editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
has growth
has number of individuals
has specific name
is growth of
is specific name of
The characteristicFor property gives the entity of the characteristic.
The hasMeasurement property gives the measurements of the observed entity.
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part of
part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
is aggregate of
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'.
(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]
proper part of continuant at all times
[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has continuant part at all times that part exists
A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
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
Definition modified from 'surrounded by'.
is in aggregate
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
See http://purl.obolibrary.org/obo/OBI_0000293
has specified input
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
See http://purl.obolibrary.org/obo/OBI_0000295
is specified input of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
See http://purl.obolibrary.org/obo/OBI_0000299
has specified output
See http://purl.obolibrary.org/obo/OBI_0000312
is specified output of
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
role of
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has quality
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
x actively participates in y if and only if x participates in y and x realizes some active role
actively participates in
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
has active participant
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
adjacent to
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
has output
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
enabled by
input of
output of
formed as result of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
causally influenced by (material entity to material entity)
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
causally influences (material entity to material entity)
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
has increased levels of
achieves
completed invasion phase
contains system
decreases effort in
alien range: range in which the species is not commonly found
has alien range
has area
has decreased effort level by
has increased effort level by
has index
has level of
native range: range in which the species is commonly found
has native range
has range
has role
has status
has value
has propagule pressure
increases effort in
is absent
is against
is alien range to
is closely related to
Two species are closely related if they split apart from each other relatively recently during their evolution..
enemy in sense of http://www.semanticweb.org/rs/ontologies/INBIO#enemy
is enemy of
is enhanced by
is in invasion phase
is influenced by
is native range to
is prey of
is range of
is similar to
shows changes in species trait
skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch.
has exact match
skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
It's the degree of veriation of life forms within a given species, ecosystem, biome, or planet. Source: wikipedia.org
The biological variation found in a defined spatial area: can refer to variation at the level of genome, phenotype, species, community or ecosystem.
The community dynamics is the study of changes over time of the structure of biological communities.
It's the difference of any parameter (size, number of deads, number of recruits etc.) between two dates.
difference
It's a quantitative measure that reflects how many different types (such as species) there are in a dataset, and can simultaneously takes into account how evenly the basic units (such as individuals) are distributed among those types. Source: wikipedia.org
The occurrence of burning in ecosystems.
A geographical region that can include land as well as water.
It's a measure of the changes in population or community size over time.
It's the number of individuals dead over time.
It's a representation of the evenness and quantifies how equal the community is numerically.
Any product of the condensation of atmospheric water vapour that falls under gravity (http://en.wikipedia.org/wiki/Precipitation)
Qualquer produto da condensação do vapor de água atmosférico que cai sob efeito da gravidade.
It's the rate on which new individuals establishes in a certain community either by new born individuals or immigration.
recruitment
Quantidade relativa de vapor de água na atmosfera
The relative amount of whater vapour in the atmosphere
The simplest measure of the character of a community that takes into account both the abundance (or biomass) patterns and the species richness (Begon et al., 2006).
Evenness is simply a measure of how similar specie are in their abundances.
the number of differnet species represented in an ecological community, landscape or region
It is a measure of the thermal energy per particle of matter or radiation; it is measured by a thermometer, which may be calibrated in any of various temperature scales, Celsius, Fahrenheit, Kelvin, etc (http://en.wikipedia.org/wiki/Temperature).
The effect or consequence of an event or condition.
A measurement of the total number of entities.
The determination of the amount of total number of entities.
The length or duration of life or viability.
Any demarcated area of the Earth; may be determined by both natural and human boundaries, such as a state or province.
Any demarcated area of the Earth; may be determined by both natural and human boundaries.
The observable characteristics in an individual resulting from the expression of genes; the clinical presentation of an individual with a particular genotype.
The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment.
A characteristic or attribute inherent or inherited to an organism.
A characteristic or attribute of a population group.
A delineated geographic area encompassing residential, commercial, and other non-residential urban land uses with a residential population of 50,000 or more people and a density of 1,000 people or more per square mile.
A non-urbanized geographic area. "Rural" encompasses densely settled small towns with a residential population of less than 2,500 people, more sparsely populated areas, and remote areas.
An organizational header for concepts representing mostly abstract entities.
How much there is of something that you can measure; the total amount or number.
A bounded physical location which may contain structures. EXAMPLE(S): ambulance, helicopter, manufacturing site, service delivery location, home, emergency department, surgical suite, patient room OTHER NAME(S): NOTE(S): Constraints: Place may be natural or man-made. The geographic position of a place may or may not be constant. Discussion: Places may be work facilities (where relevant acts occur), homes (where people live) or offices (where people work). Places may contain sub-places (floor, room, booth, bed). Places may also be sites that are investigated in the context of health care, social work, public health administration (e.g., buildings, picnic grounds, day care centers, prisons, counties, states, and other focuses of epidemiological events).
A bounded physical location which may contain structures. EXAMPLE(S): ambulance, helicopter, manufacturing site, service delivery location, home, emergency department, surgical suite, patient room. NOTE(S): Constraints: Place may be natural or man-made. The geographic position of a place may or may not be constant. Discussion: Places may be work facilities (where relevant acts occur), homes (where people live) or offices (where people work). Places may contain sub-places (floor, room, booth, bed). Places may also be sites that are investigated in the context of health care, social work, public health administration (e.g., buildings, picnic grounds, day care centers, prisons, counties, states, and other focuses of epidemiological events).
The particular portion of space occupied by a physical object or intended for a physical object.
The linear extent in space from one end of something to the other end, or the extent of something from beginning to end. (NCI)
The linear extent in space from one end of something to the other end, or the extent of something from beginning to end.
The extent or measurement of something from side to side. (NCI)
The extent or measurement of something from side to side.
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension. (NCI)
The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
The act of alteration or modification; changed or altered in form or character.
An event or sequence of events that constitute a round or succession of observable phenomena, recurring usually at regular or approximately regular time intervals and in the same sequence.
Something that happens at a given place and time.
To have a connection by participation or association or use; sharing in an activity or process.
A condition or state at a particular time.
The appearance of objects (or light sources) described in terms of a person's perception of their hue and lightness (or brightness) and saturation. (NCI)
The appearance of objects (or light sources) described in terms of a person's perception of their hue and lightness (or brightness) and saturation.
Ranked categories for the classification of organisms according to their suspected evolutionary relationships.
An area or portion of something with more or less definite boundaries designed or specified according to some established biological, administrative, economic, demographic, etc. criteria.
The place where something begins or comes from in either the sense of a physical location or a metaphysical source.
An area or region distinguished from adjacent parts by a distinctive feature or characteristic.
Specifies the location of a zone on an array. (caMAGE)
A group of organisms that differ from all other groups of organisms and that are capable of breeding and producing fertile offspring.
The negative logarithm (base 10) of the concentration of hydronium ions, which is used as a measure of the acidity or alkalinity of a fluid.
Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter.
The amount by which something increases.
The capacity of a physical system to do work.
A land mass smaller than a continent that is surrounded by water.
A distinct region or subdivision of a territorial or political area or community.
A trait or behaviour that is useful for repelling an enemy.
The size of something as given by the distance around it.
A measure of the water vapor content of air.
The ability to sustain an activity over a period of time.
The amount of water vapor in the air of a living space.
The percentage of ambient moisture of a living space.
interactions between one organism and another which it harbors or nourishes.
See http://purl.bioontology.org/ontology/CSP/1035-7240
state of close, permanent, or obligatory contact between 2 species, usually of a mutually beneficial nature.
See http://purl.bioontology.org/ontology/CSP/1035-7338
See http://purl.bioontology.org/ontology/MESH/D000078622
Various components of food that are required for nourishment.
That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.
See http://purl.bioontology.org/ontology/MESH/D008027
A group of chemical elements that are needed in minute quantities for the proper growth, development, and physiology of an organism. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
See http://purl.bioontology.org/ontology/MESH/D014131
Essential dietary elements or organic compounds that are required in only small quantities for normal physiologic processes to occur.
See http://purl.bioontology.org/ontology/MESH/D018977
a group of organisms of the same species inhabiting a given area
This class should be incorporated into ENVO.
A population comprises all the individuals of a given species in a specific area or region at a certain time.
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
specifically dependent continuant
site
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature.
A geographical feature associated with water.
A marine water body which is constitutes the majority of an astronomical body's hydrosphere.
A large expanse of saline water usually connected with an ocean.
A geographical feature associated with water with a halinity above 30 ppt (roughly 35 g/L).
A lake whose water contains a considerable concentration of dissolved salts.
A body of water or other liquid of considerable size contained in a depression on a landmass.
An vegetated area which overlaps a wetland ecosystem.
A semi-enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the open sea.
An accumulation of water of varying size.
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.
A hydrographic feature characterized by the dominance of snow or ice.
Likely to be depopulated and "glacial" made into a quality or similar.
Soil or rock and included ice or organic material at or below the freezing point of water (0 degrees Celsius or 32 degrees Fahrenheit) for two or more years.
Ice is not always present, as may be in the case of nonporous bedrock, but it frequently occurs and it may be in amounts exceeding the potential hydraulic saturation of the ground material.
An estuary which is located in regions where evaporation greatly exceeds the inflow of fresh water, forming a zone of maximum salinity towards which both riverine and marine water masses flow, before sinking and spreading along the bottom in both seaward and landward directions.
It would be more correct to say that this has_quality salty or has_part ((soil and water) and has_increased_levels_of salt.
That part of the land in immediate contact with a body of water including the area between high and low water lines.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms.
The various 'has part' and 'has quality' relations may not hold true for all soils; however, I have yet to find counter examples. Require input from a pedologist or similar. [pbuttigieg]
'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280
The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth.
An environmental material primarily composed of dihydrogen oxide in its liquid form.
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.
It is recommended to use a combination of sediment terms to describe a more specific sediment type.
A material entity which determines an environmental system.
A material entity determines an environmental system when its removal would cause the collapse of that system. For example, a seamount determines a seamount environment, acting as its 'hub'. 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.
A group of hydrous aluminium phyllosilicate (phyllosilicates being a subgroup of silicate minerals) minerals (see clay minerals), that are typically less than 2 micrometres in diameter. Clay consists of a variety of phyllosilicate minerals rich in silicon and aluminium oxides and hydroxides which include variable amounts of structural water.
A portion of enriched soil is a portion of soil with elevated levels of some material entity.
This could be demoted to an inferred class if issues with double inheritance arise.
A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system.
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
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.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here.
Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar.
https://en.wikipedia.org/wiki/ In the Udden-Wentworth scale (due to Krumbein), silt particles range between 0.0039 to 0.0625 mm, larger than clay but smaller than sand particles. ISO 14688 grades silts between 0.002 mm and 0.063 mm. In actuality, silt is chemically distinct from clay, and unlike clay, grains of silt are approximately the same size in all dimensions; furthermore, their size ranges overlap. Clays are formed from thin plate-shaped particles held together by electrostatic forces, so present a cohesion. According to the U.S. Department of Agriculture Soil Texture Classification system, the sand-silt distinction is made at the 0.05 mm particle size. The USDA system has been adopted by the Food and Agriculture Organization (FAO). In the Unified Soil Classification System (USCS) and the AASHTO Soil Classification system, the sand-silt distinction is made at the 0.075 mm particle size (i.e., material passing the #200 sieve). Silts and clays are distinguished mechanically by their plasticity.
A naturally occurring granular material composed of finely divided rock and mineral particles.
A prominent or distinctive aspect, quality, or characteristic of environments occurring within the marine water column.
Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material.
Subclasses should be assigned by inference.
particulate matter
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
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.
An abiotic environmental factor that influences the functioning of living organisms (Begon et al., 2006).
Experimental class created 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.
A system which has the disposition to environ one or more material entities.
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.
The environment of an organism consists of all those factors and phenomena outside the organism that influence it, whether these are physical and chemical (abiotic) or other organisms (biotic) (Begon et al., 2006)
A mineral material is an environmental material which is primarily composed of some substance that is naturally occurring, solid and stable at room temperature, representable by a chemical formula, usually abiogenic, and that has an ordered atomic structure.
Look for "mineral" in a chemical or geochemical ontology to formalise the composed primarily of link. From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure.
Water vapour is a vapour which is the gas phase of water.
Perhaps a better relation between water vapour and water can be found in or added to RO?
An atmosphere is a layer of gases surrounding a material body of sufficient mass that is held in place by the gravity of the body.
Atmospheric water vapour is water vapour that is part of an atmosphere.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
Unlike biomes, ecoregions are geographically defined entities. ENVO's sister project, GAZ, contains terms for instances of ecoregions (e.g. Beringia lowland tundra). Requests for new terms should be directed to GAZ. ENVO will only contain this top-level class. The class' definition is preliminary and will be aligned to BFO.
Ice is water frozen into a solid state. It can appear transparent or opaque bluish-white color, depending on the presence of impurities or air inclusions. The addition of other materials such as soil may further alter its appearance.
Ecozones delineate large areas of a planetary surface within which organisms have been evolving in relative isolation over long periods of time, separated from one another by geographic features, such as oceans, broad deserts, or high mountain ranges, that constitute barriers to migration.
ENVO contains this top-level class, but all instances will be in GAZ. The definition is preliminary and will be aligned to BFO. https://en.wikipedia.org/wiki/ Ecozones correspond to the floristic kingdoms of botany or zoogeographic regions of zoology. Ecozones are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of plants and animals to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation. Each ecozone may include a number of different biomes. A tropical moist broadleaf forest in Central America, for example, may be similar to one in New Guinea in its vegetation type and structure, climate, soils, etc., but these forests are inhabited by plants and animals with very different evolutionary histories.
A layer is a quantity of some material which is spatially continuous, has comparable thickness, and usually covers some surface.
A layer that is part of a marine water body.
An endolithic environment is an environment that exists within solid rock.
An environment which has a lower temperature than some local or global average.
The definition of the deprecated 'cold temperature habitat' class, which this class was derived from, quotes an upper threshold of 15 degrees Celsius for 'coldness'.
An anthropogenic environment is an environmental system which is the product of human activity.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
A high osmolarity environment is an environment in which entities are exposed to high concentrations of solutes.
An environment whose dynamics are strongly influenced by water.
A marine environment and enviroment which is determined by a marine water body.
A layer in a water mass, itself composed primarily of water.
This class will eventually be populated by inference, and its asserted subclasses removed.
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
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.
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.
An ecosystem which has been subject to a perturbation, that is, the ecosystem has undergone a pronounced change in response to a change in environmental conditions or other perturbation.
This is often used by plant collectors when early successional species are observed in an area.
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
"process" is included in the label to make it clear that we are not referring to the condensed material (e.g. water droplets, window fog)
hydrological condensation process
A coast is the area where land meets the sea, ocean, or lake.
Used for both marine and lake coasts. The boundary of the coast is fuzzy and it overlaps both the water body and land in quesiton. Compared to 'shore'
coast
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
"process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet)
hydrological precipitation process
Condensation is a process during which a gas undergoes a phase transition into a liquid.
condensation process
An environmental system which can sustain and allow the growth of an ecological population.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely.
This class is to be populated by inference.
gaseous environmental material
An environmental material which is in a solid state.
This is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a liquid state.
liquid environmental material
A biosphere is a part of an astronomical body which includes, as parts, all the living entities within the gravitational sphere of influence of that body, as well as the non-living and dead entities with which they interact.
A biosphere is an environmental system which includes, as parts, all the living entities within the gravitational sphere of influence of an astronomical body, and the non-living and dead entities which they interact with.
Whether this class should be grouped with classes such as "hydrosphere" and "cryosphere" requires some discussion.
The gravitational sphere of influence referenced in this class' definition is the Hill sphere: a region in which an object dominates the attraction of satellites despite gravitational perturbations.
biosphere
A cryosphere is that part of a planet which is primarily composed of water is in solid form.
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
cryosphere
A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force.
precipitation process
A hydrological process in which irregular aggregates of snow fall to a planetary surface.
snowfall
An environmental system in which minimal to no anthropisation has occurred and non-human agents are the primary determinants of the system's dynamics and composition.
In most contexts, 'natural' is defined by the lack of intervention or influence by humans and their activities. On Earth, most environments fall on a scale between completely natural and anthropised.
natural environment
A process during which a natural environmental system is altered by human action.
An area may be classified as anthropized even though it looks natural, such as grasslands that have been deforested by humans. It can be difficult to determine how much a site has been anthropized in the case of urbanization because one must be able to estimate the state of the landscape before significant human action.
anthropisation
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
This class can refer to the flow of any material in a liquid phase.
mass liquid flow
A process during which a volume of water is transported due to a disequilibria in physical forces.
water flow process
An environmental system which is determined by materials bearing roughly homogeneous qualities.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system within which an environmental material strongly influences the system's composition and properties.
Organisational class. Not intended for annotation. Subclasses describe environments which are usually permeated by an environmental material. They may also describe environments which are sufficiently close to a material, that their dynamics are strongly influenced by it (e.g. a patch of forest ecosystem neighbouring a uranium dump).
environmental system determined by a material
An environmental system which is determined by a living organism.
environmental system determined by an organism
An environmental system determined by an animal.
animal-associated environment
A lake which has formed as the result of processes that are not or are only minimally driven by human activity.
This class is to be filled by inference.
natural lake
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
Requires addition of waves for full axiomatisation. This should be linked to "subatomic particle" with an "or". Note that ENVO represents space as an environmental material (a hard vacuum with sparse material inclusions).
radiation
An environment which is determined by materials which bear significant concentrations of salts.
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.
saline environment
An environmental system which has its properties and dynamics determined by soil.
soil environment
An environmental system which has its properties and dynamics determined by sediment.
sediment environment
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with an animal part or small animal
An environmental system determined by part of a living or dead plant, or a whole small plant.
environment associated with a plant part or small plant
A material which is composed primarily of one or more pure metals and which shows their properties.
Far more axiomatisation can be done should the qualities of metals be added to PATO or a similar quality ontology. However, note that there are many exceptions to the typical qualities of the majority of metals.
While this class allows for some degree of contamination by non-metal substances, the material represented should show at least some of the typical features of a pure metal: hardness (except for liquid metals), opacity, lustre, malleability, fusibility, ductile and good electrical and thermal conductivity.
metallic material
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
An ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
This class is defined logically - any material that is frozen is considered a subclass. Note that ice may be formed at very high temperatures, due to gravitational effects and/or pressure.
ice
An environment which has its properties and composition largely determined by the presence of a metazoan which lacks a vetebral column and which has a habitat that is found in an aquatic environmental system.
environment associated with an aquatic invertebrate
Not currently live, may need to be switched to alternative PURLs.
water surface
The surface layer of a mass of sediment.
sediment surface
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
terrestrial environmental zone
An environmental zone which is bounded by material parts of a marine environment.
This class will eventually be populated by inference alone, with its subclasses distributed in more process-linked hierarchies to improve semantic density.
marine environmental zone
A terrestrial ecosystem which is inundated or saturated by surface or ground water at a frequency and duration sufficient to support, and that under normal circumstances does support, a prevalence of vegetation typically adapted for life in saturated soil conditions.
wetland ecosystem
A natural environment which is located on a land mass.
terrestrial natural environment
A natural environment which is within a water body.
aquatic natural environment
A layer which is primarily composed of some liquid material.
liquid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
solid layer
water ice layer
An environmental zone which is part of an atmosphere.
atmospheric zone
A layer of liquid that is part of an estuary.
aquatic estuarine layer
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
A liquid surface layer which is in contact with air.
liquid air-water interface layer
A surface layer which is composed primarily of solid environmental material.
solid surface layer
A material transport process during which a volume of material is displaced due to a disequilibrium in physical forces and during which 1) the qualities that inhere in that volume and 2) the processes that are unfolding within it are largely unchanged.
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
An action of exogenic processes (such as water flow or wind) which remove environmental material from one location on the surface of an astronomical body, transporting it to another location where it is deposited.
erosion
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
anthropogenic ecosystem conversion process
A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions.
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
Land which is below the freezing point of water.
Perennially and seasonally frozen ground can vary from being partially to extensively frozen depending on the extent of the phase change. It may be described as hard frozen ground, plastic frozen ground, or dry frozen ground, depending on the pore ice and unfrozen water contents and its compressibility under load.
frozen land
Soil which is below the freezing point of water.
frozen soil
A water surface that is part of a water body.
surface layer of a water body
An ecoregion which is located on a landmass.
terrestrial ecoregion
A surface layer of a water body which is part of an ocean or sea.
At this level, the depth of this layer is ambiguous. Some methods (telemetry) measure only the first few centimeters of the sea or ocean surface. In situ methods often sample the first few meters. Subclasses can be created for such cases.
sea surface layer
A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water.
land
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
ecosystem process
A process in which includes the components of an environmental system as participants.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process which occurs within an atmosphere.
This class will be populated by inference and is primarily organisational.
atmospheric process
An environmental process which is driven by the action of humans.
An action of exogenic processes (such as water flow or wind) which remove environmental material from one part of a planet's crust, transporting it to another location where it is deposited.
An environmental process which has water - in any of its states - as a participant.
This classes asserted subclasses will be moved away as it should be an inferred class.
A process during which the mass of one or more materials, present within a given site, increases.
Experimental class for structural purposes not recommended for annotation. A material accumulation process ends a material transport process.
material accumulation process
A process during which material is displaced from its original location and transported either to a new location or back to the original location.
Experimental class for structural purposes not recommended for annotation.
material transport process
Sediment which has been transported through the marine water column, settling on the seafloor.
Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input.
marine sediment
A material accumulation process during which solid particles are pulled through a water body by gravitation or centrifugal force and which ends when they settle on a solid surface.
sedimentation in a water body
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
A different material transformation process class (or similarly named class) pertaining to the conversion of a specific chemical into another belongs in CHEBI and or REX ontologies.
Experimental class for structural purposes not recommended for annotation. A material transformation process only refers to ENVO:environmental material classes (e.g. bulk and typically impure substances), rather than transformations converting a specific chemical into another.
material transformation process
An environment which is determined by an anatomical entity.
subcontinental land mass
per the definition of 'contiguous' of "being in actual contact : touching along a boundary or at a point", these land masses share boundaries with other land masses that are part of the same continent, and thus are not surrounded by water like an island. At some point, we need an 'adjacent to' relation if BFO doesn't provide it. One question is whether this class encompasses fiat parts of islands.
contiguous land mass
A subcontinental land mass that is part of an island and includes part of the land surface of the island.
It cannot be a part of the island, for example, that is below water.
contiguous island land mass
aggregate of contiguous land masses
A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface.
François Modave
Mathias Brochhausen
Matt Diller
William R. Hogan
geographical region
land mass
aggregate of islands
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
The increase in size or mass of an entire organism, a part of an organism or a cell.
See also the biological process term 'cell growth ; GO:0016049'.
The usual or expected function of something; the part something plays in an action or event.
See http://purl.obolibrary.org/obo/NCIT_C48835
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
See http://purl.obolibrary.org/obo/OBI_0100026
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy.
A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion).
A permeability quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
A quality inhering in a bearer by virtue of the bearer's power or force.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology.
A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction.
A mass which is higher than normal or average.
A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A composition quality inhering in a bearer by virtue of the bearer's containing granules.
A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid.
A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid.
A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.
A positional quality inhering in a bearer by virtue the bearer's being changed in position.
A quality inhering in a bearer by virtue of its constitution.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
A collection of organisms, all of the same species, that live in the same place.
population of organisms
A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species.
single-species collection of organisms
A collection of organisms that consists of two or more organisms from at least two species.
multi-species collection of organisms
A material entity consisting of multiple components that are causally integrated.
See http://purl.obolibrary.org/obo/RO_0002577
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology.
1) The variety of plant and animal taxa, including genes, amino acids, flowers, species, or populations. 2) The variety of plant and animal communities, forest types, stand conditions, age classes, and landscape components.
diversity
The number of individuals per unit area.
densidad de población
densité de population
population density
густота популяции
Blackwell’s concise encyclopedia of ecology, 1999
It's the amount of individuals in a population
population size
taille d'une population
tamaño de la población
размер популяции
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
See http://www.ifomis.org/bfo/1.1/span#ProcessualEntity
the effective number of different species that are represented in a collection of individuals, it consists of two components: species richness and species evenness. From http://cerrado.linkeddata.es/ecology/ccon#SpeciesDiversity
Not existing in a specified place at a specified time. (NCI)
Not existing in a specified place at a specified time.
An area in which a species occurs even though it lies outside its native range.
Species whose presence in a region is attributable to human actions that enable them to overcome biogeographical barriers.
after https://www.thefreedictionary.com/allocation
To set apart or re-distribute for a special purpose
Variety of animal species present in a location
chemical element required by animals to perform functions necessary for life
disturbance brought about by human activity
Any change in the behaviour of a species
from https://en.wikipedia.org/wiki/Beta_diversity
In ecology, beta diversity (β-diversity or true beta diversity) is the ratio between regional and local species diversity.
Any change in the environment, e.g. concerning temperature, soil nutrients or biodiversity
Any change in an individual organism, e.g. concerning its size or life cycle stage
definition from: http://purl.obolibrary.org/obo/PCO_000000
A community of at least two different species, living in a particular area. Must have at least two populations of different species as members.
A species is strongly competitive, if its way of using shared resources usually leads to a reduction in survivorship, growth and/or reproduction of at least some of the competing individuals of the other species.
Attribute resulting from a combination of several traits
from http://vivoweb.org/ontology/core#Continent
A large contiguous landmass that is at least partially surrounded by water, together with any islands on its continental shelf.
A disturbance is an event or process that disrupts ecosystem, community or population structure, and changes resources, substrate availability or the physical environment. Disturbances can have anthropogenic or non-anthropogenic causes.
A measurable change to the properties of an ecosystem by a non-native species.
metric for qualifying ecologically relevant characteristics, e.g. biodiversity or body length
from http://www.openness-project.eu/taxonomy/term/73
Attributes which characterize an ecosystem, such as its size, biodiversity, stability, degree of organization, as well as its functions and processes (i.e. the internal exchanges of materials, energy and information among different pools).
from http://www.projecthalo.com/aura#Ectoparasite
A parasite that lives on and feeds from the external surface of the host's body.
An organism that is a predator, consumer, parasite, parasitoid or pathogen of another organism.
after Reiss, J., Bridle, J.R., Montoya, J.M. and Woodward, G. 2009. Emerging horizons in biodiversity and ecosystem functioning research. Trends Ecol. Evol., 24: 505-514, and McGill BJ, Enquist BJ, Weiher E, Westoby M (2006) Rebuilding community ecology from functional traits Trends Ecol Evol 21:178-185
A trait that strongly influences organismal performance, and that determines its effect on processes and its response to environmental factors
A species that can survive and reproduce in a wide range of environmental conditions using a wide variety of resouces to do so.
Information about the genetic characteristics
from https://en.wikipedia.org/wiki/Genetic_diversity
Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.
from https://encyclopedia2.thefreedictionary.com/geographic+entity
An entity or geographic feature that occupies a position in space about which data describing the attributes of the entity and its geographic location are recorded.
Actions of human beings that have an influence on the environment and that are characteristic for human societies, i.e. they are linked to social, economic or other cultural processes.
The process of transportation, establishment and spread of organisms outside of their native range.
phase of establishment in the alien range as part of the invasion process
Sequential phases during the invasion process. Typically, four different phases are distinguished: transport, introduction, establishment and spread.
phase of spreading in the alien range as part of the invasion process
Completing one or all phases of the invasion process.
phase of transportation to the alien range as part of the invasion process
Alien species that become established and spread beyond the place of introduction are called invasive species.
Alien species that sustain self-replacing populations over several life cycles, produce reproductive offspring, often in very large numbers at considerable distance from the parent and/or site of introduction, and have the potential to spread over long distances.
Adapted from https://en.wikipedia.org/wiki/Mineral_%28nutrient%29
Chemical element required by organisms to perform functions necessary for life.
Any change in the morpholoy of a species
The form and structure of an organism and its parts, including cells, that result from the interaction of its genotype and the environment. From Bio-Assay Ontology.
The rate in which new borns are added to a population, or in other words, the number of new borns over time.
A range in which a species has evolved or in which it has arrived by natural means.
Species that have evolved in a given area or that arrived there by natural means, without the intentional or accidental intervention of humans from an area where they are native.
disturbance that happened by some event not directly caused by human activity, e.g. storms or land slides
Alien species which are not in the subgroup of invasive species are part of the subgroup non-invasive species.
Alien species that is not an invasive species.
Amount of nutrients contained in something, e.g in a defined volume of soil or water
Nutrient occurring in the chemical form of salt
from https://www.thefreedictionary.com/parasite
An organism that lives and feeds on or in an organism of a different species and causes harm to its host.
Any change in the phenology of a species
The capacity of a genotype to produce different phenotypes in different environments.
Any change in the physioloy of a species
Variety of plant species present in a location
chemical element required by plants to perform functions necessary for life
The process of remaining alive or in existence.
population survival
from https://www.thefreedictionary.com/predator
An organism that lives by preying on other organisms.
Being or existing in a specified place or at the specified time. (NCI)
Being or existing in a specified place or at the specified time.
chemical elements required by organisms in large amounts; for plants, these are nitrogen, phosphorus, and potassium
A composite measure consisting of the number of individuals introduced per introduction event and the frequency of introduction events.
An area where a species is found in the wild.
staying essentially unchanged despite the presence of disturbances
Abiotic environmental factor necessary for survival, growth, and reproduction, such as water, light, mineral nutrients, and various forms of fixed carbon (e.g. plant material or meat).
chemical elements required by organisms in moderate amounts; for plants, these are e.g. sulfur, calcium and magnesium
A species that can survive and reproduce only within a narrow range of environmental conditions using specific resources (e.g., a specific diet).
A well-defined, measurable property of organisms, usually measured at the individual level and used comparatively across species.
from https://www.thefreedictionary.com/subcontinent
A large landmass, such as India, that is part of a continent but is considered either geographically or politically as an independent entity.
from http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25447
The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
An ecosystem that has not been subject to disturbance.