From 054c71589a48cf36965c2860e81d5f51ddc33cb9 Mon Sep 17 00:00:00 2001 From: pbuttigieg Date: Thu, 29 Jun 2017 17:06:17 +0200 Subject: [PATCH] addressing #490 --- src/envo/envo-edit.owl | 1 + src/envo/imports/bfo_seed.owl | 3 +- src/envo/imports/pato_import.owl | 29 ++++++ src/envo/imports/pato_seed.owl | 4 +- src/envo/modules/catalog-v001.xml | 8 ++ src/envo/modules/entity_attribute.csv | 1 + src/envo/modules/entity_attribute.obo | 99 +++++++++++++++++++ src/envo/modules/entity_attribute.omn | 127 +++++++++++++++++++++++++ src/envo/modules/entity_attribute.owl | 27 ++++++ src/envo/modules/entity_attribute_location.obo | 123 ++++++++++++++++++++++++ src/envo/modules/entity_quality_location.obo | 39 ++++++++ 11 files changed, 459 insertions(+), 2 deletions(-) create mode 100644 src/envo/modules/catalog-v001.xml create mode 100644 src/envo/modules/entity_attribute.obo create mode 100644 src/envo/modules/entity_attribute.omn create mode 100644 src/envo/modules/entity_attribute_location.obo create mode 100644 src/envo/modules/entity_quality_location.obo diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 93d4a72..028dd75 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -25789,6 +25789,7 @@ SubClassOf( "Air which has increased levels of water vapour.") AnnotationAssertion(rdfs:label "humid air"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (water vapour saturated air) diff --git a/src/envo/imports/bfo_seed.owl b/src/envo/imports/bfo_seed.owl index 3a21523..98998b3 100644 --- a/src/envo/imports/bfo_seed.owl +++ b/src/envo/imports/bfo_seed.owl @@ -16,4 +16,5 @@ Ontology: Class: # fiat object part Class: # continuant fiat boundary Class: # two-dimensional continuant fiat boundary -Class: # one-dimensional continuant fiat boundary \ No newline at end of file +Class: # one-dimensional continuant fiat boundary +Class: # spatial region diff --git a/src/envo/imports/pato_import.owl b/src/envo/imports/pato_import.owl index e034f6b..cc33051 100644 --- a/src/envo/imports/pato_import.owl +++ b/src/envo/imports/pato_import.owl @@ -2227,6 +2227,35 @@ + + + + humidity + + + + + + + + + increased humidity + + + + + + + + + + decreased humidity + + + + + + diff --git a/src/envo/imports/pato_seed.owl b/src/envo/imports/pato_seed.owl index f2ce4f2..e058699 100644 --- a/src/envo/imports/pato_seed.owl +++ b/src/envo/imports/pato_seed.owl @@ -15,7 +15,9 @@ AnnotationProperty: rdfs:label Datatype: xsd:string -# Class: <> # +Class: # humidity +Class: # increased humidity +Class: # decreased humidity Class: # intermittent Class: # blue Class: # horizontal diff --git a/src/envo/modules/catalog-v001.xml b/src/envo/modules/catalog-v001.xml new file mode 100644 index 0000000..0db12be --- /dev/null +++ b/src/envo/modules/catalog-v001.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/src/envo/modules/entity_attribute.csv b/src/envo/modules/entity_attribute.csv index 69b1862..9f0bef0 100644 --- a/src/envo/modules/entity_attribute.csv +++ b/src/envo/modules/entity_attribute.csv @@ -10,3 +10,4 @@ ENVO:09200011,,PATO:0001025,pressure,ENVO:00002005,air ENVO:09200012,,PATO:0000146,temperature,ENVO:00001998,soil ENVO:09200013,,PATO:0001822,wetness,ENVO:00001998,soil ENVO:09200014,,PATO:0000146,temperature,ENVO:00002006,water +ENVO:09200015,,PATO:0015009,humidity,ENVO:00001998,soil \ No newline at end of file diff --git a/src/envo/modules/entity_attribute.obo b/src/envo/modules/entity_attribute.obo new file mode 100644 index 0000000..ed51cfb --- /dev/null +++ b/src/envo/modules/entity_attribute.obo @@ -0,0 +1,99 @@ +format-version: 1.2 +ontology: envo/modules/entity_attribute + +[Term] +id: ENVO:09200000 +name: temperature of environmental material +def: "The temperature of some environmental material." [] +synonym: "environmental material temperature" EXACT [] +intersection_of: PATO:0000146 +intersection_of: RO:0000052 ENVO:00010483 + +[Term] +id: ENVO:09200001 +name: temperature of air +def: "The temperature of some air." [] +synonym: "air temperature" EXACT [] +intersection_of: PATO:0000146 +intersection_of: RO:0000052 ENVO:00002005 + +[Term] +id: ENVO:09200004 +name: porosity of soil +def: "The porosity of some soil." [] +synonym: "soil porosity" EXACT [] +intersection_of: PATO:0000973 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200005 +name: mass density of soil +def: "The mass density of some soil." [] +synonym: "soil mass density" EXACT [] +intersection_of: PATO:0001019 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200008 +name: composition of soil +def: "The composition of some soil." [] +synonym: "soil composition" EXACT [] +intersection_of: PATO:0000025 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200009 +name: structure of soil +def: "The structure of some soil." [] +synonym: "soil structure" EXACT [] +intersection_of: PATO:0000141 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200010 +name: acidity of soil +def: "The acidity of some soil." [] +synonym: "soil acidity" EXACT [] +intersection_of: PATO:0001842 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200011 +name: pressure of air +def: "The pressure of some air." [] +synonym: "air pressure" EXACT [] +intersection_of: PATO:0001025 +intersection_of: RO:0000052 ENVO:00002005 + +[Term] +id: ENVO:09200012 +name: temperature of soil +def: "The temperature of some soil." [] +synonym: "soil temperature" EXACT [] +intersection_of: PATO:0000146 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200013 +name: wetness of soil +def: "The wetness of some soil." [] +synonym: "soil wetness" EXACT [] +intersection_of: PATO:0001822 +intersection_of: RO:0000052 ENVO:00001998 + +[Term] +id: ENVO:09200014 +name: temperature of water +def: "The temperature of some water." [] +synonym: "water temperature" EXACT [] +intersection_of: PATO:0000146 +intersection_of: RO:0000052 ENVO:00002006 + +[Term] +id: ENVO:09200015 +name: humidity of soil +def: "The humidity of some soil." [] +synonym: "soil humidity" EXACT [] +intersection_of: PATO:0015009 +intersection_of: RO:0000052 ENVO:00001998 + diff --git a/src/envo/modules/entity_attribute.omn b/src/envo/modules/entity_attribute.omn new file mode 100644 index 0000000..9e544f6 --- /dev/null +++ b/src/envo/modules/entity_attribute.omn @@ -0,0 +1,127 @@ +Prefix: : +Prefix: IAO: +Prefix: DOSDP: +Prefix: oio: +Prefix: CHEBI: +Prefix: PATO: +Prefix: ENVO: +Prefix: RO: + + ## Auto-generated + +Ontology: +AnnotationProperty: IAO:0000115 +AnnotationProperty: envo-p/patterns/entity_attribute/attribute +AnnotationProperty: envo-p/patterns/entity_attribute/entity +AnnotationProperty: DOSDP:applies-pattern +AnnotationProperty: oio:hasExactSynonym +ObjectProperty: RO:0000052 ## inheres in +## Auto-generated classes + +Class: PATO:0000146 ## temperature +Class: ENVO:00010483 ## environmental material +## {"attribute": "PATO:0000146", "entity": "ENVO:00010483"} +Class: ENVO:09200000 + Annotations: rdfs:label "temperature of environmental material" + Annotations: IAO:0000115 "The temperature of some environmental material." + Annotations: oio:hasExactSynonym "environmental material temperature" + EquivalentTo: PATO:0000146 and RO:0000052 some ENVO:00010483 ## temperature and 'inheres in' some environmental material + +Class: PATO:0000146 ## temperature +Class: ENVO:00002005 ## air +## {"attribute": "PATO:0000146", "entity": "ENVO:00002005"} +Class: ENVO:09200001 + Annotations: rdfs:label "temperature of air" + Annotations: IAO:0000115 "The temperature of some air." + Annotations: oio:hasExactSynonym "air temperature" + EquivalentTo: PATO:0000146 and RO:0000052 some ENVO:00002005 ## temperature and 'inheres in' some air + +Class: PATO:0000973 ## porosity +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0000973", "entity": "ENVO:00001998"} +Class: ENVO:09200004 + Annotations: rdfs:label "porosity of soil" + Annotations: IAO:0000115 "The porosity of some soil." + Annotations: oio:hasExactSynonym "soil porosity" + EquivalentTo: PATO:0000973 and RO:0000052 some ENVO:00001998 ## porosity and 'inheres in' some soil + +Class: PATO:0001019 ## mass density +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0001019", "entity": "ENVO:00001998"} +Class: ENVO:09200005 + Annotations: rdfs:label "mass density of soil" + Annotations: IAO:0000115 "The mass density of some soil." + Annotations: oio:hasExactSynonym "soil mass density" + EquivalentTo: PATO:0001019 and RO:0000052 some ENVO:00001998 ## mass density and 'inheres in' some soil + +Class: PATO:0000025 ## composition +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0000025", "entity": "ENVO:00001998"} +Class: ENVO:09200008 + Annotations: rdfs:label "composition of soil" + Annotations: IAO:0000115 "The composition of some soil." + Annotations: oio:hasExactSynonym "soil composition" + EquivalentTo: PATO:0000025 and RO:0000052 some ENVO:00001998 ## composition and 'inheres in' some soil + +Class: PATO:0000141 ## structure +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0000141", "entity": "ENVO:00001998"} +Class: ENVO:09200009 + Annotations: rdfs:label "structure of soil" + Annotations: IAO:0000115 "The structure of some soil." + Annotations: oio:hasExactSynonym "soil structure" + EquivalentTo: PATO:0000141 and RO:0000052 some ENVO:00001998 ## structure and 'inheres in' some soil + +Class: PATO:0001842 ## acidity +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0001842", "entity": "ENVO:00001998"} +Class: ENVO:09200010 + Annotations: rdfs:label "acidity of soil" + Annotations: IAO:0000115 "The acidity of some soil." + Annotations: oio:hasExactSynonym "soil acidity" + EquivalentTo: PATO:0001842 and RO:0000052 some ENVO:00001998 ## acidity and 'inheres in' some soil + +Class: PATO:0001025 ## pressure +Class: ENVO:00002005 ## air +## {"attribute": "PATO:0001025", "entity": "ENVO:00002005"} +Class: ENVO:09200011 + Annotations: rdfs:label "pressure of air" + Annotations: IAO:0000115 "The pressure of some air." + Annotations: oio:hasExactSynonym "air pressure" + EquivalentTo: PATO:0001025 and RO:0000052 some ENVO:00002005 ## pressure and 'inheres in' some air + +Class: PATO:0000146 ## temperature +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0000146", "entity": "ENVO:00001998"} +Class: ENVO:09200012 + Annotations: rdfs:label "temperature of soil" + Annotations: IAO:0000115 "The temperature of some soil." + Annotations: oio:hasExactSynonym "soil temperature" + EquivalentTo: PATO:0000146 and RO:0000052 some ENVO:00001998 ## temperature and 'inheres in' some soil + +Class: PATO:0001822 ## wetness +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0001822", "entity": "ENVO:00001998"} +Class: ENVO:09200013 + Annotations: rdfs:label "wetness of soil" + Annotations: IAO:0000115 "The wetness of some soil." + Annotations: oio:hasExactSynonym "soil wetness" + EquivalentTo: PATO:0001822 and RO:0000052 some ENVO:00001998 ## wetness and 'inheres in' some soil + +Class: PATO:0000146 ## temperature +Class: ENVO:00002006 ## water +## {"attribute": "PATO:0000146", "entity": "ENVO:00002006"} +Class: ENVO:09200014 + Annotations: rdfs:label "temperature of water" + Annotations: IAO:0000115 "The temperature of some water." + Annotations: oio:hasExactSynonym "water temperature" + EquivalentTo: PATO:0000146 and RO:0000052 some ENVO:00002006 ## temperature and 'inheres in' some water + +Class: PATO:0015009 ## humidity +Class: ENVO:00001998 ## soil +## {"attribute": "PATO:0015009", "entity": "ENVO:00001998"} +Class: ENVO:09200015 + Annotations: rdfs:label "humidity of soil" + Annotations: IAO:0000115 "The humidity of some soil." + Annotations: oio:hasExactSynonym "soil humidity" + EquivalentTo: PATO:0015009 and RO:0000052 some ENVO:00001998 ## humidity and 'inheres in' some soil diff --git a/src/envo/modules/entity_attribute.owl b/src/envo/modules/entity_attribute.owl index 581bfcf..5850254 100644 --- a/src/envo/modules/entity_attribute.owl +++ b/src/envo/modules/entity_attribute.owl @@ -337,6 +337,27 @@ + + + + humidity of soil + + + + + + + + + + + + soil humidity + The humidity of some soil. + + + + @@ -382,6 +403,12 @@ + + + + + + diff --git a/src/envo/modules/entity_attribute_location.obo b/src/envo/modules/entity_attribute_location.obo new file mode 100644 index 0000000..78b4919 --- /dev/null +++ b/src/envo/modules/entity_attribute_location.obo @@ -0,0 +1,123 @@ +format-version: 1.2 +ontology: envo/modules/entity_attribute_location + +[Term] +id: ENVO:09000001 +name: solubility of carbon atom in environmental material +def: "The solubility of a carbon atom when measured in environmental material." [] +synonym: "environmental material carbon atom solubility" EXACT [] + +[Term] +id: ENVO:09000002 +name: solubility of carbon atom in soil +def: "The solubility of a carbon atom when measured in soil." [] +synonym: "soil carbon atom solubility" EXACT [] + +[Term] +id: ENVO:09000003 +name: solubility of carbon atom in water +def: "The solubility of a carbon atom when measured in water." [] +synonym: "water carbon atom solubility" EXACT [] + +[Term] +id: ENVO:09000004 +name: amount of carbon atom in environmental material +def: "The amount of a carbon atom when measured in environmental material." [] +synonym: "environmental material carbon atom amount" EXACT [] + +[Term] +id: ENVO:09000005 +name: amount of carbon atom in soil +def: "The amount of a carbon atom when measured in soil." [] +synonym: "soil carbon atom amount" EXACT [] + +[Term] +id: ENVO:09000006 +name: amount of carbon atom in water +def: "The amount of a carbon atom when measured in water." [] +synonym: "water carbon atom amount" EXACT [] + +[Term] +id: ENVO:09000007 +name: concentration of of carbon atom in environmental material +def: "The concentration of of a carbon atom when measured in environmental material." [] +synonym: "environmental material carbon atom concentration of" EXACT [] + +[Term] +id: ENVO:09000008 +name: concentration of of carbon atom in soil +def: "The concentration of of a carbon atom when measured in soil." [] +synonym: "soil carbon atom concentration of" EXACT [] + +[Term] +id: ENVO:09000009 +name: concentration of of carbon atom in water +def: "The concentration of of a carbon atom when measured in water." [] +synonym: "water carbon atom concentration of" EXACT [] + +[Term] +id: ENVO:09000010 +name: solubility of nitrogen atom in environmental material +def: "The solubility of a nitrogen atom when measured in environmental material." [] +synonym: "environmental material nitrogen atom solubility" EXACT [] + +[Term] +id: ENVO:09000011 +name: solubility of nitrogen atom in soil +def: "The solubility of a nitrogen atom when measured in soil." [] +synonym: "soil nitrogen atom solubility" EXACT [] + +[Term] +id: ENVO:09000012 +name: solubility of nitrogen atom in water +def: "The solubility of a nitrogen atom when measured in water." [] +synonym: "water nitrogen atom solubility" EXACT [] + +[Term] +id: ENVO:09000013 +name: amount of nitrogen atom in environmental material +def: "The amount of a nitrogen atom when measured in environmental material." [] +synonym: "environmental material nitrogen atom amount" EXACT [] + +[Term] +id: ENVO:09000014 +name: amount of nitrogen atom in soil +def: "The amount of a nitrogen atom when measured in soil." [] +synonym: "soil nitrogen atom amount" EXACT [] + +[Term] +id: ENVO:09000015 +name: amount of nitrogen atom in water +def: "The amount of a nitrogen atom when measured in water." [] +synonym: "water nitrogen atom amount" EXACT [] + +[Term] +id: ENVO:09000016 +name: concentration of of nitrogen atom in environmental material +def: "The concentration of of a nitrogen atom when measured in environmental material." [] +synonym: "environmental material nitrogen atom concentration of" EXACT [] + +[Term] +id: ENVO:09000017 +name: concentration of of nitrogen atom in soil +def: "The concentration of of a nitrogen atom when measured in soil." [] +synonym: "soil nitrogen atom concentration of" EXACT [] + +[Term] +id: ENVO:09000018 +name: concentration of of nitrogen atom in water +def: "The concentration of of a nitrogen atom when measured in water." [] +synonym: "water nitrogen atom concentration of" EXACT [] + +[Term] +id: ENVO:09200006 +name: concentration of of ammonium in soil +def: "The concentration of of a ammonium when measured in soil." [] +synonym: "soil ammonium concentration of" EXACT [] + +[Term] +id: ENVO:09200007 +name: concentration of of nitrate in soil +def: "The concentration of of a nitrate when measured in soil." [] +synonym: "soil nitrate concentration of" EXACT [] + diff --git a/src/envo/modules/entity_quality_location.obo b/src/envo/modules/entity_quality_location.obo new file mode 100644 index 0000000..706e866 --- /dev/null +++ b/src/envo/modules/entity_quality_location.obo @@ -0,0 +1,39 @@ +format-version: 1.2 +ontology: envo/modules/entity_quality_location + +[Term] +id: ENVO:09100001 +name: dissolved carbon atom in environmental material +def: "The carbon atom in a dissolved state when measured in environmental material." [] +synonym: "environmental material dissolved carbon atom" EXACT [] + +[Term] +id: ENVO:09100002 +name: dissolved carbon atom in soil +def: "The carbon atom in a dissolved state when measured in soil." [] +synonym: "soil dissolved carbon atom" EXACT [] + +[Term] +id: ENVO:09100003 +name: dissolved carbon atom in water +def: "The carbon atom in a dissolved state when measured in water." [] +synonym: "water dissolved carbon atom" EXACT [] + +[Term] +id: ENVO:09100004 +name: dissolved nitrogen atom in environmental material +def: "The nitrogen atom in a dissolved state when measured in environmental material." [] +synonym: "environmental material dissolved nitrogen atom" EXACT [] + +[Term] +id: ENVO:09100005 +name: dissolved nitrogen atom in soil +def: "The nitrogen atom in a dissolved state when measured in soil." [] +synonym: "soil dissolved nitrogen atom" EXACT [] + +[Term] +id: ENVO:09100006 +name: dissolved nitrogen atom in water +def: "The nitrogen atom in a dissolved state when measured in water." [] +synonym: "water dissolved nitrogen atom" EXACT [] +