Human ancestry ontology for the NHGRI GWAS Catalog
Human Ancestry Ontology
2024-02-07
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred term
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
definition
term editor
alternative_term
definition_source
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
has ontology root term
term replaced by
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
is a defining property chain axiom
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
database_cross_reference
has_exact_synonym
is defined by
is defined by
This is an experimental annotation
label
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
https://wiki.geneontology.org/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.
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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
has part
has_part
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.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
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.
precedes
hasEthnicPopulation
true
hasAncestryStatus
hasCountryOfOrigin
hasDemonym
isDemonymOf
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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.
bearer_of
is bearer of
has characteristic
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
participates_in
participates in
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
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.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
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.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
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
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
location_of
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
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
located_in
https://wiki.geneontology.org/Located_in
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.
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.
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
2017-05-24T09:30:46Z
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
2017-05-24T09:31:01Z
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
2017-05-24T09:49:21Z
has component process
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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
true
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
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.
has function realized in
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.
has function in
capable of part of
true
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
has input
https://wiki.geneontology.org/Has_input
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
https://wiki.geneontology.org/Acts_upstream_of_or_within
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
characteristic of part of
true
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
https://wiki.geneontology.org/Enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
involved in
https://wiki.geneontology.org/Involved_in
inverse of enables
enabled by
https://wiki.geneontology.org/Enabled_by
inverse of regulates
regulated by (processual)
regulated by
inverse of negatively regulates
negatively regulated by
inverse of positively regulates
positively regulated by
inverse of has input
input of
A lump of clay and a statue
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
inverse of upstream of
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
indirectly positively regulates
https://wiki.geneontology.org/Indirectly_positively_regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
indirectly negatively regulates
https://wiki.geneontology.org/Indirectly_negatively_regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or reguates
involved in or involved in regulation of
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.
Considering relabeling as 'pairwise interacts with'
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly activates
molecularly increases activity of
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
is kinase activity
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
causally influenced by (entity-centric)
causally influenced by
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
causally influences (entity-centric)
causally influences
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
directly regulates
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
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
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.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
https://wiki.geneontology.org/Directly_positively_regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
https://wiki.geneontology.org/Directly_negatively_regulates
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
enables subfunction
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
2018-01-26T23:53:14Z
acts upstream of, positive effect
https://wiki.geneontology.org/Acts_upstream_of,_positive_effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
2018-01-26T23:53:22Z
acts upstream of, negative effect
https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
regulates activity of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
2022-09-26T06:08:01Z
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
GAZ:00006882
Afghanistan
GAZ:00000457
Africa
GAZ:00002953
Albania
GAZ:00000563
Algeria
GAZ:00003957
American Samoa
GAZ:00002948
Andorra
GAZ:00001095
Angola
GAZ:00009159
Anguilla
GAZ:00006883
Antigua and Barbuda
GAZ:00002928
Argentina
GAZ:00004094
Armenia
GAZ:00004025
Aruba
GAZ:00000465
Asia
GAZ:00000463
Australia
GAZ:00002942
Austria
GAZ:00004941
Azerbaijan
GAZ:00005281
Bahrain
GAZ:00003750
Bangladesh
GAZ:00001251
Barbados
GAZ:00006886
Belarus
GAZ:00002938
Belgium
GAZ:00002934
Belize
GAZ:00000904
Benin
GAZ:00001264
Bermuda
GAZ:00003920
Bhutan
GAZ:00002511
Bolivia
GAZ:00006887
Bosnia and Herzegovina
GAZ:00001097
Botswana
GAZ:00002828
Brazil
GAZ:00003961
British Virgin Islands
GAZ:00003901
Brunei Darussalam
Brunei
GAZ:00002950
Bulgaria
GAZ:00000905
Burkina Faso
GAZ:00001090
Burundi
GAZ:00006888
Cambodia
GAZ:00001093
Cameroon
GAZ:00002560
Canada
GAZ:00001227
Cape Verde
Caribbean
GAZ:00003986
Cayman Islands
Middle Africa
GAZ:00000588
Central Africa
GAZ:00001089
Central African Republic
GAZ:00002891
Central America
GAZ:00000586
Chad
GAZ:00001539
Channel Islands
GAZ:00002825
Chile
GAZ:00002845
China
GAZ:00005915
Christmas Island
GAZ:00002929
Colombia
GAZ:00005820
Comoros
GAZ:00053798
Cook Islands
GAZ:00002901
Costa Rica
GAZ:00002719
Croatia
GAZ:00003762
Cuba
GAZ:00012582
Curacao
GAZ:00453362
Cyprus
GAZ:00002954
Czech Republic
GAZ:00001086
Democratic Republic of the Congo
GAZ:00002635
Denmark
GAZ:00000582
Djibouti
GAZ:00006890
Dominica
GAZ:00003952
Dominican Republic
GAZ:00006913
Timor-Leste
East Timor
GAZ:00000556
Eastern Africa
GAZ:00002471
Eastern Asia
Eastern Europe
GAZ:00002912
Ecuador
GAZ:00003934
Egypt
GAZ:00002935
El Salvador
GAZ:00001091
Equatorial Guinea
GAZ:00000581
Eritrea
GAZ:00002959
Estonia
GAZ:00001099
Eswatini
GAZ:00000567
Ethiopia
GAZ:00000464
Europe
Faroe Islands
GAZ:00059206
Faeroe Islands
GAZ:00001412
Falkland Islands (Malvinas)
Falkland Islands
GAZ:00006897
Micronesia (Federated States of)
GAZ:00006891
Fiji
GAZ:00002937
Finland
GAZ:00002940
France
GAZ:00002516
French Guiana
GAZ:00002918
French Polynesia
GAZ:00001092
Gabon
GAZ:00002646
Germany
GAZ:00000908
Ghana
GAZ:00003987
Gibraltar
GAZ:00002945
Greece
GAZ:00001507
Greenland
GAZ:02000573
Grenada
GAZ:00067135
Guadeloupe
GAZ:00006933
Guam
GAZ:00002936
Guatemala
GAZ:00000909
Guinea
GAZ:00000910
Guinea-Bissau
GAZ:00002522
Guyana
GAZ:00003953
Haiti
GAZ:00003103
Holy See
GAZ:00002894
Honduras
GAZ:00003203
China, Hong Kong SAR
Hong Kong
GAZ:00002952
Hungary
GAZ:00000843
Iceland
GAZ:00002839
India
GAZ:00003727
Indonesia
GAZ:00004474
Iran (Islamic Republic of)
Iran
GAZ:00004483
Iraq
GAZ:00052477
Isle of Man
GAZ:00002476
Israel
GAZ:00002650
Italy
GAZ:00000906
Ivory Coast
Côte d'Ivoire
GAZ:00003781
Jamaica
GAZ:00002747
Japan
GAZ:00002473
Jordan
GAZ:00004999
Kazakhstan
GAZ:00001101
Kenya
GAZ:00006894
Kiribati
GAZ:00011337
Kosovo
GAZ:00005285
Kuwait
GAZ:00006893
Kyrgyzstan
GAZ:00006889
Lao People's Democratic Republic
Laos
GAZ:00000459
Latin America and the Caribbean
GAZ:00002958
Latvia
GAZ:00002478
Lebanon
GAZ:00001098
Lesotho
GAZ:00000911
Liberia
GAZ:00000566
Libyan Arab Jamahiriya
Libya
GAZ:00003858
Liechtenstein
GAZ:00002960
Lithuania
GAZ:00002947
Luxembourg
GAZ:00003202
China, Macao SAR
Macau
GAZ:00001108
Madagascar
GAZ:00001105
Malawi
GAZ:00003902
Malaysia
GAZ:00006896
Maldives
GAZ:00000584
Mali
GAZ:00004017
Malta
GAZ:00007161
Marshall Islands
GAZ:00003947
Martinique
GAZ:00000583
Mauretania
Mauritania
GAZ:00003745
Mauritius
GAZ:00003943
Mayotte
GAZ:00005860
Melanesia
GAZ:00002852
Mexico
GAZ:00005862
Micronesia
http://dbpedia.org/resource/Central_Africa
true
GAZ:00003897
Republic of Moldova
Moldova
GAZ:00003857
Monaco
GAZ:00008744
Mongolia
GAZ:00006898
Montenegro
GAZ:00003988
Montserrat
GAZ:00000565
Morocco
GAZ:00001100
Mozambique
GAZ:00006899
Burma
Myanmar
GAZ:00001096
Namibia
GAZ:00006900
Nauru
GAZ:00004399
Nepal
GAZ:00001549
Netherlands
GAZ:00004019
Netherlands Antilles
GAZ:00005206
New Caledonia
GAZ:00000469
New Zealand
GAZ:00002978
Nicaragua
GAZ:00000585
Niger
GAZ:00000912
Nigeria
Niue Fekai
GAZ:00006902
Niue
GAZ:00005913
Norfolk Island
GAZ:00002801
Democratic People's Republic of Korea
North Korea
GAZ:00000555
Northern Africa
GAZ:00000458
Northern America
Northern Europe
GAZ:00003958
Northern Mariana Islands
Kingdom of Norway
GAZ:00002699
Norway
GAZ:00000468
Oceania
GAZ:00005283
Oman
GAZ:00005246
Pakistan
GAZ:00006905
Palau
GAZ:00002475
Occupied Palestinian Territory
Palestinian Territories
GAZ:00002892
Panama
GAZ:00003922
Papua New Guinea
GAZ:00002933
Paraguay
GAZ:00002932
Peru
The Philippines
GAZ:00004525
Philippines
Pitcairn
GAZ:00005867
Pitcairn, Henderson, Ducie and Oeno Islands
Pitcairn Islands
GAZ:00002939
Poland
GAZ:00005861
Polynesia
Portugese Republic
GAZ:00002944
Portugal
Commonwealth of Puerto Rico
GAZ:00006935
Puerto Rico
GAZ:00005286
Qatar
GAZ:00002943
Ireland
Republic of Ireland
GAZ:00006895
The former Yugoslav Republic of Macedonia
Republic of Macedonia
GAZ:00001088
Congo
Republic of the Congo
GAZ:00002951
Romania
GAZ:00002721
Russian Federation
Russia
GAZ:00001087
Rwanda
GAZ:00053746
Réunion
GAZ:00000849
St. Helena
Saint Helena
GAZ:00006906
Saint Kitts and Nevis
GAZ:00006909
Saint Lucia
GAZ:00005841
Saint Martin
GAZ:00003942
Saint-Pierre-et-Miquelon
Saint Pierre and Miquelon
GAZ:02000565
Saint Vincent and the Grenadines
GAZ:00006910
Samoa
GAZ:00003102
San Marino
GAZ:00005279
Saudi Arabia
Scandinavia
GAZ:00002639
Scotland
GAZ:00000913
Senegal
GAZ:00002957
Serbia
GAZ:00005821
Seychelles
GAZ:00000914
Sierra Leone
GAZ:00003923
Singapore
GAZ:00012579
Sint Maarten
GAZ:00002956
Slovakia
GAZ:00002955
Slovenia
GAZ:00005275
Solomon Islands
GAZ:00001104
Somalia
GAZ:00000559
South-Eastern Asia
South-Central Asia
GAZ:00000459
South America
GAZ:00000553
South Africa
GAZ:00002472
South Asia
GAZ:00002802
Republic of Korea
South Korea
GAZ:00233439
South Sudan
GAZ:00000553
Southern Africa
Southern Europe
GAZ:00000591
Spain
GAZ:00003924
Sri Lanka
GAZ:00000560
Sudan
GAZ:00002525
Suriname
http://dbpedia.org/resource/Eswatini
obsolete Swaziland
true
GAZ:00002729
Sweden
GAZ:00002941
Switzerland
GAZ:00002474
Syria
GAZ:00006927
São Tomé and Príncipe
GAZ:00005341
Taiwan
GAZ:00006912
Tajikistan
GAZ:00001103
United Republic of Tanzania
Tanzania
GAZ:00003744
Thailand
GAZ:00002733
Bahamas
The Bahamas
GAZ:00000907
Gambia
The Gambia
GAZ:00000915
Togo
GAZ:00006914
Tokelau
GAZ:00006916
Tonga
GAZ:00003767
Trinidad and Tobago
GAZ:00000562
Tunisia
GAZ:00000558
Turkey
GAZ:00005018
Turkmenistan
GAZ:00003955
Turks and Caicos Islands
GAZ:00009715
Tuvalu
GAZ:00001102
Uganda
GAZ:00002724
Ukraine
GAZ:00005282
United Arab Emirates
GAZ:00002637
U.K.
United Kingdom
U.S.
GAZ:00002459
United States of America
United States
GAZ:00003959
U.S. Virgin Islands
United States Virgin Islands
GAZ:00002930
Uruguay
GAZ:00004979
Uzbekistan
GAZ:00006918
Vanuatu
GAZ:00002931
Venezuela
GAZ:00003756
Vietnam
GAZ:00007191
Wallis and Futuna Islands
Wallis and Futuna
GAZ:00000554
Western Africa
Western Asia
Western Europe
GAZ:00000564
Western Sahara
GAZ:00005284
Yemen
GAZ:00001107
Zambia
GAZ:00001106
Zimbabwe
GAZ:00009721
Cocos (Keeling) Islands
GAZ:00004942
Georgia
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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
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]
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
ic
IndependentContinuant
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
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]
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
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]
spatial region
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
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.
specifically dependent continuant
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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
function
material
MaterialEntity
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
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]
immaterial entity
geographical location
One of the large, unbroken masses of land into which the Earth's surface is divided.
major area
continent
true
Any geographic area greater than an individual country but smaller than a continent, used as a convenience reference. Please note that most geographic areas may not be formally defined and exact boundaries can be debatable.
geographical area
region
A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
NCIT:C25464
http://purl.obolibrary.org/obo/NCIT_C25464
obsolete country
true
Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data
ancestral group
ancestry category
Includes individuals who either self-report or have been described by authors as
European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations.
Caucasian
white
European
Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap
BEB, GIH, ITU, PJL and STU populations.
South Asian
Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations.
South East Asian
Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian.
Asian unspecified
Asian
Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations.
East Asian
Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African.
African unspecified
African
Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban).
This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations.
Sub-Saharan African
Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
American Indian
Native American
Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations
from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations
Jackie MacArthur
Joannella Morales
Hispanic or Latin American
Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
Middle Eastern/North African
Greater Middle Eastern (Middle Eastern or North African or Persian)
Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations.
African American or Afro-Caribbean
Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap.
Oceanian
A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories
uncategorised population
Japanese
non-aboriginal Taiwanese
Taiwanese
Chinese
Korean
Mongolian
Macanese
Singaporean Chinese
Hong Kong Chinese
Han Chinese
obsolete Africa
true
obsolete Asia
true
obsolete Europe
true
obsolete Oceania
true
obsolete Latin America and the Caribbean
true
obsolete Northern America
true
obsolete Eastern Africa
true
obsolete Middle Africa
true
obsolete Northern Africa
true
obsolete Southern Africa
true
obsolete Western Africa
true
obsolete South Central Asia
true
obsolete South-Eastern Asia
true
obsolete Western Asia
true
obsolete Eastern Europe
true
obsolete Northern Europe
true
obsolete Southern Europe
true
obsolete Western Europe
true
obsolete Caribbean
true
obsolete South America
true
obsolete Central America
true
Australia/New Zealand
obsolete Melanesia
true
obsolete Micronesia
true
obsolete Polynesia
true
obsolete Eastern Asia
true
Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap.
Central Asian
obsolete Scandinavia
true
obsolete South Asia
true
A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation
founder population
population isolate
genetically isolated population
General characterisation of the ancestry of a population or individual
ancestry status
ancestry status
Ancestry that is the result of cultural or geographic isolation. Generally characterised by increased genetic homogeneity and reduced genetic variation
genetically isolated ancestry
Ancestry which is an admixture of more than one defined ancestral population. The degree and type of admixture may vary within a population and the accuracy of classification requires well-defined reference samples
admixed ancestry
Italian
Sardinian
Val Borbera
Friuli Venezia Giulia
Carlantino
Old Order Amish
Sorbian
Hutterite
Amish
Erasmus Rucphen
Orcadian
Korculan
Dutch
Finnish
Finnish founder
Dutch founder
Ashkenazi Jew
obsolete_Caribbean
true
Sudanese
Sahrawi
Anguillan
Antiguan or Barbudan
Barbadian
Haitian
Jamaican
Tajikistani
Turkmen
Uzbekistani
Afghan
Kazakhstani
Kyrgyzstani
Albanian
Andorran
Australian
Austrian
Belarusian
Belgian
Bermudian
Bosnian or Herzegovinian
Brazilian
Bulgarian
Canadian
Channel Islander
Chilean
Croatian
Czech
Danish
Estonian
Faroese
Falkland Islander
French
German
Gibraltarian
Greek
Greenlander
Hungarian
Icelandic
Manx
Latvian
Liechtensteiner
Lithuanian
Luxembourgish
Maltese
Monegasque
Montenegrin
New Zealandish
Norfolk Islander
Norwegian
Polish
Portugese
Irish
Moldovan
Romanian
Russian
Saint-Pierrais or Miquelonnais
Sammarinese
Serb
Slovak
Slovene
Spanish
Swedish
Swiss
Macedonian
Ukrainian
Argentine
Bahamian
Belizean
Bolivian
British Virgin Islander
Caymanian
Colombian
Costa Rican
Cuban
Dominican
Ecuadorian
Salvadoran
French Guianese
Grenadian
Guatemalan
Guyanese
Honduran
Martinican
Mexican
Montserratian
Nicaraguan
Panamanian
Paraguayan
Peruvian
Puerto Rican
Kittitian or Nevisian
Saint Lucian
Saint Vincentian
Surinamer
Surinamese
Trinidadian or Tobagonian
Turks and Caicos Islander
Virgin Islander
Uruguayan
Venezuelan
Algerian
Armenian
Azerbaijani
Bahraini
Cypriote
Egyptian
Georgian
Iranian
Iraqi
Israeli
Jordanian
Kuwaiti
Lebanese
Libyan
Moroccan
Palestinian
Omani
Qatari
Saudi Arab
Saudi
Tunisian
Turkish
Emirati
Yemeni
Aruban
Christmas Islander
Cocos Islander
Curacaoan
Kosovar
Northern Mariana Islander
South Sudanese
Syrian
British
American
American Samoan
Cook Islander
Fijian
French Polynesian
Guamanian
I-Kiribati
Marshallese
Micronesian
Nauruan
New Caledonian
Niuean
Palauan
Papua New Guinean
Pitcairn Islander
Samoan
Solomon Islander
Tokelauan
Tongan
Tuvaluan
Ni-Vanuato
Wallis and Futuna Islander
Bangladeshi
Bhutanese
Asian Indian
Indian Asian
Indian
Maldivian
Nepalese
Pakistani
Sri Lankan
Bruneian
Cambodian
Indonesian
Lao
Malaysian
Burmese
Filipino
Thai
Timorese
Vietnamese
Cameroonian
Cape Verdean
Chadian
Ethiopian
Kenyan
Liberian
Malagasy
Mauritanian
Mauritian
Mahoran
Namibian
Sao Tomean
Senegalese
Seychellois
Sierra Leonean
Somali
South African
St. Helenian
Ugandan
Angolan
Beninese
Motswana
Burkinabe
Burundian
Central African
Comoran
Congolese
Ivoirian
Djiboutian
Equatorial Guinean
Eritrean
Gabonese
Gambian
Ghanaian
Guinean
Bissau-Guinean
Mosotho
Malawian
Malian
Mozambican
Nigerien
Nigerian
Rwandan
Swazi
Togolese
Tanzanian
Zambian
Zimbabweian
Irish founder
genetically homogenous Irish
Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation.
Aboriginal Australian
Includes native populations of Alaska, Siberia, and the Aleutian Archipelago. This
category does not include all native populations within the Arctic circle for example the Finnish Saami who are descended from Europeans and are therefore included within the European ancestry category.
obsolete_Circumpolar people
true
Silk Road founder
Israeli Arab
Arab Israeli founder
Cilento
Costa Rican founder
French Canadian founder
Italian founder
Northern Finnish founder
Romanian founder
South Tyrolean
Vis founder
Split founder
Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American
undefined ancestry population
African Caribbean
Afro-Caribbean
African American
Talana
Pima Indian
Plains American Indian
Kosraen
Native Hawaiian
Pacific Islander
Yoruban
West African
Dai Chinese
Hui Chinese
Jingpo Chinese
Malaysian Chinese
Uigur Chinese
Uygur Chinese
Tibetan
Han Taiwanese
Taiwanese Han
Sri Lankan Sinhalese
Tatar
Bashkir
Includes individuals who either self-report or have been described by authors as Aboriginal Australian of Martu ancestry. The Martu Australian Aboriginal people are from the Western Desert region located across the Pilbara in Western Australia
Mardu Aboriginal Australian
Mardu Australian Aboriginal
Martu Aboriginal Australian
PMID:27070114
Martu Australian Aboriginal
Jewish Israeli
Punjabi Sikh
American of European ancestry
European American
The Esan people are one of the major ethnic groups in Edo State, Nigeria who speak the Esan language. (PMID:10146569) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Esan-in-Nigeria-ESN)
Esan
The Luhya are the second-largest ethnic group in Kenya and are comprised of subgroups that speak a common Bantu language. (PMID: 27813082) The Luhya ancestry group was assembled as part of phase III of the HapMap project and used in a number of rare variant density studies (PMID:22373165, PMID:26673965)
Luhya
The Maasai are an indigenous African ethnic group of semi-nomadic people located in northern Tanzania and Kenya. (PMID:29868928) The Maasai ancestry group was assembled as part of phase III of the HapMap project and used as reference in a range of population genetic studies (PMID:28049708).
Maasai
The Mende people are one of the largest ethnic groups in Sierra Leone who speak a language of the Mande branch of the Niger-Congo family. (PMID:15761855) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Mende-in-Sierra-Leone-MSL)
Mende
Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia
PMID:25884279
PMID:29220501
Class previously labelled as "Eskimo", which is outdated and culturally inappropriate. Outdated label may be added as an appropriately flagged synonym at a later stage.
Inuit
Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa
PMID:27393651
PMID:28106113
Arab
Includes individuals who either self-report or have been described by authors as Singaporean Malay.
PMID:19700652
PMID:31626772
Singaporean Malay
Includes individuals who either self-report or have been described by authors as Singaporean Indian.
PMID:19700652
PMID:31626772
Singaporean Indian
A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states.
Country
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms:
http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
population
population
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
GROUP: OBI
organization
obsolete_Punjabi Sikh
true
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).