INO: Interaction Network Ontology
Junguk Hur
An ontology for the annotation of the interaction network domain.
OWL-DL
Product version
The Interaction Network Ontology (INO) is an ontology in the domain of interaction network. INO aims to standardize interaction network annotation, integrate various interaction network data, and support computer-assisted reasoning. It is aimed to represent general interactions (e.g., molecular interactions) and interaction networks (e.g., Bayesian network). INO was initiated by supporting literature mining related to interactions and interaction networks. INO aligns with BFO. INO is a community-based ontology. Its development follows the OBO Foundry principles.
Vision Release; 1.0.107
Yongqun "Oliver" He (YH)
Zuoshuang "Allen" Xiang
BFO OWL specification label
Really of interest to developers only
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
BFO CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred term
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
example of usage
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
example
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
curator note
An administrative note of use for a curator but of no use for a user
imported from
expand expression to
OBO foundry unique label
elucidation
Person:Barry Smith
Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms
person:Alan Ruttenberg
has associated axiom(nl)
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
Person:Alan Ruttenberg
has literature mining keywords
an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition.
example of literature mining keyword usage
an example of usage for literature mining
has keyword dependency pattern
an annotation property that specifies the dependency pattern of the literature keywords that match to the ontology interaction type.
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
logical macro assertion
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion on a property
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on an object property
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
Contributor
An entity responsible for making contributions to the content of the resource.
Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
Coverage
Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Creator
An entity primarily responsible for making the content of the resource.
Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
Date
A date associated with an event in the life cycle of the resource.
Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
Format
The physical or digital manifestation of the resource.
Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
Resource Identifier
An unambiguous reference to the resource within a given context.
Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
Relation
Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
A reference to a related resource.
Rights Management
Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
Information about rights held in and over the resource.
Source
A reference to a resource from which the present resource is derived.
The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
Subject and Keywords
The topic of the content of the resource.
Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
Title
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
part of
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'.
a core relation that holds between a part and its whole
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)
part_of
this day is part of this year (occurrent parthood)
has part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
a core relation that holds between a whole and its part
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)
realized in
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
is realized by
realized_in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
realizes
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
obsolete preceded by
accidentally included in BFO 1.2 proposal - should have been BFO_0000062
preceded by
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
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.
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.
has activator
an object property between an activation process and a material entity that acts as an activator during the process.
has_controller
controls
has_next_step
lacks part
has interaction type
An object property that represents a relation between an interaction process (domain) and another interaction process (range) where the interaction proces (domain) has a specific type of the other interaction process (range)
A host-pathogen interaction that has a specific interaction type (e.g., activation).
inheres in
A dependent inheres in its bearer at all times for which the dependent exists.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
inheres_in
this fragility inheres in this vase
this red color inheres in this apple
bearer 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.
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
bearer_of
is bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
participates in
a relation between a continuant and a process, in which the continuant is somehow involved in the process
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
has participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has_participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
has role
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.
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has_role
this person has role this investigator role (more colloquially: this person has this role of investigator)
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
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.
before or simultaneous with
Primitive instance level timing relation between events
simultaneous with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
before
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
during which ends
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
ends after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
immediately preceded by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
during which starts
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
starts before
immediately precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
starts during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
happens during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
ends during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
overlaps
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
x overlaps y if and only if there exists some z such that x has part z and z part of y
has component
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.
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.
regulates
Regulation precludes parthood; the regulatory process may not be within the regulated process.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
negatively regulates
Chris Mungall
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
negatively regulates (process to process)
positively regulates
positively regulates (process to process)
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
temporally related to
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
starts
starts with
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends
ends with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
has input
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.
has output
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
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
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
inheres in part of
q inheres in 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 inheres in part of
mereotopologically related to
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
functionally related to
This is a grouping relation that collects relations used for the purpose of connecting structure and function
regulated by
negatively regulated by
positively regulated by
input of
output of
has direct input
'protein catabolic process' SubClassOf has_direct_input some protein
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
translation SubClassOf has_direct_output some protein
causally downstream of
immediately causally downstream of
directly activates
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
indirectly activates
directly inhibits
indirectly inhibits
causally related to
This relation groups causal relations between material entities and causal relations between processes
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
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.
causally upstream of
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
immediately causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
directly provides input for
directly provides input for (process to process)
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
transitively provides input for
transitive form of directly_provides_input_for
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
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 of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Process(P1) directly regulates process(P2) 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.
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Process(P1) directly postively regulates process(P2) 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 P1 directly positively regulates P2.
directly positively regulates (process to process)
directly negatively regulates (process to process)
Process(P1) directly negatively regulates process(P2) 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 P1 directly negatively regulates P2.
entity
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
continuant
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
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.
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
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])
occurrent
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
independent continuant
(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]
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
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])
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
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])
the bottom right portion of a human torso
the interior of your mouth
temporal region
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
process
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
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])
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
disposition
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
an atom of element X has the disposition to decay to an atom of element Y
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
realizable entity
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
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.
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
quality
(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]
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])
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])
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
specifically dependent continuant
(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.
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
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.
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])
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 shape of this hole.
the smell of this portion of mozzarella
role
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.
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
site
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
object
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
atom
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
generically dependent continuant
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
function
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
one-dimensional temporal region
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
the temporal region during which a process occurs.
material entity
(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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
(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]
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])
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
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: 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.
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
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
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
the undetached arm of a human being
immaterial entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
zero-dimensional temporal region
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
a temporal region that is occupied by a process boundary
right now
temporal instant.
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.
The aggregation, arrangement and bonding together of a set of components to form a protein complex.
The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
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.
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
The covalent attachment of a myristoyl group to a protein.
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
data item
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
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
information content entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
A generically dependent continuant that is about some thing.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
pathogen role
A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles.
pathogen
A material entity with a pathogenic disposition.
host role
A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
Interaction network is a process that includes a network of at least two interactions.
If the interaction is physical and molecular, the interaction network is molecular interactions usually found in cells.
interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts
Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
an interaction network that includes at least two interactions and has a start point(s) and an end point(s).
an interaction network model that is represented by a probabilistic graphical model (a type of statistical model) that represents a set of random variables and their conditional dependencies via a directed acyclic graph (DAG).
WEB: http://en.wikipedia.org/wiki/Bayesian_network
regulator role
an regulator role that is borne by a material entity that regulates an interaction.
up-regulation
a positive regulation that one interactor up-regulates another.
up-regulate, up-regulations, up-regulated, up-regulating, upregulate, upregulations, upregulated, upregulating
interaction regulator
an interactor that regulates an interaction.
an interactor role that is borne by a material entity that acts as an input of an interaction.
an interactor role that is borne by a material entity that acts as an output of an interaction.
activator role
a positive regulator role that is borne by a material entity that activates an interaction.
WEB: http://en.wikipedia.org/wiki/Mutual_information
an interaction network model that is represented by at least two mutual information interactions.
a node is an object that represents an interactor in a graph of an interaction or interaction network.
an edge is an object that represents a graphic line that links two interactors in an interaction.
a role that is borne by a material entity to act as a participant in an interaction process.
interactor
an interactor is a material entity that participates in an interaction.
activator
a positive interaction regulator that activates an interaction.
organism-organism interaction
YL.YH. ZX.
a biological interaction that occurs in the organism level.
Examples: a bacterium interacts with a mouse, a cat interacts with a dog
A two-way interaction is an interaction that includes two different directions among two interactors.
human molecular pathway
up-regulation of secretion
an up-regulation that one interactor up-regulates the secretion of another interactor.
human molecular interaction
an interaction involving human molecules
YH: This branch may be made obsolete since we now have human INO (HINO).
a positive regulation that one interactor activates another.
activate, activated, activates, activating, activation, activator, activators, activity
gene-cell interaction
an interaction that includes a gene and a cell as interactors.
protein activation
protein activation, protein activated, activates protein, activating protein, activated protein
an activation process where one protein is activated by a material entity
YH: in literature mining, the protein can be any specific protein symbol or protein name.
cell-cell interaction
a biological interaction that involves two cells as interactors.
protein activation by mutant
an activation process where one protein is activated by a gene mutant
YH: in literature mining, the protein can be any specific protein symbol or protein name. In addition, the mutant can be a mutant of any gene and the name of the mutant can be any specific name given by the research who generated the mutant.
protein activation by mutant, protein activated by mutant, mutant activates protein, activating protein by mutant, mutant activated protein
antagonise, antagonised, antagonises, antagonising, antagonist, antagonists, antagonize, antagonized, antagonizes, antagonizing
a biochemical binding where a substance binds to the same site an agonist would bind to without causing activation of the receptor
WEB: http://en.wikipedia.org/wiki/Receptor_antagonist
gene-enviroment interaction
an interaction that involves a gene and its environment (e.g., calcium in blood).
regulation of protein location
"Localization of SpoIIE was shown to be dependent on the essential cell division protein FtsZ" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10747015)
location // (protein) // dependent, location // (protein) // depends
a regulation process that regulates the location of a protein
regulation of transcription
a gene expression regulation process that involves the regulation of a gene transcription.
transcribed, transcribed by, regulates the transcription of, regulated the transcription of, regulates // transcription, regulated // transcription, under the control of // transcription, essential for // transcription, trascription depends, transcription // dependent, control // transcription, controlling // transcription, requires // transcription
amod(transcription, controlling), amod(transcription, dependent), amod(expression, dependent), nsubj(dependent, transcription), nsubj(control, expression), nmod:for(regulator, transcription), nmod:of(activator, transcription), nsubjpass(recognized, promoter)
attenuate, attenuated, attenuates, attenuating
a negative regulation that attenuates the virulence of a pathogenic microbe.
regulation of translation
translation depends, translation // dependent, regulates // translation, regulated // translation, regulates the translation of, regulated the translation of, regulation // production, regulated // production, regulate // production
a gene expression regulation process that involves the regulation of a protein translation process.
"Transcription of ydhD was dependent on SigE" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148)
a phosphorylation process that adds a phosphate to a protein kinase (possibly affecting its activity) by virtue of its own enzymic activity.
autophosphorylate, autophosphorylated, autophosphorylates, autophosphorylating, autophosphorylation
regulation of gene activation
"sequestration of SpoIIE protein into the prespore plays an important role in the control of sigmaF activation and in coupling this activation to septation." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10476035)
WEB: http://www.medilexicon.com/medicaldictionary.php?t=970
a regulation process that regulates the activation of a gene so that the gene is expressed at a particular time
essential for // activation, essential for // activation, activated // expression, activates // expression, control // activation, controlling // activation, requires // activation, requiredd // activation
positive regulation of gene expression
a regulation process that positively regulates gene expression level
positive regulation // expression, increase // expression, induced // dependent, induced // via, induced // by, induced // dependent // presence
"YtxH and YvyD seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10913081)
negative regulation of gene expression
"These results suggest that YfhP may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and yfhP." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10463184)
essential for // negative regulation, negatively regulated // expression, negatively regulates // expression, negative regulator // transcription
a regulation process that negatively regulates gene expression level
human biochemical reaction
a human molecular reaction that is specifically a biochemical reaction
physical entity
negative regulation of gene transcription
a negative regulation process that down-regulates gene expression level
negatively regulated // transcription, negatively regulates // transcription, negatively controls // transcription, negatively controled // transcription
negative regulation of protein translation
a negative regulation process that down-regulates protein translation level
negatively regulated // translation, negatively regulates // translation, limits // production, limited // production
gene expression regulation
a regulation process that regulates gene expression level
"SigK and GerE were essential for ykvP expression" (Reference: http://www.ncbi.nlm.nih.gov/pubmed/11011148)
regulated // expression, regulates // expression, essential // expression, control // expression, controlled // expression, controlling // expression, controls // expression, expression under control, essential for // expression, responsible for production, essential for production, regulates the production of, regulated the production of, responsible // production, responsible // production, affect // production, affected // production, depend // expression, dependent // expression, level // (gene) // dependent, requires // expression, required // expression, regulated by // pathway // relying on, regulon // includes, member of // regulon
protein translation
translation, translated, translating, encoding, encodes, protein production
a gene expression process that results in protein production from a gene DNA sequence.
WEB: http://en.wikipedia.org/wiki/Translation_%28biology%29
inhibition of gene transcription
inhibited // transcription, inhibits // transcription, repressed // transcription, repress // transcription, prevented // transcription, prevents // transcription, prevent // transcription
a negative regulation of gene transcription process that specifiies the negative regulation being an inhibition.
"GerE protein inhibits transcription in vitro of the sigK gene." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
chemical reaction catalyst
an interactor that starts or speeds up a chemical reaction while undergoing no permanent change itself.
a coprecipitation that occurs through an immunoprecipitation process.
coimmunoprecipitate, coimmunoprecipitated, coimmunoprecipitates, coimmunoprecipitating, coimmunoprecipitation, coimmunopreticipate, coimmunopreticipated, coimmunopreticipates, coimmunopreticipating, co-immunoprecipitate, co-immunoprecipitated, co-immunoprecipitates, co-immunoprecipitating, co-immunoprecipitation, co-immunopreticipate, co-immunopreticipated, co-immunopreticipates, co-immunopreticipating
positive regulation of gene transcription
positively regulated // transcription, negatively regulates // transcription, stimulating // transcription, stimulates // transcription, stimulated // transcription, induction // transcription, induced // transcription, induces // transcription, inducing // transcription, driven // transcription, drives // transcription
a regulation of transcription process that inviolves a positive regulation.
an indirect association that one interactor competes with another interactor in a specfiic process.
activation of gene transcription
a positive regulation of gene transcription process that inviolves an activation of the gene transcription.
activated // transcription, activates // transcription
"Transcription of the cotB, cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called GerE." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508)
activation of gene transcription by low level protein
"A low level of GerE activated transcription of cotD by sigmaK." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
an activation of gene transcription that is achieved by a low level of a protein
low level // activated // transcription, low level // activates // transcription, low concentration // activated // transcription
positive regulation of protein translation
a regulation of translation process that positively regulates protein translation level
"ComK ... thereby increasing the production of the FlgM." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775)
positively regulated // translation, positively regulates // translation, increases // production, increased // production, increasing // production, increasing // production
WEB: http://en.wikipedia.org/wiki/Antigen-antibody_interaction
a direct interaction where an antigen interacts with an antibody physically.
regulation of protein activity
If you can detect your protein on a western blot, and it is migrating to the apparent molecular weight that you expect, you can say for definite that the protein is being expressed. This means that the primary structure (i.e. the amino acid chain) has been synthesised. Activity depends on, for example, correct folding of the enzyme, the presence of any required cofactors, proper targetting (e.g. if its a membrane protein) and that there are mutations crucial catalytic residues. Western blotting tells you nothing about these things. (Reference: http://www.protocol-online.org/biology-forums/posts/30248.html)
regulated // activity, regulates // activity, essential // activity, controlled // activity, controls // activity, activity under control, essential for // activity
a regulation process that regulates an activity of a protein
downexpression
a gene expression that has decreased volume.
a regulation that one interactor controls the quality of another interactor to a specific range
control, controled, controling, controlled, controlling, controls
conversion, convert, converted, converting, converts, derived, derives, derivation
a direct physical association that one interactor is converted from another interactor.
an indirect association that one interactor cooperates with another interactor in a specfiic process.
cooperate, cooperated, cooperates, cooperating
coprecipitate, coprecipitated, coprecipitates, coprecipitating, coprecipitation, copreticipate, copreticipated, copreticipates, copreticipating, co-precipitate, co-precipitated, co-precipitates, co-precipitating, co-precipitation, co-preticipate, co-preticipated, co-preticipates, co-preticipating
a colocalization that two interactors are precipitated together.
an indirect association that two interactors are correlated in a process without defined influence of each other.
costimulate, costimulated, costimulating
Example: A and B costimulate C. The relations between A and C or between B and C are regulation. However, the relation between A and B is an association.
cell-environment interaction
an interaction that involves a cell and its environment as interactors
an immuno-precipitation that one interactor is precipitated based on an cross- immunological precipitation process.
cross-immunoprecipitate, cross-immunoprecipitated, cross-immunoprecipitates, cross-immunoprecipitating, cross-immunoprecipitation, crossimmunoprecipitate, crossimmunoprecipitated, crossimmunoprecipitates, crossimmunoprecipitating, crossimmunoprecipitation
organism-environment interaction
an interaction that involves an organism and its environment as interactors
an antigen-antibody interaction where an antibody interats with an antigen that differs from the immunogen used to generate antibody.
negative regulation of protein activity
a regulation of protein activitiy process that involves a negative regulation
negatively regulated // activity, negatively regulates // activity
a regulation in which one interactor has a negative effect on another interactor
down-regulate, down-regulations, down-regulated, down-regulating, downregulate, downregulations, downregulated, downregulating
YH: different types of negative regulations exist. These types are related to different qualities and phenotyes of regulated targets.
chemical reaction catalyst role
an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself.
inhibition of protein activity
inhibited // activity, inhibites // activity, inhibition // activity
"... FlgM antisigma factor that inhibits sigmaD activity." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9696775)
a negative regulation of protein activitiy process that involves an inhibition of a protein activity
regulation of transcription by binding to promoter
binds // promoter, bound to // promoter, binding // promoter, recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter
a regulation of transcription process that occurs through the binding to a promotor of a gene
Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the genes that they regulate. Depending on the transcription factor, the transcription of the adjacent gene is either up- or down-regulated. (Ref: https://en.wikipedia.org/wiki/Transcription_factor).
"We show that GerE binds to two sites that span the -35 region of the cotD promoter." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
positive regulation of transcription by binding to promoter
a regulation of transcription by binding to promoter that is further classified as a positive regulation
induce // expression // promoter, induced // transcription // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter, activated // transcription // promoter, activated // promoter, dependent // promoter // drives // expression, dependent // promoter // responsible // transcription, expressed // controlled // promoter
decrease, decreased, decreases, decreasing, decreasing, reduce, reduced, reduces, reducing, diminish, diminished, diminishes, diminishing, declining, declines, declination, limit, limited, limiting, limits
a negative regulation that results in the decrease of one interactor volume.
negative regulation of transcription by binding to promoter
negatively regulate // promoter, negatively regulated // promoter, repressed // promoter, represses // promoter, repress // promoter, binds // transcriptional start site // repressor, bound // transcriptional start site // repressor
gene activation
activation // (gene), activated // (gene), activates // // (gene), activated // action
a positive regulation of gene expression process that activates a gene so that the gene is expressed at a particular time
an enzymatic reaction that leads to the breakdown of a biochemical entity.
degradation, degradations, degrade, degraded, degrades, degrading
co-regulation of transcription
transcription // combined action, transcription // results from // combined action
a regulation of transcription process where two or more regulators regulate a gene transcription
"In vitro transcription experiments suggest that the differential pattern of cot gene expression results from the combined action of GerE and another transcription factor, SpoIIID." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10788508)
activation of gene transcription by high level protein
"A low concentration of GerE activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10075739)
an activation of gene transcription that is achieved by a high level of a protein
high level // activated // transcription, high level // activate // transcription, high concentration // activated // transcription
promoter-based regulation of transcription
recognize // promoter, recognized // promoter, expressed // promoter, dependent // promoter. depdenent // promoter of (or proceding, procedes), repress // promoter, activate // promoter, regulate // promoter, regulated // promoter, stimulate // promoter, stimulate // transcription // promoter, induced // promoter
"The -10 and -35 sequences of the sigmaB- and sigmaF-dependent promoters of katX overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10503549)
a regulation of transcription process through binding to a promoter or regulating the promoter binding activity
activation of gene transcription by phosphorylated protein
phosphorylated // activator // transcription, phosphorylated // activates // transcription, phosphorylated // activate // transcription, phosphorylated // activated // transcription
"Spo0A, which when phosphorylated is an activator of sigE transcription." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/10383978)
an activation of gene transcription that is achieved by a phosphorylated protein
human molecular catalysis
a negative regulation that results in a destabilization.
destabilization, destabilize, destabilized, destabilizes, destabilizing
gene expression inhibition
a negative regulation process that inhibits gene expression level
inhibits // expression, inhibited // expression, suppressor // expression, suppress // expression, repress // expression, acts // repressor
"CtsR protein acts as a global repressor of the clpC operon." (Reference: http://www.ncbi.nlm.nih.gov/pubmed/9852015)
determine, determined, determines, determining, cause, caused, causes, causing, lead, leading, leads, led, govern, governed, governing, governs
a regulation that one interactor has a dominant effect on the quality of another interactor. This differs from the accessory regulation.
a protein complex assembly that involves two proteins that form a dimer.
dimerize, dimerized, dimerizes, dimerizing
co-regulation
co-regulation, co-regulated, co-regulate, co-regulating
a regulation process that involves in two interactors co-regulate a third interactor.
molecular complex
a negative regulation that results in a disruption.
disrupt, disrupted, disrupting, disrupts
dissociate, dissociated, dissociating, dissociation
down-regulate, down-regulated, down-regulates, down-regulating, down-regulation, downregulate, downregulated, downregulates, downregulating, downregulation, downmodulation, depress, depressed, depresses, depressing, suppress, suppressed, suppresses, suppressing, suppression, suppressor, repress, repressed, represses, repressing, repression, repressor, repressors
a negative regulation that one interactor down-regulates another.
gene expression up-regulation
essential for // up-regulation, up-regulated // expression, up-regulates // expression
a positive regulation of gene expression process that up-regulates gene expression level
gene expression down-regulation
down-regulated // expression, down-regulates // expression
induction of production
an induction that leads to the production of an entity
induction of the production, induces the production, induced the production
YH: For example, "IL-2 and IL-15 induced the production of IL-17 and IFN-γ in a dose dependent manner by PBMCs.”
a negative regulation that one interactor eliminates another.
eliminate, eliminated, eliminates, eliminating, abolish, abolished, abolishes, abolishing, abrogation
bacterial conjugation
a cell-cell interaction that the transfers genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells.
WEB: http://en.wikipedia.org/wiki/Bacterial_conjugation
hydrogen binding
WEB: http://www.ncbi.nlm.nih.gov/books/NBK22567/
Interaction leading to the formation of hydrogen bond between two molecules
regulation of assembly
a regulation process where one gene product regulates an assembly process which forms an assembly having another gene product.
human molecular control interaction
a human molecular interaction where one molecule controls another molecule.
express, expressed, expresses, expressing, expression, expressions
a biological interaction that uses the information from a gene to synthesize a functional gene product.
facilitate, facilitates, facilitating, faciliteted, help, helps, helped
a positive regulation that one interactor facilitates a phenomenon such as a phenotype. This is an accessory effect not a major one.
positive regulation of protein activity
a regulation of protein activitiy process that involves a positive regulation
positively regulated // activity, positively regulates // activity, dependent // stimulation
host-pathogen interaction
An interaction that involves a host (host organism or host cell) and pathogen organism at a specific condition.
a genetic interaction that forms a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion.
WEB: http://en.wikipedia.org/wiki/Gene_fusion
host cell-pathogen interaction
An host-pathogen interaction where the host is a cell.
induction by binding to protein
The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1
induction ... by binding to // induces .. through binding// induced ... by binding to // caused ... by binding to // causes ... through ... binding
an induction that is achieved by binding to a protein
macrophage-pathogen interaction
An host cell-pathogen interaction where the host cell is a macrophage.
human molecular degradation
heterodimerize, heterodimerized, heterodimerizes, heterodimerizing
a protein dimerization where two proteins are different.
homodimerize, homodimerized, homodimerizes, homodimerizing
a protein dimerization where two proteins are the same.
macrophage-pathogen protein-protein interaction
The Salmonella invasin SipB induces macrophage apoptosis by binding to caspase-1. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26795/
A macrophage-pathogen interaction that involves a macrophage protein and a pathogen protein.
a gene expression that has increased volume.
hyper-expression, hyperactivate, hyperactivated, hyperactivates, hyperactivation, hyperexpression, overexpression
hyperphosphorylate, hyperphosphorylated, hyperphosphorylates, hyperphosphorylation
immuno-precipitate, immuno-precipitated, immuno-precipitates, immuno-precipitating, immuno-precipitation, immunoprecipitate, immunoprecipitated, immunoprecipitates, immunoprecipitating, immunoprecipitation, immunopreticipate, immunopreticipated, immunopreticipates, immunopreticipating
a translocation that one interactor is precipitated based on an immunological precipitation process.
YH: different types of positive regulations exist. These types are related to different qualities and phenotyes of regulated targets.
positively regulate, positive regulations, positively regulated, positively regulating, promote, promoted, promotes, promoting
impair, impaired, impairing, impairs, cripple, crippled, cripples, crippling, sever, severed, severs
A negative regulation that disables, damages, or impairs the functioning of another entity.
inactivate, inactivated, inactivates, inactivating, inactivation
a negative regulation that one interactor inactivates another.
increase, increased, increases, increasing, augment, augmented, augmenting, augments, elavating, elevate, elevated, elevates, elevating, raise, raised, raises, raising, enhance, enhanced, enhances, enhancing, enhancement
a positive regulation that leads to the increase of a quality of an entity.
human molecular synthesis
induce, induced, induces, inducing, induction, trigger, triggered, triggering, triggerring, triggers, initiate, initiated, initiates, initiating, stimulate, stimulation, stimulated, stimulating, dependent // inducible
a positive regulation that leads to the induction of a new interactor due to the presence of another interactor.
human molecular regulatory reaction
a negative regulation that one interactor inhibites another.
inhibit, inhibited, inhibiting, inhibition, inhibitor, inhibitors, inhibits, block, blocked, blocking, blocks
an interactor that is an input of an interaction.
interfere, interferes, interfered, interfering, perturb, perturbed, perturbing, perturbs, obstruction
a negative regulation that one interactor interferes a process.
human molecular modulation
human template reaction regulation
host gene mutant-pathogen interaction
An host-pathogen interaction where the host is a gene mutant
human molecular conversion
a human molecular interaction where one molecule converts to another molecule.
human molecular template reaction
small molecule
host
positive regulator role
an interactor role that is borne by a material entity that positively regulates an interaction.
pathway step
negative regulator role
an interactor role that is borne by a material entity that negatively regulates an interaction.
macrophage-pathogen PPI inducing cell death
A macrophage-pathogen protein-protein interaction that induces cell death.
neutralise, neutralised, neutralises, neutralising, neutralize, neutralized, neutralizes, neutralizing
a biochemical reaction that one interactor neutrolizes another.
positive regulator
an interaction regulator that positively regulates an interaction.
oxidate, oxidated, oxidates, oxidating, oxidation, oxidise, oxidised, oxidises, oxidising, oxidize, oxidized, oxidizes, oxidizing
an enzymatic reaction where a molecule gains oxygen.
host-pathogen mutant interaction
An host-pathogen interaction where the pathogen is a gene mutant
negative regulator
an interaction regulator that negatively regulates an interaction.
deactivator role
a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme).
An host cell-pathogen interaction where the host is a macrophage cell
motivator role
an input interactor role that is borne by a material entity that motivates a process.
an indirect association that one interactor is preceded by another interactor.
prevent, prevented, preventing, prevents
hygiene factor role
an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation.
an interactor that is an output of an interaction.
An host cell-pathogen interaction where the host is an epithelial cell
reactivate, reactivated, reactivates, reactivating, reactivation
recruit, recruite, recruited, recruites, recruiting, recruits
a positive regulation that leads the recruitment of one interactor from one location to another.
epithelial cell-pathogen protein-protein interaction
We show that caspase-2 functions as an initiator caspase during Staphylococcus aureus α-toxin- and Aeromonas aerolysin-mediated apoptosis in epithelial cells. From: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365430/
regulate, regulated, regulates, regulating, regulation, regulator, modulate, modulated, modulates, modulating, modulation, mediate, mediated, mediates, mediating, influence, influenced, influences, influencing, affect, affected, affecting, affects, impact, impacted, impacting, impacts, effect, effected, effecting, effects, require, required, requires, requiring, respond, responded, responding, responds, responsive, change, changed, changes, changing, alter, altered, altering, alters, modified, modifies, modify, modifying, depend, depended, depending, depends, direct, directed, directing, directs, drive, driven, drives, driving, cause, caused, causes, causing, lead, leading, leads, led, target, targeted, targeting, targets, dependent, essential for
A regulation represents a regulatory interaction between two interactors.
interaction network model
An information content entity that models interaction network
stabilization, stabilize, stabilized, stabilizes, stabilizing
a postive interaction that one interactor increases the stability of another interactor.
a regulation process that involves in two interactors that are synergized in affecting a phenomenon (e.g., phenotype).
synergise, synergised, synergises, synergising, synergize, synergized, synergizes, synergizing
terminate, terminated, terminates, terminating
a negative regulation that leads to a process termination.
WEB: http://en.wikipedia.org/wiki/Transactivation
trans-activate, trans-activated, trans-activates, trans-activating, trans-activation, trans-activator, trans-activators, transactivate, transactivated, transactivates, transactivating, transactivation, transactivator, transactivators
a gene expression regulation that leads to an increased rate of gene expression triggered either by biological processes or by artificial means.
WEB: http://en.wikipedia.org/wiki/Transcription_%28genetics%29
transcribe, transcribed, transcribes, transcribing, transcription
an interaction process that creates a complementary RNA copy of a sequence of DNA.
a cell-cell interaction that transfers viral, bacterial, or both bacterial and viral DNA from one cell to another using a bacteriophage vector.
transduce, transduced, transducer, transducers, transduces, transducing, transduction
translocation, transloated, translocating, translocates, migrated, migration, migrates migrating, mobilization, mobilize, mobilized, mobilizes, mobilizing, mobilisation, mobilise, mobilised, mobilises, mobilising
A process that changes the location of a material entity.
a correlation association that two genes are co-expressed in a system.
a negative regulation that results in the deregulation of one interactor on a process.
A one-way interaction is an interaction that shows one direction between interactors.
a translocation that one interactor exports from one location
a translocation that one interactor imports from one location
a translocation that one interactor secretes from the inside of another interactor
an interaction that involves in a gene DNA and a protein
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues.
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
S-farnesyl-L-cysteined is cleaved and returns a C residue.
N6-formyl-L-lysine is cleaved and returns a K residue.
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
N6-myristoyl-L-lysine is cleaved and returns a K residue.
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
Reversible reaction that can affect C residue.
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
Covalent or non covalent binding of lipid group on a protein residue.
Cleavage of a lipid group covalently bound to a protein residue.
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
Interaction between molecules that are in direct contact with each other.
Covalent bond mediated by 2 sulfur atoms.
terms aiming to represent biochemical reactions referring to their resulting product modifications.
Gln-Lys cross-link catalyzed by a transglutaminase.
Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
synthetic genetic interaction (sensu inequality)
synthetic genetic interaction defined by inequality
asynthetic genetic interaction (sensu inequality)
suppressive genetic interaction (sensu inequality)
epistatic genetic interaction (sensu inequality)
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
noninteractive genetic interaction (sensu inequality)
noninteractive genetic interaction defined by inequality
oxidoreductase activity electron transfer reaction
An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
The removal of an amine group from a molecule.
The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
A modification that converts an L-histidine residue to diphthamide.
Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
Intra-molecular interaction between two or more regions of the same molecule.
The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
Aminoacylation is the process of adding an aminoacyl group to a compound.
Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
The catalysis of the structural rearrangement of isomers.
The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
Measure of hydrolytic reactions that release ADP-ribose.
Reaction where a sulfate group is transferred between two proteins
gene
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
protein
The definition was compiled based on a number of available defintions in various dictionaries.
The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics.
The definition was compiled based on a number of definitions available in various dictionaries.
The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways.
The definition was complied based on a number of definitions available in several dictionaries
The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning.
Complex human diseases encompass a spectrum of genetic and environmental attributes that together affect the normal functioning of several molecular and cellular pathways. Their combined and accumulated effect is manifested in the anomalous phenotype of the complex condition.
The pharmacokinetics and the pharmacodynamics pathway elicited by the administration of specific drugs. The systems involved in drug processing and responses are also those handling exogenous, xenobiotic compounds in the cellular detoxification pathway. The distinction between a random encounter with a foreign compound and the processing of a substance administered for treatment along with the importance of genetic variation for the individual responses to particular drugs warrant their separate consideration.
DNA
RNA
ready for release
pending final vetting
requires discussion
axiom holds for all times
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
OBO Relations Ontology
The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.