From 7188171c88fcfb12727ebbe0156413048a3f074d Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 5 Aug 2024 15:05:52 -0700 Subject: [PATCH 1/2] Adding bioremediation processes. Adding intermediate level between pollution control and anthropogenic process --- src/envo/envo-edit.owl | 90 ++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 86 insertions(+), 4 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index ae84f031..8a8b7e1b 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3415,6 +3415,15 @@ 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()) @@ -17325,8 +17334,8 @@ SubClassOf( (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( "ant's nest") AnnotationAssertion( "ENVO") AnnotationAssertion( "ant hill") AnnotationAssertion( "ENVO:00005804") @@ -25858,7 +25867,7 @@ SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (recycling process) +# Class: (waste recycling process) AnnotationAssertion(Annotation( "https://stats.oecd.org/glossary/detail.asp?ID=2260") "A process during which materials deemed as waste are separated and converted into a form which can be used as input by the same processes which generated them."@en) AnnotationAssertion( ) @@ -25870,8 +25879,8 @@ AnnotationAssertion( "資源回收"@zh) AnnotationAssertion( "envoPlastics") AnnotationAssertion(rdfs:comment "This has been created for SDGIO. Revision is likely, but the general meaning should be stable. The frame of reference for determining what is 'waste' and what is a 'resource' is unclear.") -AnnotationAssertion(rdfs:label "recycling process"@en) -SubClassOf( ) +AnnotationAssertion(rdfs:label "waste recycling process"@en) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (carbon-bearing gas emission process) @@ -30867,6 +30876,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion(Annotation( "https://eupathdb.org/eupathdb/") "A process during which materials deemed to be waste are removed from a site and transported to another site designated for its storage.") AnnotationAssertion(rdfs:label "transport of waste to a designated storage site"@en) SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (waste disposal process) @@ -38604,6 +38614,77 @@ AnnotationAssertion( "spider web"@en) SubClassOf( ) +# Class: (bioremediation) + +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:20:12Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:comment "A process of pollution degradation involving the deliberate use of cultured or modified organisms to remove or neutralize contaminants, typically within controlled systems.") +AnnotationAssertion(rdfs:label "bioremediation"@en) +SubClassOf( ) + +# Class: (pollution degradation) + +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:20:56Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "pollution degradation"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (anthropogenic modulation of pollution) + +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:21:15Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "anthropogenic modulation of pollution"@en) +SubClassOf( ) + +# Class: (hydrocarbon bioremediation) + +AnnotationAssertion( "A process of bioremediation that specifically targets the breakdown of hydrocarbon pollutants, using engineered or adapted microorganisms to convert these organic compounds into less harmful substances.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:31:42Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "hydrocarbon bioremediation"@en) +SubClassOf( ) + +# Class: (metal bioremediation) + +AnnotationAssertion( "A bioremediation technique involving the use of specially engineered organisms, often microbes, that can sequester, mobilize, or transform metal contaminants into non-toxic forms.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:32:21Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "metal bioremediation"@en) +SubClassOf( ) + +# Class: (persistent organic pollutant bioremediation) + +AnnotationAssertion( "A specialized form of bioremediation focusing on the degradation or transformation of persistent organic pollutants (POPs), employing engineered organisms capable of breaking down compounds that are resistant to environmental degradation.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:32:50Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "persistent organic pollutant bioremediation"@en) +SubClassOf( ) + +# Class: (terephthalate remediation) + +AnnotationAssertion( "A bioremediation process directed at the degradation of terephthalate compounds, utilizing genetically modified or specially adapted microorganisms to metabolize these synthetic polymers.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:33:02Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "terephthalate remediation"@en) +SubClassOf( ) + +# Class: (tetrachloroethylene or tetrachloroethylene derivative remediation) + +AnnotationAssertion( "A form of bioremediation that targets tetrachloroethylene and its derivatives, employing organisms that have been engineered to detoxify these chlorinated organic solvents.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:33:20Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "tetrachloroethylene or tetrachloroethylene derivative remediation"@en) +SubClassOf( ) + +# Class: (thiocyanate remediation) + +AnnotationAssertion( "A bioremediation process specifically designed for the breakdown of thiocyanates, using modified organisms to convert thiocyanate into less harmful substances through biological pathways.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T21:33:32Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "thiocyanate remediation"@en) +SubClassOf( ) + # Class: (environmental system process) AnnotationAssertion( "A process in which includes the components of an environmental system as participants.") @@ -38939,6 +39020,7 @@ AnnotationAssertion( "pollution prevention") AnnotationAssertion(rdfs:label "pollution control") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (pollution monitoring) From df5a423ef2438df6b4d284e5cfa383b1ec4a30fd Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 5 Aug 2024 15:36:39 -0700 Subject: [PATCH 2/2] Added biotransformation process definitions --- src/envo/envo-edit.owl | 47 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index 8a8b7e1b..bea1cd6a 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -3424,6 +3424,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -38685,6 +38690,48 @@ AnnotationAssertion( "thiocyanate remediation"@en) SubClassOf( ) +# Class: (biotransformation process) + +AnnotationAssertion( "A planned process involving the deliberate use of biological agents, such as microbes or enzymes, to chemically modify substances in a controlled setting. This process is typically utilized to enhance the value or reduce the environmental impact of various materials.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T22:07:41Z"^^xsd:dateTime) +AnnotationAssertion( "biotransformation") +AnnotationAssertion(rdfs:label "biotransformation process"@en) +SubClassOf( ) + +# Class: (biotransformation of coal) + +AnnotationAssertion( "A biotransformation process that targets coal, using engineered biological organisms to alter its chemical composition or properties, potentially enhancing its energy efficiency or reducing its environmental footprint.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T22:09:19Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "biotransformation of coal"@en) +SubClassOf( ) + +# Class: (microbial enhanced oil recovery) + +AnnotationAssertion( "A biotransformation that uses microorganisms to increase the extraction efficiency of oil from reservoirs. This process may involve the alteration of oil viscosity, the modification of reservoir properties, or the production of biosurfactants.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T22:10:07Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "microbial enhanced oil recovery"@en) +SubClassOf( ) + +# Class: (microbial solubization of coal) + +AnnotationAssertion( "A biotransformation that uses microbes to convert solid coal into a more soluble form, enhancing its utility for energy production or further chemical processing.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T22:10:33Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "microbial solubization of coal"@en) +SubClassOf( ) + +# Class: (biotransformation of biomass into mixed alcohols) + +AnnotationAssertion( "A biotransformation process that produces mixed alcohols from from biomass via fermentation.") +AnnotationAssertion( ) +AnnotationAssertion( "2024-08-05T22:13:50Z"^^xsd:dateTime) +AnnotationAssertion( "mixed alcohol bioreactor process") +AnnotationAssertion(rdfs:label "biotransformation of biomass into mixed alcohols"@en) +SubClassOf( ) + # Class: (environmental system process) AnnotationAssertion( "A process in which includes the components of an environmental system as participants.")