Birgitta König-Ries birgitta.koenig-ries@uni-jena.de
Alsayed Algergawy alsayed.algergawy@uni-jena.de
Merle Gänßinger merle.gaenssinger@uni-jena.de
Hrishikesh Jadhav jadhav02@ads.uni-passau.de
The Invasion Biology Ontology (INBIO) contains terms and concepts relevant in the field of invasion biology, which is a research area dealing with the translocation, establishment, spread, impact and management of species outside of their native ranges, where they are called non-native or alien species. This first version of the ontology covers terms and concepts needed to describe twelve major invasion hypotheses building the hierarchical hypothesis network (see also Jeschke JM, Heger T (Eds) (2018) Invasion Biology: Hypotheses and Evidence. CABI, Wallingford, UK).
PERSON:Daniel Schober
editor note
An entity responsible for making contributions to the resource.
has growth
has number of individuals
is growth of
The characteristicFor property gives the entity of the characteristic.
The hasMeasurement property gives the measurements of the observed entity.
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
a core relation that holds between a part and its whole
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'.
has part
a core relation that holds between a whole and its part
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
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)
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])
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])
[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
has spatial occupant at some time
[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 measurement unit label
A relation between a value specification and its unit of measurement.
this input material (or this output material) participates in this process
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
this process has participant this input material (or this output material)
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.
has participant
a relation between a process and a continuant, in which the continuant is somehow involved in the process
this red color is a quality of this apple
A quality inheres in its bearer at all times for which the quality exists.
quality of
a relation between a quality and an independent continuant (the bearer), in which the quality 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
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
this apple has quality this red color
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
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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
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 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
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
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
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
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)
contained in
contains
this rat is located in this cage
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
located in
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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.
ends during
overlaps
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
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.
surrounded by
This relation acts as a join point with BSPO
adjacent to
x adjacent to y if and only if x and y share a boundary.
surrounds
ends
ends with
has input
has output
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
output of
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
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.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
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
produced by
has increased levels of
is absent
facilitate
has increased effort level by
completed invasion phase
has index
is native range to
has status
has range
is in invasion phase
increases effort in
has level of
decreases effort in
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
has decreased effort level by
is enhanced by
enhance
is range of
achieves
alien range: range in which the species is not commonly found
has alien range
allocates
has area
has propagule pressure
shows changes in species trait
is prey of
has value
is similar to
is alien range to
is against
has role
native range: range in which the species is commonly found
has native range
General influence or effect on ecological or biological systems.
affects
Conducts a detailed examination of the elements or structure of something.
analyzes
Refers to the process of pushing out or replacing one species or ecological component by another.
displaces
Interrupts by causing a disturbance or problem.
disrupts
Causes or motivates a change or process.
drives
Improves or augments a particular ecological or biological property or process.
enhances
Studies or investigates a subject or area in detail.
examines
Indicates undergoing or being subjected to a particular process or condition.
experiences
Makes an action or process easy or easier.
facilitates
Acts as a host for other organisms, often referring to invasive species.
hosts
Describes significant effects on ecosystems or species.
impacts
Influences biological or ecological processes.
influences
provides
quantifies
reduces
A relation between a scalar measurement data item and a number that quantifies it.
The range should probably not be restricted to "float". It makes sense to set it to "real". However we do not know how this change will affect SPARQL queries, so we have left the range as-is for now.
has measurement value
has invasion success likelihood
has amount of species
has amount of closely related species
has specific name
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).
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
continuant
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])
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.
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])
a spatial region
an organism
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
specifically dependent 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.
site
generically dependent continuant
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.
a hurricane
a puff of smoke
a sea wave
a tornado
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.
material entity
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])
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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])
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.
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.
An accumulation of water of varying size.
Likely to be depopulated and "glacial" made into a quality or similar.
A hydrographic feature characterized by the dominance of snow or ice.
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.
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.
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.
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.
A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids.
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
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 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.
It is recommended to use a combination of sediment terms to describe a more specific sediment type.
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.
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 material entity which determines an environmental system.
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.
This could be demoted to an inferred class if issues with double inheritance arise.
A portion of enriched soil is a portion of soil with elevated levels of some material entity.
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 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.
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.
A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings.
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.
Silt is granular material of a size somewhere between sand and clay whose mineral origin is quartz and feldspar.
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.
Subclasses should be assigned by inference.
particulate matter
Particulate material is an environmental material which is composed of microscopic portions of solid or liquid material suspended in another environmental material.
Environmental material derived from living organisms and composed primarily of one or more biomacromolecules.
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.
An environmental condition is a range of a determinate quality or combination of qualities that are present in an environmental system.
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 system which has the disposition to environ one or more material entities.
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.
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.
Perhaps a better relation between water vapour and water can be found in or added to RO?
Water vapour is a vapour which is the gas phase of water.
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.
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.
A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions.
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.
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.
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.
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.
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 environment which has a lower temperature than some local or global average.
Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic.
An anthropogenic environment is an environmental system which is the product of human activity.
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.
This class will eventually be populated by inference, and its asserted subclasses removed.
A layer in a water mass, itself composed primarily of water.
Snow is an environmental material which is primarily composed of flakes of crystalline water ice.
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.
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.
This is often used by plant collectors when early successional species are observed in an area.
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.
"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
Hydrological condensation is a process in which atmospheric water vapour undergoes a phase transition from the gas phase to the liquid phase.
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
A coast is the area where land meets the sea, ocean, or lake.
"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
Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity.
condensation process
Condensation is a process during which a gas undergoes a phase transition into a liquid.
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
An environmental system which can sustain and allow the growth of an ecological population.
This class is to be populated by inference.
gaseous environmental material
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 is a defined class: its subclasses will not be asserted, but filled by inference.
solid environmental material
An environmental material which is in a solid state.
liquid environmental material
An environmental material which is in a liquid state.
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 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.
This is a very broad and, in practice, poorly defined term. Please consider using or requesting a more specific class.
cryosphere
A cryosphere is that part of a planet which is primarily composed of water is in solid form.
precipitation process
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.
snowfall
A hydrological process in which irregular aggregates of snow fall to a planetary surface.
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
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.
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 during which a natural environmental system is altered by human action.
This class can refer to the flow of any material in a liquid phase.
mass liquid flow
A process whereby a volume of liquid moves due to a disequilibrium of physical forces.
water flow process
A process during which a volume of water is transported due to a disequilibria in physical forces.
Organisational class. Not intended for annotation.
environmental system determined by a quality
An environmental system which is determined by materials bearing roughly homogeneous qualities.
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 within which an environmental material strongly influences the system's composition and properties.
environmental system determined by an organism
An environmental system which is determined by a living organism.
animal-associated environment
An environmental system determined by an animal.
This class is to be filled by inference.
natural lake
A lake which has formed as the result of processes that are not or are only minimally driven by human activity.
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
A process during which energy is emitted or transmitted in the form of waves or particles through space or a material medium.
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 environment which is determined by materials which bear significant concentrations of salts.
soil environment
An environmental system which has its properties and dynamics determined by soil.
sediment environment
An environmental system which has its properties and dynamics determined by sediment.
environment associated with an animal part or small animal
An environmental system determined by part of a living or dead animal, or a whole small animal.
environment associated with a plant part or small plant
An environmental system determined by part of a living or dead plant, or a whole small plant.
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
A material which is composed primarily of one or more pure metals and which shows their properties.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
An environmental system which includes both living and non-living components.
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 ice is an environmental material which is either frozen or which is maintained in a solid state by gravitational forces or pressure.
environment associated with an aquatic invertebrate
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.
Not currently live, may need to be switched to alternative PURLs.
water surface
sediment surface
The surface layer of a mass of sediment.
terrestrial environmental zone
An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it.
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
An environmental zone which is bounded by material parts of a marine environment.
wetland ecosystem
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.
terrestrial natural environment
A natural environment which is located on a land mass.
aquatic natural environment
A natural environment which is within a water body.
liquid layer
A layer which is primarily composed of some liquid material.
solid layer
A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid.
water ice layer
atmospheric zone
An environmental zone which is part of an atmosphere.
aquatic estuarine layer
A layer of liquid that is part of an estuary.
A vegetated area is a geographic feature which has ground cover dominated by plant communities.
liquid air-water interface layer
A liquid surface layer which is in contact with air.
solid surface layer
A surface layer which is composed primarily of solid environmental material.
Advective processes are disjoint from diffusive processes. Typically, fluids are advected.
advective transport process
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.
erosion
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.
anthropogenic ecosystem conversion process
A process during which an ecosystem - natural or anthropised - is changed by the actions of humans.
Sometimes the increase in viscosity is great enough to crystallize or solidify the substance in question.
material congelation process
A material transformation process during which a material's viscosity increase either through a reduction in temperature or through chemical reactions.
frozen soil
Soil which is below the freezing point of water.
surface layer of a water body
A water surface that is part of a water body.
terrestrial ecoregion
An ecoregion which is located on a landmass.
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 a water body which is part of an ocean or sea.
land
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.
ecosystem process
An environmental process either driven by or primarily impacting the parts or emergent properties of an ecosystem.
This is a convenience class for organisation and should not be used for annotation.
environmental system process
A process in which includes the components of an environmental system as participants.
This class will be populated by inference and is primarily organisational.
atmospheric process
A process which occurs within an atmosphere.
An environmental process which is driven by the action of humans.
This classes asserted subclasses will be moved away as it should be an inferred class.
An environmental process which has water - in any of its states - as a participant.
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 the mass of one or more materials, present within a given site, increases.
Experimental class for structural purposes not recommended for annotation.
material transport 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.
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
Sediment which has been transported through the marine water column, settling on the seafloor.
sedimentation in a water body
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.
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
A process during which a portion of some environmental material is converted into a different material or a collection of materials.
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
It cannot be a part of the island, for example, that is below water.
contiguous island land mass
A subcontinental land mass that is part of an island and includes part of the land surface of the island.
aggregate of contiguous land masses
François Modave
Mathias Brochhausen
Matt Diller
William R. Hogan
geographical region
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.
land mass
aggregate of islands
geodetic coordinate measurement datum
A measurement of location on the Earth that uses a single number to specify a coordinate in a coordinate system known as a geodetic datum.
Josh Hanna
latitude and longitude are key subtypes
geodetic datum
A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects).
Wikipedia: https://en.wikipedia.org/wiki/Geodetic_datum Date accessed: 2015-04-13
Every latitude and longitude measurement is with respect to a geodetic datum. Most common ones in use are NAD83 and WGS84.
planar angular measurement unit label
plane angle measurement unit label
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.
See also the biological process term 'cell growth ; GO:0016049'.
The increase in size or mass of an entire organism, a part of an organism or a cell.
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A data item label that denotes a unit of measure.
2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
data item label
An information content entity that is part of some data item and is used to partially define the denotation of that data item.
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
GROUP: IAO
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data item
A generically dependent continuant that is about some thing.
information content entity
scalar measurement datum
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part
measurement datum
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
obsolescence reason specification
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology.
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module.
A subset ontology module that is intended to be imported from another ontology.
TODO: add axioms that indicate this is the output of a module extraction process.
An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms.
A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation.
An ontology module that is intended for usage in analysis or discovery applications.
A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint.
A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes.
An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach.
A subset ontology that is crafted to either include or exclude a taxonomic grouping of species.
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV.
TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process
An ontology module that is automatically generated from a template specification and fillers for slots in that template.
ontology module subsetted by expressivity
A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports
ontology module subsetted by owl profile
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.
Any demarcated area of the Earth; may be determined by both natural and human boundaries, such as a state or province.
The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment.
The observable characteristics in an individual resulting from the expression of genes; the clinical presentation of an individual with a particular genotype.
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. 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.
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.
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.
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.
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 negative logarithm (base 10) of the concentration of hydronium ions, which is used as a measure of the acidity or alkalinity of a fluid.
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.
latitude coordinate measurement datum
A measurement datum that is the measure of the latitude coordinate of a site.
latitude
NIAID GSCID-BRC metadata working group
Person: Chris Stoeckert, Jie Zheng
longitude coordinate measurement datum
A measurement datum that is the measure of the longitude coordinate of a site.
longitude
Specimen Collection Location - Longitude
A value specification that consists of two parts: a numeral and a unit label
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
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 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.
multiply inhering quality of a physical entity
A quality which inheres in a continuant.
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 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.
collection of organisms
A material entity that consists of two or more organisms, viruses, or viroids.
population of organisms
A collection of organisms, all of the same species, that live in the same place.
single-species collection 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.
multi-species collection of organisms
A collection of organisms that consists of two or more organisms from at least two species.
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.
A unit which is a standard measure of the amount of a 2-dimensional flat surface.
See http://purl.obolibrary.org/obo/RO_0002577
A material entity consisting of multiple components that are causally integrated.
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.
See http://purl.bioontology.org/ontology/MESH/D018977
Essential dietary elements or organic compounds that are required in only small quantities for normal physiologic processes to occur.
From http://www.fao.org/aims/aos/cwr.owl#PopulationSize
population size
taille d'une population
tamaño de la población
размер популяции
It's the amount of individuals in a population
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.
See http://purl.bioontology.org/ontology/CSP/1035-7240
interactions between one organism and another which it harbors or nourishes.
Information about the genetic characteristics
from https://www.thefreedictionary.com/predator
An organism that lives by preying on other organisms.
Adapted from https://en.wikipedia.org/wiki/Mineral_%28nutrient%29
Chemical element required by organisms to perform functions necessary for life.
A composite measure consisting of the number of individuals introduced per introduction event and the frequency of introduction events.
See http://purl.bioontology.org/ontology/MESH/D000078622
Various components of food that are required for nourishment.
Nutrient occurring in the chemical form of salt
See http://purl.bioontology.org/ontology/MESH/D008027
That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.
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.
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).
Any change in the environment, e.g. concerning temperature, soil nutrients or biodiversity
staying essentially unchanged despite the presence of disturbances
A species that can survive and reproduce in a wide range of environmental conditions using a wide variety of resouces to do so.
See http://purl.obolibrary.org/obo/NCIT_C48835
The usual or expected function of something; the part something plays in an action or event.
phase of spreading in the alien range as part of the invasion process
See http://www.ifomis.org/bfo/1.1/span#ProcessualEntity
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.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Sequential phases during the invasion process. Typically, four different phases are distinguished: transport, introduction, establishment and spread.
chemical elements required by organisms in moderate amounts; for plants, these are e.g. sulfur, calcium and magnesium
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
Being or existing in a specified place or at the specified time.
phase of transportation to the alien range as part of the invasion process
See http://purl.bioontology.org/ontology/CSP/1035-7338
state of close, permanent, or obligatory contact between 2 species, usually of a mutually beneficial nature.
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.
Any change in the phenology of a species
disturbance that happened by some event not directly caused by human activity, e.g. storms or land slides
An area in which a species occurs even though it lies outside its native range.
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
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.
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.
From http://www.fao.org/aims/aos/cwr.owl#Diversity
diversity
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.
metric for qualifying ecologically relevant characteristics, e.g. biodiversity or body length
An area where a species is found in the wild.
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.
Any change in an individual organism, e.g. concerning its size or life cycle stage
Any change in the morpholoy of a species
A well-defined, measurable property of organisms, usually measured at the individual level and used comparatively across species.
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.
Variety of animal species present in a location
Species whose presence in a region is attributable to human actions that enable them to overcome biogeographical barriers.
See http://purl.obolibrary.org/obo/OBI_0100026
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.
A species that can survive and reproduce only within a narrow range of environmental conditions using specific resources (e.g., a specific diet).
A range in which a species has evolved or in which it has arrived by natural means.
from http://purl.obolibrary.org/obo/NCIT_C25447
The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
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.
chemical element required by plants to perform functions necessary for life
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.
chemical element required by animals to perform functions necessary for life
The process of transportation, establishment and spread of organisms outside of their native range.
Amount of nutrients contained in something, e.g in a defined volume of soil or water
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.
after https://www.thefreedictionary.com/allocation
To set apart or re-distribute for a special purpose
Completing one or all phases of the invasion process.
phase of establishment in the alien range as part of the invasion process
from http://www.projecthalo.com/aura#Ectoparasite
A parasite that lives on and feeds from the external surface of the host's body.
chemical elements required by organisms in large amounts; for plants, these are nitrogen, phosphorus, and potassium
Any change in the behaviour of a species
Not existing in a specified place at a specified time.
population survival
The process of remaining alive or in existence.
The rate in which new borns are added to a population, or in other words, the number of new borns over time.
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).
Variety of plant species present in a location
An ecosystem that has not been subject to disturbance.
Blackwell’s concise encyclopedia of ecology, 1999
From http://www.fao.org/aims/aos/cwr.owl#PopulationDensity
densidad de población
densité de population
population density
густота популяции
The number of individuals per unit area.
Attribute resulting from a combination of several traits
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.
Any change in the physioloy of a species
See http://purl.bioontology.org/ontology/MESH/D014131
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)
A measurable change to the properties of an ecosystem by a non-native species.
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.
The capacity of a genotype to produce different phenotypes in different environments.
An organism that is a predator, consumer, parasite, parasitoid or pathogen of another organism.
disturbance brought about by human activity
From http://purl.dataone.org/odo/ECSO_00000311.
This class should be incorporated into ENVO.
a group of organisms of the same species inhabiting a given area
A population comprises all the individuals of a given species in a specific area or region at a certain time.
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.
biotic acceptance
Biotic acceptance is a concept in invasion biology that suggests that ecosystems with high native species diversity are more likely to accept invasive species, as opposed to resisting them.
community resilience
Community resilience refers to the ability of a community of organisms to withstand, recover, and adapt to the impacts of invasive species, maintaining its structure, function, and dynamics.
community study
A community study refers to the examination and analysis of the interactions, dynamics, and characteristics of a community of organisms, particularly focusing on the impact and role of invasive species within that community.
detritivore
A detritivore is an organism that feeds on dead organic material, particularly plant detritus, playing a crucial role in the decomposition process and nutrient cycling within ecosystems.
dominance
Dominance refers to the ability of an invasive species to exert control over a community by outcompeting native species for resources, thereby altering community dynamics and ecosystem processes.
ecological disruption
Ecological disruption involves significant changes to ecosystem structure and function due to invasive species, leading to loss of biodiversity and altered ecosystem services.
ecosystem dynamics
Ecosystem dynamics cover the changes and processes within ecosystems driven by both native and invasive species, including nutrient flows and energy cycles.
ecosystem stability
Ecosystem stability in invasion biology refers to the ability of an ecosystem to maintain its structure and function in the face of external stressors, including the introduction and spread of invasive species.
fire frequency
Fire frequency refers to the rate at which fires occur in a given area over a specified period of time. In the context of invasion biology, it is an important factor influencing the dynamics of ecosystems, particularly in how it affects the establishment and spread of invasive species.
generalist herbivore
A generalist herbivore is an organism that feeds on a wide variety of plant species, rather than specializing in a particular type of plant. In the context of invasion biology, generalist herbivores can have significant impacts on ecosystems by consuming native and non-native plant species, potentially facilitating the spread of invasive plants.
host availability
Host availability refers to the presence and accessibility of suitable hosts for a species, particularly in the context of invasive species and their ability to establish and spread in a new environment.
dispersal mechanisms
Insight into dispersal mechanisms in invasion biology involves understanding the various ways invasive species spread across landscapes, including natural dispersal processes like wind and water, and anthropogenic factors such as global trade.
invasion biology
Invasion biology is the study of the causes and consequences of the introduction of species to new environments, where they establish, spread, and have impacts on native ecosystems and biodiversity.
invasion event
An invasion event refers to the occurrence of a species entering and establishing itself in a new ecosystem, potentially causing ecological impacts.
invasion pattern
Invasion pattern refers to the specific sequence or manner in which an invasive species spreads and establishes itself in a new environment. It encompasses the stages of introduction, establishment, and spread, and is influenced by various ecological, biological, and environmental factors.
invasion process
The invasion process refers to the sequence of events and mechanisms through which non-native species establish, spread, and impact new environments, often leading to ecological changes.
invasion rate
Invasion rate refers to the speed or frequency at which an invasive species spreads into new areas within a given time frame. It is a critical measure in invasion biology to assess the potential impact and management needs of invasive species.
invasive plant
An invasive plant is a species of plant that is not native to a specific location and has a tendency to spread, which can cause damage to the environment, human economy, or human health.
invasive species populations
Invasive species populations in invasion biology refer to the groups of non-native organisms that establish, proliferate, and expand across new territories, often impacting local ecosystems.
invasive weed
An invasive weed is a type of plant that is not native to a specific location and has a tendency to spread, which can cause damage to the environment, human economy, or human health.
local ecosystems
Local ecosystems in invasion biology refer to specific ecological communities within a defined geographical area, each with unique interactions and susceptibilities to the impacts of invasive species.
manual removal
Manual removal refers to the physical extraction of invasive species by human effort, often used as a management strategy in invasion biology to control or eradicate non-native species from an ecosystem.
mutualistic interaction
A mutualistic interaction is a type of symbiosis where two or more species interact in a way that is beneficial to all involved parties. In the context of invasion biology, mutualistic interactions can influence the success and impact of invasive species by providing them with advantages such as increased resources, protection, or dispersal opportunities.
native biodiversity
Native biodiversity in invasion biology refers to the variety and variability of native species within an ecological community, crucial for ecosystem resilience and stability.
native ecosystems
Native ecosystems in invasion biology are those ecosystems that have developed naturally without human intervention and are characterized by well-established native species populations and ecological processes.
native species decline
Native species decline in invasion biology examines the decrease in native species populations due to factors such as habitat loss, competition from invasive species, and environmental changes.
native vegetation
Native vegetation refers to plant species that are indigenous to a region, playing a critical role in maintaining ecological balance and resisting invasive species.
nutrient cycling
Nutrient cycling examines how invasive species can alter the rates of nutrient intake, recycling, and distribution within an ecosystem.
original community
Original community refers to the assemblage of native species and their interactions within a specific ecosystem prior to the introduction of alien species.
pathways of species introduction
Pathways of species introduction are the routes through which non-native species are introduced into new environments, including natural dispersal and human-related activities.
population dynamics
Population dynamics in invasion biology refers to the study of how invasive species populations change over time and space, affected by births, deaths, and migration rates.
species coexistence
Species coexistence in invasion biology examines how different species live together in the same habitat, focusing on the mechanisms that enable competing species to coexist and how these mechanisms are disrupted by invasive species.
species distribution
Species distribution in invasion biology studies the geographical spread of species, particularly how invasive species expand beyond their native ranges, influencing biodiversity and ecosystem structure.
species interactions
Species interactions in invasion biology involve the various ways species influence each other within an ecosystem, including competition, predation, parasitism, and mutualism, which can be significantly altered by invasive species.
species number
Species number refers to the count of distinct species present in a given area or ecosystem, often used as a measure of biodiversity and an indicator of ecological health, particularly in the context of invasion biology where it can reflect the impact of invasive species on native biodiversity.
species survival
Species survival in invasion biology refers to the capability of native or invasive species to maintain populations under environmental pressures and competitive interactions.
ecosystem diversity
The diversity of ecosystems refers to the range of different ecosystems found within a specific geographic area, each with unique structures, species compositions, and ecological functions, which can be impacted variably by invasive species.