Issue 1251

[pbuttigieg]

Supercedes #1252

[cmungall]

Hi @pbuttigieg

Unfortunately reviewing this PR is very difficult as it was started from an old PR and has many of the changes that happened on master merged in, so everything is all mixed together in the PR.

I'm going to consult with some others on the best way to proceed here. (There are many approaches ranging from cherry picking through to rebasing through to simply redoing the work). I will report back later.

[cmungall]

It looks like all intended changes were in one commit. I did a diff of this to help us review: diff.txt

• ADD AnnotationAssertion([definition] [cave entrance] "A two-dimensional continuant fiat boundary which is used to demarcate the interior from the exterior of a cave."@en)
• ADD AnnotationAssertion([definition] [marine water body] "A lentic water body which is composed primarily of marine water."@en)
• DEL AnnotationAssertion([definition] [marine water body] "A significant accumulation of water which is part of a marine biome.")
• ADD AnnotationAssertion([definition] [sacred site] "A fiat object part which contains entities of high spiritual or cultural significance to one or more human groups."@en)
• DEL AnnotationAssertion([definition] [sacred site] "A site which is bounded or relativised by a material entity which is of spiritual significance to one or more human groups.")
• ADD AnnotationAssertion([definition] [marine environmental zone] "An astronomical body part which is part of a marine environment."@en)
• DEL AnnotationAssertion([definition] [marine environmental zone] "An environmental zone which is bounded by material parts of a marine environment.")
• ADD AnnotationAssertion([definition] [area of low atmospheric pressure] "A gaseous part of an atmosphere in which gases have reduced atmospheric pressure."@en)
• DEL AnnotationAssertion([definition] [area of low atmospheric pressure] "An atmospheric zone in which atmospheric gaseous masses have reduced atmospheric pressure.")
• ADD AnnotationAssertion([definition] [liquid astronomical body part] "A part of an astronomical body which is primarily composed of liquid material."@en)
• ADD AnnotationAssertion([definition] [gaseous astronomical body part] "A part of an astronomical body which is primarily composed of gaseous material."@en)
• DEL AnnotationAssertion([definition] [two-dimensional fiat ice surface] "An two-dimensional continuant fiat boundary which overlaps the surface layer of a mass of ice.")
• ADD AnnotationAssertion([definition] [two-dimensional fiat ice surface] "An two-dimensional continuant fiat boundary which overlaps the surface layer of a mass of ice."@en)
• DEL AnnotationAssertion([definition] [two-dimensional fiat water ice surface] "A two-dimensional fiat ice surface which is composed primarily of water ice.")
• ADD AnnotationAssertion([definition] [two-dimensional fiat water ice surface] "A two-dimensional fiat ice surface which overlaps the surface layer of a mass of water ice."@en)
• ADD AnnotationAssertion([definition] [fiat part of an astronomical object] "A part of an environmental system whose boundaries are determined by fiat."@en)
• ADD AnnotationAssertion([definition] [area of high atmospheric pressure] "A gaseous part of an atmosphere in which gases have increased atmospheric pressure."@en)
• DEL AnnotationAssertion([editor note] [atmospheric column] "This should be relocated under \"fiat object part\" of the BFO during next refactoring. Also, the \"part of\" relation to atomosphere should be updated to express that this is a fiat part of the atmosphere.")
• ADD AnnotationAssertion([editor note] [astronomical body part] "Also note that some astronomical body parts (ABPs) may have fiat boundaries: if there's strong debate about where an ABP begins or ends (over and above fuzzy boundaries), with different official classifications setting different thresholds or limits, axiomatise the class with fiat boundaries of the appropriate dimension."@en)
• ADD AnnotationAssertion([editor note] [astronomical body part] "Note that material entities may have immaterial entities (e.g. sites) as parts."@en)
• ADD AnnotationAssertion([editor note] [astronomical body part] "This class includes material parts of astronomical bodies. Immaterial parts, such as magnetospheres, are represented as sites under the influence of magnetic fields.Please post countercases in the ENVO tracker for revision of this hierarchy if needed."@en)
• ADD AnnotationAssertion( [seam surface] https://orcid.org/0000-0002-4366-3088)
• ADD AnnotationAssertion( [seam surface] https://orcid.org/0000-0002-2738-824X)
• DEL AnnotationAssertion( [layer] "ORCID:0000-0002-4366-3088")
• ADD AnnotationAssertion( [layer] https://orcid.org/0000-0002-4366-3088)
• DEL AnnotationAssertion( [Taylor column] "ORCID:0000-0002-4366-3088")
• ADD AnnotationAssertion( [Taylor column] https://orcid.org/0000-0002-4366-3088)
• DEL AnnotationAssertion( [seam surface] https://orcid.org/0000-0002-2738-824X)
• ADD AnnotationAssertion([has_exact_synonym] [area of snow cover] "area of snow cover"@en)
• ADD AnnotationAssertion([has_exact_synonym] [area of snow cover] "land covered by snow"@en)
• ADD AnnotationAssertion([has_exact_synonym] [area of snow cover] "snow covered land"@en)
• DEL AnnotationAssertion([has_obo_namespace] [national geopolitical entity] "ENVO")
• DEL AnnotationAssertion([has_obo_namespace] [populated place] "ENVO")
• DEL AnnotationAssertion([has_obo_namespace] [supranational geopolitical entity] "ENVO")
• DEL AnnotationAssertion([has_obo_namespace] [buffer zone] "ENVO")
• DEL AnnotationAssertion([has_obo_namespace] [scree] "ENVO")
• DEL AnnotationAssertion([has_obo_namespace] [plunge pool] "ENVO")
• ADD AnnotationAssertion([has_related_synonym] [cave entrance] "cave exit"@en)
• DEL AnnotationAssertion( [national geopolitical entity] "ENVO:00000009")
• DEL AnnotationAssertion( [populated place] "ENVO:00000062")
• DEL AnnotationAssertion( [supranational geopolitical entity] "ENVO:00000124")
• DEL AnnotationAssertion( [buffer zone] "ENVO:00000135")
• DEL AnnotationAssertion( [scree] "ENVO:00000194")
• DEL AnnotationAssertion( [plunge pool] "ENVO:00000483")
• ADD AnnotationAssertion( [water body] "The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water."@en)
• DEL AnnotationAssertion( [water body] "https://en.wikipedia.org/wiki/ The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water.")
• ADD AnnotationAssertion( [cave entrance] "The term \"cave entrance\" is typically used when ingress or entry to the cave is desired. The same fiat bondary can serve as a cave exit, although that may be less feasible due to the shape or other physical properties of the cave."@en)
• ADD AnnotationAssertion( [vadose zone] "If the vadose zone includes portions of soil, the water contained therein is termed soil moisture. In fine grained soils, capillary action can cause the pores of the soil to be fully saturated above the water table at a pressure less than atmospheric. In such soils, therefore, the unsaturated zone is the upper section of the vadose zone and not identical to it."@en)
• DEL AnnotationAssertion( [vadose zone] "https://en.wikipedia.org/wiki/ If the vadose zone envelops soil, the water contained therein is termed soil moisture. In fine grained soils, capillary action can cause the pores of the soil to be fully saturated above the water table at a pressure less than atmospheric. In such soils, therefore, the unsaturated zone is the upper section of the vadose zone and not identical to it.")
• DEL AnnotationAssertion( [marine water body] "Ideas like \"significant\" are fuzzy and need to be modelled more accurately. The definition is a candidate for review.")
• DEL AnnotationAssertion( [sediment] "It is recommended to use a combination of sediment terms to describe a more specific sediment type.")
• ADD AnnotationAssertion( [sediment] "Sediment is typically deposited on the bed or bottom of a body of water or other liquid."@en)
• ADD AnnotationAssertion( [environmental material] "Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, \"ENVO:water\" is to be understood as \"environmental material composed primarly of some CHEBI:water\"."@en)
• DEL AnnotationAssertion( [environmental material] "Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, \"ENVO:water\" is to be understood as \"environmental material composed primarly of some CHEBI:water\". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.")
• ADD AnnotationAssertion( [environmental material] "Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket."@en)
• DEL AnnotationAssertion( [layer] "Preliminary definition.")
• DEL AnnotationAssertion( [sedimentary stratum] "Preliminary definition. Concepts such as \"characteristic\" may be problematic.")
• ADD AnnotationAssertion( [atmospheric column] "Once defined, an atmospheric column can be used to quantify an atmospheric parameter such as pressure, ozone or precipitable water."@en)
• ADD AnnotationAssertion( [regolith] "Regolith typically includes dust, soil, broken rock, and similar materials, but can be highly variable."@en)
• ADD AnnotationAssertion( [astronomical body part] "Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information."@en)
• ADD AnnotationAssertion( [two-dimensional fiat ice surface] "This class was created during a semantic harmonisation exercise with the SWEET resource, currently adminstered by Earth Science Information Partners. Its subclass(es) are mapped to the corresponding SWEET terms, which were determined to align with fiat boundaries rather than physical ones."@en)
• ADD AnnotationAssertion( [two-dimensional fiat water ice surface] "This class was created during a semantic harmonisation exercise with the SWEET resource, currently adminstered by Earth Science Information Partners. It is mapped to the corresponding SWEET term, which was determined to align with fiat boundaries rather than physical ones."@en)
• ADD AnnotationAssertion( [area of seasonal sea ice] "As this part of the environment is defined by a seasonal process, some of its differentia aren't physically there at all times of its existence.Thus, all boundaries of this entity are fiat."@en)
• ADD AnnotationAssertion( [fiat part of an astronomical object] "Subclasses of this class have fiat (and only fiat) boundaries - that is, boundaries which are determined by human consensus or opinion rather than (and sometimes in contrast to) well-defined physical discontinuities. We distinguish these from entities that have fuzzy or hard to define boundaries that do overlap some form of physical discontinuity."@en)
• ADD AnnotationAssertion( [area of high atmospheric pressure] "Air is not specified directly (although the definition subsumes air masses) to allow for other forms of low pressure areas in planetary atmospheres.")
• ADD AnnotationAssertion( [fiat part of an astronomical object] "fiat part of an astronomical object"@en)
• ADD AnnotationAssertion( [area of high atmospheric pressure] "area of high atmospheric pressure"@en)
• DEL AnnotationAssertion( [area of snow cover] "area of snow cover"@en)
• ADD AnnotationAssertion( [area of snow cover] "snow-covered land"@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "ADL:FTT") [has_related_synonym] [woodland area] "wood")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "DOI:10.1186/2041-1480-4-43") Annotation([database_cross_reference] "MA:ma") Annotation([database_cross_reference] "ORCID:0000-0002-4366-3088") Annotation([database_cross_reference] "URL:http://ontology.buffalo.edu/smith/articles/niches.html") [definition] [environmental material] "A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "USGS:SDTS") [has_related_synonym] [woodland area] "tropical rain forest")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "USGS:SDTS") [has_related_synonym] [woodland area] "wood")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "Wiktionary:layer") [definition] [layer] "A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "http://wasg.iinet.net.au/terminol.html") Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Vadose_zone") [definition] [vadose zone] "A zone beneath the land surface and above the level of permanent groundwater or phreatic zone in which water has a hydraulic head less than atmospheric pressure and is retained by a combination of adhesion and capillary action.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "http://wasg.iinet.net.au/terminol.html") Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Vadose_zone") [definition] [vadose zone] "An interface layer which 1) is primarily composed of solid materials, 2) separates the land surface and phreatic zone, and 3) contains groundwater at atmospheric pressure."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Buffer_zone") [definition] [buffer zone] "A geographical region that serves the purpose of keeping two or more other areas (often, but not necessarily, countries) distant from one another, for whatever reason.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Buffer_zone") [definition] [buffer zone] "A geographical region that serves the purpose of keeping two or more other areas (often, but not necessarily, countries) distant from one another, for whatever reason."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Landform") [definition] [solid astronomical body part] "A part of an astronomical body which is primarily composed of a continuous volume of solid material, shaped by one or more environmental processes.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Landform") [definition] [solid astronomical body part] "A part of an astronomical body which is primarily composed of solid material."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Landform") [definition] [liquid astronomical body part] "A part of an astronomical body which is primarily composed of a continuous volume of liquid material, shaped by one or more environmental processes.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Landform") [definition] [gaseous astronomical body part] "A part of an astronomical body which is primarily composed of a continuous volume of gaseous material, shaped by one or more environmental processes.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Landform") [definition] [fluid astronomical body part] "A part of an astronomical body which is primarily composed of a continuous volume of liquid or gaseous material, shaped by one or more environmental processes.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Regolith") [definition] [regolith] "A layer of loose, heterogeneous, superficial material covering solid rock. It includes dust, soil, broken rock, and other related materials.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Regolith") [definition] [regolith] "A solid layer which is composed primarily of loose, heterogeneous, superficial material covering solid rock."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Sediment") [definition] [sediment] "Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Sediment") [definition] [sediment] "Sediment is an environmental substance comprised of any particulate matter that can be transported by fluid flow and which eventually is deposited as a layer of solid particles on the bedor bottom of a body of water or other liquid.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Stratum") [definition] [sedimentary stratum] "A solid layer which is composed primarily of sedimentary rock or soil."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://en.wikipedia.org/wiki/Stratum") [definition] [sedimentary stratum] "A stratum is a layer which is composed of sedimentary rock or soil with internally consistent characteristics that distinguish it from other layers.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://github.com/EnvironmentOntology/envo/issues/940") [definition] [fluid environmental material] "A liquid or a gas.")
• ADD AnnotationAssertion(Annotation([database_cross_reference] "https://mynasadata.larc.nasa.gov/glossary/atmospheric-column-2/") [definition] [atmospheric column] "A fiat part of an atmosphere which is defined as a vertical, three-dimensional pillar extending from a unit area on a planetary surface and bounded by the top of the atmosphere."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] "https://mynasadata.larc.nasa.gov/glossary/atmospheric-column-2/") [definition] [atmospheric column] "A vertical pillar defined by a unit area on a planetary surface and bounded by the top of the atmosphere that is used to quantify an atmospheric parameter such as pressure, ozone or precipitable water.")
• DEL AnnotationAssertion(Annotation([database_cross_reference] http://glossary.ametsoc.org/wiki/Front) [definition] [atmospheric frontal zone] "An environmental zone which contains a weather front, bounded by frontal surfaces."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] http://glossary.ametsoc.org/wiki/Front) [definition] [atmospheric frontal zone] "Part of an atmosphere which contains a weather front, bounded by frontal surfaces."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] http://ontology.buffalo.edu/smith/articles/niches.html) Annotation([database_cross_reference] https://dx.doi.org/10.1186/2041-1480-4-43) Annotation([database_cross_reference] https://en.wikipedia.org/wiki/Material) [definition] [environmental material] "A material entity which other material entities in an environmental system are primarily or partially composed of."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] http://vocab.getty.edu/page/aat/300228472) [definition] [seam surface] "A two-dimensional spatial region where one material entity touches or is attached to itself or another material entity along some length which is exposed to an environment."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] http://vocab.getty.edu/page/aat/300228472) [definition] [seam surface] "An interface layer which is formed where either two parts of a material entity or two separate material entities touch or are attached to one another along some length."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] https://en.wikipedia.org/wiki/Fluid) [definition] [fluid astronomical body part] "A part of an astronomical body which is primarily composed of fluid."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] https://en.wikipedia.org/wiki/Fluid) Annotation([database_cross_reference] "https://github.com/EnvironmentOntology/envo/issues/940") [definition] [fluid environmental material] "An environmental material which is unable to resist shear forces and continuously deforms when subject to them."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] https://en.wiktionary.org/wiki/layer) [definition] [layer] "A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] https://orcid.org/0000-0003-4808-4736) [definition] [area of snow cover] "An environmental zone which is covered or partially covered by snow."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] https://orcid.org/0000-0003-4808-4736) [definition] [area of snow cover] "Land which is covered or partially covered by snow."@en)
• ADD AnnotationAssertion(Annotation([database_cross_reference] https://orcid.org/0000-0003-4808-4736) [area of snow cover] "The threshold at which land is considered covered by snow varies. Please define such thresholds on the instance level, or request a subclass of this class if a threshold you know of is used by a large community of practice or in an official definition. This is one of three classes representing the idea of snow cover in the GCW glossary in addition to depth of snow and snow cover. In the GCW this refers to 1. The areal extent of snow-covered ground, usually expressed as percent of total area in a given region."@en)
• DEL AnnotationAssertion(Annotation([database_cross_reference] https://orcid.org/0000-0003-4808-4736) [area of snow cover] "This is one of three classes representing the idea of snow cover in the GCW glossary in addition to depth of snow and snow cover. In the GCW this refers to 1. The areal extent of snow-covered ground, usually expressed as percent of total area in a given region."@en)
• ADD Declaration(Class([fiat part of an astronomical object]))
• ADD Declaration(Class([area of high atmospheric pressure]))
• DEL EquivalentClasses([hydrographic feature] ObjectIntersectionOf([geographic feature] ObjectUnionOf(ObjectSomeValuesFrom([partially_surrounded_by] [liquid water]) ObjectSomeValuesFrom([adjacent to] [water body]))))
• DEL EquivalentClasses([scree] ObjectIntersectionOf([environmental material] ObjectSomeValuesFrom([has part] [piece of rock]) ObjectSomeValuesFrom([derives from] [rock])))
• ADD EquivalentClasses([astronomical body part] ObjectIntersectionOf([material entity] ObjectSomeValuesFrom([part of] [astronomical body])))
• DEL EquivalentClasses([marine environmental zone] ObjectIntersectionOf([environmental zone] ObjectSomeValuesFrom([part of] [marine environment])))
• ADD EquivalentClasses([fluid astronomical body part] ObjectIntersectionOf([astronomical body part] ObjectSomeValuesFrom([composed primarily of] [fluid environmental material])))
• DEL EquivalentClasses([fluid astronomical body part] ObjectIntersectionOf([astronomical body part] ObjectSomeValuesFrom([composed primarily of] ObjectUnionOf([gaseous environmental material] [liquid environmental material]))))
• ADD EquivalentClasses([fluid environmental material] ObjectIntersectionOf([environmental material] ObjectSomeValuesFrom([composed primarily of] ObjectUnionOf([gaseous environmental material] [plasma] [liquid environmental material]))))
• DEL EquivalentClasses([fluid environmental material] ObjectUnionOf([gaseous environmental material] [plasma] [liquid environmental material]))
• DEL SubClassOf([administrative region] [site])
• ADD SubClassOf([administrative region] [fiat part of an astronomical object])
• ADD SubClassOf([hydrographic feature] ObjectSomeValuesFrom([determined by] [water body]))
• ADD SubClassOf([water body] ObjectSomeValuesFrom([formed as result of] [water accumulation process]))
• DEL SubClassOf([cave entrance] [site])
• ADD SubClassOf([cave entrance] [two-dimensional continuant fiat boundary])
• ADD SubClassOf([political entity] [fiat object part])
• DEL SubClassOf([political entity] [administrative region])
• ADD SubClassOf([political entity] ObjectSomeValuesFrom([has part] [administrative region]))
• DEL SubClassOf([scree] [environmental material])
• ADD SubClassOf([scree] [solid environmental material])
• ADD SubClassOf([scree] ObjectSomeValuesFrom([has part] [piece of rock]))
• DEL SubClassOf([vadose zone] [environmental zone])
• ADD SubClassOf([vadose zone] [interface layer])
• ADD SubClassOf([vadose zone] ObjectSomeValuesFrom([has part] [groundwater]))
• ADD SubClassOf([vadose zone] ObjectSomeValuesFrom([adjacent to] [phreatic zone]))
• ADD SubClassOf([vadose zone] ObjectSomeValuesFrom([adjacent to] [land]))
• ADD SubClassOf([vadose zone] ObjectSomeValuesFrom([composed primarily of] [solid environmental material]))
• ADD SubClassOf([archeological site] [fiat object part])
• DEL SubClassOf([archeological site] [site])
• DEL SubClassOf([marine water body] ObjectSomeValuesFrom([part of] [marine biome]))
• DEL SubClassOf([marine water body] ObjectSomeValuesFrom([part of] [marine environment]))
• DEL SubClassOf([sediment] [environmental material])
• ADD SubClassOf([sediment] [particulate environmental material])
• ADD SubClassOf([anthropogenic contamination feature] ObjectSomeValuesFrom([formed as result of] [anthropisation]))
• DEL SubClassOf([rhizosphere] [environmental zone])
• ADD SubClassOf([rhizosphere] [ecosystem])
• ADD SubClassOf([rhizosphere] ObjectSomeValuesFrom([part of] [soil]))
• ADD SubClassOf([rhizosphere] ObjectSomeValuesFrom([has part] [microbial community]))
• ADD SubClassOf([rhizosphere] ObjectSomeValuesFrom([has part] ObjectIntersectionOf([ecosystem] ObjectSomeValuesFrom([determined by part of] [root system]))))
• DEL SubClassOf([rhizosphere] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf([ecosystem] ObjectSomeValuesFrom([determined by part of] [soil]))))
• DEL SubClassOf([rhizosphere] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf([ecosystem] ObjectSomeValuesFrom([determined by part of] [root system]))))
• DEL SubClassOf([environmental material] [fiat object part])
• ADD SubClassOf([environmental material] [material entity])
• DEL SubClassOf([gravel] [environmental material])
• ADD SubClassOf([gravel] [solid environmental material])
• ADD SubClassOf([layer] ObjectSomeValuesFrom([has quality] [continuous]))
• ADD SubClassOf([environmental zone] [fiat object part])
• DEL SubClassOf([environmental zone] [site])
• ADD SubClassOf([roadside] [anthropogenic geographic feature])
• DEL SubClassOf([roadside] [environmental zone])
• ADD SubClassOf([roadside] ObjectSomeValuesFrom([formed as result of] [anthropisation]))
• ADD SubClassOf([lentic water body] ObjectSomeValuesFrom([composed primarily of] [sea water]))
• DEL SubClassOf([tephra] [environmental material])
• ADD SubClassOf([tephra] [solid environmental material])
• DEL SubClassOf([area of open water] [environmental zone])
• ADD SubClassOf([area of open water] [fiat part of an astronomical object])
• DEL SubClassOf([atmospheric column] [gaseous astronomical body part])
• ADD SubClassOf([atmospheric column] [fiat part of an astronomical object])
• DEL SubClassOf([area of perennial water ice] [environmental zone])
• ADD SubClassOf([area of perennial water ice] [area of perennial ice or snow])
• DEL SubClassOf([area of perennial water ice] ObjectSomeValuesFrom([part of] [planetary surface]))
• DEL SubClassOf([area of perennial water ice] ObjectSomeValuesFrom([part of] [area of perennial ice or snow]))
• ADD SubClassOf([area of perennial water ice] ObjectSomeValuesFrom([part of] ObjectIntersectionOf([planetary surface] ObjectSomeValuesFrom([composed primarily of] [water ice]))))
• DEL SubClassOf([area of perennial snow] [environmental zone])
• ADD SubClassOf([area of perennial snow] [area of perennial ice or snow])
• ADD SubClassOf([area of perennial snow] ObjectSomeValuesFrom([part of] ObjectIntersectionOf([planetary surface] ObjectSomeValuesFrom([composed primarily of] [snow]))))
• DEL SubClassOf([area of perennial ice or snow] [environmental zone])
• ADD SubClassOf([area of perennial ice or snow] [fiat part of an astronomical object])
• ADD SubClassOf([area of perennial ice or snow] ObjectSomeValuesFrom([part of] ObjectIntersectionOf([planetary surface] ObjectSomeValuesFrom([composed primarily of] ObjectUnionOf([snow] [ice])))))
• DEL SubClassOf([area of perennial ice or snow] ObjectSomeValuesFrom([overlaps] ObjectUnionOf([snow] ObjectIntersectionOf([planetary surface] ObjectSomeValuesFrom([composed primarily of] [ice])))))
• DEL SubClassOf([regolith] ObjectSomeValuesFrom([has quality] [broken]))
• ADD SubClassOf([biosphere] [astronomical body part])
• DEL SubClassOf([biosphere] [compound astronomical body part])
• ADD SubClassOf([pedosphere] [astronomical body part])
• DEL SubClassOf([pedosphere] [compound astronomical body part])
• ADD SubClassOf([planetary photic zone] ObjectSomeValuesFrom([part of] [planet]))
• DEL SubClassOf([technosphere] ObjectSomeValuesFrom([has part] [human construction]))
• DEL SubClassOf([technosphere] ObjectSomeValuesFrom([has part] [manufactured product]))
• ADD SubClassOf([technosphere] ObjectSomeValuesFrom([composed primarily of] [human construction]))
• ADD SubClassOf([technosphere] ObjectSomeValuesFrom([composed primarily of] [manufactured product]))
• ADD SubClassOf([manufacturing process] ObjectSomeValuesFrom([has part] [anthropisation]))
• ADD SubClassOf([human-directed construction process] ObjectSomeValuesFrom([has part] [anthropisation]))
• ADD SubClassOf([Karman vortex street] ObjectSomeValuesFrom([formed as result of] ObjectIntersectionOf([material transport process] ObjectSomeValuesFrom([has participant] [fluid environmental material]))))
• DEL SubClassOf([Karman vortex street] ObjectUnionOf([aeroform] ObjectSomeValuesFrom([composed primarily of] [hydroform])))
• DEL SubClassOf([ice] [environmental material])
• ADD SubClassOf([ice] [solid environmental material])
• ADD SubClassOf([sacred site] [fiat object part])
• DEL SubClassOf([sacred site] [site])
• ADD SubClassOf([magnetosphere] [site])
• DEL SubClassOf([magnetosphere] [environmental zone])
• DEL SubClassOf([marine environmental zone] [environmental zone])
• ADD SubClassOf([marine environmental zone] [astronomical body part])
• ADD SubClassOf([marine environmental zone] ObjectSomeValuesFrom([part of] [marine environment]))
• ADD SubClassOf([Hill sphere] [site])
• DEL SubClassOf([Hill sphere] [environmental zone])
• ADD SubClassOf([Lagrangian point] [site])
• DEL SubClassOf([Lagrangian point] [environmental zone])
• DEL SubClassOf([area designated for human defecation] [environmental zone])
• ADD SubClassOf([area designated for human defecation] [fiat part of an astronomical object])
• DEL SubClassOf([area designated for waste storage] [environmental zone])
• ADD SubClassOf([area designated for waste storage] [fiat part of an astronomical object])
• DEL SubClassOf([area of low atmospheric pressure] [atmospheric zone])
• ADD SubClassOf([area of low atmospheric pressure] [gaseous part of an atmosphere])
• DEL SubClassOf([area of low atmospheric pressure] ObjectSomeValuesFrom([contains] ObjectIntersectionOf([gaseous environmental material] ObjectSomeValuesFrom([has quality] [decreased pressure]))))
• DEL SubClassOf([area of low atmospheric pressure] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf([gaseous environmental material] ObjectSomeValuesFrom([has quality] [decreased pressure]))))
• ADD SubClassOf([area of low atmospheric pressure] ObjectSomeValuesFrom([composed primarily of] ObjectIntersectionOf([gaseous environmental material] ObjectSomeValuesFrom([has quality] [decreased pressure]))))
• DEL SubClassOf([area of attached faunal communities] [environmental zone])
• ADD SubClassOf([area of attached faunal communities] [fiat part of an astronomical object])
• ADD SubClassOf([area of attached faunal communities] ObjectSomeValuesFrom([has part] ObjectIntersectionOf([ecological community] ObjectSomeValuesFrom([composed primarily of] [Metazoa]))))
• DEL SubClassOf([area of attached faunal communities] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf([ecological community] ObjectSomeValuesFrom([composed primarily of] [Metazoa]))))
• ADD SubClassOf([planned environmental usage process] ObjectSomeValuesFrom([has part] [anthropisation]))
• DEL SubClassOf([area of pack ice] [environmental zone])
• ADD SubClassOf([area of pack ice] [fiat part of an astronomical object])
• ADD SubClassOf([area of pack ice] ObjectSomeValuesFrom([part of] [water body]))
• ADD SubClassOf([area of pack ice] ObjectSomeValuesFrom([has part] ObjectIntersectionOf(ObjectIntersectionOf([object aggregate] ObjectSomeValuesFrom([composed primarily of] [drift ice mass])) ObjectSomeValuesFrom([has quality] [increased concentration]))))
• DEL SubClassOf([area of pack ice] ObjectSomeValuesFrom([overlaps] [water body]))
• DEL SubClassOf([area of pack ice] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf(ObjectIntersectionOf([object aggregate] ObjectSomeValuesFrom([composed primarily of] [drift ice mass])) ObjectSomeValuesFrom([has quality] [increased concentration]))))
• DEL SubClassOf([area of sea ice] [environmental zone])
• ADD SubClassOf([area of sea ice] [fiat part of an astronomical object])
• ADD SubClassOf([area of sea ice] ObjectSomeValuesFrom([part of] [water body]))
• ADD SubClassOf([area of sea ice] ObjectSomeValuesFrom([has part] [sea ice]))
• DEL SubClassOf([area of sea ice] ObjectSomeValuesFrom([overlaps] [water body]))
• DEL SubClassOf([area of sea ice] ObjectSomeValuesFrom([overlaps] [sea ice]))
• DEL SubClassOf([area of drift ice] [environmental zone])
• ADD SubClassOf([area of drift ice] [fiat part of an astronomical object])
• ADD SubClassOf([area of drift ice] ObjectSomeValuesFrom([part of] [water body]))
• ADD SubClassOf([area of drift ice] ObjectSomeValuesFrom([has part] ObjectIntersectionOf([object aggregate] ObjectSomeValuesFrom([composed primarily of] [drift ice mass]))))
• DEL SubClassOf([area of drift ice] ObjectSomeValuesFrom([overlaps] [water body]))
• DEL SubClassOf([area of drift ice] ObjectSomeValuesFrom([overlaps] ObjectIntersectionOf([object aggregate] ObjectSomeValuesFrom([composed primarily of] [drift ice mass]))))
• DEL SubClassOf([area of seasonal sea ice] [environmental zone])
• ADD SubClassOf([area of seasonal sea ice] [fiat part of an astronomical object])
• DEL SubClassOf([protected area] [environmental zone])
• ADD SubClassOf([protected area] [fiat part of an astronomical object])
• DEL SubClassOf([atmospheric frontal zone] [environmental zone])
• ADD SubClassOf([atmospheric frontal zone] [gaseous part of an atmosphere])
• ADD SubClassOf([atmospheric frontal zone] ObjectSomeValuesFrom([part of] [atmosphere]))
• ADD SubClassOf([frost] ObjectSomeValuesFrom([has quality] [quality of a solid]))
• ADD SubClassOf([well intervention] ObjectSomeValuesFrom([has part] [anthropisation]))
• ADD SubClassOf([fiat part of an astronomical object] [fiat object part])
• ADD SubClassOf([fiat part of an astronomical object] ObjectSomeValuesFrom([part of] [astronomical object]))
• ADD SubClassOf([area of high atmospheric pressure] [gaseous part of an atmosphere])
• ADD SubClassOf([area of high atmospheric pressure] ObjectSomeValuesFrom([composed primarily of] ObjectIntersectionOf([gaseous environmental material] ObjectSomeValuesFrom([has quality] [increased pressure]))))
• ADD SubClassOf([hydrogen production process] ObjectSomeValuesFrom([has output] [dihydrogen]))
• DEL SubClassOf([iceberg calving process] ObjectSomeValuesFrom([has input] [glacier]))
• DEL SubClassOf([iceberg calving process] ObjectSomeValuesFrom([has output] [glacier]))
• DEL SubClassOf([iceberg calving process] ObjectSomeValuesFrom([has output] [marine iceberg]))
• ADD SubClassOf([iceberg calving process] ObjectSomeValuesFrom([has output] ObjectIntersectionOf([marine iceberg] ObjectSomeValuesFrom([derives from part of] [glacier]))))
• DEL SubClassOf([calving of ice from an iceberg] ObjectSomeValuesFrom([has output] [ice mass]))
• ADD SubClassOf([calving of ice from an iceberg] ObjectSomeValuesFrom([has output] ObjectIntersectionOf([ice mass] ObjectSomeValuesFrom([derives from part of] [iceberg]))))
• DEL SubClassOf([area of snow cover] [environmental zone])
• ADD SubClassOf([area of snow cover] [land])
• ADD SubClassOf([area of snow cover] ObjectSomeValuesFrom([adjacent to] ObjectUnionOf([snow mass] [snow layer])))
• DEL SubClassOf([area of ice cover] [environmental zone])
• ADD SubClassOf([area of ice cover] [fiat part of an astronomical object])
• ADD SubClassOf([area of ice cover] ObjectSomeValuesFrom([has part] [ice surface layer]))
• DEL SubClassOf([seam surface] [spatial region])
• ADD SubClassOf([seam surface] [interface layer])

[cmungall]

This is a really important PR. There are lots of much needed changes in these, for example, moving a lot of currently very useful classes from immaterial to material entities. I'm going to prioritize rescuing this.

[cmungall]

Replaced by #1430