concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of tetraphosphorus decaoxide in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of sulfate in soil) + +AnnotationAssertion( "The concentration of sulfate when measured in soil."^^xsd:string) +AnnotationAssertion( "soil sulfate concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of sulfate in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + +# Class: (concentration of salt in soil) + +AnnotationAssertion( "The concentration of salt when measured in soil."^^xsd:string) +AnnotationAssertion( "soil salt concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of salt in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + # Class: (area of alpine tundra) AnnotationAssertion(Annotation( ) Annotation( ) "An area of tundra which is present in a region subject to alpine conditions.") diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e6edf3b8..e0877ebe 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -101,3 +101,23 @@ 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,,ENVO:00002982,clay,ENVO:00001998,soil +ENVO:3200062,,ENVO:01000016,slit,ENVO:00001998,soil +ENVO:3200063,,ENVO:01000017,sand,ENVO:00001998,soil +ENVO:3200064,,ENVO:01000018,gravel,ENVO:00001998,soil +ENVO:3200065,,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:3200066,,CHEBI:25154,manganese molecular entity,ENVO:00001998,soil +ENVO:3200067,,CHEBI:24873,iron molecular entity,ENVO:00001998,soil +ENVO:3200068,,CHEBI:33620,aluminium molecular entity,ENVO:00001998,soil +ENVO:3200069,,CHEBI:25108,magnesium molecular entity,ENVO:00001998,soil +ENVO:3200070,,CHEBI:26712,sodium molecular entity,ENVO:00001998,soil +ENVO:3200071,,CHEBI:50335,organic nitrogen anion,ENVO:00001998,soil +ENVO:3200072,,CHEBI:25710,organophosphorus compound,ENVO:00001998,soil +ENVO:3200073,,CHEBI:26082,phosphorus molecular entity,ENVO:00001998,soil +ENVO:3200074,,CHEBI:26217,potassium molecular entity,ENVO:00001998,soil +ENVO:3200075,,CHEBI:3311,calcium carbonate,ENVO:00001998,soil +ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil +ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil +ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil +ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 1b9ea83a..dc33ac5e 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -69,249 +69,63 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -321,99 +135,33 @@ - - - - - - - + - + - + - + - + - + - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -423,126 +171,33 @@ - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of Adenosine 5-triphosphate when measured in liquid water. - liquid water Adenosine 5-triphosphate concentration - concentration of Adenosine 5-triphosphate in liquid water - + - + - - - - - - - - - - - - - - - - - - - - - - - The concentration of alloxanthine when measured in liquid water. - liquid water alloxanthine concentration - concentration of alloxanthine in liquid water - + - + - - - - - - - - - - - - - - - - - - - - - - - The concentration of alpha-carotene when measured in liquid water. - liquid water alpha-carotene concentration - concentration of alpha-carotene in liquid water - + - + - + @@ -552,10 +207,10 @@ - + - + @@ -564,16 +219,16 @@ - The concentration of ammonium when measured in liquid water. - liquid water ammonium concentration - concentration of ammonium in liquid water + The concentration of oxygen when measured in soil. + soil oxygen concentration + concentration of oxygen in soil - + - + @@ -583,10 +238,10 @@ - + - + @@ -595,16 +250,16 @@ - The concentration of bacteriochlorophyll a when measured in liquid water. - liquid water bacteriochlorophyll a concentration - concentration of bacteriochlorophyll a in liquid water + The concentration of clay when measured in soil. + soil clay concentration + concentration of clay in soil - + - + @@ -614,10 +269,10 @@ - + - + @@ -626,16 +281,16 @@ - The concentration of beta-carotene when measured in liquid water. - liquid water beta-carotene concentration - concentration of beta-carotene in liquid water + The concentration of slit when measured in soil. + soil slit concentration + concentration of slit in soil - + - + @@ -645,10 +300,10 @@ - + - + @@ -657,16 +312,16 @@ - The concentration of carotene when measured in liquid water. - liquid water carotene concentration - concentration of carotene in liquid water + The concentration of sand when measured in soil. + soil sand concentration + concentration of sand in soil - + - + @@ -676,10 +331,10 @@ - + - + @@ -688,16 +343,16 @@ - The concentration of chlorophyll a when measured in liquid water. - liquid water chlorophyll a concentration - concentration of chlorophyll a in liquid water + The concentration of gravel when measured in soil. + soil gravel concentration + concentration of gravel in soil - + - + @@ -707,10 +362,10 @@ - + - + @@ -719,16 +374,16 @@ - The concentration of chlorophyll b when measured in liquid water. - liquid water chlorophyll b concentration - concentration of chlorophyll b in liquid water + The concentration of liquid water when measured in soil. + soil liquid water concentration + concentration of liquid water in soil - + - + @@ -738,10 +393,10 @@ - + - + @@ -750,16 +405,16 @@ - The concentration of chlorophyllide a when measured in liquid water. - liquid water chlorophyllide a concentration - concentration of chlorophyllide a in liquid water + The concentration of manganese molecular entity when measured in soil. + soil manganese molecular entity concentration + concentration of manganese molecular entity in soil - + - + @@ -769,10 +424,10 @@ - + - + @@ -781,16 +436,16 @@ - The concentration of dioxygen when measured in liquid water. - liquid water dioxygen concentration - concentration of dioxygen in liquid water + The concentration of iron molecular entity when measured in soil. + soil iron molecular entity concentration + concentration of iron molecular entity in soil - + - + @@ -800,10 +455,10 @@ - + - + @@ -812,16 +467,16 @@ - The concentration of divinyl chlorophyll a when measured in liquid water. - liquid water divinyl chlorophyll a concentration - concentration of divinyl chlorophyll a in liquid water + The concentration of aluminium molecular entity when measured in soil. + soil aluminium molecular entity concentration + concentration of aluminium molecular entity in soil - + - + @@ -831,10 +486,10 @@ - + - + @@ -843,16 +498,16 @@ - The concentration of divinyl chlorophyll b when measured in liquid water. - liquid water divinyl chlorophyll b concentration - concentration of divinyl chlorophyll b in liquid water + The concentration of magnesium molecular entity when measured in soil. + soil magnesium molecular entity concentration + concentration of magnesium molecular entity in soil - + - + @@ -862,10 +517,10 @@ - + - + @@ -874,16 +529,16 @@ - The concentration of fucoxanthin when measured in liquid water. - liquid water fucoxanthin concentration - concentration of fucoxanthin in liquid water + The concentration of sodium molecular entity when measured in soil. + soil sodium molecular entity concentration + concentration of sodium molecular entity in soil - + - + @@ -893,10 +548,10 @@ - + - + @@ -905,16 +560,16 @@ - The concentration of Guanosine 5-triphosphate when measured in liquid water. - liquid water Guanosine 5-triphosphate concentration - concentration of Guanosine 5-triphosphate in liquid water + The concentration of organic nitrogen anion when measured in soil. + soil organic nitrogen anion concentration + concentration of organic nitrogen anion in soil - + - + @@ -924,10 +579,10 @@ - + - + @@ -936,16 +591,16 @@ - The concentration of hydrogen peroxide when measured in liquid water. - liquid water hydrogen peroxide concentration - concentration of hydrogen peroxide in liquid water + The concentration of organophosphorus compound when measured in soil. + soil organophosphorus compound concentration + concentration of organophosphorus compound in soil - + - + @@ -955,10 +610,10 @@ - + - + @@ -967,16 +622,16 @@ - The concentration of hydrogen sulfide when measured in liquid water. - liquid water hydrogen sulfide concentration - concentration of hydrogen sulfide in liquid water + The concentration of phosphorus molecular entity when measured in soil. + soil phosphorus molecular entity concentration + concentration of phosphorus molecular entity in soil - + - + @@ -986,10 +641,10 @@ - + - + @@ -998,16 +653,16 @@ - The concentration of lutein when measured in liquid water. - liquid water lutein concentration - concentration of lutein in liquid water + The concentration of potassium molecular entity when measured in soil. + soil potassium molecular entity concentration + concentration of potassium molecular entity in soil - + - + @@ -1017,2459 +672,10 @@ - - - - - - - - - - - - - The concentration of methane when measured in liquid water. - liquid water methane concentration - concentration of methane in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of neoxanthin when measured in liquid water. - liquid water neoxanthin concentration - concentration of neoxanthin in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of nitrate when measured in liquid water. - liquid water nitrate concentration - concentration of nitrate in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of nitrite when measured in liquid water. - liquid water nitrite concentration - concentration of nitrite in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of nitrous oxide when measured in liquid water. - liquid water nitrous oxide concentration - concentration of nitrous oxide in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of peridinin when measured in liquid water. - liquid water peridinin concentration - concentration of peridinin in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of phosphate when measured in liquid water. - liquid water phosphate concentration - concentration of phosphate in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silicate(4-) when measured in liquid water. - liquid water silicate(4-) concentration - concentration of silicate(4-) in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of violaxanthin when measured in liquid water. - liquid water violaxanthin concentration - concentration of violaxanthin in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of zeaxanthin when measured in liquid water. - liquid water zeaxanthin concentration - concentration of zeaxanthin in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silicic acid when measured in liquid water. - liquid water silicic acid concentration - concentration of silicic acid in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of chlorophyll when measured in liquid water. - liquid water chlorophyll concentration - concentration of chlorophyll in liquid water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of nitrate when measured in sea water. - sea water nitrate concentration - concentration of nitrate in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of phosphate when measured in sea water. - sea water phosphate concentration - concentration of phosphate in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silicic acid when measured in sea water. - sea water silicic acid concentration - concentration of silicic acid in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of ammonium when measured in sea water. - sea water ammonium concentration - concentration of ammonium in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of nitrite when measured in sea water. - sea water nitrite concentration - concentration of nitrite in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of carbon-13 atom when measured in sea water. - sea water carbon-13 atom concentration - concentration of carbon-13 atom in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of carbon atom when measured in sea water. - sea water carbon atom concentration - concentration of carbon atom in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of chloroflurocarbon when measured in sea water. - sea water chloroflurocarbon concentration - concentration of chloroflurocarbon in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of tritium when measured in sea water. - sea water tritium concentration - concentration of tritium in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of helium-3 when measured in sea water. - sea water helium-3 concentration - concentration of helium-3 in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of carbon-14 atom when measured in sea water. - sea water carbon-14 atom concentration - concentration of carbon-14 atom in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sulfur hexafluoride when measured in sea water. - sea water sulfur hexafluoride concentration - concentration of sulfur hexafluoride in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of calcium carbonate when measured in sea water. - sea water calcium carbonate concentration - concentration of calcium carbonate in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of dioxygen when measured in sea water. - sea water dioxygen concentration - concentration of dioxygen in sea water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of bromine when measured in lake water. - lake water bromine concentration - concentration of bromine in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cerium when measured in lake water. - lake water cerium concentration - concentration of cerium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cobalt when measured in lake water. - lake water cobalt concentration - concentration of cobalt in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of dysprosium when measured in lake water. - lake water dysprosium concentration - concentration of dysprosium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of europium when measured in lake water. - lake water europium concentration - concentration of europium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of gadolinium when measured in lake water. - lake water gadolinium concentration - concentration of gadolinium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lanthanum when measured in lake water. - lake water lanthanum concentration - concentration of lanthanum in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lithium when measured in lake water. - lake water lithium concentration - concentration of lithium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of methanesulfonic acid when measured in lake water. - lake water methanesulfonic acid concentration - concentration of methanesulfonic acid in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of molybdenum when measured in lake water. - lake water molybdenum concentration - concentration of molybdenum in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of neodymium when measured in lake water. - lake water neodymium concentration - concentration of neodymium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of niobium when measured in lake water. - lake water niobium concentration - concentration of niobium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of praseodymium when measured in lake water. - lake water praseodymium concentration - concentration of praseodymium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of samarium when measured in lake water. - lake water samarium concentration - concentration of samarium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silver when measured in lake water. - lake water silver concentration - concentration of silver in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of thallium when measured in lake water. - lake water thallium concentration - concentration of thallium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of tin when measured in lake water. - lake water tin concentration - concentration of tin in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of titanium when measured in lake water. - lake water titanium concentration - concentration of titanium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of yttrium when measured in lake water. - lake water yttrium concentration - concentration of yttrium in lake water - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of bromine when measured in water ice. - water ice bromine concentration - concentration of bromine in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cerium when measured in water ice. - water ice cerium concentration - concentration of cerium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cobalt when measured in water ice. - water ice cobalt concentration - concentration of cobalt in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of dysprosium when measured in water ice. - water ice dysprosium concentration - concentration of dysprosium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of europium when measured in water ice. - water ice europium concentration - concentration of europium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of gadolinium when measured in water ice. - water ice gadolinium concentration - concentration of gadolinium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lanthanum when measured in water ice. - water ice lanthanum concentration - concentration of lanthanum in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lithium when measured in water ice. - water ice lithium concentration - concentration of lithium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of methanesulfonic acid when measured in water ice. - water ice methanesulfonic acid concentration - concentration of methanesulfonic acid in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of molybdenum when measured in water ice. - water ice molybdenum concentration - concentration of molybdenum in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of neodymium when measured in water ice. - water ice neodymium concentration - concentration of neodymium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of niobium when measured in water ice. - water ice niobium concentration - concentration of niobium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of praseodymium when measured in water ice. - water ice praseodymium concentration - concentration of praseodymium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of samarium when measured in water ice. - water ice samarium concentration - concentration of samarium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silver when measured in water ice. - water ice silver concentration - concentration of silver in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of thallium when measured in water ice. - water ice thallium concentration - concentration of thallium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of tin when measured in water ice. - water ice tin concentration - concentration of tin in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of titanium when measured in water ice. - water ice titanium concentration - concentration of titanium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of yttrium when measured in water ice. - water ice yttrium concentration - concentration of yttrium in water ice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of bromine when measured in snow. - snow bromine concentration - concentration of bromine in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cerium when measured in snow. - snow cerium concentration - concentration of cerium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of cobalt when measured in snow. - snow cobalt concentration - concentration of cobalt in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of dysprosium when measured in snow. - snow dysprosium concentration - concentration of dysprosium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of europium when measured in snow. - snow europium concentration - concentration of europium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of gadolinium when measured in snow. - snow gadolinium concentration - concentration of gadolinium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lanthanum when measured in snow. - snow lanthanum concentration - concentration of lanthanum in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of lithium when measured in snow. - snow lithium concentration - concentration of lithium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of methanesulfonic acid when measured in snow. - snow methanesulfonic acid concentration - concentration of methanesulfonic acid in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of molybdenum when measured in snow. - snow molybdenum concentration - concentration of molybdenum in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of neodymium when measured in snow. - snow neodymium concentration - concentration of neodymium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of niobium when measured in snow. - snow niobium concentration - concentration of niobium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of praseodymium when measured in snow. - snow praseodymium concentration - concentration of praseodymium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of samarium when measured in snow. - snow samarium concentration - concentration of samarium in snow - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of silver when measured in snow. - snow silver concentration - concentration of silver in snow - - - - - - - - - - - - - - - - - + - + @@ -3478,16 +684,16 @@ - The concentration of thallium when measured in snow. - snow thallium concentration - concentration of thallium in snow + The concentration of calcium carbonate when measured in soil. + soil calcium carbonate concentration + concentration of calcium carbonate in soil - + - + @@ -3497,10 +703,10 @@ - + - + @@ -3509,16 +715,16 @@ - The concentration of tin when measured in snow. - snow tin concentration - concentration of tin in snow + The concentration of organic molecular entity when measured in soil. + soil organic molecular entity concentration + concentration of organic molecular entity in soil - + - + @@ -3528,10 +734,10 @@ - + - + @@ -3540,16 +746,16 @@ - The concentration of titanium when measured in snow. - snow titanium concentration - concentration of titanium in snow + The concentration of tetraphosphorus decaoxide when measured in soil. + soil tetraphosphorus decaoxide concentration + concentration of tetraphosphorus decaoxide in soil - + - + @@ -3559,10 +765,10 @@ - + - + @@ -3571,16 +777,16 @@ - The concentration of yttrium when measured in snow. - snow yttrium concentration - concentration of yttrium in snow + The concentration of sulfate when measured in soil. + soil sulfate concentration + concentration of sulfate in soil - + - + @@ -3590,10 +796,10 @@ - + - + @@ -3602,9 +808,9 @@ - The concentration of urea when measured in liquid water. - liquid water urea concentration - concentration of urea in liquid water + The concentration of salt when measured in soil. + soil salt concentration + concentration of salt in soil From e74d8aa842b45fbab7f6aef16c2c83e8b6695fc0 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Fri, 29 Oct 2021 18:27:58 -0400 Subject: [PATCH 02/23] Added CC pattern class per issue #394 Ran dosdp run per previous commit with current class substitution. --- src/envo/envo-edit.owl | 9 + src/envo/modules/chemical_concentration.csv | 1 + src/envo/modules/chemical_concentration.owl | 719 +------------------- 3 files changed, 18 insertions(+), 711 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 60da1957..e13ff060 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -74,6 +74,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3759,6 +3760,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -41937,6 +41939,13 @@ AnnotationAssertion( "concentration of salt in soil"^^xsd:string) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) +# Class: (concentration of nitrogen molecular entity in soil) + +AnnotationAssertion( "The concentration of nitrogen molecular entity when measured in soil."^^xsd:string) +AnnotationAssertion( "soil nitrogen molecular entity concentration"^^xsd:string) +AnnotationAssertion(rdfs:label "concentration of nitrogen molecular entity in soil"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + # Class: (area of alpine tundra) AnnotationAssertion(Annotation( ) Annotation( ) "An area of tundra which is present in a region subject to alpine conditions.") diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e0877ebe..adf985e3 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -121,3 +121,4 @@ ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil +ENVO:3200080,,CHEBI:51143,nitrogen molecular entity,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index dc33ac5e..17a2b433 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -69,93 +69,9 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -165,628 +81,9 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of oxygen when measured in soil. - soil oxygen concentration - concentration of oxygen in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of clay when measured in soil. - soil clay concentration - concentration of clay in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of slit when measured in soil. - soil slit concentration - concentration of slit in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sand when measured in soil. - soil sand concentration - concentration of sand in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of gravel when measured in soil. - soil gravel concentration - concentration of gravel in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of liquid water when measured in soil. - soil liquid water concentration - concentration of liquid water in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of manganese molecular entity when measured in soil. - soil manganese molecular entity concentration - concentration of manganese molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of iron molecular entity when measured in soil. - soil iron molecular entity concentration - concentration of iron molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of aluminium molecular entity when measured in soil. - soil aluminium molecular entity concentration - concentration of aluminium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of magnesium molecular entity when measured in soil. - soil magnesium molecular entity concentration - concentration of magnesium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sodium molecular entity when measured in soil. - soil sodium molecular entity concentration - concentration of sodium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organic nitrogen anion when measured in soil. - soil organic nitrogen anion concentration - concentration of organic nitrogen anion in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organophosphorus compound when measured in soil. - soil organophosphorus compound concentration - concentration of organophosphorus compound in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of phosphorus molecular entity when measured in soil. - soil phosphorus molecular entity concentration - concentration of phosphorus molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of potassium molecular entity when measured in soil. - soil potassium molecular entity concentration - concentration of potassium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of calcium carbonate when measured in soil. - soil calcium carbonate concentration - concentration of calcium carbonate in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organic molecular entity when measured in soil. - soil organic molecular entity concentration - concentration of organic molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of tetraphosphorus decaoxide when measured in soil. - soil tetraphosphorus decaoxide concentration - concentration of tetraphosphorus decaoxide in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sulfate when measured in soil. - soil sulfate concentration - concentration of sulfate in soil - - - - - + - + @@ -796,7 +93,7 @@ - + @@ -808,9 +105,9 @@ - The concentration of salt when measured in soil. - soil salt concentration - concentration of salt in soil + The concentration of nitrogen molecular entity when measured in soil. + soil nitrogen molecular entity concentration + concentration of nitrogen molecular entity in soil From 5200c8529eb8c674bd7f02b7582fbccedc29d052 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 1 Nov 2021 18:35:50 -0400 Subject: [PATCH 03/23] Revert "Added CC pattern class per issue #394" This reverts commit e74d8aa842b45fbab7f6aef16c2c83e8b6695fc0. --- src/envo/envo-edit.owl | 9 - src/envo/modules/chemical_concentration.csv | 1 - src/envo/modules/chemical_concentration.owl | 719 +++++++++++++++++++- 3 files changed, 711 insertions(+), 18 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index e13ff060..60da1957 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -74,7 +74,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3760,7 +3759,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -41939,13 +41937,6 @@ AnnotationAssertion( "concentration of salt in soil"^^xsd:string) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -# Class: (concentration of nitrogen molecular entity in soil) - -AnnotationAssertion( "The concentration of nitrogen molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil nitrogen molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of nitrogen molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - # Class: (area of alpine tundra) AnnotationAssertion(Annotation( ) Annotation( ) "An area of tundra which is present in a region subject to alpine conditions.") diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index adf985e3..e0877ebe 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -121,4 +121,3 @@ ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil -ENVO:3200080,,CHEBI:51143,nitrogen molecular entity,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 17a2b433..dc33ac5e 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -69,9 +69,93 @@ - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -81,9 +165,628 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of oxygen when measured in soil. + soil oxygen concentration + concentration of oxygen in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of clay when measured in soil. + soil clay concentration + concentration of clay in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of slit when measured in soil. + soil slit concentration + concentration of slit in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sand when measured in soil. + soil sand concentration + concentration of sand in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of gravel when measured in soil. + soil gravel concentration + concentration of gravel in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of liquid water when measured in soil. + soil liquid water concentration + concentration of liquid water in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of manganese molecular entity when measured in soil. + soil manganese molecular entity concentration + concentration of manganese molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of iron molecular entity when measured in soil. + soil iron molecular entity concentration + concentration of iron molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of aluminium molecular entity when measured in soil. + soil aluminium molecular entity concentration + concentration of aluminium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of magnesium molecular entity when measured in soil. + soil magnesium molecular entity concentration + concentration of magnesium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sodium molecular entity when measured in soil. + soil sodium molecular entity concentration + concentration of sodium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic nitrogen anion when measured in soil. + soil organic nitrogen anion concentration + concentration of organic nitrogen anion in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organophosphorus compound when measured in soil. + soil organophosphorus compound concentration + concentration of organophosphorus compound in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of phosphorus molecular entity when measured in soil. + soil phosphorus molecular entity concentration + concentration of phosphorus molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of potassium molecular entity when measured in soil. + soil potassium molecular entity concentration + concentration of potassium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of calcium carbonate when measured in soil. + soil calcium carbonate concentration + concentration of calcium carbonate in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic molecular entity when measured in soil. + soil organic molecular entity concentration + concentration of organic molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tetraphosphorus decaoxide when measured in soil. + soil tetraphosphorus decaoxide concentration + concentration of tetraphosphorus decaoxide in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sulfate when measured in soil. + soil sulfate concentration + concentration of sulfate in soil + + + + + - + @@ -93,7 +796,7 @@ - + @@ -105,9 +808,9 @@ - The concentration of nitrogen molecular entity when measured in soil. - soil nitrogen molecular entity concentration - concentration of nitrogen molecular entity in soil + The concentration of salt when measured in soil. + soil salt concentration + concentration of salt in soil From 895c962d0576028d03c7ea3bbca97f7fe2448d64 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 1 Nov 2021 18:35:54 -0400 Subject: [PATCH 04/23] Revert "Added CC pattern classes (desc for issues list)" This reverts commit 0064be2fe7a39bf4defe479160ae716de9067720. --- src/envo/envo-edit.owl | 180 -- src/envo/modules/chemical_concentration.csv | 20 - src/envo/modules/chemical_concentration.owl | 3146 +++++++++++++++++-- 3 files changed, 2970 insertions(+), 376 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 60da1957..12140e92 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -40,24 +40,14 @@ Annotation( "https://github.com/Envir Annotation( "ENVO"^^xsd:string) Annotation( "http://environmentontology.org/"^^xsd:anyURI) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -65,15 +55,10 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3737,34 +3722,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3777,7 +3739,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -3786,7 +3747,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -41797,146 +41757,6 @@ AnnotationAssertion( "ionizing radiation") SubClassOf( ) -# Class: (concentration of oxygen in soil) - -AnnotationAssertion( "The concentration of oxygen when measured in soil."^^xsd:string) -AnnotationAssertion( "soil oxygen concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of oxygen in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of clay in soil) - -AnnotationAssertion( "The concentration of clay when measured in soil."^^xsd:string) -AnnotationAssertion( "soil clay concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of clay in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of slit in soil) - -AnnotationAssertion( "The concentration of slit when measured in soil."^^xsd:string) -AnnotationAssertion( "soil slit concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of slit in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of sand in soil) - -AnnotationAssertion( "The concentration of sand when measured in soil."^^xsd:string) -AnnotationAssertion( "soil sand concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of sand in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of gravel in soil) - -AnnotationAssertion( "The concentration of gravel when measured in soil."^^xsd:string) -AnnotationAssertion( "soil gravel concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of gravel in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of liquid water in soil) - -AnnotationAssertion( "The concentration of liquid water when measured in soil."^^xsd:string) -AnnotationAssertion( "soil liquid water concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of liquid water in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of manganese molecular entity in soil) - -AnnotationAssertion( "The concentration of manganese molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil manganese molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of manganese molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of iron molecular entity in soil) - -AnnotationAssertion( "The concentration of iron molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil iron molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of iron molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of aluminium molecular entity in soil) - -AnnotationAssertion( "The concentration of aluminium molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil aluminium molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of aluminium molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of magnesium molecular entity in soil) - -AnnotationAssertion( "The concentration of magnesium molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil magnesium molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of magnesium molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of sodium molecular entity in soil) - -AnnotationAssertion( "The concentration of sodium molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil sodium molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of sodium molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of organic nitrogen anion in soil) - -AnnotationAssertion( "The concentration of organic nitrogen anion when measured in soil."^^xsd:string) -AnnotationAssertion( "soil organic nitrogen anion concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of organic nitrogen anion in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of organophosphorus compound in soil) - -AnnotationAssertion( "The concentration of organophosphorus compound when measured in soil."^^xsd:string) -AnnotationAssertion( "soil organophosphorus compound concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of organophosphorus compound in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of phosphorus molecular entity in soil) - -AnnotationAssertion( "The concentration of phosphorus molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil phosphorus molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of phosphorus molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of potassium molecular entity in soil) - -AnnotationAssertion( "The concentration of potassium molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil potassium molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of potassium molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of calcium carbonate in soil) - -AnnotationAssertion( "The concentration of calcium carbonate when measured in soil."^^xsd:string) -AnnotationAssertion( "soil calcium carbonate concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of calcium carbonate in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of organic molecular entity in soil) - -AnnotationAssertion( "The concentration of organic molecular entity when measured in soil."^^xsd:string) -AnnotationAssertion( "soil organic molecular entity concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of organic molecular entity in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of tetraphosphorus decaoxide in soil) - -AnnotationAssertion( "The concentration of tetraphosphorus decaoxide when measured in soil."^^xsd:string) -AnnotationAssertion( "soil tetraphosphorus decaoxide concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of tetraphosphorus decaoxide in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of sulfate in soil) - -AnnotationAssertion( "The concentration of sulfate when measured in soil."^^xsd:string) -AnnotationAssertion( "soil sulfate concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of sulfate in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - -# Class: (concentration of salt in soil) - -AnnotationAssertion( "The concentration of salt when measured in soil."^^xsd:string) -AnnotationAssertion( "soil salt concentration"^^xsd:string) -AnnotationAssertion(rdfs:label "concentration of salt in soil"^^xsd:string) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - # Class: (area of alpine tundra) AnnotationAssertion(Annotation( ) Annotation( ) "An area of tundra which is present in a region subject to alpine conditions.") diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e0877ebe..e6edf3b8 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -101,23 +101,3 @@ 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,,ENVO:00002982,clay,ENVO:00001998,soil -ENVO:3200062,,ENVO:01000016,slit,ENVO:00001998,soil -ENVO:3200063,,ENVO:01000017,sand,ENVO:00001998,soil -ENVO:3200064,,ENVO:01000018,gravel,ENVO:00001998,soil -ENVO:3200065,,ENVO:00002006,liquid water,ENVO:00001998,soil -ENVO:3200066,,CHEBI:25154,manganese molecular entity,ENVO:00001998,soil -ENVO:3200067,,CHEBI:24873,iron molecular entity,ENVO:00001998,soil -ENVO:3200068,,CHEBI:33620,aluminium molecular entity,ENVO:00001998,soil -ENVO:3200069,,CHEBI:25108,magnesium molecular entity,ENVO:00001998,soil -ENVO:3200070,,CHEBI:26712,sodium molecular entity,ENVO:00001998,soil -ENVO:3200071,,CHEBI:50335,organic nitrogen anion,ENVO:00001998,soil -ENVO:3200072,,CHEBI:25710,organophosphorus compound,ENVO:00001998,soil -ENVO:3200073,,CHEBI:26082,phosphorus molecular entity,ENVO:00001998,soil -ENVO:3200074,,CHEBI:26217,potassium molecular entity,ENVO:00001998,soil -ENVO:3200075,,CHEBI:3311,calcium carbonate,ENVO:00001998,soil -ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil -ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil -ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil -ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index dc33ac5e..1b9ea83a 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -69,63 +69,249 @@ + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -135,33 +321,99 @@ - + + + + + + + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -171,33 +423,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -207,10 +459,10 @@ - + - + @@ -219,16 +471,16 @@ - The concentration of oxygen when measured in soil. - soil oxygen concentration - concentration of oxygen in soil + The concentration of Adenosine 5-triphosphate when measured in liquid water. + liquid water Adenosine 5-triphosphate concentration + concentration of Adenosine 5-triphosphate in liquid water - + - + @@ -238,10 +490,10 @@ - + - + @@ -250,16 +502,16 @@ - The concentration of clay when measured in soil. - soil clay concentration - concentration of clay in soil + The concentration of alloxanthine when measured in liquid water. + liquid water alloxanthine concentration + concentration of alloxanthine in liquid water - + - + @@ -269,10 +521,10 @@ - + - + @@ -281,16 +533,16 @@ - The concentration of slit when measured in soil. - soil slit concentration - concentration of slit in soil + The concentration of alpha-carotene when measured in liquid water. + liquid water alpha-carotene concentration + concentration of alpha-carotene in liquid water - + - + @@ -300,10 +552,10 @@ - + - + @@ -312,16 +564,16 @@ - The concentration of sand when measured in soil. - soil sand concentration - concentration of sand in soil + The concentration of ammonium when measured in liquid water. + liquid water ammonium concentration + concentration of ammonium in liquid water - + - + @@ -331,10 +583,10 @@ - + - + @@ -343,16 +595,16 @@ - The concentration of gravel when measured in soil. - soil gravel concentration - concentration of gravel in soil + The concentration of bacteriochlorophyll a when measured in liquid water. + liquid water bacteriochlorophyll a concentration + concentration of bacteriochlorophyll a in liquid water - + - + @@ -362,10 +614,10 @@ - + - + @@ -374,16 +626,16 @@ - The concentration of liquid water when measured in soil. - soil liquid water concentration - concentration of liquid water in soil + The concentration of beta-carotene when measured in liquid water. + liquid water beta-carotene concentration + concentration of beta-carotene in liquid water - + - + @@ -393,10 +645,10 @@ - + - + @@ -405,16 +657,16 @@ - The concentration of manganese molecular entity when measured in soil. - soil manganese molecular entity concentration - concentration of manganese molecular entity in soil + The concentration of carotene when measured in liquid water. + liquid water carotene concentration + concentration of carotene in liquid water - + - + @@ -424,10 +676,10 @@ - + - + @@ -436,16 +688,16 @@ - The concentration of iron molecular entity when measured in soil. - soil iron molecular entity concentration - concentration of iron molecular entity in soil + The concentration of chlorophyll a when measured in liquid water. + liquid water chlorophyll a concentration + concentration of chlorophyll a in liquid water - + - + @@ -455,10 +707,10 @@ - + - + @@ -467,16 +719,16 @@ - The concentration of aluminium molecular entity when measured in soil. - soil aluminium molecular entity concentration - concentration of aluminium molecular entity in soil + The concentration of chlorophyll b when measured in liquid water. + liquid water chlorophyll b concentration + concentration of chlorophyll b in liquid water - + - + @@ -486,10 +738,10 @@ - + - + @@ -498,16 +750,16 @@ - The concentration of magnesium molecular entity when measured in soil. - soil magnesium molecular entity concentration - concentration of magnesium molecular entity in soil + The concentration of chlorophyllide a when measured in liquid water. + liquid water chlorophyllide a concentration + concentration of chlorophyllide a in liquid water - + - + @@ -517,10 +769,10 @@ - + - + @@ -529,16 +781,16 @@ - The concentration of sodium molecular entity when measured in soil. - soil sodium molecular entity concentration - concentration of sodium molecular entity in soil + The concentration of dioxygen when measured in liquid water. + liquid water dioxygen concentration + concentration of dioxygen in liquid water - + - + @@ -548,10 +800,10 @@ - + - + @@ -560,16 +812,16 @@ - The concentration of organic nitrogen anion when measured in soil. - soil organic nitrogen anion concentration - concentration of organic nitrogen anion in soil + The concentration of divinyl chlorophyll a when measured in liquid water. + liquid water divinyl chlorophyll a concentration + concentration of divinyl chlorophyll a in liquid water - + - + @@ -579,10 +831,10 @@ - + - + @@ -591,16 +843,16 @@ - The concentration of organophosphorus compound when measured in soil. - soil organophosphorus compound concentration - concentration of organophosphorus compound in soil + The concentration of divinyl chlorophyll b when measured in liquid water. + liquid water divinyl chlorophyll b concentration + concentration of divinyl chlorophyll b in liquid water - + - + @@ -610,10 +862,10 @@ - + - + @@ -622,16 +874,16 @@ - The concentration of phosphorus molecular entity when measured in soil. - soil phosphorus molecular entity concentration - concentration of phosphorus molecular entity in soil + The concentration of fucoxanthin when measured in liquid water. + liquid water fucoxanthin concentration + concentration of fucoxanthin in liquid water - + - + @@ -641,10 +893,10 @@ - + - + @@ -653,16 +905,16 @@ - The concentration of potassium molecular entity when measured in soil. - soil potassium molecular entity concentration - concentration of potassium molecular entity in soil + The concentration of Guanosine 5-triphosphate when measured in liquid water. + liquid water Guanosine 5-triphosphate concentration + concentration of Guanosine 5-triphosphate in liquid water - + - + @@ -672,10 +924,2552 @@ - + + + + + + + + + + + + + The concentration of hydrogen peroxide when measured in liquid water. + liquid water hydrogen peroxide concentration + concentration of hydrogen peroxide in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of hydrogen sulfide when measured in liquid water. + liquid water hydrogen sulfide concentration + concentration of hydrogen sulfide in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lutein when measured in liquid water. + liquid water lutein concentration + concentration of lutein in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of methane when measured in liquid water. + liquid water methane concentration + concentration of methane in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of neoxanthin when measured in liquid water. + liquid water neoxanthin concentration + concentration of neoxanthin in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrate when measured in liquid water. + liquid water nitrate concentration + concentration of nitrate in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrite when measured in liquid water. + liquid water nitrite concentration + concentration of nitrite in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrous oxide when measured in liquid water. + liquid water nitrous oxide concentration + concentration of nitrous oxide in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of peridinin when measured in liquid water. + liquid water peridinin concentration + concentration of peridinin in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of phosphate when measured in liquid water. + liquid water phosphate concentration + concentration of phosphate in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silicate(4-) when measured in liquid water. + liquid water silicate(4-) concentration + concentration of silicate(4-) in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of violaxanthin when measured in liquid water. + liquid water violaxanthin concentration + concentration of violaxanthin in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of zeaxanthin when measured in liquid water. + liquid water zeaxanthin concentration + concentration of zeaxanthin in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silicic acid when measured in liquid water. + liquid water silicic acid concentration + concentration of silicic acid in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of chlorophyll when measured in liquid water. + liquid water chlorophyll concentration + concentration of chlorophyll in liquid water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrate when measured in sea water. + sea water nitrate concentration + concentration of nitrate in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of phosphate when measured in sea water. + sea water phosphate concentration + concentration of phosphate in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silicic acid when measured in sea water. + sea water silicic acid concentration + concentration of silicic acid in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of ammonium when measured in sea water. + sea water ammonium concentration + concentration of ammonium in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of nitrite when measured in sea water. + sea water nitrite concentration + concentration of nitrite in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of carbon-13 atom when measured in sea water. + sea water carbon-13 atom concentration + concentration of carbon-13 atom in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of carbon atom when measured in sea water. + sea water carbon atom concentration + concentration of carbon atom in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of chloroflurocarbon when measured in sea water. + sea water chloroflurocarbon concentration + concentration of chloroflurocarbon in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tritium when measured in sea water. + sea water tritium concentration + concentration of tritium in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of helium-3 when measured in sea water. + sea water helium-3 concentration + concentration of helium-3 in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of carbon-14 atom when measured in sea water. + sea water carbon-14 atom concentration + concentration of carbon-14 atom in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sulfur hexafluoride when measured in sea water. + sea water sulfur hexafluoride concentration + concentration of sulfur hexafluoride in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of calcium carbonate when measured in sea water. + sea water calcium carbonate concentration + concentration of calcium carbonate in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of dioxygen when measured in sea water. + sea water dioxygen concentration + concentration of dioxygen in sea water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of bromine when measured in lake water. + lake water bromine concentration + concentration of bromine in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cerium when measured in lake water. + lake water cerium concentration + concentration of cerium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cobalt when measured in lake water. + lake water cobalt concentration + concentration of cobalt in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of dysprosium when measured in lake water. + lake water dysprosium concentration + concentration of dysprosium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of europium when measured in lake water. + lake water europium concentration + concentration of europium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of gadolinium when measured in lake water. + lake water gadolinium concentration + concentration of gadolinium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lanthanum when measured in lake water. + lake water lanthanum concentration + concentration of lanthanum in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lithium when measured in lake water. + lake water lithium concentration + concentration of lithium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of methanesulfonic acid when measured in lake water. + lake water methanesulfonic acid concentration + concentration of methanesulfonic acid in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of molybdenum when measured in lake water. + lake water molybdenum concentration + concentration of molybdenum in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of neodymium when measured in lake water. + lake water neodymium concentration + concentration of neodymium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of niobium when measured in lake water. + lake water niobium concentration + concentration of niobium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of praseodymium when measured in lake water. + lake water praseodymium concentration + concentration of praseodymium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of samarium when measured in lake water. + lake water samarium concentration + concentration of samarium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silver when measured in lake water. + lake water silver concentration + concentration of silver in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of thallium when measured in lake water. + lake water thallium concentration + concentration of thallium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tin when measured in lake water. + lake water tin concentration + concentration of tin in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of titanium when measured in lake water. + lake water titanium concentration + concentration of titanium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of yttrium when measured in lake water. + lake water yttrium concentration + concentration of yttrium in lake water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of bromine when measured in water ice. + water ice bromine concentration + concentration of bromine in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cerium when measured in water ice. + water ice cerium concentration + concentration of cerium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cobalt when measured in water ice. + water ice cobalt concentration + concentration of cobalt in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of dysprosium when measured in water ice. + water ice dysprosium concentration + concentration of dysprosium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of europium when measured in water ice. + water ice europium concentration + concentration of europium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of gadolinium when measured in water ice. + water ice gadolinium concentration + concentration of gadolinium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lanthanum when measured in water ice. + water ice lanthanum concentration + concentration of lanthanum in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lithium when measured in water ice. + water ice lithium concentration + concentration of lithium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of methanesulfonic acid when measured in water ice. + water ice methanesulfonic acid concentration + concentration of methanesulfonic acid in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of molybdenum when measured in water ice. + water ice molybdenum concentration + concentration of molybdenum in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of neodymium when measured in water ice. + water ice neodymium concentration + concentration of neodymium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of niobium when measured in water ice. + water ice niobium concentration + concentration of niobium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of praseodymium when measured in water ice. + water ice praseodymium concentration + concentration of praseodymium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of samarium when measured in water ice. + water ice samarium concentration + concentration of samarium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silver when measured in water ice. + water ice silver concentration + concentration of silver in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of thallium when measured in water ice. + water ice thallium concentration + concentration of thallium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tin when measured in water ice. + water ice tin concentration + concentration of tin in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of titanium when measured in water ice. + water ice titanium concentration + concentration of titanium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of yttrium when measured in water ice. + water ice yttrium concentration + concentration of yttrium in water ice + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of bromine when measured in snow. + snow bromine concentration + concentration of bromine in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cerium when measured in snow. + snow cerium concentration + concentration of cerium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of cobalt when measured in snow. + snow cobalt concentration + concentration of cobalt in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of dysprosium when measured in snow. + snow dysprosium concentration + concentration of dysprosium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of europium when measured in snow. + snow europium concentration + concentration of europium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of gadolinium when measured in snow. + snow gadolinium concentration + concentration of gadolinium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lanthanum when measured in snow. + snow lanthanum concentration + concentration of lanthanum in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of lithium when measured in snow. + snow lithium concentration + concentration of lithium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of methanesulfonic acid when measured in snow. + snow methanesulfonic acid concentration + concentration of methanesulfonic acid in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of molybdenum when measured in snow. + snow molybdenum concentration + concentration of molybdenum in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of neodymium when measured in snow. + snow neodymium concentration + concentration of neodymium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of niobium when measured in snow. + snow niobium concentration + concentration of niobium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of praseodymium when measured in snow. + snow praseodymium concentration + concentration of praseodymium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of samarium when measured in snow. + snow samarium concentration + concentration of samarium in snow + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of silver when measured in snow. + snow silver concentration + concentration of silver in snow + + + + + + + + + + + + + + + + + - + @@ -684,16 +3478,16 @@ - The concentration of calcium carbonate when measured in soil. - soil calcium carbonate concentration - concentration of calcium carbonate in soil + The concentration of thallium when measured in snow. + snow thallium concentration + concentration of thallium in snow - + - + @@ -703,10 +3497,10 @@ - + - + @@ -715,16 +3509,16 @@ - The concentration of organic molecular entity when measured in soil. - soil organic molecular entity concentration - concentration of organic molecular entity in soil + The concentration of tin when measured in snow. + snow tin concentration + concentration of tin in snow - + - + @@ -734,10 +3528,10 @@ - + - + @@ -746,16 +3540,16 @@ - The concentration of tetraphosphorus decaoxide when measured in soil. - soil tetraphosphorus decaoxide concentration - concentration of tetraphosphorus decaoxide in soil + The concentration of titanium when measured in snow. + snow titanium concentration + concentration of titanium in snow - + - + @@ -765,10 +3559,10 @@ - + - + @@ -777,16 +3571,16 @@ - The concentration of sulfate when measured in soil. - soil sulfate concentration - concentration of sulfate in soil + The concentration of yttrium when measured in snow. + snow yttrium concentration + concentration of yttrium in snow - + - + @@ -796,10 +3590,10 @@ - + - + @@ -808,9 +3602,9 @@ - The concentration of salt when measured in soil. - soil salt concentration - concentration of salt in soil + The concentration of urea when measured in liquid water. + liquid water urea concentration + concentration of urea in liquid water From d8e1124d3fcc5041be541c1f0865cc17aa360192 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 1 Nov 2021 21:15:48 -0400 Subject: [PATCH 05/23] Rerun pattern add using make recipe --- src/envo/modules/chemical_concentration.csv | 20 + src/envo/modules/chemical_concentration.owl | 728 ++++++++++++++++++++ 2 files changed, 748 insertions(+) diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e6edf3b8..e0877ebe 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -101,3 +101,23 @@ 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,,ENVO:00002982,clay,ENVO:00001998,soil +ENVO:3200062,,ENVO:01000016,slit,ENVO:00001998,soil +ENVO:3200063,,ENVO:01000017,sand,ENVO:00001998,soil +ENVO:3200064,,ENVO:01000018,gravel,ENVO:00001998,soil +ENVO:3200065,,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:3200066,,CHEBI:25154,manganese molecular entity,ENVO:00001998,soil +ENVO:3200067,,CHEBI:24873,iron molecular entity,ENVO:00001998,soil +ENVO:3200068,,CHEBI:33620,aluminium molecular entity,ENVO:00001998,soil +ENVO:3200069,,CHEBI:25108,magnesium molecular entity,ENVO:00001998,soil +ENVO:3200070,,CHEBI:26712,sodium molecular entity,ENVO:00001998,soil +ENVO:3200071,,CHEBI:50335,organic nitrogen anion,ENVO:00001998,soil +ENVO:3200072,,CHEBI:25710,organophosphorus compound,ENVO:00001998,soil +ENVO:3200073,,CHEBI:26082,phosphorus molecular entity,ENVO:00001998,soil +ENVO:3200074,,CHEBI:26217,potassium molecular entity,ENVO:00001998,soil +ENVO:3200075,,CHEBI:3311,calcium carbonate,ENVO:00001998,soil +ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil +ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil +ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil +ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 1b9ea83a..3efb9906 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -105,6 +105,12 @@ + + + + + + @@ -165,24 +171,72 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -375,6 +429,12 @@ + + + + + + @@ -387,6 +447,12 @@ + + + + + + @@ -399,6 +465,18 @@ + + + + + + + + + + + + @@ -417,6 +495,12 @@ + + + + + + @@ -429,6 +513,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -3609,6 +3717,626 @@ + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of oxygen when measured in soil. + soil oxygen concentration + concentration of oxygen in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of clay when measured in soil. + soil clay concentration + concentration of clay in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of slit when measured in soil. + soil slit concentration + concentration of slit in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sand when measured in soil. + soil sand concentration + concentration of sand in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of gravel when measured in soil. + soil gravel concentration + concentration of gravel in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of liquid water when measured in soil. + soil liquid water concentration + concentration of liquid water in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of manganese molecular entity when measured in soil. + soil manganese molecular entity concentration + concentration of manganese molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of iron molecular entity when measured in soil. + soil iron molecular entity concentration + concentration of iron molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of aluminium molecular entity when measured in soil. + soil aluminium molecular entity concentration + concentration of aluminium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of magnesium molecular entity when measured in soil. + soil magnesium molecular entity concentration + concentration of magnesium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sodium molecular entity when measured in soil. + soil sodium molecular entity concentration + concentration of sodium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic nitrogen anion when measured in soil. + soil organic nitrogen anion concentration + concentration of organic nitrogen anion in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organophosphorus compound when measured in soil. + soil organophosphorus compound concentration + concentration of organophosphorus compound in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of phosphorus molecular entity when measured in soil. + soil phosphorus molecular entity concentration + concentration of phosphorus molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of potassium molecular entity when measured in soil. + soil potassium molecular entity concentration + concentration of potassium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of calcium carbonate when measured in soil. + soil calcium carbonate concentration + concentration of calcium carbonate in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic molecular entity when measured in soil. + soil organic molecular entity concentration + concentration of organic molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tetraphosphorus decaoxide when measured in soil. + soil tetraphosphorus decaoxide concentration + concentration of tetraphosphorus decaoxide in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sulfate when measured in soil. + soil sulfate concentration + concentration of sulfate in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of salt when measured in soil. + soil salt concentration + concentration of salt in soil + + + + From f018778fb4ebb5f7358510d0ee8cfadf006de76d Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 15 Nov 2021 13:55:33 -0500 Subject: [PATCH 06/23] Revert "Rerun pattern add using make recipe" This reverts commit d8e1124d3fcc5041be541c1f0865cc17aa360192. --- src/envo/modules/chemical_concentration.csv | 20 - src/envo/modules/chemical_concentration.owl | 728 -------------------- 2 files changed, 748 deletions(-) diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e0877ebe..e6edf3b8 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -101,23 +101,3 @@ 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,,ENVO:00002982,clay,ENVO:00001998,soil -ENVO:3200062,,ENVO:01000016,slit,ENVO:00001998,soil -ENVO:3200063,,ENVO:01000017,sand,ENVO:00001998,soil -ENVO:3200064,,ENVO:01000018,gravel,ENVO:00001998,soil -ENVO:3200065,,ENVO:00002006,liquid water,ENVO:00001998,soil -ENVO:3200066,,CHEBI:25154,manganese molecular entity,ENVO:00001998,soil -ENVO:3200067,,CHEBI:24873,iron molecular entity,ENVO:00001998,soil -ENVO:3200068,,CHEBI:33620,aluminium molecular entity,ENVO:00001998,soil -ENVO:3200069,,CHEBI:25108,magnesium molecular entity,ENVO:00001998,soil -ENVO:3200070,,CHEBI:26712,sodium molecular entity,ENVO:00001998,soil -ENVO:3200071,,CHEBI:50335,organic nitrogen anion,ENVO:00001998,soil -ENVO:3200072,,CHEBI:25710,organophosphorus compound,ENVO:00001998,soil -ENVO:3200073,,CHEBI:26082,phosphorus molecular entity,ENVO:00001998,soil -ENVO:3200074,,CHEBI:26217,potassium molecular entity,ENVO:00001998,soil -ENVO:3200075,,CHEBI:3311,calcium carbonate,ENVO:00001998,soil -ENVO:3200076,,CHEBI:50860,organic molecular entity,ENVO:00001998,soil -ENVO:3200077,,CHEBI:37376,tetraphosphorus decaoxide,ENVO:00001998,soil -ENVO:3200078,,CHEBI:16189,sulfate,ENVO:00001998,soil -ENVO:3200079,soil salinity,CHEBI:24866,salt,ENVO:00001998,soil diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 3efb9906..1b9ea83a 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -105,12 +105,6 @@ - - - - - - @@ -171,72 +165,24 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -429,12 +375,6 @@ - - - - - - @@ -447,12 +387,6 @@ - - - - - - @@ -465,18 +399,6 @@ - - - - - - - - - - - - @@ -495,12 +417,6 @@ - - - - - - @@ -513,30 +429,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - @@ -3717,626 +3609,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of oxygen when measured in soil. - soil oxygen concentration - concentration of oxygen in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of clay when measured in soil. - soil clay concentration - concentration of clay in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of slit when measured in soil. - soil slit concentration - concentration of slit in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sand when measured in soil. - soil sand concentration - concentration of sand in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of gravel when measured in soil. - soil gravel concentration - concentration of gravel in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of liquid water when measured in soil. - soil liquid water concentration - concentration of liquid water in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of manganese molecular entity when measured in soil. - soil manganese molecular entity concentration - concentration of manganese molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of iron molecular entity when measured in soil. - soil iron molecular entity concentration - concentration of iron molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of aluminium molecular entity when measured in soil. - soil aluminium molecular entity concentration - concentration of aluminium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of magnesium molecular entity when measured in soil. - soil magnesium molecular entity concentration - concentration of magnesium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sodium molecular entity when measured in soil. - soil sodium molecular entity concentration - concentration of sodium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organic nitrogen anion when measured in soil. - soil organic nitrogen anion concentration - concentration of organic nitrogen anion in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organophosphorus compound when measured in soil. - soil organophosphorus compound concentration - concentration of organophosphorus compound in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of phosphorus molecular entity when measured in soil. - soil phosphorus molecular entity concentration - concentration of phosphorus molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of potassium molecular entity when measured in soil. - soil potassium molecular entity concentration - concentration of potassium molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of calcium carbonate when measured in soil. - soil calcium carbonate concentration - concentration of calcium carbonate in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of organic molecular entity when measured in soil. - soil organic molecular entity concentration - concentration of organic molecular entity in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of tetraphosphorus decaoxide when measured in soil. - soil tetraphosphorus decaoxide concentration - concentration of tetraphosphorus decaoxide in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of sulfate when measured in soil. - soil sulfate concentration - concentration of sulfate in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of salt when measured in soil. - soil salt concentration - concentration of salt in soil - - - - From 167dbe698004aad31fdc6afda27619280c162e8a Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Mon, 15 Nov 2021 14:31:48 -0500 Subject: [PATCH 07/23] 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 --- src/envo/modules/chemical_concentration.csv | 14 + src/envo/modules/chemical_concentration.owl | 512 ++++++++++++++++++ .../modules/entity_attribute_location.csv | 10 + .../modules/entity_attribute_location.owl | 412 +++++++++++++- 4 files changed, 936 insertions(+), 12 deletions(-) diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e6edf3b8..e3611c8a 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -101,3 +101,17 @@ 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 diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 1b9ea83a..31031efe 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -105,6 +105,12 @@ + + + + + + @@ -165,24 +171,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -375,6 +423,12 @@ + + + + + + @@ -387,6 +441,12 @@ + + + + + + @@ -399,6 +459,18 @@ + + + + + + + + + + + + @@ -417,6 +489,12 @@ + + + + + + @@ -3609,6 +3687,440 @@ + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of oxygen when measured in soil. + soil oxygen concentration + concentration of oxygen in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of manganese molecular entity when measured in soil. + soil manganese molecular entity concentration + concentration of manganese molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of iron molecular entity when measured in soil. + soil iron molecular entity concentration + concentration of iron molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of aluminium molecular entity when measured in soil. + soil aluminium molecular entity concentration + concentration of aluminium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of magnesium molecular entity when measured in soil. + soil magnesium molecular entity concentration + concentration of magnesium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sodium molecular entity when measured in soil. + soil sodium molecular entity concentration + concentration of sodium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic nitrogen anion when measured in soil. + soil organic nitrogen anion concentration + concentration of organic nitrogen anion in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organophosphorus compound when measured in soil. + soil organophosphorus compound concentration + concentration of organophosphorus compound in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of phosphorus molecular entity when measured in soil. + soil phosphorus molecular entity concentration + concentration of phosphorus molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of potassium molecular entity when measured in soil. + soil potassium molecular entity concentration + concentration of potassium molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of calcium carbonate when measured in soil. + soil calcium carbonate concentration + concentration of calcium carbonate in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of organic molecular entity when measured in soil. + soil organic molecular entity concentration + concentration of organic molecular entity in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of tetraphosphorus decaoxide when measured in soil. + soil tetraphosphorus decaoxide concentration + concentration of tetraphosphorus decaoxide in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of sulfate when measured in soil. + soil sulfate concentration + concentration of sulfate in soil + + + + diff --git a/src/envo/modules/entity_attribute_location.csv b/src/envo/modules/entity_attribute_location.csv index c13a522d..170fb0a0 100644 --- a/src/envo/modules/entity_attribute_location.csv +++ b/src/envo/modules/entity_attribute_location.csv @@ -22,3 +22,13 @@ ENVO:09200007,,PATO:0000033,concentration,CHEBI:17632,nitrate,ENVO:00001998,soil ENVO:09000019,,PATO:0000033,concentration,CHEBI:17996,chloride,ENVO:00002006,water ENVO:09200020,,PATO:0000033,concentration,CHEBI:17632,nitrate,ENVO:01001004,groundwater ENVO:09200021,,PATO:0000033,concentration,CHEBI:15379,oxygen,ENVO:00002006,water +ENVO:09200022,,PATO:0000033,concentration,ENVO:00002982,clay,ENVO:00001998,soil +ENVO:09200023,,PATO:0000033,concentration,ENVO:01000016,slit,ENVO:00001998,soil +ENVO:09200024,,PATO:0000033,concentration,ENVO:01000017,sand,ENVO:00001998,soil +ENVO:09200025,,PATO:0000033,concentration,ENVO:01000018,gravel,ENVO:00001998,soil +ENVO:09200026,,PATO:0000033,concentration,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:09200027,,PATO:0000033,concentration,CHEBI:24866,salt,ENVO:00001998,soil +ENVO:09200028,,ENVO:02500034,evaporation,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:09200029,,PATO:0000161,rate,ENVO:01000704,hydrological evaporation,ENVO:00001998,soil +ENVO:09200030,,PATO:0000033,concentration,ENVO:04000008,soil organic matter,ENVO:00001998,soil +ENVO:09200031,,PATO:0000033,concentration,CHEBI:25944,pesticide,ENVO:00002042,surface water \ No newline at end of file diff --git a/src/envo/modules/entity_attribute_location.owl b/src/envo/modules/entity_attribute_location.owl index fd8fbdb9..684bb2a7 100644 --- a/src/envo/modules/entity_attribute_location.owl +++ b/src/envo/modules/entity_attribute_location.owl @@ -29,12 +29,6 @@ - - - - - - @@ -93,12 +87,24 @@ + + + + + + + + + + + + @@ -123,18 +129,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -820,12 +874,340 @@ - OBSOLETE The concentration of a oxygen when measured in water. - + + + + + + + + + + + + + + + + + + + + + + The concentration of a oxygen when measured in water. water oxygen concentration - https://github.com/EnvironmentOntology/envo/pull/839 - obsolete concentration of oxygen in water - true + concentration of oxygen in water + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a clay when measured in soil. + soil clay concentration + concentration of clay in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a slit when measured in soil. + soil slit concentration + concentration of slit in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a sand when measured in soil. + soil sand concentration + concentration of sand in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a gravel when measured in soil. + soil gravel concentration + concentration of gravel in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a liquid water when measured in soil. + soil liquid water concentration + concentration of liquid water in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a salt when measured in soil. + soil salt concentration + concentration of salt in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The evaporation of a liquid water when measured in soil. + soil liquid water evaporation + evaporation of liquid water in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The rate of a hydrological evaporation when measured in soil. + soil hydrological evaporation rate + rate of hydrological evaporation in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a soil organic matter when measured in soil. + soil soil organic matter concentration + concentration of soil organic matter in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a pesticide when measured in surface water. + surface water pesticide concentration + concentration of pesticide in surface water @@ -842,6 +1224,12 @@ + + + + + + @@ -849,5 +1237,5 @@ - + From 6857ffb060de0a17b42904757536e7ffb8b070ce Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Tue, 16 Nov 2021 10:32:32 -0500 Subject: [PATCH 08/23] #368 [EA] Added class 'color of soil' --- src/envo/modules/entity_attribute.csv | 3 +- src/envo/modules/entity_attribute.owl | 75 +++++++++++++++++++++++++++ 2 files changed, 77 insertions(+), 1 deletion(-) diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 1ef67131..c7bcafa3 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -19,4 +19,5 @@ ENVO:09200020,,PATO:0001595,depth,ENVO:01000406,snow ENVO:3100030,,PATO:0001842,acidity,ENVO:00002006,water ENVO:3100031,,PATO:0001595,depth,ENVO:00002006,water ENVO:3100032,,PATO:0000018,fluorescence,ENVO:00002006,water -ENVO:3100033,,PATO:0001025,pressure,ENVO:00002006,water \ No newline at end of file +ENVO:3100033,,PATO:0001025,pressure,ENVO:00002006,water +ENVO:3100035,,PATO:0000014,color,ENVO:00001998,soil \ No newline at end of file diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 0822fbec..337c8413 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -87,6 +87,12 @@ + + + + + + @@ -402,6 +408,48 @@ + + + + + + + + + + + + + + + The mass density of some snow. + snow mass density + mass density of snow + + + + + + + + + + + + + + + + + + + The depth of some snow. + snow depth + depth of snow + + + + @@ -486,6 +534,33 @@ + + + + + + + + + + + + + + + The color of some soil. + soil color + color of soil + + + + + + + + + + From ce3f1feaa3c11c155e15199c478f7f80d55e864b Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Tue, 16 Nov 2021 13:43:41 -0500 Subject: [PATCH 09/23] #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 --- src/envo/envo-edit.owl | 2 + src/envo/imports/pato_import.owl | 1063 ++++++++++++++++- src/envo/imports/pato_terms.txt | 1 + src/envo/modules/entity_attribute.csv | 3 +- src/envo/modules/entity_attribute.owl | 76 +- .../modules/entity_attribute_location.csv | 24 +- .../modules/entity_attribute_location.owl | 172 +-- 7 files changed, 1214 insertions(+), 127 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 12140e92..f482a1b9 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -42232,6 +42232,8 @@ AnnotationAssertion( "envoPlastics"@en) AnnotationAssertion( "ground water nitrate concentration") AnnotationAssertion(rdfs:label "concentration of nitrate in groundwater") +AnnotationAssertion( "sunshine hours") +AnnotationAssertion(rdfs:label "hours of sunshine") AnnotationAssertion(rdfs:label "editor preferred term~editor preferred label") AnnotationAssertion(rdfs:label "imported from") AnnotationAssertion(rdfs:label "expand expression to") diff --git a/src/envo/imports/pato_import.owl b/src/envo/imports/pato_import.owl index 2548442c..427e9af5 100644 --- a/src/envo/imports/pato_import.owl +++ b/src/envo/imports/pato_import.owl @@ -94,9 +94,18 @@ + + + + entity + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant @@ -107,6 +116,7 @@ + An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -134,6 +144,27 @@ + + + + + + disposition + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + @@ -153,11 +184,41 @@ + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + object + object + + + + + + + + + function + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity material entity @@ -191,6 +252,288 @@ + + + + + molecular entity + + + + + + + + + chemical entity + + + + + + + + + + nitrogen atom + + + + + + + + + nonmetal atom + + + + + + + + + oxygen molecular entity + + + + + + + + + + sulfur atom + + + + + + + + + sulfur molecular entity + + + + + + + + + + carbon atom + + + + + + + + + atom + + + + + + + + + pnictogen + + + + + + + + + pnictogen molecular entity + + + + + + + + + chalcogen + + + + + + + + + chalcogen molecular entity + + + + + + + + + carbon group element atom + + + + + + + + + main group element atom + + + + + + + + + p-block element atom + + + + + + + + + main group molecular entity + + + + + + + + + carbon group molecular entity + + + + + + + + + p-block molecular entity + + + + + + + + + + biomacromolecule + + + + + + + + + macromolecule + + + + + + + + + subatomic particle + + + + + + + + + polyatomic entity + + + + + + + + + mineral + + + + + + + + + organic molecular entity + + + + + + + + + nitrogen molecular entity + + + + + + + + + chemical substance + + + + + + + + obsolete aerial habitat + + + + + + + + + environmental system + + + + + + + + + system process + + + + + + + + + excretion + + + + @@ -205,6 +548,162 @@ + + + + + multicellular organismal process + + + + + + + + + root + + + + + + + + + Viruses + + + + + + + + + cellular organisms + + + + + + + + + + Bacteria + + + + + + + + + Archaea + + + + + + + + + + Eukaryota + + + + + + + + + Opisthokonta + + + + + + + + + Metazoa + + + + + + + + + Bilateria + + + + + + + + + Deuterostomia + + + + + + + + + Eumetazoa + + + + + + + + + Chordata + + + + + + + + + Vertebrata <vertebrates> + + + + + + + + + Craniata <chordates> + + + + + + + + + + + + + + + + + + + organism + + + + @@ -339,7 +838,6 @@ - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology @@ -1618,6 +2116,7 @@ + A quality which inheres in a continuant. monadic quality of a continuant @@ -1700,6 +2199,18 @@ + + + + + A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. + period + time + duration + + + + @@ -2282,7 +2793,7 @@ - A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimenision. + A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. depth @@ -2392,7 +2903,6 @@ A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. preceding - ventral_to anterior to @@ -2681,7 +3191,7 @@ - An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entitity by natural process. + An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process. shedability @@ -3486,7 +3996,7 @@ - A broken quality inhering in a bearer by virtue of the bearer's being seperated into two contiguous wholes. + A broken quality inhering in a bearer by virtue of the bearer's being separated into two contiguous wholes. broken into two pieces @@ -3517,7 +4027,7 @@ - A spatial pattern inhering in a bearer by virtue of the bearer's structureresembling an irregular meshwork with cross-linking struts. + A spatial pattern inhering in a bearer by virtue of the bearer's structure resembling an irregular meshwork with cross-linking struts. trabecular @@ -4514,6 +5024,547 @@ A rate of occurrence that is relatively low. decreased rate of occurrence + + + + + + + + system + + + + + + + + + + Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. + portion of skin + region of skin + skin + skin region + skin zone + zone of skin + + + + + + + + + Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. + anatomical tube + duct + tube + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + biological structure + connected biological structure + anatomical structure + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + anatomical unit + body organ + element + organ + + + + + + + + + A multicellular structure that is a part of an organ. + cardinal organ part + regional part of organ + organ part + + + + + + + + + Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. + bowel + intestinal tract + intestine + + + + + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + regio oralis + adult mouth + cavital oralis + cavitas oris + cavum oris + mouth cavity + oral region + oral vestibule + rima oris + stoma + stomatodaeum + trophic apparatus + vestibule of mouth + vestibulum oris + mouth + + + + + + + + + A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity + excreted substance + portion of excreted substance + waste substance + excretion + excreta + + + + + + + + + + A fluid that is composed of blood plasma and erythrocytes. + portion of blood + vertebrate blood + whole blood + blood + + + + + + + + + Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. + blood or blood analog + circulating fluid + haemolymphatic fluid + + + + + + + + + A portion of organism substance that is produced by exocrine glands. + secretion + bodily secretion + exocrine gland fluid/secretion + secreted substance + exocrine gland fluid + exocrine gland fluid or secretion + exocrine gland secretion + external secretion + secretion of exocrine gland + + + + + + + + + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + body fluid or substance + body substance + organism substance + portion of body substance + portion of organism substance + organism substance + + + + + + + + + + Anatomical entity that has mass. + material anatomical entity + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + system + body system + connected anatomical system + organ system + anatomical systems + anatomical system + + + + + + + + + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + portion of tissue + tissue portion + simple tissue + tissue + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + + + + + + A zone of skin that is part of a head [Automatically generated definition]. + adult head zone of skin + head skin + head zone of skin + zone of skin of adult head + zone of skin of head + skin of head + + + + + + + + + + Joint fluid is a transudate of plasma that is actively secreted by synovial cells. + joint fluid + synovial fluid + + + + + + + + + + Skeletal element that is composed of bone tissue. + bone organ + bone + bones + bone element + + + + + + + + + + A tube extending from the mouth to the anus. + gut + digestive tube + enteric tract + alimentary canal + alimentary tract + digestive canal + gut tube + digestive tract + + + + + + + + + + A thick watery refractive medium that fills the space between the lens and the cornea[WP]. + aqueous humor + aqueous humour + humor aquosus + aqueous humor of eyeball + + + + + + + + + + The liquid component of blood, in which erythrocytes are suspended. + plasma + portion of plasma + blood plasm + portion of blood plasma + blood plasma + + + + + + + + + Portion of semisolid bodily waste discharged through the anus[MW,modified] + excreta + faeces + fecal material + fecal matter + piece of shit + portion of excrement + portion of faeces + portion of fecal material + portion of fecal matter + portion of feces + portionem cacas + stool + cow dung + cow pat + dung + fewmet + frass + guano + portion of dung + portion of guano + portion of scat + scat + spraint + droppings + excrement + ordure + spoor + feces + + + + + + + + + + Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. + integumentary system + body surface + dermal system + external covering of organism + integumentum commune + organism surface + surface + integumental system + + + + + + + + + Any tube, opening or passage that connects two distinct anatomical spaces. + foramen + foramina + opening + ostia + ostium + anatomical conduit + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the ectoderm. + ectodermal deriviative + ectoderm-derived structure + + + + + + + + + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. + skeletal element + + + + + + + + + + A proximal-distal subdivision of the digestive tract. + alimentary system subdivision + intestinal tract + segment of intestinal tract + subdivision of alimentary system + subdivision of digestive tract + + + + + + + + + + Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. + ocular refractive media + + + + + + + + + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + fluid + body fluid + bodily fluid + + + + + + + + + + Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces + plasma ultrafiltrate + transudate + + + + + + + + + + Any fluid produced by a serous gland. + serous fluid + serosal fluid + serous gland fluid + secretion of serous gland + + + + + + + + + An anatomical structure that has more than one cell as a part. + multicellular structure + multicellular anatomical structure + + + + + + + + + A zone of skin that is part of a craniocervical region. + head or neck skin + + + + + + + + + subdivision of tube + + + + + + + + + organ sector + organ zonal region + organ zone + organ region with floating fiat boundary + zone of organ + + + + + + + + + Material anatomical entity that forms the outermost boundary of an anatomical structure. + anatomical surface region + + + + + + + + + A zone of skin that is part of the face. + face skin + facial skin + skin of face + diff --git a/src/envo/imports/pato_terms.txt b/src/envo/imports/pato_terms.txt index e55d47db..7c3538ac 100644 --- a/src/envo/imports/pato_terms.txt +++ b/src/envo/imports/pato_terms.txt @@ -272,3 +272,4 @@ 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 \ No newline at end of file diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index c7bcafa3..9dbe4c3f 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -20,4 +20,5 @@ ENVO:3100030,,PATO:0001842,acidity,ENVO:00002006,water ENVO:3100031,,PATO:0001595,depth,ENVO:00002006,water ENVO:3100032,,PATO:0000018,fluorescence,ENVO:00002006,water ENVO:3100033,,PATO:0001025,pressure,ENVO:00002006,water -ENVO:3100035,,PATO:0000014,color,ENVO:00001998,soil \ No newline at end of file +ENVO:09200021,,PATO:0000014,color,ENVO:00001998,soil +ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation \ No newline at end of file diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 337c8413..0926dc8d 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -93,6 +93,12 @@ + + + + + + @@ -450,6 +456,47 @@ + + + + + + + + + + + + + + + The color of some soil. + soil color + color of soil + + + + + + + + + + + + + + + + + + + The duration of some stellar radiation. + stellar radiation duration + + + + @@ -534,27 +581,6 @@ - - - - - - - - - - - - - - - The color of some soil. - soil color - color of soil - - - - @@ -603,6 +629,12 @@ + + + + + + @@ -634,5 +666,5 @@ - + diff --git a/src/envo/modules/entity_attribute_location.csv b/src/envo/modules/entity_attribute_location.csv index 170fb0a0..46bb554c 100644 --- a/src/envo/modules/entity_attribute_location.csv +++ b/src/envo/modules/entity_attribute_location.csv @@ -20,15 +20,15 @@ ENVO:09000018,,PATO:0000033,concentration,CHEBI:25555,nitrogen atom,ENVO:0000200 ENVO:09200006,,PATO:0000033,concentration,CHEBI:28938,ammonium,ENVO:00001998,soil ENVO:09200007,,PATO:0000033,concentration,CHEBI:17632,nitrate,ENVO:00001998,soil ENVO:09000019,,PATO:0000033,concentration,CHEBI:17996,chloride,ENVO:00002006,water -ENVO:09200020,,PATO:0000033,concentration,CHEBI:17632,nitrate,ENVO:01001004,groundwater -ENVO:09200021,,PATO:0000033,concentration,CHEBI:15379,oxygen,ENVO:00002006,water -ENVO:09200022,,PATO:0000033,concentration,ENVO:00002982,clay,ENVO:00001998,soil -ENVO:09200023,,PATO:0000033,concentration,ENVO:01000016,slit,ENVO:00001998,soil -ENVO:09200024,,PATO:0000033,concentration,ENVO:01000017,sand,ENVO:00001998,soil -ENVO:09200025,,PATO:0000033,concentration,ENVO:01000018,gravel,ENVO:00001998,soil -ENVO:09200026,,PATO:0000033,concentration,ENVO:00002006,liquid water,ENVO:00001998,soil -ENVO:09200027,,PATO:0000033,concentration,CHEBI:24866,salt,ENVO:00001998,soil -ENVO:09200028,,ENVO:02500034,evaporation,ENVO:00002006,liquid water,ENVO:00001998,soil -ENVO:09200029,,PATO:0000161,rate,ENVO:01000704,hydrological evaporation,ENVO:00001998,soil -ENVO:09200030,,PATO:0000033,concentration,ENVO:04000008,soil organic matter,ENVO:00001998,soil -ENVO:09200031,,PATO:0000033,concentration,CHEBI:25944,pesticide,ENVO:00002042,surface water \ No newline at end of file +ENVO:09000020,,PATO:0000033,concentration,CHEBI:17632,nitrate,ENVO:01001004,groundwater +ENVO:09000021,,PATO:0000033,concentration,CHEBI:15379,oxygen,ENVO:00002006,water +ENVO:09000022,,PATO:0000033,concentration,ENVO:00002982,clay,ENVO:00001998,soil +ENVO:09000023,,PATO:0000033,concentration,ENVO:01000016,slit,ENVO:00001998,soil +ENVO:09000024,,PATO:0000033,concentration,ENVO:01000017,sand,ENVO:00001998,soil +ENVO:09000025,,PATO:0000033,concentration,ENVO:01000018,gravel,ENVO:00001998,soil +ENVO:09000026,,PATO:0000033,concentration,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:09000027,,PATO:0000033,concentration,CHEBI:24866,salt,ENVO:00001998,soil +ENVO:09000028,,ENVO:02500034,evaporation,ENVO:00002006,liquid water,ENVO:00001998,soil +ENVO:09000029,,PATO:0000161,rate,ENVO:01000704,hydrological evaporation,ENVO:00001998,soil +ENVO:09000030,,PATO:0000033,concentration,ENVO:04000008,soil organic matter,ENVO:00001998,soil +ENVO:09000031,,PATO:0000033,concentration,CHEBI:25944,pesticide,ENVO:00002042,surface water diff --git a/src/envo/modules/entity_attribute_location.owl b/src/envo/modules/entity_attribute_location.owl index 684bb2a7..b6cc7fc2 100644 --- a/src/envo/modules/entity_attribute_location.owl +++ b/src/envo/modules/entity_attribute_location.owl @@ -778,71 +778,9 @@ - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of a ammonium when measured in soil. - soil ammonium concentration - concentration of ammonium in soil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The concentration of a nitrate when measured in soil. - soil nitrate concentration - concentration of nitrate in soil - - - - - + - + @@ -871,9 +809,9 @@ - + - + @@ -902,9 +840,9 @@ - + - + @@ -933,9 +871,9 @@ - + - + @@ -964,9 +902,9 @@ - + - + @@ -995,9 +933,9 @@ - + - + @@ -1026,9 +964,9 @@ - + - + @@ -1057,9 +995,9 @@ - + - + @@ -1088,9 +1026,9 @@ - + - + @@ -1119,9 +1057,9 @@ - + - + @@ -1150,9 +1088,9 @@ - + - + @@ -1181,9 +1119,9 @@ - + - + @@ -1212,6 +1150,68 @@ + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a ammonium when measured in soil. + soil ammonium concentration + concentration of ammonium in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of a nitrate when measured in soil. + soil nitrate concentration + concentration of nitrate in soil + + + + From 70ef56aa9f81b1b79fd9b172e8ae5bfb456ab3f7 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Tue, 16 Nov 2021 19:31:29 -0500 Subject: [PATCH 10/23] #366 Add class 'pressure of vapour' --- src/envo/modules/entity_attribute.csv | 3 ++- src/envo/modules/entity_attribute.owl | 30 ++++++++++++++++++++++++++- 2 files changed, 31 insertions(+), 2 deletions(-) diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 9dbe4c3f..874b2281 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -21,4 +21,5 @@ ENVO:3100031,,PATO:0001595,depth,ENVO:00002006,water ENVO:3100032,,PATO:0000018,fluorescence,ENVO:00002006,water ENVO:3100033,,PATO:0001025,pressure,ENVO:00002006,water ENVO:09200021,,PATO:0000014,color,ENVO:00001998,soil -ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation \ No newline at end of file +ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation +ENVO:09200023,,PATO:0001025,pressure,ENVO:01000268,atmospheric water vapour diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 0926dc8d..def614ff 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -87,6 +87,12 @@ + + + + + + @@ -493,6 +499,28 @@ The duration of some stellar radiation. stellar radiation duration + duration of stellar radiation + + + + + + + + + + + + + + + + + + + The pressure of some atmospheric water vapour. + atmospheric water vapour pressure + pressure of atmospheric water vapour @@ -666,5 +694,5 @@ - + From 8dbadf3a7b644ca691a3f5859f82c4f1f66af0f6 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Thu, 18 Nov 2021 12:37:25 -0500 Subject: [PATCH 11/23] #361 [EA] Added class 'runoff volume' closes #361 --- src/envo/modules/entity_attribute.csv | 1 + src/envo/modules/entity_attribute.owl | 33 +++++++++++++++++++++++++++ 2 files changed, 34 insertions(+) diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 874b2281..47ff4d2c 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -23,3 +23,4 @@ ENVO:3100033,,PATO:0001025,pressure,ENVO:00002006,water ENVO:09200021,,PATO:0000014,color,ENVO:00001998,soil ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation ENVO:09200023,,PATO:0001025,pressure,ENVO:01000268,atmospheric water vapour +ENVO:09200024,,PATO:0000918,volume,ENVO:06105211,runoff diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index def614ff..10b837da 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -105,6 +105,12 @@ + + + + + + @@ -525,6 +531,27 @@ + + + + + + + + + + + + + + + The volume of some runoff. + runoff volume + volume of runoff + + + + @@ -639,6 +666,12 @@ + + + + + + From 6dada0012657eaa025983c07018b624f5e6a9c66 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Thu, 18 Nov 2021 13:53:56 -0500 Subject: [PATCH 12/23] #353,#354,#355 [EA] Added 'evaporation', 'evapotranspiration', 'rain' volumes --- src/envo/modules/entity_attribute.csv | 3 + src/envo/modules/entity_attribute.owl | 81 +++++++++++++++++++++++++++ 2 files changed, 84 insertions(+) diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 47ff4d2c..093ee63d 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -24,3 +24,6 @@ ENVO:09200021,,PATO:0000014,color,ENVO:00001998,soil ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation ENVO:09200023,,PATO:0001025,pressure,ENVO:01000268,atmospheric water vapour ENVO:09200024,,PATO:0000918,volume,ENVO:06105211,runoff +ENVO:09200025,,PATO:0000918,volume,ENVO:02500034,evaporation +ENVO:09200026,,PATO:0000918,volume,ENVO:02500033,evapotranspiration +ENVO:09200027,,PATO:0000918,volume,ENVO:01001564,rain diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 10b837da..84baf550 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -105,6 +105,24 @@ + + + + + + + + + + + + + + + + + + @@ -552,6 +570,69 @@ + + + + + + + + + + + + + + + The volume of some evaporation. + evaporation volume + volume of evaporation + + + + + + + + + + + + + + + + + + + The volume of some evapotranspiration. + evapotranspiration volume + volume of evapotranspiration + + + + + + + + + + + + + + + + + + + The volume of some rain. + rain volume + volume of rain + + + + From 48ac44c65ed51bdfbcbd75f6bca0edbb4b2f95dd Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Sun, 19 Dec 2021 19:47:45 -0500 Subject: [PATCH 13/23] Added classes for water infiltration Added classes: - water infiltration - soil water infiltration --- src/envo/envo-edit.owl | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 38edbeba..0e8060a2 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3909,6 +3909,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44006,6 +44008,23 @@ AnnotationAssertion( "weathering of plastic"@en) SubClassOf( ) +# Class: (water infiltration) + +AnnotationAssertion( "A movement quality in which water infiltrates a material and fills in the pores."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-20T00:35:50Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "water infiltration"@en) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (soil water infiltration) + +AnnotationAssertion( "A water infiltration process in which water is filling in the pores of a soil."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-20T00:41:35Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "soil water infiltration"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From 5c40b30926977c5fed101deb4364f4b2b9da75c7 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Sun, 19 Dec 2021 22:33:19 -0500 Subject: [PATCH 14/23] #415 added classes for exchangeable potassium Added classes: - exchangeable potassium - exchangeable ion --- src/envo/envo-edit.owl | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 38edbeba..e36ede6c 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3909,6 +3909,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44006,6 +44008,24 @@ AnnotationAssertion( "weathering of plastic"@en) SubClassOf( ) +# Class: (exchangeable ion) + +AnnotationAssertion(Annotation( "https://lawr.ucdavis.edu/classes/ssc219/biogeo/exchca.htm") "A molecular quantity where the bearer of the entity is easily displaced into the soil solution making the entity readily available for plant and microorganism utilization."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-20T01:24:00Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "The exchangeable ion pool is the dominant storage pool for Ca2+, Mg2+, and K+."@en) +AnnotationAssertion(rdfs:label "exchangeable ion"@en) +SubClassOf( ) + +# Class: (exchangeable potassium) + +AnnotationAssertion(Annotation( "https://www.alberta.ca/potassium-management-in-crops.aspx") "An exchangable ion of potassium is that which is loosely held on the negatively charged exchange sites on the surface of clay minerals."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-20T03:22:11Z"^^xsd:dateTime) +AnnotationAssertion( "K+"@en) +AnnotationAssertion(rdfs:label "exchangeable potassium"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From e9927f7eb06afe9cb4ee9784c6024fdfc5736d41 Mon Sep 17 00:00:00 2001 From: Krishna Udaiwal Date: Sun, 19 Dec 2021 22:46:32 -0500 Subject: [PATCH 15/23] #417 added class 'residual water' --- src/envo/envo-edit.owl | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 12140e92..8b475f64 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3654,6 +3654,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -41163,6 +41164,14 @@ AnnotationAssertion( "weathering of plastic"@en) SubClassOf( ) +# Class: (residual water) + +AnnotationAssertion(Annotation( "https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.87.3867&rep=rep1&type=pdf") "Liquid water which has a water phase that is discontinuous and isolated with thin films of water surrounding the soil and air."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-20T03:37:25Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "residual water"@en) +SubClassOf( ) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From da31cc42df6fe1bdd3f84e13168adede47a9151d Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 11:37:51 -0500 Subject: [PATCH 16/23] Added class 'exchangeable calcium' --- src/envo/envo-edit.owl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index e36ede6c..61c0e033 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3911,6 +3911,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44026,6 +44027,15 @@ AnnotationAssertion( "exchangeable potassium"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (exchangeable calcium) + +AnnotationAssertion(Annotation( "https://www.eco-gem.com/soil-science-available-calcium-cation-exchange-complex/") "An exchangable ion of calcium which is attached to the cation exchange complex on soil particles or organic matter, which carries a negative charge."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-22T16:30:54Z"^^xsd:dateTime) +AnnotationAssertion( "Ca2+") +AnnotationAssertion(rdfs:label "exchangeable calcium"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From 30d655759f74409b7fd0fb5dd1159314035e5bae Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 11:53:04 -0500 Subject: [PATCH 17/23] Added class 'cation exchange capacity' --- src/envo/envo-edit.owl | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index e36ede6c..99492bea 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3911,6 +3911,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44026,6 +44027,17 @@ AnnotationAssertion( "exchangeable potassium"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (cation exchange capacity) + +AnnotationAssertion(Annotation( "https://www.extension.purdue.edu/extmedia/ay/ay-238.html") "A molecular quality which inheres in the relative ability of clay and organic matter particles in soils to store cations."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-22T16:39:01Z"^^xsd:dateTime) +AnnotationAssertion( "CEC"@en) +AnnotationAssertion(rdfs:comment "CEC is measured in millequivalents per 100 grams of soil (meq/100g). A meq is the number of ions which total a specific quantity of electrical charges."@en) +AnnotationAssertion(rdfs:comment "Common soil cations include: calcium (Ca++), magnesium (Mg++), potassium (K+), ammonium (NH4+), hydrogen (H+) and sodium (Na+)."@en) +AnnotationAssertion(rdfs:label "cation exchange capacity"@en) +SubClassOf( ) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From bc5b1f0bbf91eaf6eb4990e6a6d8c958063597a4 Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 12:02:01 -0500 Subject: [PATCH 18/23] update DL 'exchangeable ion' relation to 'CEC' --- src/envo/envo-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 99492bea..80decd35 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -44036,7 +44036,7 @@ AnnotationAssertion( "CEC is measured in millequivalents per 100 grams of soil (meq/100g). A meq is the number of ions which total a specific quantity of electrical charges."@en) AnnotationAssertion(rdfs:comment "Common soil cations include: calcium (Ca++), magnesium (Mg++), potassium (K+), ammonium (NH4+), hydrogen (H+) and sodium (Na+)."@en) AnnotationAssertion(rdfs:label "cation exchange capacity"@en) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (axilla skin environment) From 7780bea4559427b827c4409b7bd4e5627d2ebcb7 Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 12:41:45 -0500 Subject: [PATCH 19/23] #422 added class 'percentage base saturation' --- src/envo/envo-edit.owl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 80decd35..1e5ba8b3 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3912,6 +3912,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -44038,6 +44039,16 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "cation exchange capacity"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (percentage base saturation) + +AnnotationAssertion(Annotation( "https://extension.uga.edu/publications/detail.html?number=C1040") "Cation exchange capacity (CEC) where the percentage value refers to the occupied portion of the total CEC by basic cations."@en) +AnnotationAssertion( ) +AnnotationAssertion( "2021-12-22T17:32:00Z"^^xsd:dateTime) +AnnotationAssertion( "BS"@en) +AnnotationAssertion(rdfs:comment "The percentage base saturation is expressed as follows: %BS = [(Ca2+ + Mg2+ + K+)/CEC] × 100"@en) +AnnotationAssertion(rdfs:label "percentage base saturation"@en) +SubClassOf( ) + # Class: (axilla skin environment) AnnotationAssertion(Annotation( "GOC:TermGenie"^^xsd:string) "An environment that is determined by an axilla skin."^^xsd:string) From dac398fa4a8f8989f5fccfe82bf11b6779f33f48 Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 23:40:02 -0500 Subject: [PATCH 20/23] #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 --- src/envo/modules/chemical_concentration.csv | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/envo/modules/chemical_concentration.csv b/src/envo/modules/chemical_concentration.csv index e3611c8a..a14054ee 100644 --- a/src/envo/modules/chemical_concentration.csv +++ b/src/envo/modules/chemical_concentration.csv @@ -115,3 +115,6 @@ 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 From c6586642bcf365b193c413c8bd9105aa721e8679 Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 23:48:44 -0500 Subject: [PATCH 21/23] Update 'water infiltration' DL --- src/envo/envo-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 0e8060a2..4b773dd1 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -44014,7 +44014,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2021-12-20T00:35:50Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "water infiltration"@en) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ) # Class: (soil water infiltration) From 3b99e5640d2b68c9db6701570f414b235c5f1d48 Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Wed, 22 Dec 2021 23:57:47 -0500 Subject: [PATCH 22/23] #395 #398 #420 #432 Added classes in EA pattern Added classes: - soil water infiltration speed - topsoil thickness - soil drainage speed - air temperature amplitude --- src/envo/modules/entity_attribute.csv | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 093ee63d..4106b15c 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -27,3 +27,7 @@ ENVO:09200024,,PATO:0000918,volume,ENVO:06105211,runoff ENVO:09200025,,PATO:0000918,volume,ENVO:02500034,evaporation ENVO:09200026,,PATO:0000918,volume,ENVO:02500033,evapotranspiration ENVO:09200027,,PATO:0000918,volume,ENVO:01001564,rain +ENVO:09200028,,PATO:0000008,speed,ENVO:06105231,soil water infiltration +ENVO:09200029,,PATO:0000915,thickness,PATO:0000915,topsoil +ENVO:09200030,,PATO:0000008,speed,ENVO:06105241,soil drainage +ENVO:09200031,,PATO:0000080,amplitude,ENVO:01000753,air temperature From d8a1e03081d31e8ce8c244d6e6121087a7d3784c Mon Sep 17 00:00:00 2001 From: krishnaTO Date: Thu, 23 Dec 2021 00:17:42 -0500 Subject: [PATCH 23/23] run robot dosdp patterns for CC & EA Imported PATO term corrected EA IRI --- src/envo/imports/pato_terms.txt | 1 + src/envo/modules/chemical_concentration.owl | 111 +++++++++++++++++ src/envo/modules/entity_attribute.csv | 2 +- src/envo/modules/entity_attribute.owl | 126 ++++++++++++++++++++ 4 files changed, 239 insertions(+), 1 deletion(-) diff --git a/src/envo/imports/pato_terms.txt b/src/envo/imports/pato_terms.txt index c87d17c0..fabebcfa 100644 --- a/src/envo/imports/pato_terms.txt +++ b/src/envo/imports/pato_terms.txt @@ -274,3 +274,4 @@ 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_0000915 # thickness diff --git a/src/envo/modules/chemical_concentration.owl b/src/envo/modules/chemical_concentration.owl index 31031efe..76f71294 100644 --- a/src/envo/modules/chemical_concentration.owl +++ b/src/envo/modules/chemical_concentration.owl @@ -525,6 +525,24 @@ + + + + + + + + + + + + + + + + + + @@ -4121,6 +4139,99 @@ + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of exchangeable potassium when measured in soil. + soil exchangeable potassium concentration + concentration of exchangeable potassium in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of residual water when measured in soil. + soil residual water concentration + concentration of residual water in soil + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The concentration of exchangeable calcium when measured in soil. + soil exchangeable calcium concentration + concentration of exchangeable calcium in soil + + + + diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 4106b15c..b724c9b8 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -28,6 +28,6 @@ ENVO:09200025,,PATO:0000918,volume,ENVO:02500034,evaporation ENVO:09200026,,PATO:0000918,volume,ENVO:02500033,evapotranspiration ENVO:09200027,,PATO:0000918,volume,ENVO:01001564,rain ENVO:09200028,,PATO:0000008,speed,ENVO:06105231,soil water infiltration -ENVO:09200029,,PATO:0000915,thickness,PATO:0000915,topsoil +ENVO:09200029,,PATO:0000915,thickness,ENVO:02000059,topsoil ENVO:09200030,,PATO:0000008,speed,ENVO:06105241,soil drainage ENVO:09200031,,PATO:0000080,amplitude,ENVO:01000753,air temperature diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 84baf550..e7e6c4c2 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -99,6 +99,12 @@ + + + + + + @@ -111,6 +117,12 @@ + + + + + + @@ -129,6 +141,18 @@ + + + + + + + + + + + + @@ -633,6 +657,90 @@ + + + + + + + + + + + + + + + The speed of some soil water infiltration. + soil water infiltration speed + speed of soil water infiltration + + + + + + + + + + + + + + + + + + + The thickness of some topsoil. + topsoil thickness + thickness of topsoil + + + + + + + + + + + + + + + + + + + The speed of some soil drainage. + soil drainage speed + speed of soil drainage + + + + + + + + + + + + + + + + + + + The amplitude of some air temperature. + air temperature amplitude + amplitude of air temperature + + + + @@ -717,6 +825,12 @@ + + + + + + @@ -735,6 +849,12 @@ + + + + + + @@ -747,6 +867,12 @@ + + + + + +