RBO is an ontology for the effects of radiation on biota in terrestrial and space environments.
Radiation Biology Ontology
2023-09-05
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO:0000112
uberon
example_of_usage
true
example_of_usage
example of usage
example of usage
definition
definition
textual definition
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.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
alternative term
definition source
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
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
abbreviation
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.
http://purl.org/dc/elements/1.1/creator
uberon
dc-creator
true
dc-creator
An entity primarily responsible for making the content
of the resource.
Creator
Creator
creator
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.
A date associated with an event in the life cycle of the
resource.
Date
Date
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.
uberon
dc-description
true
dc-description
An account of the content of the resource.
Description
Description
description
Typically, a Title will be a name by which the resource is
formally known.
uberon
dc-title
true
dc-title
A name given to the resource.
Title
Title
title
Mark Miller
2018-05-11T13:47:29Z
uberon
dcterms-license
true
dcterms-license
license
created_by
has_alternative_id
has_broad_synonym
database_cross_reference
An alternative label for a given entity such as a commonly used abbreviation or synonym.
has_exact_synonym
has_obo_namespace
has_related_synonym
in_subset
label
label
is part of
is part of
my brain is part of my body (continuant parthood, two material entities)
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)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
this day is part of this year (occurrent parthood)
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
a core relation that holds between a part and its whole
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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'.
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part_of
http://www.ebi.ac.uk/efo/part_of
BFO:0000050
OBO_REL:part_of
part of
external
human_stages_ontology
plant_ontology
protein
quality
relationship
spatial
uberon
part_of
part_of
EFO_0000822
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
has part
my body has part my brain (continuant parthood, two material entities)
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)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
this year has part this day (occurrent parthood)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
a core relation that holds between a whole and its part
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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 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'.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
has_part
http://www.ebi.ac.uk/efo/has_part
BFO:0000051
chebi_ontology
external
protein
quality
spatial
uberon
has_part
false
has_part
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
has part
has part
has_part
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
PATOC:CJM
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
is realized by
realized_in
[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])
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
realized in
realizes
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])
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
realizes
BFO:0000057
has participant
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
external
uberon
preceded_by
preceded_by
preceded by
preceded by
preceded_by
is preceded by
SIO:000249
takes place after
Allen:precedes
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.
BFO:0000063
external
uberon
precedes
precedes
precedes
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
BFO:0000067
uberon
contains_process
contains_process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
contains process
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
cjm
2009-07-31T02:15:46Z
BSPO:0000096
rostral_to
spatial
uberon
anterior_to
anterior_to
anterior to
anterior_to
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000098
spatial
uberon
dorsal_to
dorsal_to
dorsal to
dorsal_to
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
BSPO:0000099
caudal to
caudal_to
spatial
uberon
posterior_to
posterior_to
posterior to
posterior_to
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
caudal to
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000102
spatial
uberon
ventral_to
ventral_to
ventral to
ventral_to
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
spatial
uberon
deep_to
deep_to
deep to
deep_to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:cjm
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
spatial
uberon
superficial_to
superficial_to
superficial to
superficial_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:cjm
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:0000120
spatial
uberon
in_left_side_of
in_left_side_of
in left side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:PATO_mtg_2009
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:0000121
spatial
uberon
in_right_side_of
in_right_side_of
in right side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:PATO_mtg_2009
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
spatial
uberon
in_posterior_side_of
in_posterior_side_of
in posterior side of
in_posterior_side_of
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
BSPO:PATO_mtg_2009
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:PATO_mtg_2009
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
spatial
uberon
in_anterior_side_of
in_anterior_side_of
in anterior side of
in_anterior_side_of
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
BSPO:PATO_mtg_2009
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:PATO_mtg_2009
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:0000124
spatial
uberon
in_proximal_side_of
in_proximal_side_of
in proximal side of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:0000125
spatial
uberon
in_distal_side_of
in_distal_side_of
in distal side of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:PATO_mtg_2009
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
BSPO:0000126
spatial
uberon
in_lateral_side_of
in_lateral_side_of
in lateral side of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
UBERON:cjm
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
BSPO:0001106
spatial
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost part of
proximalmost_part_of
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
https://orcid.org/0000-0002-6601-2165
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:0001107
spatial
uberon
immediately_deep_to
immediately_deep_to
immediately deep to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:curators
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
BSPO:0001108
spatial
uberon
distalmost_part_of
distalmost_part_of
distalmost part of
distalmost_part_of
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
https://orcid.org/0000-0002-6601-2165
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
X intersects median plane of iff X crosses the midine plane of Y.
BSPO:0005001
spatial
uberon
intersects_midsagittal_plane_of
intersects_midsagittal_plane_of
intersects midsagittal plane of
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:0015014
spatial
uberon
immediately_superficial_to
immediately_superficial_to
immediately superficial to
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:curators
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:0015101
spatial
uberon
in_dorsal_side_of
in_dorsal_side_of
in dorsal side of
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:cjm
concretizes
intended to realize
realizes
A duck swimming in a pond is partially surrounded by air and partially surrounded by water.
x partially_surrounded_by y if and only if (1) x is adjacent to y and for the region r that is adjacent to x, r partially overlaps y (2) the shared boundary between x and y occupies a non-trivial proportion of the outermost boundary of x
Definition modified from 'surrounded by'.
partially_surrounded_by
Afforestation results in the expansion of a forest.
A process, p, results in the expansion of a material entity, m, if the spatial extent of m is increased as a result of participating in p.
results in expansion of
A relation between a process and a disposition such that the existence of the disposition is caused by the execution of the process.
Consider ceding to RO
cjm
2018-11-03T20:58:13Z
generates
hasAncestryStatus
has measurement unit label
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
Person:Alan Ruttenberg
is quality measured as
is_supported_by_data
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
OBI
OBI
Philly 2011 workshop
is_supported_by_data
has_specified_input
has_specified_input
see is_input_of example_of_usage
The inverse property of is_specified_input_of
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
http://www.ebi.ac.uk/efo/has_input
OBI:0000293
has specified input
has_input
has_specified_input
has_specified_input
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
http://www.ebi.ac.uk/efo/is_input_of
is specified input of
is_input_of
is_specified_input_of
has_specified_output
has_specified_output
The inverse property of is_specified_output_of
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
OBI:0000299
has specified output
has_output
has_specified_output
has_specified_output
is_specified_output_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
PERSON:Bjoern Peters
is specified output of
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
objective_achieved_by
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
OBI
OBI
objective_achieved_by
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
http://www.ebi.ac.uk/efo/EFO_0000829
RO:0000052
fly_anatomy.ontology
characteristic_of
inheres_in
characteristic_of
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
characteristic_of
inheres in
inheres in
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
external
uberon
bearer_of
bearer_of
bearer of
bearer of
has characteristic
has characteristic
https://github.com/oborel/obo-relations/pull/284
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
Participates in is a primitive instance-level relation between a continuant and a process in which it participates. For example a scanner participates in a scanning process at some specific time.
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
external
uberon
participates_in
participates_in
participates in
participates in
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the A 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 is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
external
has_participant
has_participant
has participant
has participant
has_participant
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
http://www.ebi.ac.uk/efo/has_quality
RO:0000086
protein
uberon
has_quality
false
has_quality
has quality
has quality
has_quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
chebi_ontology
has_role
false
false
has_role
has role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
RO:0001015
uberon
location_of
location_of
location of
contained in
RO:0001019
uberon
contains
contains
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
uberon
located_in
located_in
located in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
2D boundary of
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
RO:0002005
uberon
innervated_by
innervated_by
innervated_by
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
David Osumi-Sutherland
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
dos
2017-05-24T09:30:46Z
RO:0002013
external
has_regulatory_component_activity
has_regulatory_component_activity
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
dos
2017-05-24T09:31:01Z
RO:0002014
external
has_negative_regulatory_component_activity
has_negative_regulatory_component_activity
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
dos
2017-05-24T09:31:17Z
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
dos
2017-05-24T09:49:21Z
has component process
dos
2017-09-17T13:52:24Z
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
GOC:dos
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
GOC:dos
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
dos
2017-09-17T13:52:47Z
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
GOC:dos
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.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
GOC:dos
before or simultaneous with
RO:0002082
uberon
simultaneous_with
simultaneous_with
simultaneous with
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
external
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately preceded by
immediately_preceded_by
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
external
immediately_precedes
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
immediately_precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
external
spatial
uberon
overlaps
overlaps
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
overlaps
true
x overlaps y iff they have some part in common.
BSPO:cjm
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
T innervates some R
Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
RO:0002134
uberon
innervates
innervates
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
RO:0002150
uberon
continuous_with
continuous_with
continuous with
lactation SubClassOf 'only in taxon' some 'Mammalia'
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
never_outside_taxon
specific_to
specific_to_taxon
protein
uberon
only_in_taxon
false
only_in_taxon
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
only in taxon
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
ROC:Waclaw
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
RO:0002176
uberon
connects
connects
connects
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
true
true
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
RO:0002178
uberon
supplies
supplies
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
external
protein
uberon
has_component
qualifier
false
has_component
qualifier
For use in recording has_part with a cardinality constraint.
placeholder relation to indicate normality/abnormality.
has component
has component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
Chris Mungall
David Osumi-Sutherland
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
RO:0002207
uberon
directly_develops_from
directly_develops_from
directly develops from
inverse of directly develops from
directly develops into
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.
process(P1) regulates process(P2) iff:Â 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.
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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
regulates (processual)
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.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
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.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO_0000053 some (RO_0000054 only ?Y)
RO:0002215
external
protein
uberon
capable_of
false
capable_of
capable of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))
RO:0002216
external
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
spatial
uberon
adjacent_to
adjacent_to
adjacent to
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
inverse of surrounded_by
RO:0002221
uberon
surrounds
surrounds
surrounds
inverse of surrounded_by
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
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.
Chris Mungall
started by
RO:0002224
external
uberon
starts_with
starts_with
starts with
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
RO:0002225
uberon
develops_from_part_of
develops_from_part_of
develops from part of
x develops_in y if x is located in y whilst x is developing
RO:0002226
uberon
develops_in
develops_in
develops in
Relation between occurrents, shares an end boundary with.
inverse of ends with
Chris Mungall
RO:0002229
finishes
uberon
ends
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
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.
Chris Mungall
finished by
RO:0002230
external
uberon
ends_with
ends_with
ends with
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
p has 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.
Chris Mungall
consumes
RO:0002233
external
has_input
has_input
has input
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
Chris Mungall
produces
RO:0002234
external
has_output
has_output
has output
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
GO:0001759
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
Chris Mungall
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
results in formation of
Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'
where
'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview
x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.
Pier Buttigieg
adapted for living in
A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y.
has habitat
has habitat
cjm
RO:0002304
external
causally_upstream_of,_positive_effect
causally_upstream_of,_positive_effect
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
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
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
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 characteristic of part of
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
characteristic of part of
inheres in part of
inheres in part of
true
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
ecologically related to
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
RO:0002334
external
regulated_by
regulated_by
regulated by
regulated by
inverse of negatively regulates
Chris Mungall
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
negatively regulated by
inverse of positively regulates
Chris Mungall
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
is member of
member part of
SIO
RO:0002350
uberon
member_of
member_of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
external
protein
uberon
output_of
false
output_of
output of
output of
Chris Mungall
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
RO:0002371
uberon
attaches_to
attaches_to
attached to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
RO:0002372
uberon
has_muscle_origin
has_muscle_origin
has muscle origin
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
RO:0002373
uberon
has_muscle_insertion
has_muscle_insertion
has muscle insertion
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
in branching relationship with
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary of
drains into
dbpowl:drainsTo
x spatially_coextensive_with y if and inly if x and y have the same location
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
RO:0002404
external
causally_downstream_of
causally_downstream_of
causally downstream of
causally downstream of
Chris Mungall
RO:0002405
external
immediately_causally_downstream_of
immediately_causally_downstream_of
immediately causally downstream of
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
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.
Chris Mungall
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
immediately causally upstream of
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
Chris Mungall
influences (processual)
RO:0002418
external
affects
causally_upstream_of_or_within
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
RO:0002427
external
causally_downstream_of_or_within
causally_downstream_of_or_within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
Chris Mungall
RO:0002473
uberon
RO:0002473
composed_primarily_of
composed_primarily_of
composed primarily of
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
Chris Mungall
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence overlaps
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
RO:0002491
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
existence starts and ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Chris Mungall
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
existence_ends_during
existence_ends_during
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
https://orcid.org/0000-0002-6601-2165
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
Chris Mungall
RO:0002493
uberon
existence_ends_with
existence_ends_with
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
immediately transforms from
SIO:000658
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
Chris Mungall
determined by (system to material entity)
Chris Mungall
Pier Buttigieg
determined by
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
Chris Mungall
determined by part of
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
biomechanically related to
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
RO:0002568
uberon
has_muscle_antagonist
has_muscle_antagonist
has muscle antagonist
inverse of branching part of
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
RO:0002571
uberon
lumen_of
lumen_of
lumen of
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
inverse of has skeleton
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
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.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
results in breakdown of
RO:0002588
external
results_in_assembly_of
results_in_assembly_of
results in assembly of
results_in_assembly_of
RO:0002590
external
results_in_disassembly_of
results_in_disassembly_of
results in disassembly of
results_in_disassembly_of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
RO:0002592
external
results_in_organization_of
results_in_organization_of
results in organization of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
RO:0002608
external
process_has_causal_agent
process_has_causal_agent
process has causal agent
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 positively regulates
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.
directly negatively regulates (process to process)
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
RO:0003000
uberon
produces
produces
produces
a produced_by b iff some process that occurs_in b has_output a.
RO:0003001
uberon
produced_by
produced_by
produced by
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
cjm
2018-12-13T11:26:17Z
RO:0004007
external
has_primary_input_or_output
has_primary_input_or_output
has primary input or output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
cjm
2018-12-13T11:26:32Z
RO:0004008
external
has_primary_output
has_primary_output
has primary output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
cjm
2017-12-26T19:45:49Z
realized in response to stimulus
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
Austin Meier
Chris Mungall
David Osumi-Sutherland
Marie Angelique Laporte
triggered by process
realized in response to
https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit
triggered by process
RO:cjm
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
different in magnitude relative to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased in magnitude relative to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
https://orcid.org/0000-0002-6601-2165
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
https://orcid.org/0000-0001-9625-1899
https://orcid.org/0000-0003-2620-0345
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff:Â P results in the existence of C OR affects the intensity or magnitude of C.
RO:0019000
gene_ontology
regulates_characteristic
regulates_characteristic
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff:Â P results in an increase in the intensity or magnitude of C.
RO:0019001
gene_ontology
positively_regulates_characteristic
positively_regulates_characteristic
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff:Â P results in a decrease in the intensity or magnitude of C.
RO:0019002
gene_ontology
negatively_regulates_characteristic
negatively_regulates_characteristic
negatively regulates characteristic
p has anatomical participant c iff p has participant c, and c is an anatomical entity
cjm
2018-09-26T01:08:58Z
results in changes to anatomical or cellular structure
chebi_ontology
has_parent_hydride
false
false
has parent hydride
chebi_ontology
is_conjugate_acid_of
true
false
is conjugate acid of
chebi_ontology
is_conjugate_base_of
true
false
is conjugate base of
chebi_ontology
is_substituent_group_from
false
false
is substituent group from
chebi_ontology
is_tautomer_of
true
is tautomer of
protein
has_gene_template
false
has_gene_template
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
uberon
anteriorly_connected_to
anteriorly connected to
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
uberon
distally_connected_to
distally connected to
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
uberon
extends_fibers_into
extends_fibers_into
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
add to RO
uberon
indirectly_supplies
indirectly_supplies
uberon
layer_part_of
layer part of
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
posteriorly_connected_to
posteriorly connected to
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
protects
protects
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
uberon
proximally_connected_to
proximally connected to
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
c site_of p if c is the bearer of a disposition that is realized by a process that has p as part.
uberon
capable_of_has_part
site_of
site_of
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
uberon
synapsed_by
synapsed by
has atomic number
Number of protons in an atomic nucleus
We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning
has atomic number
has number of atomic nuclei
has measurement value
has specified numeric value
A relation between a value specification and a number that quantifies it.
A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
PERSON: James A. Overton
OBI
has specified numeric value
has specified value
A relation between a value specification and a literal.
This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
OBI
has specified value
The atomic mass (ma or m) is the mass of an atom. The protons and neutrons of the nucleus account for nearly all of the total mass of atoms, with the electrons and nuclear binding energy making minor contributions.
has atomic mass
mass number
A planned process that has specified output a software product and that involves the creation of source code.
Mathias Brochhausen
William R. Hogan
http://en.wikipedia.org/wiki/Software_development
A planned process resulting in a software product involving the creation of source code.
software development
creating a data set
A planned process that has a data set as its specified output.
William R. Hogan
data set creation
dataset creation
dataset creating
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
BFO:0000002
continuant
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
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.
per discussion with Barry Smith
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a chair
a heart
a heart
a leg
a leg
a molecule
a molecule
a spatial region
a spatial region
an atom
an atom
an orchestra.
an orchestra.
an organism
an organism
the bottom right portion of a human torso
the bottom right portion of a human torso
the interior of your mouth
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
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])
http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl
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 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])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
BFO:0000004
independent continuant
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
James Malone
(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]
http://www.ebi.ac.uk/efo/EFO_0001433
true
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
http://www.ifomis.org/bfo/1.1/span#ProcessualEntity
NCIt:C29862
SNOMEDCT:415178003
BFO:0000015
process
process
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])
(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]
disposition
Disposition
For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
an atom of element X has the disposition to decay to an atom of element Y
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
A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
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.
James Malone modified from original
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disease property
http://www.ebi.ac.uk/efo/EFO_0001438
true
A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
http://www.ifomis.org/bfo/1.1/snap#Disposition
NCIt:C41205
BFO:0000016
disposition
disposition
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
realizable
RealizableEntity
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
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.
https://orcid.org/0000-0001-8815-0078
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
BFO:0000017
realizable
realizable entity
realizable_entity
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
quality
Quality
quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
James Malone
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
http://www.ebi.ac.uk/efo/EFO_0001436
true
A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
http://www.ifomis.org/bfo/1.1/snap#Quality
NCIt:C25283
SNOMEDCT:263496004
bfo
BFO:0000019
quality
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
specifically dependent continuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white.
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant 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.
James Malone
Sirarat Sarntivijai
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(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]
sample characteristic
http://www.ebi.ac.uk/efo/EFO_0001443
true
A continuant [snap: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.
http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant
BFO:0000020
SpecificallyDependentContinuant
specifically dependent continuant
BFO:0000020
material property
specifically dependent continuant
specifically dependent continuant
b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
(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]
role
Role
For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
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.
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
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.
A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
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.
James Malone
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
http://www.ebi.ac.uk/efo/EFO_0001440
true
A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
http://www.ifomis.org/bfo/1.1/snap#Role
MeSH:D012380
NCIt:C48835
BFO:0000023
role
role
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
fiat object
fiat object part
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
site
bfo
BFO:0000030
object
object
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
BFO:0000031
generically dependent continuant
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
Function
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
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
material
MaterialEntity
material entity
material entity
A heart, a human, a fly, a microarray.
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
James Malone
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
sample factor
http://www.ebi.ac.uk/efo/EFO_0001434
true
An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
material type
bfo
BFO:0000040
material entity
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
immaterial
ImmaterialEntity
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
immaterial entity
history
History
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
anatomical entity
connected anatomical structure
material anatomical entity
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
Melissa Haendel
9/18/11
organism or virus or viroid
biological entity
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
-1
0.000548579903
0.0
KEGG:C05359
PMID:21614077
Wikipedia:Electron
electron
chebi_ontology
Elektron
beta
beta(-)
beta-particle
e
e(-)
e-
negatron
CHEBI:10545
electron
PMID:21614077
Europe PMC
PMID:21614077
Europe PMC
electron
ChEBI
electron
IUPAC
electron
KEGG_COMPOUND
Elektron
ChEBI
beta
IUPAC
beta(-)
ChEBI
beta-particle
IUPAC
e
IUPAC
e(-)
UniProt
e-
KEGG_COMPOUND
negatron
IUPAC
dicarboxylic acids and O-substituted derivatives
An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included.
Wikipedia:Metalloid
chebi_ontology
metalloid
metalloids
CHEBI:137980
metalloid atom
metalloid
ChEBI
metalloids
ChEBI
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
Wikipedia:https://en.wikipedia.org/wiki/Gas
chebi_ontology
gas molecular entities
gaseous molecular entities
gaseous molecular entity
CHEBI:138675
gas molecular entity
gas molecular entities
ChEBI
gaseous molecular entities
ChEBI
gaseous molecular entity
ChEBI
-1
CH2NO2
InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1
KXDHJXZQYSOELW-UHFFFAOYSA-M
60.03212
60.00910
NC([O-])=O
Beilstein:3903503
CAS:302-11-4
Gmelin:239604
carbamate
chebi_ontology
Carbamat
Karbamat
carbamate ion
carbamic acid, ion(1-)
CHEBI:13941
carbamate
Beilstein:3903503
Beilstein
CAS:302-11-4
ChemIDplus
Gmelin:239604
Gmelin
carbamate
IUPAC
carbamate
UniProt
Carbamat
ChEBI
Karbamat
ChEBI
carbamate ion
ChemIDplus
carbamic acid, ion(1-)
ChemIDplus
24G7 epitope
electron donor
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
CHEBI:13699
CHEBI:2377
KEGG:C00028
KEGG:C16722
Acceptor
chebi_ontology
A
Akzeptor
Hydrogen-acceptor
Oxidized donor
accepteur
CHEBI:15339
acceptor
Acceptor
KEGG_COMPOUND
A
KEGG_COMPOUND
Akzeptor
ChEBI
Hydrogen-acceptor
KEGG_COMPOUND
Oxidized donor
KEGG_COMPOUND
accepteur
ChEBI
water
The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).
+1
H
InChI=1S/p+1
GPRLSGONYQIRFK-UHFFFAOYSA-N
1.00794
1.008
[H+]
CHEBI:10744
CHEBI:13357
CHEBI:5584
KEGG:C00080
Hydron
hydrogen(1+)
hydron
chebi_ontology
H(+)
H+
CHEBI:15378
hydron
Hydron
KEGG_COMPOUND
hydrogen(1+)
IUPAC
hydron
IUPAC
H(+)
UniProt
H+
KEGG_COMPOUND
dioxygen
A trace radioisotope of argon with atomic mass of 38.964313 and a half-life of 269 years.
0
[39Ar]
InChI=1S/Ar/i1-1
XKRFYHLGVUSROY-BJUDXGSMSA-N
38.964
38.96431
[Ar]
CAS:25729-41-3
PMID:16429279
PMID:17781454
PMID:17791262
PMID:28017500
PMID:28755564
PMID:30487580
chebi_ontology
(39)18Ar
(39)Ar
(39)Ar radioisotope
Ar-39
Ar-39 radioisotope
argon 39
argon, isotope of mass 39
argon-39
CHEBI:155827
argon-39 atom
CAS:25729-41-3
ChemIDplus
PMID:16429279
Europe PMC
PMID:17781454
Europe PMC
PMID:17791262
Europe PMC
PMID:28017500
Europe PMC
PMID:28755564
Europe PMC
PMID:30487580
Europe PMC
(39)18Ar
ChEBI
(39)Ar
ChemIDplus
(39)Ar radioisotope
ChEBI
Ar-39
ChEBI
Ar-39 radioisotope
ChEBI
argon 39
ChEBI
argon, isotope of mass 39
ChemIDplus
argon-39
ChEBI
A peptide containing ten or more amino acid residues.
C4H6N2O3R2(C2H2NOR)n
CHEBI:14860
CHEBI:8314
KEGG:C00403
Polypeptide
polypeptides
chebi_ontology
Polypeptid
polipeptido
CHEBI:15841
polypeptide
Polypeptide
KEGG_COMPOUND
polypeptides
IUPAC
Polypeptid
ChEBI
polipeptido
ChEBI
A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
0
(C5H8O6PR)n.C10H17O10PR2
CHEBI:13672
CHEBI:14859
CHEBI:8312
KEGG:C00419
Polynucleotide
chebi_ontology
polynucleotides
CHEBI:15986
polynucleotide
Polynucleotide
KEGG_COMPOUND
polynucleotides
ChEBI
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
0
H3N
InChI=1S/H3N/h1H3
QGZKDVFQNNGYKY-UHFFFAOYSA-N
17.03056
17.02655
[H]N([H])[H]
CHEBI:13405
CHEBI:13406
CHEBI:13407
CHEBI:13771
CHEBI:22533
CHEBI:44269
CHEBI:44284
CHEBI:44404
CHEBI:7434
Beilstein:3587154
CAS:7664-41-7
Drug_Central:4625
Gmelin:79
HMDB:HMDB0000051
KEGG:C00014
KEGG:D02916
KNApSAcK:C00007267
MetaCyc:AMMONIA
MolBase:930
PDBeChem:NH3
PMID:110589
PMID:11139349
PMID:11540049
PMID:11746427
PMID:11783653
PMID:13753780
PMID:14663195
PMID:15092448
PMID:15094021
PMID:15554424
PMID:15969015
PMID:16008360
PMID:16050680
PMID:16348008
PMID:16349403
PMID:16614889
PMID:16664306
PMID:16842901
PMID:17025297
PMID:17439666
PMID:17569513
PMID:17737668
PMID:18670398
PMID:22002069
PMID:22081570
PMID:22088435
PMID:22100291
PMID:22130175
PMID:22150211
PMID:22240068
PMID:22290316
PMID:22342082
PMID:22385337
PMID:22443779
PMID:22560242
Reaxys:3587154
Wikipedia:Ammonia
AMMONIA
Ammonia
ammonia
azane
chebi_ontology
Ammoniak
NH3
R-717
[NH3]
ammoniac
amoniaco
spirit of hartshorn
CHEBI:16134
ammonia
Beilstein:3587154
Beilstein
CAS:7664-41-7
ChemIDplus
CAS:7664-41-7
KEGG COMPOUND
CAS:7664-41-7
NIST Chemistry WebBook
Drug_Central:4625
DrugCentral
Gmelin:79
Gmelin
PMID:110589
Europe PMC
PMID:11139349
Europe PMC
PMID:11540049
Europe PMC
PMID:11746427
Europe PMC
PMID:11783653
Europe PMC
PMID:13753780
Europe PMC
PMID:14663195
Europe PMC
PMID:15092448
Europe PMC
PMID:15094021
Europe PMC
PMID:15554424
Europe PMC
PMID:15969015
Europe PMC
PMID:16008360
Europe PMC
PMID:16050680
Europe PMC
PMID:16348008
Europe PMC
PMID:16349403
Europe PMC
PMID:16614889
Europe PMC
PMID:16664306
Europe PMC
PMID:16842901
Europe PMC
PMID:17025297
Europe PMC
PMID:17439666
Europe PMC
PMID:17569513
Europe PMC
PMID:17737668
Europe PMC
PMID:18670398
Europe PMC
PMID:22002069
Europe PMC
PMID:22081570
Europe PMC
PMID:22088435
Europe PMC
PMID:22100291
Europe PMC
PMID:22130175
Europe PMC
PMID:22150211
Europe PMC
PMID:22240068
Europe PMC
PMID:22290316
Europe PMC
PMID:22342082
Europe PMC
PMID:22385337
Europe PMC
PMID:22443779
Europe PMC
PMID:22560242
Europe PMC
Reaxys:3587154
Reaxys
AMMONIA
PDBeChem
Ammonia
KEGG_COMPOUND
ammonia
IUPAC
azane
IUPAC
Ammoniak
ChemIDplus
NH3
IUPAC
NH3
KEGG_COMPOUND
NH3
UniProt
R-717
ChEBI
[NH3]
MolBase
ammoniac
ChEBI
amoniaco
ChEBI
spirit of hartshorn
ChemIDplus
hyaluronic acid
carbon dioxide
A naturally occurring polypeptide synthesized at the ribosome.
CHEBI:8526
KEGG:C00017
chebi_ontology
Protein
a protein
polypeptide chain
protein polypeptide chains
CHEBI:16541
protein polypeptide chain
Protein
KEGG_COMPOUND
a protein
UniProt
polypeptide chain
ChEBI
protein polypeptide chains
ChEBI
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
0
(C2H2NOR)nC2H3NOR
CHEBI:14753
CHEBI:25906
CHEBI:7990
KEGG:C00012
Peptide
peptides
chebi_ontology
Peptid
peptido
peptidos
CHEBI:16670
peptide
Peptide
KEGG_COMPOUND
peptides
IUPAC
Peptid
ChEBI
peptido
ChEBI
peptidos
ChEBI
glycan
bilirubin IXalpha
glycoprotein
A minor stable isotope of calcium with relative atomic mass 42.95877 and 0.135 atom percent natural abundance.
0
[43Ca]
InChI=1S/Ca/i1+3
OYPRJOBELJOOCE-AKLPVKDBSA-N
42.959
42.95877
[43Ca]
CAS:14333-06-3
PMID:11859764
PMID:19117733
PMID:20463996
PMID:20574585
PMID:23163540
PMID:23398971
PMID:24874995
PMID:25306191
PMID:29770988
PMID:6548252
((43)Ca)calcium
chebi_ontology
(43)20Ca
(43)Ca
(43)calcium
Ca-43
calcium, isotope of mass 43
calcium-43
calcium-43 isotope
CHEBI:176566
calcium-43 atom
CAS:14333-06-3
ChemIDplus
PMID:11859764
Europe PMC
PMID:19117733
Europe PMC
PMID:20463996
Europe PMC
PMID:20574585
Europe PMC
PMID:23163540
Europe PMC
PMID:23398971
Europe PMC
PMID:24874995
Europe PMC
PMID:25306191
Europe PMC
PMID:29770988
Europe PMC
PMID:6548252
Europe PMC
((43)Ca)calcium
IUPAC
(43)20Ca
ChEBI
(43)Ca
ChemIDplus
(43)calcium
ChEBI
Ca-43
ChEBI
calcium, isotope of mass 43
ChemIDplus
calcium-43
ChemIDplus
calcium-43 isotope
ChEBI
A stable isotope of molybdenum with relative atomic mass 97.90541, 24.29 atom percent natural abundance and nuclear spin 0.
0
[98Mo]
InChI=1S/Mo/i1+2
ZOKXTWBITQBERF-NJFSPNSNSA-N
97.905
97.90541
[98Mo]
CAS:14392-20-2
PMID:19720541
PMID:22796396
PMID:22970917
PMID:24593536
PMID:25087173
PMID:25168118
PMID:25880611
PMID:26397967
PMID:26808401
((98)Mo)molybdenum
chebi_ontology
(98)42Mo
(98)Mo
Mo-98
molybdenum, isotope of mass 98
molybdenum-98
CHEBI:176570
molybdenum-98 atom
CAS:14392-20-2
ChemIDplus
PMID:19720541
Europe PMC
PMID:22796396
Europe PMC
PMID:22970917
Europe PMC
PMID:24593536
Europe PMC
PMID:25087173
SUBMITTER
PMID:25168118
Europe PMC
PMID:25880611
Europe PMC
PMID:26397967
Europe PMC
PMID:26808401
Europe PMC
((98)Mo)molybdenum
IUPAC
(98)42Mo
ChEBI
(98)Mo
ChemIDplus
Mo-98
ChEBI
molybdenum, isotope of mass 98
ChemIDplus
molybdenum-98
ChemIDplus
A major stable isotope of strontium with relative atomic mass 87.90561 and 82.58 atom percent natural abundance.
0
[88Sr]
InChI=1S/Sr/i1+0
CIOAGBVUUVVLOB-IGMARMGPSA-N
87.906
87.90561
[88Sr]
CAS:14119-10-9
PMID:11893161
PMID:27829691
PMID:32350478
PMID:33328666
PMID:33834832
PMID:6337617
((88)Sr)strontium
chebi_ontology
(88)38Sr
(88)Sr
(88)strontium
Sr-88
strontium, isotope of mass 88
strontium-88
strontium-88 isotope
CHEBI:176571
strontium-88 atom
CAS:14119-10-9
ChemIDplus
PMID:11893161
Europe PMC
PMID:27829691
Europe PMC
PMID:32350478
Europe PMC
PMID:33328666
Europe PMC
PMID:33834832
Europe PMC
PMID:6337617
SUBMITTER
((88)Sr)strontium
IUPAC
(88)38Sr
ChEBI
(88)Sr
ChemIDplus
(88)strontium
ChEBI
Sr-88
ChEBI
strontium, isotope of mass 88
ChemIDplus
strontium-88
ChemIDplus
strontium-88 isotope
ChEBI
A stable isotope of rubidium with relative atomic mass 84.91179, 72.17 atom percent natural abundance and nuclear spin 5/2.
0
[85Rb]
InChI=1S/Rb/i1+0
IGLNJRXAVVLDKE-IGMARMGPSA-N
84.912
84.91179
[85Rb]
CAS:13982-12-2
PMID:18026483
PMID:18033464
PMID:18291893
PMID:18382518
PMID:19855587
PMID:25087142
PMID:32909800
PMID:33709729
PMID:34170158
((85)Rb)rubidium
chebi_ontology
(85)37Rb
(85)Rb
Rb-85
rubidium, isotope of mass 85
rubidium-85
CHEBI:176572
rubidium-85 atom
CAS:13982-12-2
ChemIDplus
PMID:18026483
Europe PMC
PMID:18033464
Europe PMC
PMID:18291893
Europe PMC
PMID:18382518
Europe PMC
PMID:19855587
Europe PMC
PMID:25087142
SUBMITTER
PMID:32909800
Europe PMC
PMID:33709729
Europe PMC
PMID:34170158
Europe PMC
((85)Rb)rubidium
IUPAC
(85)37Rb
ChEBI
(85)Rb
ChemIDplus
Rb-85
ChEBI
rubidium, isotope of mass 85
ChemIDplus
rubidium-85
ChemIDplus
A stable isotope of selenium with relative atomic mass 81.91670, 8.82 atom percent natural abundance and nuclear spin 0.
0
[82Se]
InChI=1S/Se/i1+3
BUGBHKTXTAQXES-AKLPVKDBSA-N
81.917
81.91670
[82Se]
CAS:14687-58-2
Chemspider:4892236
PMID:16028633
PMID:18781022
PMID:21139275
PMID:22258472
PMID:23575454
PMID:29932707
PMID:30881205
PMID:31386478
PMID:31951429
PMID:33576665
PMID:6337549
((82)Se)selenium
chebi_ontology
(82)34Se
(82)Se
Se-82
selenium, isotope of mass 82
selenium-82
CHEBI:176573
selenium-82 atom
CAS:14687-58-2
ChemIDplus
PMID:16028633
Europe PMC
PMID:18781022
Europe PMC
PMID:21139275
Europe PMC
PMID:22258472
Europe PMC
PMID:23575454
Europe PMC
PMID:29932707
Europe PMC
PMID:30881205
Europe PMC
PMID:31386478
Europe PMC
PMID:31951429
Europe PMC
PMID:33576665
Europe PMC
PMID:6337549
SUBMITTER
((82)Se)selenium
IUPAC
(82)34Se
ChEBI
(82)Se
ChemIDplus
Se-82
ChEBI
selenium, isotope of mass 82
ChemIDplus
selenium-82
ChemIDplus
A stable isotope of zinc with relative atomic mass 65.92603, 27.7 atom percent natural abundance and nuclear spin 0.
0
[66Zn]
InChI=1S/Zn/i1+1
HCHKCACWOHOZIP-OUBTZVSYSA-N
65.926
65.92603
[66Zn]
CAS:14378-33-7
PMID:12447866
PMID:19836537
PMID:20155761
PMID:21047059
PMID:24196216
PMID:26065372
PMID:26808401
PMID:27189145
PMID:27306032
((66)Zn)zinc
chebi_ontology
(66)30Zn
(66)Zn
Zn-66
zinc, isotope of mass 66
zinc-66
CHEBI:176574
zinc-66 atom
CAS:14378-33-7
ChemIDplus
PMID:12447866
SUBMITTER
PMID:19836537
Europe PMC
PMID:20155761
Europe PMC
PMID:21047059
Europe PMC
PMID:24196216
Europe PMC
PMID:26065372
Europe PMC
PMID:26808401
Europe PMC
PMID:27189145
Europe PMC
PMID:27306032
Europe PMC
((66)Zn)zinc
IUPAC
(66)30Zn
ChEBI
(66)Zn
ChemIDplus
Zn-66
ChemIDplus
zinc, isotope of mass 66
ChemIDplus
zinc-66
ChemIDplus
A stable isotope of nickel with relative atomic mass 59.93079, 26.223 atom percent natural abundance and nuclear spin 0.
0
[60Ni]
InChI=1S/Ni/i1+1
PXHVJJICTQNCMI-OUBTZVSYSA-N
59.931
59.93079
[60Ni]
CAS:13981-80-1
PMID:15308160
PMID:22583786
PMID:23149182
PMID:25126912
PMID:25700212
PMID:26709546
PMID:29376683
((60)Ni)nickel
chebi_ontology
(60)Ni
Ni-60
nickel, isotope of mass 60
nickel-60
CHEBI:176575
nickel-60 atom
CAS:13981-80-1
ChemIDplus
PMID:15308160
Europe PMC
PMID:22583786
Europe PMC
PMID:23149182
Europe PMC
PMID:25126912
Europe PMC
PMID:25700212
Europe PMC
PMID:26709546
Europe PMC
PMID:29376683
Europe PMC
((60)Ni)nickel
IUPAC
(60)Ni
ChEBI
Ni-60
ChEBI
nickel, isotope of mass 60
ChemIDplus
nickel-60
ChemIDplus
A stable isotope of cobalt with relative atomic mass 58.93319, 100 atom percent natural abundance and nuclear spin 7/2.
0
[59Co]
InChI=1S/Co/i1+0
GUTLYIVDDKVIGB-IGMARMGPSA-N
58.933
58.93319
[59Co]
PMID:10617436
PMID:10940985
PMID:11421673
PMID:11528329
PMID:12943912
PMID:19150229
PMID:19421527
PMID:25069794
PMID:25169133
PMID:26066447
PMID:26641288
PMID:27355901
PMID:30137661
PMID:31367328
PMID:32478347
((59)Co)cobalt
chebi_ontology
(59)27Co
(59)Co
Co-59
cobalt, isotope of mass 59
cobalt-(59)Co
cobalt-59
CHEBI:176578
cobalt-59 atom
PMID:10617436
Europe PMC
PMID:10940985
Europe PMC
PMID:11421673
Europe PMC
PMID:11528329
SUBMITTER
PMID:12943912
Europe PMC
PMID:19150229
Europe PMC
PMID:19421527
Europe PMC
PMID:25069794
Europe PMC
PMID:25169133
Europe PMC
PMID:26066447
Europe PMC
PMID:26641288
Europe PMC
PMID:27355901
Europe PMC
PMID:30137661
Europe PMC
PMID:31367328
Europe PMC
PMID:32478347
Europe PMC
((59)Co)cobalt
IUPAC
(59)27Co
ChEBI
(59)Co
ChEBI
Co-59
ChEBI
cobalt, isotope of mass 59
ChEBI
cobalt-(59)Co
ChEBI
cobalt-59
ChEBI
A stable isotope of manganese with relative atomic mass 54.93804, 100 atom percent natural abundance and nuclear spin 5/2.
0
[55Mn]
InChI=1S/Mn/i1+0
PWHULOQIROXLJO-IGMARMGPSA-N
54.938
54.93804
[55Mn]
PMID:20645339
PMID:21058720
PMID:21341708
PMID:24993844
PMID:25179135
PMID:25891681
((55)Mn)manganese
chebi_ontology
(55)25Mn
(55)Mn
Mn-55
manganese, isotope of mass 55
manganese-55
CHEBI:176583
manganese-55 atom
PMID:20645339
Europe PMC
PMID:21058720
Europe PMC
PMID:21341708
Europe PMC
PMID:24993844
Europe PMC
PMID:25179135
Europe PMC
PMID:25891681
Europe PMC
((55)Mn)manganese
IUPAC
(55)25Mn
ChEBI
(55)Mn
ChEBI
Mn-55
ChEBI
manganese, isotope of mass 55
ChEBI
manganese-55
ChEBI
A stable isotope of arsenic with relative atomic mass 74.921596, 100 atom percent natural abundance and nuclear spin 3/2.
0
[75As]
InChI=1S/As/i1+0
RQNWIZPPADIBDY-IGMARMGPSA-N
74.922
74.92159
[75As]
((75)As)arsenic
chebi_ontology
(75)33As
(75)As
As-75
arsenic, isotope of mass 75
arsenic-75
CHEBI:176584
arsenic-75 atom
((75)As)arsenic
IUPAC
(75)33As
ChEBI
(75)As
ChEBI
As-75
ChEBI
arsenic, isotope of mass 75
ChEBI
arsenic-75
ChEBI
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
CHEBI:14202
CHEBI:4697
KEGG:C01351
Donor
chebi_ontology
Donator
donneur
CHEBI:17891
donor
Donor
KEGG_COMPOUND
Donator
ChEBI
donneur
ChEBI
dinitrogen
lipid
glycosaminoglycan
An iron group element atom that has atomic number 26.
0
Fe
InChI=1S/Fe
XEEYBQQBJWHFJM-UHFFFAOYSA-N
55.84500
55.93494
[Fe]
CHEBI:13322
CHEBI:24872
CHEBI:5974
CAS:7439-89-6
DrugBank:DB01592
HMDB:HMDB0015531
KEGG:C00023
Reaxys:4122945
WebElements:Fe
iron
chebi_ontology
26Fe
Eisen
Fe
Iron
fer
ferrum
hierro
iron
CHEBI:18248
iron atom
CAS:7439-89-6
ChemIDplus
CAS:7439-89-6
KEGG COMPOUND
CAS:7439-89-6
NIST Chemistry WebBook
Reaxys:4122945
Reaxys
iron
IUPAC
26Fe
IUPAC
Eisen
ChEBI
Fe
IUPAC
Fe
UniProt
Iron
KEGG_COMPOUND
fer
ChEBI
ferrum
IUPAC
hierro
ChEBI
iron
ChEBI
That part of DNA or RNA that may be involved in pairing.
CHEBI:13873
CHEBI:25598
CHEBI:2995
KEGG:C00701
Wikipedia:Nucleobase
chebi_ontology
Base
nucleobases
CHEBI:18282
nucleobase
Base
KEGG_COMPOUND
nucleobases
ChEBI
0
Mn
InChI=1S/Mn
PWHULOQIROXLJO-UHFFFAOYSA-N
54.93805
54.93804
[Mn]
CHEBI:13382
CHEBI:25153
CHEBI:6681
CAS:7439-96-5
KEGG:C00034
WebElements:Mn
manganese
chebi_ontology
25Mn
Mangan
Manganese
Mn
manganese
manganeso
manganum
CHEBI:18291
manganese atom
CAS:7439-96-5
ChemIDplus
CAS:7439-96-5
KEGG COMPOUND
manganese
IUPAC
25Mn
IUPAC
Mangan
NIST_Chemistry_WebBook
Manganese
KEGG_COMPOUND
Mn
IUPAC
Mn
UniProt
manganese
ChEBI
manganeso
ChEBI
manganum
ChEBI
A carbon group element atom with a symbol Fl and atomic number 114.
0
Fl
InChI=1S/Fl
WIHJCBVMYKIGOT-UHFFFAOYSA-N
289.000
289.00000
[Fl]
PMID:16833611
PMID:17919027
PMID:19905506
PMID:20379506
PMID:20867370
PMID:23787759
PMID:24456007
PMID:29711350
PMID:36092655
Wikipedia:Flerovium
chebi_ontology
114Fl
114Uuq
E114
Fl
Uuq
eka-lead
element 114
ununquadium
CHEBI:194531
flerovium atom
PMID:16833611
Europe PMC
PMID:17919027
Europe PMC
PMID:19905506
Europe PMC
PMID:20379506
Europe PMC
PMID:20867370
Europe PMC
PMID:23787759
Europe PMC
PMID:24456007
Europe PMC
PMID:29711350
Europe PMC
PMID:36092655
Europe PMC
114Fl
ChEBI
114Uuq
ChEBI
E114
ChEBI
Fl
ChEBI
Uuq
ChEBI
eka-lead
ChEBI
element 114
ChEBI
ununquadium
ChEBI
A boron group element atom with a symbol Nh and atomic number 113.
0
Nh
InChI=1S/Nh
KUGNSLWRKGRKGS-UHFFFAOYSA-N
286.000
286.00000
[Nh]
PMID:19049424
PMID:34142795
PMID:34917588
PMID:36149319
PMID:9913354
Wikipedia:Nihonium
chebi_ontology
113Nh
E113
Nh
Uut
eka-thallium
element 113
ununtrium
CHEBI:194533
nihonium atom
PMID:19049424
Europe PMC
PMID:34142795
Europe PMC
PMID:34917588
Europe PMC
PMID:36149319
Europe PMC
PMID:9913354
Europe PMC
113Nh
ChEBI
E113
ChEBI
Nh
ChEBI
Uut
ChEBI
eka-thallium
ChEBI
element 113
ChEBI
ununtrium
ChEBI
A pnictogen atom with a symbol Mc and atomic number 115.
0
Mc
InChI=1S/Mc
QDXZEHQJHSHEQF-UHFFFAOYSA-N
289.000
289.00000
[Mc]
PMID:24074079
PMID:34142795
Wikipedia:Moscovium
chebi_ontology
115Mc
E115
Mc
Uup
eka-bismuth
element 115
ununpentium
CHEBI:194535
moscovium atom
PMID:24074079
Europe PMC
PMID:34142795
Europe PMC
115Mc
ChEBI
E115
ChEBI
Mc
ChEBI
Uup
ChEBI
eka-bismuth
ChEBI
element 115
ChEBI
ununpentium
ChEBI
A chalcogen atom with a symbol Lv and atomic number 116.
0
Lv
InChI=1S/Lv
ONFASNXETZOODS-UHFFFAOYSA-N
293.000
293.00000
[Lv]
PMID:17381195
PMID:27554416
Wikipedia:Livermorium
chebi_ontology
116Lv
E116
Lv
Uuh
eka-polonium
element 116
ununhexium
CHEBI:194537
livermorium atom
PMID:17381195
Europe PMC
PMID:27554416
Europe PMC
116Lv
ChEBI
E116
ChEBI
Lv
ChEBI
Uuh
ChEBI
eka-polonium
ChEBI
element 116
ChEBI
ununhexium
ChEBI
A halogen atom with a symbol Ts and atomic number 117.
0
Ts
InChI=1S/Ts
INMSAURDCVBGHH-UHFFFAOYSA-N
293.000
293.00000
[Ts]
PMID:16483205
PMID:19367904
PMID:20395479
PMID:23090670
Wikipedia:Tennessine
chebi_ontology
117Ts
E117
Ts
Uus
eka-astatine
element 117
ununseptium
CHEBI:194539
tennessine atom
PMID:16483205
Europe PMC
PMID:19367904
Europe PMC
PMID:20395479
Europe PMC
PMID:23090670
Europe PMC
117Ts
ChEBI
E117
ChEBI
Ts
ChEBI
Uus
ChEBI
eka-astatine
ChEBI
element 117
ChEBI
ununseptium
ChEBI
A p-block element atom with a symbol Og and atomic number 118.
0
InChI=1S/Og
GOANEQIZDYDFCO-UHFFFAOYSA-N
294.000
294.00000
[Og]
PMID:10062781
PMID:11486061
PMID:19045133
PMID:23913741
PMID:36859080
Wikipedia:Oganesson
chebi_ontology
118Og
E118
Og
Uuo
eka-emanation
eka-radon
element 118
ununoctium
CHEBI:194541
oganesson atom
PMID:10062781
Europe PMC
PMID:11486061
Europe PMC
PMID:19045133
Europe PMC
PMID:23913741
Europe PMC
PMID:36859080
Europe PMC
118Og
ChEBI
E118
ChEBI
Og
ChEBI
Uuo
ChEBI
eka-emanation
ChEBI
eka-radon
ChEBI
element 118
ChEBI
ununoctium
ChEBI
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
acyl group
alkanoyl
chebi_ontology
acyl groups
alkanoyl group
groupe acyle
CHEBI:22221
acyl group
acyl group
IUPAC
alkanoyl
IUPAC
acyl groups
ChEBI
alkanoyl group
ChEBI
groupe acyle
IUPAC
alkaline earth metals
chebi_ontology
Erdalkalimetall
Erdalkalimetalle
alkaline earth metal
alkaline-earth metal
alkaline-earth metals
metal alcalino-terreux
metal alcalinoterreo
metales alcalinoterreos
metaux alcalino-terreux
CHEBI:22313
alkaline earth metal atom
alkaline earth metals
IUPAC
Erdalkalimetall
ChEBI
Erdalkalimetalle
ChEBI
alkaline earth metal
ChEBI
alkaline-earth metal
ChEBI
alkaline-earth metals
ChEBI
metal alcalino-terreux
ChEBI
metal alcalinoterreo
ChEBI
metales alcalinoterreos
ChEBI
metaux alcalino-terreux
ChEBI
alkali metals
chebi_ontology
Alkalimetall
Alkalimetalle
alkali metal
metal alcalin
metal alcalino
metales alcalinos
metaux alcalins
CHEBI:22314
alkali metal atom
alkali metals
IUPAC
Alkalimetall
ChEBI
Alkalimetalle
ChEBI
alkali metal
ChEBI
metal alcalin
ChEBI
metal alcalino
ChEBI
metales alcalinos
ChEBI
metaux alcalins
ChEBI
aminoglycan
A monoatomic or polyatomic species having one or more elementary charges of the electron.
Anion
anion
chebi_ontology
Anionen
aniones
anions
CHEBI:22563
anion
Anion
ChEBI
anion
ChEBI
anion
IUPAC
Anionen
ChEBI
aniones
ChEBI
anions
IUPAC
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
KEGG:C00701
Base
base
chebi_ontology
Base1
Base2
Basen
Nucleobase
bases
CHEBI:22695
base
Base
ChEBI
base
ChEBI
base
IUPAC
Base1
KEGG_COMPOUND
Base2
KEGG_COMPOUND
Basen
ChEBI
Nucleobase
KEGG_COMPOUND
bases
ChEBI
bile salt
0
Br
InChI=1S/Br
WKBOTKDWSSQWDR-UHFFFAOYSA-N
79.90400
78.91834
[Br]
WebElements:Br
bromine
chebi_ontology
35Br
Br
Brom
brome
bromine
bromo
bromum
CHEBI:22927
bromine atom
bromine
IUPAC
35Br
IUPAC
Br
ChEBI
Brom
ChEBI
brome
ChEBI
bromine
ChEBI
bromo
ChEBI
bromum
ChEBI
0
Cd
InChI=1S/Cd
BDOSMKKIYDKNTQ-UHFFFAOYSA-N
112.41100
113.90336
[Cd]
CAS:7440-43-9
KEGG:C01413
WebElements:Cd
cadmium
chebi_ontology
48Cd
Cd
Kadmium
cadmio
cadmium
CHEBI:22977
cadmium atom
CAS:7440-43-9
ChemIDplus
CAS:7440-43-9
KEGG COMPOUND
CAS:7440-43-9
NIST Chemistry WebBook
cadmium
IUPAC
48Cd
IUPAC
Cd
IUPAC
Kadmium
NIST_Chemistry_WebBook
cadmio
ChEBI
cadmium
ChEBI
0
Ca
InChI=1S/Ca
OYPRJOBELJOOCE-UHFFFAOYSA-N
40.07800
39.96259
[Ca]
CAS:7440-70-2
DrugBank:DB01373
KEGG:C00076
WebElements:Ca
calcium
chebi_ontology
20Ca
Ca
Calcium
Kalzium
calcio
calcium
CHEBI:22984
calcium atom
CAS:7440-70-2
ChemIDplus
calcium
IUPAC
20Ca
IUPAC
Ca
IUPAC
Ca
UniProt
Calcium
KEGG_COMPOUND
Kalzium
ChEBI
calcio
ChEBI
calcium
ChEBI
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
0
CH2NO
44.03272
44.01364
*C(N)=O
PMID:24168430
carbamoyl
chebi_ontology
-C(O)NH2
-CONH2
aminocarbonyl
carbamyl
carbamyl group
carboxamide
CHEBI:23004
carbamoyl group
PMID:24168430
Europe PMC
carbamoyl
IUPAC
-C(O)NH2
ChEBI
-CONH2
IUPAC
aminocarbonyl
IUPAC
carbamyl
ChEBI
carbamyl group
ChEBI
carboxamide
IUPAC
carbon oxide
0
CO
28.01010
27.99491
O=C(*)*
carbonyl
carbonyl group
chebi_ontology
>C=O
CHEBI:23019
carbonyl group
carbonyl
IUPAC
carbonyl group
ChEBI
carbonyl group
UniProt
>C=O
IUPAC
chloride salt
0
Cl
InChI=1S/Cl
ZAMOUSCENKQFHK-UHFFFAOYSA-N
35.45270
34.96885
[Cl]
WebElements:Cl
chlorine
chebi_ontology
17Cl
Chlor
Cl
chlore
chlorine
chlorum
cloro
CHEBI:23116
chlorine atom
chlorine
IUPAC
17Cl
IUPAC
Chlor
ChEBI
Cl
IUPAC
chlore
ChEBI
chlorine
ChEBI
chlorum
ChEBI
cloro
ChEBI
chlorine molecular entity
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Wikipedia:Cofactor_(biochemistry)
cofactor
cofactors
chebi_ontology
CHEBI:23357
cofactor
cofactor
IUPAC
cofactors
IUPAC
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entity
chebi_ontology
entidad molecular
entidades moleculares
entite moleculaire
molecular entities
molekulare Entitaet
CHEBI:23367
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
fake:2
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
monoatomic cation
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
enzyme inhibitor
chebi_ontology
enzyme inhibitors
inhibidor enzimatico
inhibidores enzimaticos
inhibiteur enzymatique
inhibiteurs enzymatiques
CHEBI:23924
enzyme inhibitor
enzyme inhibitor
IUPAC
enzyme inhibitors
ChEBI
inhibidor enzimatico
ChEBI
inhibidores enzimaticos
ChEBI
inhibiteur enzymatique
ChEBI
inhibiteurs enzymatiques
ChEBI
0
F
InChI=1S/F
YCKRFDGAMUMZLT-UHFFFAOYSA-N
18.99840
18.99840
[F]
CAS:7782-41-4
WebElements:F
fluorine
chebi_ontology
9F
F
Fluor
fluor
fluorine
fluorum
CHEBI:24061
fluorine atom
CAS:7782-41-4
ChemIDplus
fluorine
IUPAC
9F
IUPAC
F
IUPAC
Fluor
ChemIDplus
fluor
ChEBI
fluorine
ChEBI
fluorum
ChEBI
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
A molecular entity consisting of two or more chemical elements.
James Malone
Tomasz Adamusiak
true
chemical compound
chemical entity
heteroatomic molecular entities
heteroatomic molecular entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
A role played by the molecular entity or part thereof within a biological context.
Helen Parkinson
chebi_ontology
biological function
CHEBI:24432
biological role
biological function
ChEBI
A defined linked collection of atoms or a single atom within a molecular entity.
group
chebi_ontology
Gruppe
Rest
groupe
grupo
grupos
CHEBI:24433
group
group
IUPAC
Gruppe
ChEBI
Rest
ChEBI
groupe
IUPAC
grupo
IUPAC
grupos
IUPAC
halogen molecular entity
halogen
halogens
chebi_ontology
Halogene
group 17 elements
group VII elements
halogene
halogenes
halogeno
halogenos
CHEBI:24473
halogen
halogen
IUPAC
halogens
IUPAC
Halogene
ChEBI
group 17 elements
ChEBI
group VII elements
ChEBI
halogene
ChEBI
halogenes
ChEBI
halogeno
ChEBI
halogenos
ChEBI
A cyclic compound having as ring members atoms of carbon and at least of one other element.
chebi_ontology
organic heterocycle
organic heterocyclic compounds
CHEBI:24532
organic heterocyclic compound
organic heterocycle
ChEBI
organic heterocyclic compounds
ChEBI
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
+1
[1H]
InChI=1S/p+1/i/hH
GPRLSGONYQIRFK-FTGQXOHASA-N
1.007
1.00728
[1H+]
CAS:12408-02-5
KEGG:C00080
protium(1+)
proton
chebi_ontology
(1)1H(+)
(1)H(+)
p
p(+)
CHEBI:24636
proton
CAS:12408-02-5
ChemIDplus
CAS:12408-02-5
NIST Chemistry WebBook
protium(1+)
IUPAC
proton
ChEBI
proton
IUPAC
(1)1H(+)
IUPAC
(1)H(+)
IUPAC
p
IUPAC
p(+)
IUPAC
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
chebi_ontology
CHEBI:24651
hydroxides
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
oxoacid
oxoacids
chebi_ontology
oxacids
oxiacids
oxo acid
oxy-acids
oxyacids
CHEBI:24833
oxoacid
oxoacid
IUPAC
oxoacids
IUPAC
oxacids
ChEBI
oxiacids
ChEBI
oxo acid
ChEBI
oxy-acids
ChEBI
oxyacids
ChEBI
chebi_ontology
inorganic anions
CHEBI:24834
inorganic anion
inorganic anions
ChEBI
A molecular entity that contains no carbon.
chebi_ontology
anorganische Verbindungen
inorganic compounds
inorganic entity
inorganic molecular entities
inorganics
CHEBI:24835
inorganic molecular entity
anorganische Verbindungen
ChEBI
inorganic compounds
ChEBI
inorganic entity
ChEBI
inorganic molecular entities
ChEBI
inorganics
ChEBI
inorganic salt
Chemical element with atomic number 53.
0
I
InChI=1S/I
ZCYVEMRRCGMTRW-UHFFFAOYSA-N
126.90447
126.90447
[I]
WebElements:I
iodine
chebi_ontology
53I
I
Iod
J
Jod
iode
iodine
iodium
yodo
CHEBI:24859
iodine atom
iodine
IUPAC
53I
IUPAC
I
ChEBI
Iod
ChEBI
J
ChEBI
Jod
ChEBI
iode
ChEBI
iodine
ChEBI
iodium
ChEBI
yodo
ChEBI
salt
monoatomic ion
organic salt
A molecular entity having a net electric charge.
Ion
ion
chebi_ontology
Ionen
iones
ions
CHEBI:24870
ion
Ion
ChEBI
ion
ChEBI
ion
IUPAC
Ionen
ChEBI
iones
ChEBI
ions
ChEBI
iron molecular entity
0
Pb
InChI=1S/Pb
WABPQHHGFIMREM-UHFFFAOYSA-N
207.20000
207.97665
[Pb]
KEGG:C06696
WebElements:Pb
lead
chebi_ontology
82Pb
Blei
Pb
lead
plomb
plomo
plumbum
CHEBI:25016
lead atom
lead
IUPAC
82Pb
IUPAC
Blei
ChEBI
Pb
IUPAC
lead
ChEBI
plomb
ChEBI
plomo
ChEBI
plumbum
IUPAC
linear tetrapyrrole
0
Mg
InChI=1S/Mg
FYYHWMGAXLPEAU-UHFFFAOYSA-N
24.30500
23.98504
[Mg]
CAS:7439-95-4
DrugBank:DB01378
Gmelin:16207
KEGG:C00305
WebElements:Mg
magnesium
chebi_ontology
12Mg
Magnesium
Mg
magnesio
magnesium
CHEBI:25107
magnesium atom
CAS:7439-95-4
ChemIDplus
Gmelin:16207
Gmelin
magnesium
IUPAC
12Mg
IUPAC
Magnesium
ChEBI
Mg
IUPAC
Mg
UniProt
magnesio
ChEBI
magnesium
ChEBI
0
Hg
InChI=1S/Hg
QSHDDOUJBYECFT-UHFFFAOYSA-N
200.59000
201.97064
[Hg]
CAS:7439-97-6
WebElements:Hg
mercury
chebi_ontology
80Hg
Hg
Quecksilber
azogue
hydrargyrum
liquid silver
mercure
mercurio
mercury
quicksilver
CHEBI:25195
mercury atom
CAS:7439-97-6
ChemIDplus
mercury
IUPAC
80Hg
IUPAC
Hg
IUPAC
Quecksilber
ChemIDplus
azogue
ChEBI
hydrargyrum
IUPAC
liquid silver
ChemIDplus
mercure
ChemIDplus
mercurio
ChEBI
mercury
ChEBI
quicksilver
ChemIDplus
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
CHEBI:26619
CHEBI:35220
metabolite
chebi_ontology
metabolites
primary metabolites
secondary metabolites
CHEBI:25212
metabolite
metabolite
IUPAC
metabolites
ChEBI
primary metabolites
ChEBI
secondary metabolites
ChEBI
metal cation
elemental molecule
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
molecule
chebi_ontology
Molekuel
molecula
molecules
neutral molecular compounds
CHEBI:25367
molecule
molecule
IUPAC
Molekuel
ChEBI
molecula
IUPAC
molecules
IUPAC
neutral molecular compounds
IUPAC
monoatomic monocation
0
N
14.007
14.00307
WebElements:N
nitrogen
chebi_ontology
7N
N
Stickstoff
azote
nitrogen
nitrogeno
CHEBI:25555
nitrogen atom
nitrogen
IUPAC
7N
IUPAC
N
IUPAC
Stickstoff
ChEBI
azote
IUPAC
nitrogen
ChEBI
nitrogeno
ChEBI
nonmetal
chebi_ontology
Nichtmetall
Nichtmetalle
no metal
no metales
non-metal
non-metaux
nonmetal
nonmetals
CHEBI:25585
nonmetal atom
nonmetal
IUPAC
Nichtmetall
ChEBI
Nichtmetalle
ChEBI
no metal
ChEBI
no metales
ChEBI
non-metal
ChEBI
non-metaux
ChEBI
nonmetal
ChEBI
nonmetals
ChEBI
Any organic ion with a net negative charge.
chebi_ontology
organic anions
CHEBI:25696
organic anion
organic anions
ChEBI
chebi_ontology
organic ions
CHEBI:25699
organic ion
organic ions
ChEBI
organic oxide
organic sulfate
An oxide is a chemical compound of oxygen with other chemical elements.
oxide
chebi_ontology
oxides
CHEBI:25741
oxide
oxide
ChEBI
oxides
ChEBI
0
O
InChI=1S/O
QVGXLLKOCUKJST-UHFFFAOYSA-N
15.99940
15.99491
[O]
KEGG:C00007
WebElements:O
oxygen
chebi_ontology
8O
O
Sauerstoff
oxigeno
oxygen
oxygene
CHEBI:25805
oxygen atom
oxygen
IUPAC
8O
IUPAC
O
IUPAC
Sauerstoff
ChEBI
oxigeno
ChEBI
oxygen
ChEBI
oxygene
ChEBI
oxygen molecular entity
chebi_ontology
oxygen molecular entities
CHEBI:25806
oxygen molecular entity
oxygen molecular entity
ChEBI
oxygen molecular entities
ChEBI
0
K
InChI=1S/K
ZLMJMSJWJFRBEC-UHFFFAOYSA-N
39.09830
38.96371
[K]
CAS:7440-09-7
DrugBank:DB01345
KEGG:C00238
WebElements:K
potassium
chebi_ontology
19K
K
Kalium
kalium
potasio
potassium
CHEBI:26216
potassium atom
CAS:7440-09-7
ChemIDplus
potassium
IUPAC
19K
IUPAC
K
IUPAC
Kalium
ChemIDplus
kalium
IUPAC
potasio
ChEBI
potassium
ChEBI
0
Na
InChI=1S/Na
KEAYESYHFKHZAL-UHFFFAOYSA-N
22.98977
22.98977
[Na]
CAS:7440-23-5
Gmelin:16221
KEGG:C01330
WebElements:Na
sodium
chebi_ontology
11Na
Na
Natrium
natrium
sodio
sodium
CHEBI:26708
sodium atom
CAS:7440-23-5
ChemIDplus
Gmelin:16221
Gmelin
sodium
IUPAC
11Na
IUPAC
Na
IUPAC
Natrium
ChemIDplus
natrium
IUPAC
sodio
ChemIDplus
sodium
ChEBI
sodium chloride
sodium molecular entity
sodium salt
sulfuric ester
sulfates
0
S
InChI=1S/S
NINIDFKCEFEMDL-UHFFFAOYSA-N
32.06600
31.97207
[S]
CAS:7704-34-9
KEGG:C00087
KEGG:D06527
PPDB:605
WebElements:S
sulfur
chebi_ontology
16S
Elemental sulfur
S
Schwefel
azufre
soufre
sulfur
sulphur
theion
CHEBI:26833
sulfur atom
CAS:7704-34-9
ChemIDplus
CAS:7704-34-9
NIST Chemistry WebBook
sulfur
IUPAC
16S
IUPAC
Elemental sulfur
KEGG_COMPOUND
S
IUPAC
S
KEGG_COMPOUND
Schwefel
ChEBI
azufre
ChEBI
soufre
ChEBI
sulfur
ChEBI