envoEmpo.owl
type: Ontology
version IRI: envoEmpo.owl
version info: 2021-05-14

definition
type: AnnotationProperty

expand assertion to
type: AnnotationProperty

term replaced by
type: AnnotationProperty

EnvO-Lite-GSC
type: AnnotationProperty
comment: EnvO-Lite-GSC
sub property of: subset_property

plurals
type: AnnotationProperty
sub property of: synonym_type_property

disconnected_from
type: AnnotationProperty
definition: A is disconnected_from B if they have no parts in common.
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
has_exact_synonym: non_overlapping_with
has_obo_namespace: ENVO
id: disconnected_from
is class level: true
is metadata tag: true

Axiom
annotated source: disconnected_from
annotated property: definition
annotated target: A is disconnected_from B if they have no parts in common.
database_cross_reference: SO:cjm

disposition slim
type: AnnotationProperty
comment: Disposition slim
sub property of: subset_property

environmental hazards
type: AnnotationProperty
comment: environmental_hazards
sub property of: subset_property

envoAstro
type: AnnotationProperty
comment: envoAstro
sub property of: subset_property

envoAtmo
type: AnnotationProperty
comment: envoAtmo
sub property of: subset_property

envoCesab
type: AnnotationProperty
comment: envoCesab
sub property of: subset_property

envoCmecs
type: AnnotationProperty
comment: envoCmecs
sub property of: subset_property

envoEOVs
type: AnnotationProperty
comment: envoEOVs
sub property of: subset_property

envoEmpo
type: AnnotationProperty
comment: envoEmpo
sub property of: subset_property

envoMarine
type: AnnotationProperty
comment: envoMarine
sub property of: subset_property

envoMeo
type: AnnotationProperty
comment: envoMeo
sub property of: subset_property

envoNceas
type: AnnotationProperty
comment: envoNceas
sub property of: subset_property

envoOmics
type: AnnotationProperty
comment: envoOmics
sub property of: subset_property

envoPlastics
type: AnnotationProperty
comment: envoPlastics
sub property of: subset_property

envoPolar
type: AnnotationProperty
comment: envoPolar
sub property of: subset_property

mpath slim
type: AnnotationProperty
comment: Pathology slim
sub property of: subset_property

nlcd2011
type: AnnotationProperty
comment: nlcd2011
sub property of: subset_property

relational slim
type: AnnotationProperty
comment: Relational slim: types of quality that require an additional entity in order to exist
sub property of: subset_property

ro-eco
type: AnnotationProperty
comment: ro-eco
sub property of: subset_property

scalar slim
type: AnnotationProperty
comment: Scalar slim
sub property of: subset_property

value slim
type: AnnotationProperty
comment: Value slim
sub property of: subset_property

wwfBiome
type: AnnotationProperty
comment: wwfBiome
sub property of: subset_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

BFO_0000050
type: ObjectProperty
database_cross_reference: BFO:0000050
has_obo_namespace: ENVO
id: part_of
shorthand: part_of

BFO_0000051
type: ObjectProperty
database_cross_reference: BFO:0000051
has_obo_namespace: ENVO
id: has_part
shorthand: has_part

BFO_0000054
type: ObjectProperty
database_cross_reference: BFO:0000054
has_obo_namespace: ENVO
id: realized_in
shorthand: realized_in

BFO_0000055
type: ObjectProperty
database_cross_reference: BFO:0000055
has_obo_namespace: ENVO
id: realizes
shorthand: realizes

BFO_0000062
type: ObjectProperty
database_cross_reference: BFO:0000062
has_obo_namespace: ENVO
id: preceded_by
shorthand: preceded_by

BFO_0000063
type: ObjectProperty
database_cross_reference: BFO:0000063
has_obo_namespace: ENVO
id: precedes
shorthand: precedes

BFO_0000066
type: ObjectProperty
database_cross_reference: BFO:0000066
has_obo_namespace: ENVO
id: occurs_in
shorthand: occurs_in

BFO_0000067
type: ObjectProperty
database_cross_reference: BFO:0000067
has_obo_namespace: ENVO
id: contains_process
shorthand: contains_process

partially_surrounded_by
type: ObjectProperty
IAO_0000112: A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
definition: x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x
database_cross_reference: ENVO:01001307
has_obo_namespace: ENVO
id: partially_surrounded_by
shorthand: partially_surrounded_by
comment: Definition modified from 'surrounded by'.

results in transformation into
type: ObjectProperty
database_cross_reference: ENVO:02500006
has_obo_namespace: ENVO
id: results_in_transformation_into
shorthand: results_in_transformation_into

results in expansion of
type: ObjectProperty
IAO_0000112: Afforestation results in the expansion of a forest.
definition: A process, p, results in the expansion of a material entity, m, if the spatial extent of m is increased as a result of participating in p.
database_cross_reference: ENVO:02500016
has_obo_namespace: ENVO
id: results_in_expansion_of
shorthand: results_in_expansion_of

results in proliferation of
type: ObjectProperty
database_cross_reference: ENVO:02500020
has_obo_namespace: ENVO
id: results_in_proliferation_of
shorthand: results_in_proliferation_of
comment: To be ceded to RO

generates
type: ObjectProperty
definition: A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process.
IAO_0000116: Consider ceding to RO
created by: cjm
creation date: 2018-11-03T20:58:13Z
database_cross_reference: ENVO:2000036
has_obo_namespace: ENVO
id: generates
shorthand: generates

obsolete determined by
type: ObjectProperty
database_cross_reference: ENVO:2100001
has_obo_namespace: ENVO
id: obsolete_determined_by
shorthand: obsolete_determined_by
deprecated: true

obsolete determined by part of
type: ObjectProperty
database_cross_reference: ENVO:2100007
has_obo_namespace: ENVO
id: obsolete_determined_by_part_of
shorthand: obsolete_determined_by_part_of
deprecated: true

RO_0000052
type: ObjectProperty
database_cross_reference: RO:0000052
has_obo_namespace: ENVO
id: inheres_in
shorthand: inheres_in

RO_0000053
type: ObjectProperty
database_cross_reference: RO:0000053
has_obo_namespace: ENVO
id: bearer_of
shorthand: bearer_of

RO_0000056
type: ObjectProperty
database_cross_reference: RO:0000056
has_obo_namespace: ENVO
id: participates_in
shorthand: participates_in

RO_0000057
type: ObjectProperty
database_cross_reference: RO:0000057
has_obo_namespace: ENVO
id: has_participant
shorthand: has_participant

RO_0000059
type: ObjectProperty
database_cross_reference: RO:0000059
has_obo_namespace: ENVO
id: concretizes
shorthand: concretizes

RO_0000085
type: ObjectProperty
database_cross_reference: RO:0000085
has_obo_namespace: ENVO
id: has_function
shorthand: has_function

RO_0000086
type: ObjectProperty
database_cross_reference: RO:0000086
has_obo_namespace: ENVO
id: has_quality
shorthand: has_quality

RO_0000087
type: ObjectProperty
database_cross_reference: RO:0000087
has_obo_namespace: ENVO
id: has_role
shorthand: has_role

RO_0000091
type: ObjectProperty
database_cross_reference: RO:0000091
has_obo_namespace: ENVO
id: has_disposition
shorthand: has_disposition

RO_0001000
type: ObjectProperty
database_cross_reference: RO:0001000
has_obo_namespace: ENVO
id: derives_from
shorthand: derives_from

RO_0001001
type: ObjectProperty
database_cross_reference: RO:0001001
has_obo_namespace: ENVO
id: derives_into
shorthand: derives_into

RO_0001015
type: ObjectProperty
database_cross_reference: RO:0001015
has_obo_namespace: ENVO
id: location_of
shorthand: location_of

RO_0001018
type: ObjectProperty
database_cross_reference: RO:0001018
has_obo_namespace: ENVO
id: contained_in
shorthand: contained_in

RO_0001019
type: ObjectProperty
database_cross_reference: RO:0001019
has_obo_namespace: ENVO
id: contains
shorthand: contains

RO_0001025
type: ObjectProperty
database_cross_reference: RO:0001025
has_obo_namespace: ENVO
id: located_in
shorthand: located_in

RO_0002007
type: ObjectProperty
database_cross_reference: RO:0002007
has_obo_namespace: ENVO
id: bounding_layer_of
shorthand: bounding_layer_of

RO_0002084
type: ObjectProperty
database_cross_reference: RO:0002084
has_obo_namespace: ENVO
id: during_which_ends
shorthand: during_which_ends

RO_0002088
type: ObjectProperty
database_cross_reference: RO:0002088
has_obo_namespace: ENVO
id: during_which_starts
shorthand: during_which_starts

RO_0002091
type: ObjectProperty
database_cross_reference: RO:0002091
has_obo_namespace: ENVO
id: starts_during
shorthand: starts_during

RO_0002131
type: ObjectProperty
database_cross_reference: RO:0002131
has_obo_namespace: ENVO
id: overlaps
shorthand: overlaps

RO_0002150
type: ObjectProperty
database_cross_reference: RO:0002150
has_obo_namespace: ENVO
id: continuous_with
shorthand: continuous_with

RO_0002151
type: ObjectProperty
database_cross_reference: RO:0002151
has_obo_namespace: ENVO
id: partially_overlaps
shorthand: partially_overlaps

RO_0002170
type: ObjectProperty
database_cross_reference: RO:0002170
has_obo_namespace: ENVO
id: connected_to
shorthand: connected_to

connects
type: ObjectProperty
database_cross_reference: RO:0002176
has_obo_namespace: ENVO
id: connects
shorthand: connects

RO_0002180
type: ObjectProperty
database_cross_reference: RO:0002180
has_obo_namespace: ENVO
id: has_component
shorthand: has_component

regulates (processual)
type: ObjectProperty
database_cross_reference: RO:0002211
has_obo_namespace: ENVO
id: regulates_(processual)
shorthand: regulates_(processual)

RO_0002212
type: ObjectProperty
database_cross_reference: RO:0002212
has_obo_namespace: ENVO
id: negatively_regulates
shorthand: negatively_regulates

RO_0002215
type: ObjectProperty
database_cross_reference: RO:0002215
has_obo_namespace: ENVO
id: capable_of
shorthand: capable_of

RO_0002218
type: ObjectProperty
database_cross_reference: RO:0002218
has_obo_namespace: ENVO
id: obsolete_has_active_participant
shorthand: obsolete_has_active_participant

surrounded by
type: ObjectProperty
database_cross_reference: RO:0002219
has_obo_namespace: ENVO
id: surrounded_by
shorthand: surrounded_by

RO_0002220
type: ObjectProperty
database_cross_reference: RO:0002220
has_obo_namespace: ENVO
id: adjacent_to
shorthand: adjacent_to

RO_0002229
type: ObjectProperty
database_cross_reference: RO:0002229
has_obo_namespace: ENVO
id: ends
shorthand: ends

RO_0002232
type: ObjectProperty
database_cross_reference: RO:0002232
has_obo_namespace: ENVO
id: has_end_location
shorthand: has_end_location

RO_0002233
type: ObjectProperty
database_cross_reference: RO:0002233
has_obo_namespace: ENVO
id: has_input
shorthand: has_input

RO_0002234
type: ObjectProperty
database_cross_reference: RO:0002234
has_obo_namespace: ENVO
id: has_output
shorthand: has_output

RO_0002297
type: ObjectProperty
database_cross_reference: RO:0002297
has_obo_namespace: ENVO
id: results_in_formation_of
shorthand: results_in_formation_of

has habitat
type: ObjectProperty
database_cross_reference: RO:0002303
has_obo_namespace: ENVO
id: has_habitat
shorthand: has_habitat

RO_0002350
type: ObjectProperty
database_cross_reference: RO:0002350
has_obo_namespace: ENVO
id: member_of
shorthand: member_of

RO_0002351
type: ObjectProperty
database_cross_reference: RO:0002351
has_obo_namespace: ENVO
id: has_member
shorthand: has_member

RO_0002352
type: ObjectProperty
database_cross_reference: RO:0002352
has_obo_namespace: ENVO
id: input_of
shorthand: input_of

RO_0002353
type: ObjectProperty
database_cross_reference: RO:0002353
has_obo_namespace: ENVO
id: output_of
shorthand: output_of

RO_0002354
type: ObjectProperty
database_cross_reference: RO:0002354
has_obo_namespace: ENVO
id: formed_as_result_of
shorthand: formed_as_result_of

RO_0002371
type: ObjectProperty
database_cross_reference: RO:0002371
has_obo_namespace: ENVO
id: attached_to
shorthand: attached_to

RO_0002376
type: ObjectProperty
database_cross_reference: RO:0002376
has_obo_namespace: ENVO
id: tributary_of
shorthand: tributary_of

RO_0002377
type: ObjectProperty
database_cross_reference: RO:0002377
has_obo_namespace: ENVO
id: distributary_of
shorthand: distributary_of

RO_0002411
type: ObjectProperty
database_cross_reference: RO:0002411
has_obo_namespace: ENVO
id: causally_upstream_of
shorthand: causally_upstream_of

RO_0002418
type: ObjectProperty
database_cross_reference: RO:0002418
has_obo_namespace: ENVO
id: causally_upstream_of_or_within
shorthand: causally_upstream_of_or_within

RO_0002427
type: ObjectProperty
database_cross_reference: RO:0002427
has_obo_namespace: ENVO
id: causally_downstream_of_or_within
shorthand: causally_downstream_of_or_within

RO_0002430
type: ObjectProperty
database_cross_reference: RO:0002430
has_obo_namespace: ENVO
id: involved_in_negative_regulation_of
shorthand: involved_in_negative_regulation_of

RO_0002473
type: ObjectProperty
database_cross_reference: RO:0002473
has_obo_namespace: ENVO
id: composed_primarily_of
shorthand: composed_primarily_of

RO_0002479
type: ObjectProperty
database_cross_reference: RO:0002479
has_obo_namespace: ENVO
id: has_part_that_occurs_in
shorthand: has_part_that_occurs_in

RO_0002500
type: ObjectProperty
database_cross_reference: RO:0002500
has_obo_namespace: ENVO
id: causal_agent_in_process
shorthand: causal_agent_in_process

RO_0002503
type: ObjectProperty
database_cross_reference: RO:0002503
has_obo_namespace: ENVO
id: towards
shorthand: towards

RO_0002507
type: ObjectProperty
database_cross_reference: RO:0002507
has_obo_namespace: ENVO
id: determined_by
shorthand: determined_by

RO_0002509
type: ObjectProperty
database_cross_reference: RO:0002509
has_obo_namespace: ENVO
id: determined_by_part_of
shorthand: determined_by_part_of

RO_0002608
type: ObjectProperty
database_cross_reference: RO:0002608
has_obo_namespace: ENVO
id: process_has_causal_agent
shorthand: process_has_causal_agent

has_condition
type: ObjectProperty
type: InverseFunctionalProperty
creation date: 2013-05-08T07:33:05Z
database_cross_reference: has_condition
has_obo_namespace: ENVO
id: has_condition
comment: Experimental relation used in EnvO. A condition defines a restricted range of a given quality or combination of qualities. If an environment class, E, has_condition C, then all qualities listed in C are restricted to the ranges defined in C in E. This is not intended as a logical conditional.

has increased levels of
type: ObjectProperty
database_cross_reference: has_increased_levels_of
has_obo_namespace: ENVO
id: has_increased_levels_of

liquid water
type: Class
subclass of: liquid environmental material
definition: An environmental material primarily composed of dihydrogen oxide in its liquid form.
has_broad_synonym: water
database_cross_reference: EcoLexicon:water
database_cross_reference: LTER:617
database_cross_reference: https://en.wikipedia.org/wiki/Water
has_obo_namespace: ENVO
id: ENVO:00002006

Axiom
annotated source: liquid water
annotated property: definition
annotated target: An environmental material primarily composed of dihydrogen oxide in its liquid form.
database_cross_reference: MA:ma

sediment
type: Class
subclass of: environmental material
definition: 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.
database_cross_reference: EcoLexicon:sediment
database_cross_reference: EcoLexicon:sedimentation
database_cross_reference: LTER:492
database_cross_reference: LTER:493
database_cross_reference: SWEETRealm:Sediment
database_cross_reference: https://en.wikipedia.org/wiki/Sediment
has_obo_namespace: ENVO
id: ENVO:00002007
in_subset: EnvO-Lite-GSC
in_subset: envoPolar
comment: It is recommended to use a combination of sediment terms to describe a more specific sediment type.

Axiom
annotated source: sediment
annotated property: definition
annotated target: 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.
database_cross_reference: https://en.wikipedia.org/wiki/Sediment

saline water
type: Class
subclass of: liquid water
definition: Water which contains a significant concentration of dissolved salts.
database_cross_reference: EcoLexicon:saltwater
database_cross_reference: SWEETRealm:SalineWater
database_cross_reference: SWEETRealm:SaltWater
database_cross_reference: https://en.wikipedia.org/wiki/Saline_water
has_exact_synonym: salt water
has_obo_namespace: ENVO
id: ENVO:00002010
comment: The threshold salt concentration for classifying water as saline varies, but typically begins at about 1,000 to 3,000 parts salt per million parts water or 0.1–0.3% salt by weight.

fresh water
type: Class
subclass of: liquid water
definition: Water which has a low concentration of dissolved solutes, particularly that of sodium chloride.
database_cross_reference: EcoLexicon:fresh_water
database_cross_reference: LTER:216
database_cross_reference: SWEETRealm:FreshWater
database_cross_reference: https://en.wikipedia.org/wiki/Fresh_water
has_exact_synonym: freshwater
has_obo_namespace: ENVO
has_related_synonym: sweet water
id: ENVO:00002011
in_subset: envoEmpo
in_subset: envoPolar
comment: The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water.

sterile water
type: Class
subclass of: liquid water
definition: Sterile water is water which does not contain lliving organisms.
has_obo_namespace: ENVO
id: ENVO:00005791

rhizosphere
type: Class
subclass of: environmental zone
definition: The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
database_cross_reference: LTER:472
has_obo_namespace: ENVO
id: ENVO:00005801

Axiom
annotated source: rhizosphere
annotated property: definition
annotated target: The narrow region of soil that is directly influenced by root secretions and associated soil microorganisms.
database_cross_reference: https://en.wikipedia.org/wiki/Rhizosphere_%28ecology%29

environmental material
type: Class
definition: A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
has_exact_synonym: portion of environmental material
has_obo_namespace: ENVO
id: ENVO:00010483
comment: 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.

Axiom
annotated source: environmental material
annotated property: definition
annotated target: A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
database_cross_reference: DOI:10.1186/2041-1480-4-43
database_cross_reference: MA:ma
database_cross_reference: ORCID:0000-0002-4366-3088
database_cross_reference: URL:http://ontology.buffalo.edu/smith/articles/niches.html

organic material
type: Class
subclass of: environmental material
definition: Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
created by: ORCID:0000-0002-4366-3088
creation date: 2010-03-20T08:40:04Z
database_cross_reference: EcoLexicon:organic_material
has_exact_synonym: biomass
has_obo_namespace: ENVO
id: ENVO:01000155

Axiom
annotated source: organic material
annotated property: definition
annotated target: Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
database_cross_reference: ISBN:978-0-618-45504-1
database_cross_reference: ORCID:0000-0002-4366-3088

environmental system
type: Class
definition: A system which has the disposition to environ one or more material entities.
creation date: 2013-09-23T16:04:08Z
database_cross_reference: EcoLexicon:environment
has_exact_synonym: environment
has_obo_namespace: ENVO
id: ENVO:01000254
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

Axiom
annotated source: environmental system
annotated property: definition
annotated target: A system which has the disposition to environ one or more material entities.
database_cross_reference: DOI:10.1186/2041-1480-4-43

freshwater environment
type: Class
equivalent class: Class
  intersection of: aquatic environment
  intersection of: Restriction
    on property: RO_0002507
    some values from: fresh water
subclass of: aquatic environment
definition: An aquatic environment which is determined by freshwater.
IAO_0000118: Water (non-saline)
has_exact_synonym: fresh water environment
has_obo_namespace: ENVO
id: ENVO:01000306
in_subset: envoEmpo
in_subset: envoOmics
in_subset: envoPolar

Axiom
annotated source: freshwater environment
annotated property: IAO_0000118
annotated target: Water (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

saline water environment
type: Class
equivalent class: Class
  intersection of: aquatic environment
  intersection of: Restriction
    on property: RO_0002507
    some values from: saline water
subclass of: aquatic environment
definition: An environmental system which has its properties and dynamics determined by saline water.
IAO_0000118: Water (saline)
has_obo_namespace: ENVO
id: ENVO:01000307
in_subset: envoEmpo
in_subset: envoOmics
in_subset: envoPolar

Axiom
annotated source: saline water environment
annotated property: IAO_0000118
annotated target: Water (saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

aquatic environment
type: Class
equivalent class: Class
  intersection of: environmental system
  intersection of: Restriction
    on property: RO_0002507
    some values from: liquid water
subclass of: environmental system
definition: An environment whose dynamics are strongly influenced by water.
has_obo_namespace: ENVO
id: ENVO:01000317

environmental zone
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: environmental system
definition: A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein.
has_obo_namespace: ENVO
has_related_synonym: environmental area
id: ENVO:01000408
in_subset: envoPolar
comment: Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition.

liquid environmental material
type: Class
subclass of: fluid environmental material
definition: An environmental material which is in a liquid state.
has_obo_namespace: ENVO
id: ENVO:01000815
in_subset: envoPolar
comment: This is a defined class: most of its subclasses will not be asserted, but filled by inference.

environmental system determined by a quality
type: Class
subclass of: environmental system
definition: An environmental system which is determined by materials bearing roughly homogeneous qualities.
has_obo_namespace: ENVO
id: ENVO:01000997
comment: Organisational class. Not intended for annotation.

rhizosphere environment
type: Class
subclass of: environmental system
subclass of: Restriction
  on property: RO_0002131
  some values from: rhizosphere
subclass of: Restriction
  on property: RO_0002131
  some values from: plant-associated environment
definition: An environmental system determined by the presence of a plant rhizosphere.
IAO_0000118: Plant rhizosphere
has_obo_namespace: ENVO
id: ENVO:01000999
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: rhizosphere environment
annotated property: IAO_0000118
annotated target: Plant rhizosphere
comment: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environmental system determined by an organism
type: Class
subclass of: environmental system
definition: An environmental system which is determined by a living organism.
has_obo_namespace: ENVO
has_related_synonym: host-associated environment
id: ENVO:01001000
in_subset: envoEmpo
in_subset: envoOmics

plant-associated environment
type: Class
definition: An environmental system determined by a green plant.
IAO_0000118: Plant
has_broad_synonym: plant environment
has_exact_synonym: Viridiplantae-associated environment
has_obo_namespace: ENVO
id: ENVO:01001001
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: plant-associated environment
annotated property: IAO_0000118
annotated target: Plant
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

animal-associated environment
type: Class
definition: An environmental system determined by an animal.
IAO_0000118: Animal
has_broad_synonym: animal environment
has_exact_synonym: Metazoan-associated environment
has_obo_namespace: ENVO
id: ENVO:01001002
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: animal-associated environment
annotated property: IAO_0000118
annotated target: Animal
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

non-saline environment
type: Class
subclass of: environmental system determined by a quality
IAO_0000118: Non-saline
has_obo_namespace: ENVO
id: ENVO:01001003
in_subset: envoEmpo
comment: This class (term) is defined by the lack of a quality (i.e. the lack of salinity or increased osmolarity), which is not best-practice ontologically. Use for annotation is generally discouraged and users should use classes which positively describe the material or environment sampled (i.e. stating the qualities the entity has, rather than those it does not).

Axiom
annotated source: non-saline environment
annotated property: IAO_0000118
annotated target: Non-saline
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

sediment permeated by freshwater
type: Class
subclass of: sediment
subclass of: Restriction
  on property: surrounded by
  some values from: fresh water
definition: Sediment which has its porespace filled by water which has very low levels of sodium chloride and/or other salts.
has_obo_namespace: ENVO
id: ENVO:01001028
in_subset: envoEmpo
in_subset: envoOmics
comment: We do not specify numeric thresholds for saline vs. non-saline here, as this is variable. Consider specifying this on the information and/or data layer for your purposes. If you require an ENVO class with a fixed threshold, please request one using our issue tracker.

fecal environment
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by feces.
IAO_0000118: Animal distal gut
has_obo_namespace: ENVO
id: ENVO:01001029
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: fecal environment
annotated property: IAO_0000118
annotated target: Animal distal gut
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
comment: The label of this EMPO class is ambiguous, but pers. comm. with L Thompson (http://orcid.org/0000-0002-3911-1280) reveals that this is essentially limited to fecal samples.

environment determined by a metazoan secretion
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by a bodily secretion of a metazoan.
IAO_0000118: Animal secretion
has_obo_namespace: ENVO
id: ENVO:01001030
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a metazoan secretion
annotated property: IAO_0000118
annotated target: Animal secretion
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment determined by a plant substance
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by a substance produced by a plant.
IAO_0000118: Plant secretion
has_obo_namespace: ENVO
id: ENVO:01001031
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a plant substance
annotated property: IAO_0000118
annotated target: Plant secretion
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment determined by a biofilm on a plant surface
type: Class
definition: An environmental system which has its properties and dynamics determined by a biofilm on the surface of a plant.
IAO_0000118: Plant surface
has_obo_namespace: ENVO
id: ENVO:01001032
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a biofilm on a plant surface
annotated property: IAO_0000118
annotated target: Plant surface
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

digestive tract environment
type: Class
subclass of: anatomical entity environment
definition: An environmental system which has its properties and dynamics determined by a digestive tract.
IAO_0000118: Animal proximal gut
has_obo_namespace: ENVO
id: ENVO:01001033
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: digestive tract environment
annotated property: IAO_0000118
annotated target: Animal proximal gut
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
comment: This EMPO class includes examples of microbial environments determined by the "gut intestine, gizzard, crop, lumen, [and] mucosa".

environment determined by a biofilm on an animal surface
type: Class
definition: An environmental system which has its properties and dynamics determined by a biofilm on the surface of a animal.
IAO_0000118: Animal surface
has_obo_namespace: ENVO
id: ENVO:01001034
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a biofilm on an animal surface
annotated property: IAO_0000118
annotated target: Animal surface
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment determined by a biofilm on a fungal surface
type: Class
definition: An environmental system which has its properties and dynamics determined by a biofilm on the surface of a fungus.
IAO_0000118: Fungus surface
has_obo_namespace: ENVO
id: ENVO:01001035
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a biofilm on a fungal surface
annotated property: IAO_0000118
annotated target: Fungus surface
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

sediment permeated by saline water
type: Class
subclass of: sediment
subclass of: Restriction
  on property: surrounded by
  some values from: saline water
definition: Sediment which has its porespace filled by water with increased levels of sodium chloride and other salts.
has_obo_namespace: ENVO
id: ENVO:01001036
in_subset: envoEmpo
in_subset: envoOmics
comment: We do not specify numeric thresholds for saline vs. non-saline here, as this is variable. Consider specifying this on the information and/or data layer for your purposes. If you require an ENVO class with a fixed threshold, please request one using our issue tracker.

saline environment
type: Class
subclass of: environmental system determined by a quality
definition: An environment which is determined by materials which bear significant concentrations of salts.
IAO_0000118: Saline
has_obo_namespace: ENVO
id: ENVO:01001040
in_subset: envoEmpo
comment: The thresholds for "significant" concentrations of salts vary widely and thus no committment is made in this class. Subclasses with more explicit thresholds can be made upon request.

Axiom
annotated source: saline environment
annotated property: IAO_0000118
annotated target: Saline
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

fungi-associated environment
type: Class
definition: An environmental system determined by a fungal structure.
IAO_0000118: Fungus
has_broad_synonym: fungus environment
has_exact_synonym: fungus-associated environment
has_obo_namespace: ENVO
id: ENVO:01001041
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: fungi-associated environment
annotated property: IAO_0000118
annotated target: Fungus
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

sterile water environment
type: Class
equivalent class: Class
  intersection of: aquatic environment
  intersection of: Restriction
    on property: RO_0002507
    some values from: sterile water
subclass of: aquatic environment
subclass of: Restriction
  on property: RO_0002473
  some values from: sterile water
definition: An environmental system which has its properties and dynamics determined by sterile water.
IAO_0000118: Negative
has_obo_namespace: ENVO
id: ENVO:01001042
in_subset: envoEmpo
in_subset: envoOmics
comment: This term can be understood as a negative experimental control primarily composed of sterile water. The quantity of sterile water used may be contaminated; to express pure sterile water, please use http://purl.obolibrary.org/obo/ENVO_00005791

Axiom
annotated source: sterile water environment
annotated property: IAO_0000118
annotated target: Negative
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

hypersaline water environment
type: Class
subclass of: saline water environment
definition: An environmental system which has its properties and dynamics determined by hypersaline water.
IAO_0000118: Hypersaline (saline)
has_obo_namespace: ENVO
id: ENVO:01001043
in_subset: envoEmpo
in_subset: envoOmics
in_subset: envoPolar

Axiom
annotated source: hypersaline water environment
annotated property: IAO_0000118
annotated target: Hypersaline (saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
comment: Examples inlcude water from hypersaline samples or brines (>50 psu)

soil environment
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by soil.
IAO_0000118: Soil (non-saline)
has_obo_namespace: ENVO
id: ENVO:01001044
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: soil environment
annotated property: IAO_0000118
annotated target: Soil (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

planetary subsurface environment
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by the subsurface zone of a planet.
has_obo_namespace: ENVO
id: ENVO:01001046
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

non-saline planetary subsurface environment
type: Class
subclass of: planetary subsurface environment
definition: An environmental system which has its properties and dynamics determined by those parts of a planetary subsurface zone which are not saline.
IAO_0000118: Subsurface (non-saline)
has_obo_namespace: ENVO
id: ENVO:01001047
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: non-saline planetary subsurface environment
annotated property: IAO_0000118
annotated target: Subsurface (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

sediment environment
type: Class
equivalent class: Class
  intersection of: environmental system
  intersection of: Restriction
    on property: RO_0002507
    some values from: sediment
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by sediment.
has_obo_namespace: ENVO
id: ENVO:01001048
in_subset: envoEmpo
in_subset: envoOmics

non-saline sediment environment
type: Class
equivalent class: Class
  intersection of: sediment environment
  intersection of: Restriction
    on property: RO_0002507
    some values from: sediment permeated by freshwater
subclass of: sediment environment
definition: An environmental system which has its properties and dynamics determined by sediment permeated by non-saline water.
IAO_0000118: Sediment (non-saline)
has_obo_namespace: ENVO
id: ENVO:01001049
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: non-saline sediment environment
annotated property: IAO_0000118
annotated target: Sediment (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

saline sediment environment
type: Class
equivalent class: Class
  intersection of: sediment environment
  intersection of: Restriction
    on property: RO_0002507
    some values from: sediment permeated by saline water
subclass of: sediment environment
definition: An environmental system which has its properties and dynamics determined by sediment permeated by saline water.
IAO_0000118: Sediment (saline)
has_obo_namespace: ENVO
id: ENVO:01001050
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: saline sediment environment
annotated property: IAO_0000118
annotated target: Sediment (saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment determined by a biofilm on a non-saline surface
type: Class
definition: An environmental system which has its properties and dynamics determined by a biofilm on a surface which is exposed to non-saline materials.
IAO_0000118: Surface (non-saline)
has_obo_namespace: ENVO
id: ENVO:01001051
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a biofilm on a non-saline surface
annotated property: IAO_0000118
annotated target: Surface (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

aerosol environment
type: Class
subclass of: environmental system
definition: An environmental system which has its properties and dynamics determined by an aerosol.
has_obo_namespace: ENVO
id: ENVO:01001052
in_subset: envoEmpo
in_subset: envoOmics

saline aerosol environment
type: Class
subclass of: aerosol environment
definition: An environmental system which has its properties and dynamics determined by a saline aerosol.
IAO_0000118: Aerosol (saline)
has_obo_namespace: ENVO
id: ENVO:01001053
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: saline aerosol environment
annotated property: IAO_0000118
annotated target: Aerosol (saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
comment: seaspray or other aerosolized saline material (>5 psu)

non-saline aerosol environment
type: Class
subclass of: aerosol environment
definition: An environmental system which has its properties and dynamics determined by an aerosol with a low concentration of dissolved solutes.
IAO_0000118: Aerosol (non-saline)
has_obo_namespace: ENVO
id: ENVO:01001054
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: non-saline aerosol environment
annotated property: IAO_0000118
annotated target: Aerosol (non-saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/
comment: aerosolized dust or liquid

environment associated with an animal part or small animal
type: Class
definition: An environmental system determined by part of a living or dead animal, or a whole small animal.
IAO_0000118: Animal corpus
has_obo_namespace: ENVO
id: ENVO:01001055
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment associated with an animal part or small animal
annotated property: IAO_0000118
annotated target: Animal corpus
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment determined by a biofilm on a saline surface
type: Class
definition: An environmental system which has its properties and dynamics determined by a biofilm on a surface which is exposed to saline materials.
IAO_0000118: Surface (saline)
has_obo_namespace: ENVO
id: ENVO:01001056
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment determined by a biofilm on a saline surface
annotated property: IAO_0000118
annotated target: Surface (saline)
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment associated with a plant part or small plant
type: Class
definition: An environmental system determined by part of a living or dead plant, or a whole small plant.
IAO_0000118: Plant corpus
has_obo_namespace: ENVO
id: ENVO:01001057
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment associated with a plant part or small plant
annotated property: IAO_0000118
annotated target: Plant corpus
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

environment associated with a fungal tissue
type: Class
definition: An environmental system determined by part of a living or dead fungus.
IAO_0000118: Fungus corpus
has_obo_namespace: ENVO
id: ENVO:01001058
in_subset: envoEmpo
in_subset: envoMeo
in_subset: envoOmics

Axiom
annotated source: environment associated with a fungal tissue
annotated property: IAO_0000118
annotated target: Fungus corpus
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

mock community culture
type: Class
subclass of: cell culture
definition: A cell culture which is composed of a microbial community of known composition.
IAO_0000118: Mock community
has_obo_namespace: ENVO
id: ENVO:01001059
in_subset: envoEmpo
in_subset: envoOmics
comment: Mock communities are typically used as positive controls in experiments.

Axiom
annotated source: mock community culture
annotated property: IAO_0000118
annotated target: Mock community
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

single strain cell culture
type: Class
subclass of: cell culture
definition: A cell culture which is composed of a single population of bacterial or archaeal cells.
IAO_0000118: Single strain
has_obo_namespace: ENVO
id: ENVO:01001060
in_subset: envoEmpo
in_subset: envoOmics

Axiom
annotated source: single strain cell culture
annotated property: IAO_0000118
annotated target: Single strain
database_cross_reference: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/emp-ontology-empo/

cell culture
type: Class
subclass of: organic material
definition: A cell culture is a growth of cells in vitro in an artificial medium for experimental research.
database_cross_reference: https://en.wikipedia.org/wiki/Cell_culture
has_obo_namespace: ENVO
id: ENVO:02000008

Axiom
annotated source: cell culture
annotated property: definition
annotated target: A cell culture is a growth of cells in vitro in an artificial medium for experimental research.

fluid environmental material
type: Class
subclass of: environmental material
definition: A liquid or a gas.
has_narrow_synonym: fluid
has_obo_namespace: ENVO
id: ENVO:02000140

Axiom
annotated source: fluid environmental material
annotated property: definition
annotated target: A liquid or a gas.
database_cross_reference: https://github.com/EnvironmentOntology/envo/issues/940

anatomical entity environment
type: Class
subclass of: environmental system
subclass of: Restriction
  on property: BFO_0000050
  some values from: environmental system determined by an organism
definition: An environment which is determined by an anatomical entity.
has_obo_namespace: ENVO
id: ENVO:2100000