From 31c49979901f664155d11e254f6e428c45e85f83 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 5 Aug 2024 14:19:16 -0700 Subject: [PATCH] new terms for animal constructions. (#1530) - created an additional level of classification as not all constructions are habitats - moved beaver dam to construction, made new term for the actual nest - made various terms for hymenopteran constructions (bees, ants, wasps) - added "ant dump" - axiomatized bee hives (made from honeycombs, made from beeswax) - subtypes for beehive for natural v artificial - made human construction term for the artificial bee hive housing. open Qs to be addressed in future PRs: - adding links between structures and the organism taxon class - adding or obtaining terms for functions or processes (e.g. housing, prey entrapment) - environmental processes for damming rivers - linking to NBO or its replacement (modeling the actual construction behavior) --- src/envo/envo-edit.owl | 194 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 189 insertions(+), 5 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 91a67700..ae84f031 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3393,10 +3393,28 @@ 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()) @@ -4392,6 +4410,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -11921,8 +11940,9 @@ AnnotationAssertion(Annotation( "USGS:SDTS") "dam") AnnotationAssertion( "FTT:243") AnnotationAssertion( "https://en.wikipedia.org/wiki/Beaver_dam") +AnnotationAssertion( "dam of beaver") AnnotationAssertion(rdfs:label "beaver dam") -SubClassOf( ) +SubClassOf( ) # Class: (submerged bed) @@ -17295,21 +17315,23 @@ SubClassOf( (animal habitation) AnnotationAssertion(Annotation( "MA:ma") "The dwelling of an animal or group of similar animals.") +AnnotationAssertion( "constructed animal dwelling") AnnotationAssertion( "den") AnnotationAssertion( "nest") AnnotationAssertion(rdfs:comment "This class represents habitations of non-human animals. This distinction may be removed in future releases.") AnnotationAssertion(rdfs:label "animal habitation") -SubClassOf( ) +SubClassOf( ) # Class: (nest of ant) AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Ant_colony#Ant-hills") "A pile of earth, sand, pine needles, or clay or a composite of these and other materials that build up at the entrances of the subterranean dwellings of ant colonies as they are excavated. A colony is built and maintained by legions of worker ants, who carry tiny bits of dirt and pebbles in their mandibles and deposit them near the exit of the colony. They normally deposit the dirt or vegetation at the top of the hill to prevent it from sliding back into the colony, but in some species they actively sculpt the materials into specific shapes, and may create nest chambers within the mound.") AnnotationAssertion( "ant's nest") +AnnotationAssertion( "ant nest") AnnotationAssertion( "ENVO") AnnotationAssertion( "ant hill") AnnotationAssertion( "ENVO:00005804") AnnotationAssertion(rdfs:label "nest of ant") -SubClassOf( ) +SubClassOf( ) # Class: (nest of bird) @@ -24450,6 +24472,7 @@ SubClassOf( "https://en.wikipedia.org/wiki/Apiary") "An apiary is a place where beehives of honey bees are kept and maintained by beekeepers.") AnnotationAssertion(rdfs:label "apiary"@en) SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (radio device) @@ -36146,6 +36169,7 @@ SubClassOf( "A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine.") AnnotationAssertion( ) AnnotationAssertion( "2019-10-29T14:50:34Z"^^xsd:dateTime) +AnnotationAssertion( "assembled material entity") AnnotationAssertion(rdfs:label "construction"@en) SubClassOf( ) @@ -38385,6 +38409,16 @@ AnnotationAssertion(rdfs:label "m EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) +# Class: (animal construction) + +AnnotationAssertion( "A construction that is assembled by a non-human animal") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:02:27Z"^^xsd:dateTime) +AnnotationAssertion( "Non-human animal assembled structure") +AnnotationAssertion( "Non-human animal construction") +AnnotationAssertion(rdfs:label "animal construction"@en) +SubClassOf( ) + # Class: (solid waste material) AnnotationAssertion( "Solid material that has a waste role.") @@ -38421,6 +38455,155 @@ AnnotationAssertion(rdfs:label "b SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (bee hive) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "An animal habitation that is assembled by colonies of organisms in the clade Anthophila (bees). Each nest is composed of multiple honeycombs, constructed using beeswax for the purposes of rearing young and storing honey and pollen.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:04:24Z"^^xsd:dateTime) +AnnotationAssertion( "beehive") +AnnotationAssertion(rdfs:label "bee hive"@en) +SubClassOf( ) +DisjointUnion( ) + +# Class: (hymenopteran habitation) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "An animal habitation assembled by organisms within the clade Hymenoptera. Examples include termite nests, beehives, and ant nests. Typically constructed to serve as habitation for a whole colony ruled by a queen.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:07:57Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "hymenopteran habitation"@en) +EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) + +# Class: (termite mound) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "A termite nest that is built above ground, and is made of soil, saliva, and feces, formed as a large mound.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:09:16Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "termite mound"@en) +SubClassOf( ) + +# Class: (termite subterranean nest) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "A termite nest that is underground, often connected to food sources through a network of tunnels.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:09:26Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "termite subterranean nest"@en) +SubClassOf( ) + +# Class: (termite arboreal nest) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "A termite nest that is built above ground in trees or on structures, often resembling large lumps attached to branches.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:09:37Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "termite arboreal nest"@en) +SubClassOf( ) + +# Class: (crocodilian nest) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "An animal habitation that is assembled by an organism in the order Crocodylia (alligators, crocodiles, caimans, and gharials). These habitations (nests), are typically built in freshwater or brackish environments. They can be mound nests, made from vegetation, mud, and organic material, or hole nests, excavated in sandy or muddy banks. These nests serve as sites for egg laying, incubation, and initial care of the young.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:15:17Z"^^xsd:dateTime) +AnnotationAssertion( "nest of crocodilian") +AnnotationAssertion( "nest of crocodylian") +AnnotationAssertion(rdfs:label "crocodilian nest"@en) +SubClassOf( ) + +# Class: (nest of crocodile) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "An animal habitation that is constructed by organisms in the family Crocodylidae (crocodiles).") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:15:34Z"^^xsd:dateTime) +AnnotationAssertion( "crocodile nest") +AnnotationAssertion(rdfs:comment "Crocodiles can nest in a variety of environments, including freshwater and brackish water habitats like rivers, lakes, wetlands, and coastal areas.") +AnnotationAssertion(rdfs:label "nest of crocodile"@en) +SubClassOf( ) + +# Class: (natural bee hive) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Beehive") "A bee hive that occurs naturally without human intervention, typically found in environments such as tree cavities, rock crevices, or underground burrows.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:24:25Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "natural bee hive"@en) +SubClassOf( ) + +# Class: (anthropogenic bee hive) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Beehive") "A bee hive that is built in a structure assembled by humans to house bee colonies, often for the purposes of honey production, pollination, or research.") +AnnotationAssertion( "For simplicitly we model anthropogenic bee hive as an animal construction, and model the structure in which it is housed as anthropogenic.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:24:51Z"^^xsd:dateTime) +AnnotationAssertion( "artificial hive") +AnnotationAssertion(rdfs:label "anthropogenic bee hive"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (anthropogenic bee hive structure) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "A human construction that serves as a structure in which bees can build their hives.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:28:42Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "anthropogenic bee hive structure"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (beeswax) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Beehive") "A natural wax that is produced by a bee.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:33:59Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "beeswax"@en) +SubClassOf( ) + +# Class: (honeycomb) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Beehive") "A modular structure created by bees (Anthophila) from beeswax, consisting of a mass of hexagonal prismatic cells used to store honey, pollen, and house brood (eggs, larvae, and pupae).") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:34:57Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "honeycomb"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (hymenopteran construction) + +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:38:06Z"^^xsd:dateTime) +AnnotationAssertion( "construction of hymenopteran") +AnnotationAssertion(rdfs:label "hymenopteran construction"@en) +SubClassOf( ) + +# Class: (nest of wasp) + +AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Nest") "An animal habitation that is assembled by a wasp. These may be in the ground, in wall cavities, or in sheltered areas.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:41:04Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "nest of wasp"@en) +SubClassOf( ) + +# Class: (beaver lodge) + +AnnotationAssertion( "An animal habitation created by a beaver, constructed within or adjacent to the pond created by the beaver dam.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T20:56:27Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "beaver lodge"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) + +# Class: (ant dump) + +AnnotationAssertion( "An animal construction created by leaf-cutter ants that is composed of various materials that result from the ants' activities and behaviors, including degraded plant material, microbial communities, organic material, dead ants and fungus.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:02:49Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "ant dump"@en) +SubClassOf( ) + +# Class: (spider web) + +AnnotationAssertion( "An animal structure that is assembled by a spider from silk, that serves as both habitation and a structure to trap prey.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:05:22Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "spider web"@en) +SubClassOf( ) + # Class: (environmental system process) AnnotationAssertion( "A process in which includes the components of an environmental system as participants.") @@ -44906,8 +45089,9 @@ SubClassOf( ) Annotation( ) "An animal habitation which is built by alligators from plants and decomposing vegetation in order to protect their eggs from predators."@en) AnnotationAssertion( ) AnnotationAssertion( "2021-07-03T00:22:16.764Z"^^xsd:dateTime) +AnnotationAssertion( "alligator nest") AnnotationAssertion(rdfs:label "nest of alligator"@en) -SubClassOf( ) +SubClassOf( ) # Class: (river plume) @@ -46804,7 +46988,7 @@ AnnotationAssertion( "ENVO") AnnotationAssertion( "ENVO:2000006") AnnotationAssertion(rdfs:label "nest of termite") -SubClassOf( ) +SubClassOf( ) # Class: (biochar)