An ontology of phenotypic qualities (properties, attributes or characteristics).
PATO - the Phenotype And Trait Ontology
quality
1.2
2023-05-18
definition
IAO:0000116
uberon
editor_note
true
editor_note
editor note
IAO:0000700
uberon
has_ontology_root_term
true
has_ontology_root_term
has ontology root term
preferred_root
term replaced by
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
RO:0002604
quality
is_opposite_of
true
true
is_opposite_of
is opposite of
is_opposite_of
Abnormal/normal slim
Absent/present slim
Attribute slim
cell_quality
Disposition slim
Human phenotype slim
Pathology slim
Relational slim: types of quality that require an additional entity in order to exist
Scalar slim
Value slim
http://purl.org/dc/elements/1.1/creator
uberon
dc-creator
true
dc-creator
creator
http://purl.org/dc/elements/1.1/description
uberon
dc-description
true
dc-description
description
http://purl.org/dc/elements/1.1/title
uberon
dc-title
true
dc-title
title
http://purl.org/dc/terms/contributor
uberon
dc-contributor
true
dc-contributor
contributor
http://purl.org/dc/terms/license
uberon
dcterms-license
true
dcterms-license
license
subset_property
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
in_subset
shorthand
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
quality
uberon
part_of
part_of
part of
part of
part_of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
external
quality
uberon
has_part
has_part
has part
has part
has_part
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
external
uberon
preceded_by
preceded_by
preceded by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
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
BFO:0000066
external
occurs_in
occurs_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
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
BSPO:0000096
uberon
anterior_to
anterior_to
anterior to
BSPO:0000097
uberon
distal_to
distal_to
distal to
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal to
BSPO:0000099
uberon
posterior_to
posterior_to
posterior to
BSPO:0000100
uberon
proximal_to
proximal_to
proximal to
BSPO:0000102
uberon
ventral_to
ventral_to
ventral to
BSPO:0000107
uberon
deep_to
deep_to
deep to
BSPO:0000108
uberon
superficial_to
superficial_to
superficial to
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in left side of
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in right side of
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in posterior side of
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in anterior side of
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in lateral side of
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost part of
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately deep to
BSPO:0001108
uberon
distalmost_part_of
distalmost_part_of
distalmost part of
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y
lacks_part
http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)
lacks_plasma_membrane_part
GOREL:0002003
external
results_in_distribution_of
results_in_distribution_of
results in distribution of
results_in_distribution_of
GOREL:0002004
external
results_in_fission_of
results_in_fission_of
results in fission of
results_in_fission_of
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
external
bearer_of
bearer_of
bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
external
uberon
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)
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
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
RO:0000086
uberon
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
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
RO:0001015
uberon
location_of
location_of
location of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
RO:0001019
uberon
contains
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
uberon
located_in
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.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
surface of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has 2D boundary
http://www.ncbi.nlm.nih.gov/pubmed/22402613
RO:0002005
uberon
innervated_by
innervated_by
innervated_by
innervated_by
has synaptic terminal of
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
RO:0002007
external
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.
bounding layer of
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
A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.
dos
2017-07-20T17:19:37Z
occurs across
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
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
David Osumi-Sutherland
RO:0002082
uberon
simultaneous_with
simultaneous_with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
simultaneous with
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
RO:0002087
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
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
Relation between a neuron and an anatomical structure that its soma is part of.
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
has soma location
Relation between a neuron and some structure its axon forms (chemical) synapses in.
<http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some (
<http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some (
<http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
axon synapses in
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
RO:0002103
uberon
synapsed_by
synapsed_by
synapsed by
synapsed by
Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
has plasma membrane part
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapsed in
http://purl.obolibrary.org/obo/BFO_0000051 some (
http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (
http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
has postsynaptic terminal in
Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
synapses in
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has presynaptic terminal in
Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
N1 synapsed_to some N2
Expands to:
N1 SubclassOf (
has_part some (
‘pre-synaptic membrane ; GO:0042734’ that part_of some (
‘synapse ; GO:0045202’ that has_part some (
‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
synapsed to
A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
has synapse in
<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
has synaptic terminal in
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
external
uberon
overlaps
overlaps
overlaps
overlaps
true
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.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
RO:0002134
uberon
innervates
innervates
innervates
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous with
FMA:85972
lactation SubClassOf 'only in taxon' some 'Mammalia'
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
RO:0002160
uberon
only_in_taxon
only_in_taxon
only in taxon
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.
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.
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
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
The M8 connects Glasgow and Edinburgh
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
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.
RO:0002176
uberon
connects
connects
connects
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
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.
attached to part of (anatomical structure to anatomical structure)
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attached to part of
true
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
RO:0002178
uberon
supplies
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.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
RO:0002179
uberon
drains
drains
drains
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
uberon
has_component
has_component
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
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops from
inverse of develops from
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.
FBbt
RO:0002207
has developmental precursor
uberon
directly_develops_from
directly_develops_from
TODO - add child relations from DOS
directly develops from
directly develops from
inverse of directly develops from
developmental precursor of
directly develops into
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
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.
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:0002215
external
uberon
capable_of
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.
has function in
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
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
RO:0002220
external
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
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
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
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
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
develops from part of
x develops_in y if x is located in y whilst x is developing
EHDAA2
Jonathan Bard, EHDAA2
RO:0002226
uberon
develops_in
develops_in
develops in
develops in
inverse of ends with
Chris Mungall
RO:0002229
uberon
ends
ends
ends
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
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
starts with process that occurs in
RO:0002231
external
has_start_location
has_start_location
has start location
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
ends with process that occurs in
RO:0002232
external
has_end_location
has_end_location
has end location
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.
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 in the same state at the beginning of p.
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
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
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 material anatomical entity type T to T', where T' develops_from T
induced by
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
GO:0001759
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
developmentally induced by
developmentally induced by
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
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
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
replaces
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally replaces
Inverse of developmentally preceded by
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity 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.
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
http://www.geneontology.org/GO.doc.development.shtml
RO:0002296
external
results_in_development_of
results_in_development_of
results in development of
results in development 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)
GOC:mtg_berkeley_2013
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
results in formation of
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
GOC:mtg_berkeley_2013
RO:0002298
external
results_in_morphogenesis_of
results_in_morphogenesis_of
results in morphogenesis of
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
GOC:mtg_berkeley_2013
RO:0002299
external
results_in_maturation_of
results_in_maturation_of
results in maturation of
results in maturation of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
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
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
causally upstream of, negative effect
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
characteristic of part of
true
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
GOC:mtg_berkeley_2013
RO:0002315
external
results_in_acquisition_of_features_of
results_in_acquisition_of_features_of
results in acquisition of features of
results in acquisition of features of
A relationship that holds via some environmental process
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
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
An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial.
adapted for
RO:0002322
uberon
confers_advantage_in
confers_advantage_in
confers advantage in
confers advantage in
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
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
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
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.
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
regulates levels of (process to entity)
RO:0002332
external
regulates_levels_of
regulates_levels_of
regulates levels of
regulates levels of
inverse of enables
enabled by
inverse of regulates
regulated by (processual)
RO:0002334
external
regulated_by
regulated_by
regulated by
regulated by
inverse of negatively regulates
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
negatively regulated by
inverse of positively regulates
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
RO:0002338
external
has_target_start_location
has_target_start_location
has target start location
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
RO:0002339
external
has_target_end_location
has_target_end_location
has target end location
has target end location
Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l
RO:0002341
external
results_in_transport_along
results_in_transport_along
results in transport along
results in transport along
Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.
RO:0002342
external
results_in_transport_across
results_in_transport_across
results in transport across
results in transport across
'pollen tube growth' results_in growth_of some 'pollen tube'
RO:0002343
external
results_in_growth_of
results_in_growth_of
results in growth of
results in growth of
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
RO:0002344
external
results_in_transport_to_from_or_in
results_in_transport_to_from_or_in
results in transport to from or in
results in transport to from or in
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
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
RO:0002353
external
uberon
output_of
output_of
output of
output of
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
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached 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.
Wikipedia:Insertion_(anatomy)
RO:0002372
uberon
has_muscle_origin
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.
Wikipedia:Insertion_(anatomy)
RO:0002373
uberon
has_muscle_insertion
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.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
https://github.com/obophenotype/uberon/issues/170
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
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.
drains into
drains to
tributary channel of
http://en.wikipedia.org/wiki/Tributary
http://www.medindia.net/glossary/venous_tributary.htm
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)
RO:0002376
uberon
tributary_of
tributary_of
tributary of
tributary of
http://en.wikipedia.org/wiki/Tributary
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
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
RO:0002380
uberon
branching_part_of
branching_part_of
branching part of
branching part of
FMA:85994
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).
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
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
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
RO:0002387
uberon
has_potential_to_develop_into
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
has potential to directly develop into
inverse of upstream of
RO:0002404
external
causally_downstream_of
causally_downstream_of
causally downstream of
causally downstream of
RO:0002405
external
immediately_causally_downstream_of
immediately_causally_downstream_of
immediately causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
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
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
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or reguates
involved in or involved in regulation of
A 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.
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.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Considering relabeling as 'pairwise interacts with'
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly activates
molecularly increases activity of
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
'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.
RO:0002473
uberon
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.
has part that occurs in
true
is kinase activity
See notes for inverse relation
receives input from
This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in.
sends output to
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
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
uberon
existence_starts_during
existence_starts_during
existence starts during
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
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))
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
exists during
uberon
existence_starts_and_ends_during
existence_starts_and_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 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).
RO:0002492
ceases_to_exist_during
uberon
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.
https://orcid.org/0000-0002-6601-2165
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).
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
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
uberon
transformation_of
transformation_of
transformation of
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
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
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
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 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.
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
depends on
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
towards
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
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.
has supporting framework
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
RO:0002551
uberon
has_skeleton
has_skeleton
has skeleton
causally influenced by (entity-centric)
causally influenced by
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
RO:0002565
external
results_in_movement_of
results_in_movement_of
results in movement of
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
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.
Wikipedia:Antagonist_(muscle)
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 is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
UBERON:cjm
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
RO:0002570
uberon
conduit_for
conduit_for
conduit for
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.
GOC:cjm
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
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
RO:0002578
external
directly_regulates
directly_regulates
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
has part structure that is capable of
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
RO:0002590
external
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.
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
A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
Groups both positive and negative correlation
correlated with
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
RO:0002629
external
directly_positively_regulates
directly_positively_regulates
directly positively regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
RO:0002630
external
directly_negatively_regulates
directly_negatively_regulates
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
external
uberon
produces
produces
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
produces
a produced_by b iff some process that occurs_in b has_output a.
RO:0003001
external
uberon
produced_by
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.
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.
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
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
2018-12-13T11:26:56Z
RO:0004009
external
has_primary_input
has_primary_input
has primary input
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
enables subfunction
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
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
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
2018-01-26T23:53:22Z
acts upstream of, negative effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
regulates activity of
p acts on population of c iff c' is a collection, has members of type c, and p has participant c
pg
2020-06-08T17:21:33Z
RO:0012003
external
acts_on_population_of
acts_on_population_of
acts on population of
acts on population of
pg
2021-02-26T07:28:29Z
RO:0012008
external
results_in_fusion_of
results_in_fusion_of
results in fusion of
results in fusion of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
pg
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
pg
2022-09-26T06:08:01Z
indirectly regulates
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
q1 decreased_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 'decreased strength', relative to the parent type, 'strength'.
decreased in magnitude relative to
q1 decreased_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
q1 similar_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.
similar in magnitude relative to
q1 similar_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
has relative magnitude
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has cross section
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
https://orcid.org/0000-0002-6601-2165
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
reciprocal of
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
https://orcid.org/0000-0002-6601-2165
'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
has high plasma membrane amount
A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.
PMID:19243617
'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
has low plasma membrane amount
A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.
PMID:19243617
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: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
2018-09-26T01:08:58Z
RO:0040036
external
results_in_changes_to_anatomical_or_cellular_structure
results_in_changes_to_anatomical_or_cellular_structure
results in changes to anatomical or cellular structure
RO:0002610
quality
correlates_with
Consider using RO:0002610 instead. See https://github.com/pato-ontology/pato/issues/454
obsolete correlates_with
true
OBSOLETE. q1 decreased_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.
RO:0015008
quality
decreased_in_magnitude_relative_to
Refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason. This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
obsolete decreased_in_magnitude_relative_to
true
OBSOLETE. q1 decreased_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.
PATOC:CJM
OBSOLETE. 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.
RO:0015006
quality
different_in_magnitude_relative_to
Refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete different_in_magnitude_relative_to
true
OBSOLETE. 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.
PATOC:CJM
OBSOLETE. q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
cjm
2009-08-26T02:50:08Z
quality
directly_associated_with
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
OBSOLETE. Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites.
Association is weaker than correlation or proportionality. These relations may be later added to PATO.
obsolete directly_associated_with
true
OBSOLETE. q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
PATOC:cjm
Wikipedia:Association_(statistics)
OBSOLETE. s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
RO:0015011
quality
has_cross_section
Refer to https://github.com/pato-ontology/pato/issues/454. Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
obsolete has_cross_section
true
OBSOLETE. s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
PATOC:CJM
quality
has_dividend_entity
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete has_dividend_entity
true
quality
has_dividend_quality
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete has_dividend_quality
true
quality
has_divisor_entity
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete has_divisor_entity
true
quality
has_divisor_quality
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete has_divisor_quality
true
quality
has_ratio_quality
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete has_ratio_quality
true
RO:0015010
quality
has_relative_magnitude
Refer to https://github.com/pato-ontology/pato/issues/454.
obsolete has_relative_magnitude
true
OBSOLETE. 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.
RO:0015007
quality
increased_in_magnitude_relative_to
Refer to https://github.com/pato-ontology/pato/issues/454. This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
obsolete increased_in_magnitude_relative_to
true
OBSOLETE. 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.
PATOC:CJM
OBSOLETE. q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
cjm
2009-08-26T02:50:24Z
quality
inversely_associated_with
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete inversely_associated_with
true
OBSOLETE. q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
PATOC:cjm
Wikipedia:Association_(statistics)
pato.ontology
is_magnitude_of
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete is_magnitude_of
true
pato.ontology
is_measurement_of
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete is_measurement_of
true
pato.ontology
is_unit_of
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete is_unit_of
true
RO:0009501
quality
realized_by
Consider using RO:0009501 instead. See https://github.com/pato-ontology/pato/issues/454
obsolete realized_by
true
OBSOLETE. q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
RO:0015012
quality
reciprocal_of
Refer to https://github.com/pato-ontology/pato/issues/454. There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
obsolete reciprocal_of
true
OBSOLETE. q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
PATOC:CJM
OBSOLETE. q1 similar_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.
RO:0015009
quality
similar_in_magnitude_relative_to
Refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
obsolete similar_in_magnitude_relative_to
true
OBSOLETE. q1 similar_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.
PATOC:CJM
monadic_form_of
quality
singly_occurring_form_of
refer to https://github.com/pato-ontology/pato/issues/454 for obsoletion reason.
OBSOLETE. PATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them.
obsolete singly_occurring_form_of
true
RO:0002503
quality
towards
Consider using RO:0002503 instead. See https://github.com/pato-ontology/pato/issues/454
obsolete towards
true
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.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
uberon
channels_into
channels_into
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.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
uberon
extends_fibers_into
extends_fibers_into
X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y
https://orcid.org/0000-0002-7073-9172
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
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.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
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.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
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
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
.
uberon
transitively_distally_connected_to
transitively distally connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
.
uberon
transitively_proximally_connected_to
transitively proximally connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
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.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
spatial region
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
immaterial 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
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
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
chebi_ontology
dicarboxylic acids and derivatives
CHEBI:131927
dicarboxylic acids and O-substituted derivatives
dicarboxylic acids and derivatives
ChEBI
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3.
-1
(C14H20NO11)n.H2O
chebi_ontology
hyaluronan
hyaluronate polyanion
CHEBI:132153
hyaluronate
hyaluronan
UniProt
hyaluronate polyanion
ChEBI
Any steroid that has beta-configuration at position 5.
chebi_ontology
5beta steroids
5beta-steroid
5beta-steroids
CHEBI:136889
5beta steroid
5beta steroids
ChEBI
5beta-steroid
ChEBI
5beta-steroids
ChEBI
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Wikipedia:Mineral_acid
chebi_ontology
inorganic acids
mineral acid
mineral acids
CHEBI:138103
inorganic acid
inorganic acids
ChEBI
mineral acid
ChEBI
mineral acids
ChEBI
Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration.
chebi_ontology
CHEBI:138366
bile acids
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
An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22.
0
C7H6N2O
134.136
134.04801
C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)*
chebi_ontology
CHEBI:142163
24G7 epitope
An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group
-1
C5H8NO4
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1
WHUUTDBJXJRKMK-UHFFFAOYSA-M
146.12136
146.04588
[NH3+]C(CCC([O-])=O)C([O-])=O
Gmelin:327908
glutamate(1-)
hydrogen glutamate
chebi_ontology
2-ammoniopentanedioate
glutamate
glutamic acid monoanion
CHEBI:14321
glutamate(1-)
Gmelin:327908
Gmelin
glutamate(1-)
JCBN
hydrogen glutamate
IUPAC
2-ammoniopentanedioate
IUPAC
glutamate
UniProt
glutamic acid monoanion
JCBN
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
Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.
+1
C7H16NO2
InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1
OIPILFWXSMYKGL-UHFFFAOYSA-N
146.20748
146.11756
CC(=O)OCC[N+](C)(C)C
CHEBI:12686
CHEBI:13715
CHEBI:22197
CHEBI:2416
CHEBI:40559
Beilstein:1764436
CAS:51-84-3
DrugBank:DB03128
Drug_Central:65
Gmelin:326108
KEGG:C01996
LINCS:LSM-5888
PDBeChem:ACH
PMID:14764638
PMID:15014918
PMID:15231705
PMID:15361288
PMID:18050502
PMID:18407448
PMID:19255787
PMID:20963497
PMID:21130809
PMID:21246223
PMID:21545631
PMID:21601579
Wikipedia:Acetylcholine
2-acetyloxy-N,N,N-trimethylethanaminium
ACETYLCHOLINE
Acetylcholine
acetylcholine
chebi_ontology
ACh
Azetylcholin
O-Acetylcholine
choline acetate
CHEBI:15355
acetylcholine
Beilstein:1764436
ChemIDplus
CAS:51-84-3
ChemIDplus
CAS:51-84-3
KEGG COMPOUND
Drug_Central:65
DrugCentral
Gmelin:326108
Gmelin
PMID:14764638
Europe PMC
PMID:15014918
Europe PMC
PMID:15231705
Europe PMC
PMID:15361288
Europe PMC
PMID:18050502
Europe PMC
PMID:18407448
Europe PMC
PMID:19255787
Europe PMC
PMID:20963497
Europe PMC
PMID:21130809
Europe PMC
PMID:21246223
Europe PMC
PMID:21545631
Europe PMC
PMID:21601579
Europe PMC
2-acetyloxy-N,N,N-trimethylethanaminium
IUPAC
ACETYLCHOLINE
PDBeChem
Acetylcholine
KEGG_COMPOUND
acetylcholine
UniProt
ACh
ChemIDplus
Azetylcholin
ChEBI
O-Acetylcholine
KEGG_COMPOUND
choline acetate
ChemIDplus
A simple monocarboxylic acid containing two carbons.
0
C2H4O2
InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)
QTBSBXVTEAMEQO-UHFFFAOYSA-N
60.05200
60.02113
CC(O)=O
CHEBI:22169
CHEBI:2387
CHEBI:40486
Beilstein:506007
CAS:64-19-7
Drug_Central:4211
Gmelin:1380
HMDB:HMDB0000042
KEGG:C00033
KEGG:D00010
KNApSAcK:C00001176
LIPID_MAPS_instance:LMFA01010002
MetaCyc:ACET
PDBeChem:ACT
PDBeChem:ACY
PMID:12005138
PMID:15107950
PMID:16630552
PMID:16774200
PMID:17190852
PMID:19416101
PMID:19469536
PMID:22153255
PMID:22173419
PPDB:1333
Reaxys:506007
Wikipedia:Acetic_acid
ACETIC ACID
Acetic acid
acetic acid
chebi_ontology
AcOH
CH3-COOH
CH3CO2H
E 260
E-260
E260
Essigsaeure
Ethanoic acid
Ethylic acid
HOAc
INS No. 260
MeCO2H
MeCOOH
Methanecarboxylic acid
acide acetique
ethoic acid
CHEBI:15366
acetic acid
Beilstein:506007
Beilstein
CAS:64-19-7
ChemIDplus
CAS:64-19-7
KEGG COMPOUND
CAS:64-19-7
NIST Chemistry WebBook
Drug_Central:4211
DrugCentral
Gmelin:1380
Gmelin
LIPID_MAPS_instance:LMFA01010002
LIPID MAPS
PMID:12005138
Europe PMC
PMID:15107950
Europe PMC
PMID:16630552
Europe PMC
PMID:16774200
Europe PMC
PMID:17190852
Europe PMC
PMID:19416101
Europe PMC
PMID:19469536
Europe PMC
PMID:22153255
Europe PMC
PMID:22173419
Europe PMC
Reaxys:506007
Reaxys
ACETIC ACID
PDBeChem
Acetic acid
KEGG_COMPOUND
acetic acid
IUPAC
AcOH
ChEBI
CH3-COOH
IUPAC
CH3CO2H
ChEBI
E 260
ChEBI
E-260
ChEBI
E260
ChEBI
Essigsaeure
ChEBI
Ethanoic acid
KEGG_COMPOUND
Ethylic acid
ChemIDplus
HOAc
ChEBI
INS No. 260
ChEBI
MeCO2H
ChEBI
MeCOOH
ChEBI
Methanecarboxylic acid
ChemIDplus
acide acetique
ChemIDplus
ethoic acid
ChEBI
0
O2
InChI=1S/O2/c1-2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
31.998
31.98983
O=O
CHEBI:10745
CHEBI:13416
CHEBI:23833
CHEBI:25366
CHEBI:30491
CHEBI:44742
CHEBI:7860
CAS:7782-44-7
Gmelin:485
HMDB:HMDB0001377
KEGG:C00007
KEGG:D00003
MetaCyc:OXYGEN-MOLECULE
MolBase:750
PDBeChem:OXY
PMID:10906528
PMID:16977326
PMID:18210929
PMID:18638417
PMID:19840863
PMID:7710549
PMID:9463773
Wikipedia:Oxygen
dioxygen
chebi_ontology
Disauerstoff
E 948
E-948
E948
O2
OXYGEN MOLECULE
Oxygen
[OO]
dioxygene
molecular oxygen
CHEBI:15379
dioxygen
CAS:7782-44-7
ChemIDplus
CAS:7782-44-7
KEGG COMPOUND
CAS:7782-44-7
NIST Chemistry WebBook
Gmelin:485
Gmelin
PMID:10906528
Europe PMC
PMID:16977326
Europe PMC
PMID:18210929
Europe PMC
PMID:18638417
Europe PMC
PMID:19840863
Europe PMC
PMID:7710549
Europe PMC
PMID:9463773
Europe PMC
dioxygen
IUPAC
Disauerstoff
ChEBI
E 948
ChEBI
E-948
ChEBI
E948
ChEBI
O2
IUPAC
O2
KEGG_COMPOUND
O2
UniProt
OXYGEN MOLECULE
PDBeChem
Oxygen
KEGG_COMPOUND
[OO]
MolBase
dioxygene
ChEBI
molecular oxygen
ChEBI
Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals.
0
C2H4O2(CH2O)n
CHEBI:13755
CHEBI:22305
CHEBI:2561
KEGG:C01370
Wikipedia:Aldose
Aldose
chebi_ontology
aldoses
an aldose
CHEBI:15693
aldose
Aldose
KEGG_COMPOUND
aldoses
ChEBI
an aldose
UniProt
Any alpha-amino acid having L-configuration at the alpha-carbon.
0
C2H4NO2R
74.05870
74.02420
N[C@@H]([*])C(O)=O
CHEBI:13072
CHEBI:13243
CHEBI:13797
CHEBI:21224
CHEBI:6175
KEGG:C00151
L-alpha-amino acid
L-alpha-amino acids
chebi_ontology
L-2-Amino acid
L-Amino acid
L-alpha-amino acids
CHEBI:15705
L-alpha-amino acid
L-alpha-amino acid
IUPAC
L-alpha-amino acids
IUPAC
L-2-Amino acid
KEGG_COMPOUND
L-Amino acid
KEGG_COMPOUND
L-alpha-amino acids
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
An optically active form of glutamic acid having D-configuration.
0
C5H9NO4
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1
WHUUTDBJXJRKMK-GSVOUGTGSA-N
147.12930
147.05316
N[C@H](CCC(O)=O)C(O)=O
CHEBI:21023
CHEBI:4183
Beilstein:1723800
CAS:6893-26-1
DrugBank:DB02517
Gmelin:201189
HMDB:HMDB0003339
KEGG:C00217
KNApSAcK:C00019577
MetaCyc:D-GLT
PDBeChem:DGL
Reaxys:1723800
(2R)-2-aminopentanedioic acid
D-Glutamic acid
D-glutamic acid
chebi_ontology
(R)-2-aminopentanedioic acid
D-2-Aminoglutaric acid
D-Glutaminic acid
D-Glutaminsaeure
DGL
glutamic acid D-form
CHEBI:15966
D-glutamic acid
Beilstein:1723800
Beilstein
CAS:6893-26-1
ChemIDplus
CAS:6893-26-1
KEGG COMPOUND
CAS:6893-26-1
NIST Chemistry WebBook
Gmelin:201189
Gmelin
Reaxys:1723800
Reaxys
(2R)-2-aminopentanedioic acid
IUPAC
D-Glutamic acid
KEGG_COMPOUND
D-glutamic acid
IUPAC
(R)-2-aminopentanedioic acid
ChEBI
D-2-Aminoglutaric acid
KEGG_COMPOUND
D-Glutaminic acid
KEGG_COMPOUND
D-Glutaminsaeure
ChEBI
DGL
PDBeChem
glutamic acid D-form
ChemIDplus
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 optically active form of glutamic acid having L-configuration.
0
C5H9NO4
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
WHUUTDBJXJRKMK-VKHMYHEASA-N
147.12930
147.05316
N[C@@H](CCC(O)=O)C(O)=O
CHEBI:21304
CHEBI:42825
CHEBI:6224
BPDB:2297
Beilstein:1723801
CAS:56-86-0
DrugBank:DB00142
Drug_Central:1310
Gmelin:3502
HMDB:HMDB0000148
KEGG:C00025
KEGG:D00007
KNApSAcK:C00001358
LINCS:LSM-36375
MetaCyc:GLT
PDBeChem:GLU_LFOH
PMID:15739367
PMID:15930465
PMID:16719819
PMID:16892196
PMID:19581495
PMID:22219301
PMID:22735334
Reaxys:1723801
Wikipedia:L-Glutamic_Acid
(2S)-2-aminopentanedioic acid
L-Glutamic acid
L-glutamic acid
chebi_ontology
(S)-2-aminopentanedioic acid
(S)-glutamic acid
E
GLUTAMIC ACID
Glu
Glutamate
L-Glu
L-Glutaminic acid
L-Glutaminsaeure
acide glutamique
acido glutamico
acidum glutamicum
glutamic acid
CHEBI:16015
L-glutamic acid
Beilstein:1723801
Beilstein
CAS:56-86-0
ChemIDplus
CAS:56-86-0
KEGG COMPOUND
CAS:56-86-0
NIST Chemistry WebBook
Drug_Central:1310
DrugCentral
Gmelin:3502
Gmelin
PMID:15739367
Europe PMC
PMID:15930465
Europe PMC
PMID:16719819
Europe PMC
PMID:16892196
Europe PMC
PMID:19581495
Europe PMC
PMID:22219301
Europe PMC
PMID:22735334
Europe PMC
Reaxys:1723801
Reaxys
(2S)-2-aminopentanedioic acid
IUPAC
L-Glutamic acid
KEGG_COMPOUND
L-glutamic acid
IUPAC
(S)-2-aminopentanedioic acid
ChEBI
(S)-glutamic acid
NIST_Chemistry_WebBook
E
ChEBI
GLUTAMIC ACID
PDBeChem
Glu
ChEBI
Glutamate
KEGG_COMPOUND
L-Glu
ChEBI
L-Glutaminic acid
KEGG_COMPOUND
L-Glutaminsaeure
ChEBI
acide glutamique
ChEBI
acido glutamico
ChEBI
acidum glutamicum
ChEBI
glutamic acid
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
A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.
-2
O4S
InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
QAOWNCQODCNURD-UHFFFAOYSA-L
96.06360
95.95283
[O-]S([O-])(=O)=O
CHEBI:15135
CHEBI:45687
CHEBI:9335
Beilstein:3648446
CAS:14808-79-8
Gmelin:2120
HMDB:HMDB0001448
KEGG:C00059
KEGG:D05963
MetaCyc:SULFATE
PDBeChem:SO4
PMID:11200094
PMID:11452993
PMID:11581495
PMID:11798107
PMID:12166931
PMID:12668033
PMID:14597181
PMID:15093386
PMID:15984785
PMID:16186560
PMID:16345535
PMID:16347366
PMID:16348007
PMID:16483812
PMID:16534979
PMID:16656509
PMID:16742508
PMID:16742518
PMID:17120760
PMID:17420092
PMID:17439666
PMID:17709180
PMID:18398178
PMID:18815700
PMID:18846414
PMID:19047345
PMID:19244483
PMID:19544990
PMID:19628332
PMID:19812358
PMID:30398859
Reaxys:3648446
Wikipedia:Sulfate
Sulfate
sulfate
tetraoxidosulfate(2-)
tetraoxosulfate(2-)
tetraoxosulfate(VI)
chebi_ontology
SO4(2-)
SULFATE ION
Sulfate anion(2-)
Sulfate dianion
Sulfate(2-)
Sulfuric acid ion(2-)
[SO4](2-)
sulphate
sulphate ion
CHEBI:16189
sulfate
Beilstein:3648446
Beilstein
CAS:14808-79-8
ChemIDplus
CAS:14808-79-8
NIST Chemistry WebBook
Gmelin:2120
Gmelin
PMID:11200094
Europe PMC
PMID:11452993
Europe PMC
PMID:11581495
Europe PMC
PMID:11798107
Europe PMC
PMID:12166931
Europe PMC
PMID:12668033
Europe PMC
PMID:14597181
Europe PMC
PMID:15093386
Europe PMC
PMID:15984785
Europe PMC
PMID:16186560
Europe PMC
PMID:16345535
Europe PMC
PMID:16347366
Europe PMC
PMID:16348007
Europe PMC
PMID:16483812
Europe PMC
PMID:16534979
Europe PMC
PMID:16656509
Europe PMC
PMID:16742508
Europe PMC
PMID:16742518
Europe PMC
PMID:17120760
Europe PMC
PMID:17420092
Europe PMC
PMID:17439666
Europe PMC
PMID:17709180
Europe PMC
PMID:18398178
Europe PMC
PMID:18815700
Europe PMC
PMID:18846414
Europe PMC
PMID:19047345
Europe PMC
PMID:19244483
Europe PMC
PMID:19544990
Europe PMC
PMID:19628332
Europe PMC
PMID:19812358
Europe PMC
PMID:30398859
Europe PMC
Reaxys:3648446
Reaxys
Sulfate
KEGG_COMPOUND
sulfate
IUPAC
sulfate
UniProt
tetraoxidosulfate(2-)
IUPAC
tetraoxosulfate(2-)
IUPAC
tetraoxosulfate(VI)
IUPAC
SO4(2-)
IUPAC
SULFATE ION
PDBeChem
Sulfate anion(2-)
HMDB
Sulfate dianion
HMDB
Sulfate(2-)
HMDB
Sulfuric acid ion(2-)
HMDB
[SO4](2-)
IUPAC
sulphate
ChEBI
sulphate ion
ChEBI
A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells.
0
(C14H21NO12)n
CHEBI:14412
CHEBI:24622
CHEBI:24623
CHEBI:5772
Beilstein:8538277
CAS:9004-61-9
HMDB:HMDB0010366
KEGG:C00518
KEGG:D08043
KEGG:G10505
PMID:11122186
PMID:18056362
PMID:18290544
Reaxys:8187837
Wikipedia:Hyaluronan
Hyaluronic acid
chebi_ontology
Hyaluronsaeure
[beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n
[beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n
acide hyaluronique
acido hialuronico
hyaluronan
CHEBI:16336
hyaluronic acid
Beilstein:8538277
Beilstein
CAS:9004-61-9
ChemIDplus
CAS:9004-61-9
KEGG COMPOUND
PMID:11122186
Europe PMC
PMID:18056362
Europe PMC
PMID:18290544
Europe PMC
Reaxys:8187837
Reaxys
Hyaluronic acid
KEGG_COMPOUND
Hyaluronsaeure
ChEBI
[beta-D-glucopyranuronosyl-(1->3)-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl-(1->4)]n
ChEBI
[beta-N-Acetyl-D-glucosaminyl(1,4)beta-D-glucuronosyl(1,3)]n
KEGG_COMPOUND
acide hyaluronique
ChEBI
acido hialuronico
ChEBI
hyaluronan
ChEBI
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
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
CHEBI:15131
CHEBI:23008
CHEBI:9318
Wikipedia:Carbohydrate
carbohydrate
carbohydrates
chebi_ontology
Kohlenhydrat
Kohlenhydrate
a carbohydrate
carbohidrato
carbohidratos
glucide
glucides
glucido
glucidos
hydrates de carbone
saccharide
saccharides
saccharidum
CHEBI:16646
carbohydrate
carbohydrate
IUPAC
carbohydrates
IUPAC
Kohlenhydrat
ChEBI
Kohlenhydrate
ChEBI
a carbohydrate
UniProt
carbohidrato
IUPAC
carbohidratos
IUPAC
glucide
ChEBI
glucides
ChEBI
glucido
ChEBI
glucidos
ChEBI
hydrates de carbone
ChEBI
saccharide
IUPAC
saccharides
IUPAC
saccharidum
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
+1
C8H12NO3
InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/p+1
SFLSHLFXELFNJZ-UHFFFAOYSA-O
170.187
170.08117
C1=CC(=CC(=C1O)O)C(C[NH3+])O
chebi_ontology
noradrenaline
CHEBI:166902
noradrenaline(1+)
noradrenaline
UniProt
0
C2H4NO2R
74.05870
74.02420
N[C@H]([*])C(O)=O
CHEBI:12909
CHEBI:13625
CHEBI:20906
CHEBI:4097
KEGG:C00405
D-alpha-amino acid
D-alpha-amino acids
chebi_ontology
D-Amino acid
D-alpha-amino acids
CHEBI:16733
D-alpha-amino acid
D-alpha-amino acid
ChEBI
D-alpha-amino acids
IUPAC
D-Amino acid
KEGG_COMPOUND
D-alpha-amino acids
ChEBI
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
chebi_ontology
glycans
CHEBI:167559
glycan
glycans
ChEBI
An aminoalkylindole consisting of indole having a 2-aminoethyl group at the 3-position.
0
C10H12N2
InChI=1S/C10H12N2/c11-6-5-8-7-12-10-4-2-1-3-9(8)10/h1-4,7,12H,5-6,11H2
APJYDQYYACXCRM-UHFFFAOYSA-N
160.21570
160.10005
NCCc1c[nH]c2ccccc12
CHEBI:15274
CHEBI:27161
CHEBI:46157
CHEBI:9767
Beilstein:125513
CAS:61-54-1
DrugBank:DB08653
Gmelin:603448
HMDB:HMDB0000303
KEGG:C00398
KNApSAcK:C00001434
MetaCyc:TRYPTAMINE
PDBeChem:TSS
PMID:16126914
PMID:22770225
PMID:24345948
PMID:24558969
Reaxys:125513
Wikipedia:Tryptamine
2-(1H-indol-3-yl)ethanamine
Tryptamine
chebi_ontology
1H-indole-3-ethanamine
2-(1H-INDOL-3-YL)ETHANAMINE
2-(3-indolyl)ethylamine
3-(2-Aminoethyl)indole
CHEBI:16765
tryptamine
Beilstein:125513
Beilstein
CAS:61-54-1
ChemIDplus
CAS:61-54-1
KEGG COMPOUND
CAS:61-54-1
NIST Chemistry WebBook
Gmelin:603448
Gmelin
PMID:16126914
Europe PMC
PMID:22770225
Europe PMC
PMID:24345948
Europe PMC
PMID:24558969
Europe PMC
Reaxys:125513
Reaxys
2-(1H-indol-3-yl)ethanamine
IUPAC
Tryptamine
KEGG_COMPOUND
1H-indole-3-ethanamine
NIST_Chemistry_WebBook
2-(1H-INDOL-3-YL)ETHANAMINE
PDBeChem
2-(3-indolyl)ethylamine
ChemIDplus
3-(2-Aminoethyl)indole
KEGG_COMPOUND
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
0
C33H36N4O6
InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-
BPYKTIZUTYGOLE-IFADSCNNSA-N
584.673
584.26348
CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(N2)\C=C2/NC(=O)C(C=C)=C2C)N1
CHEBI:13898
CHEBI:22870
CHEBI:3099
Beilstein:74376
CAS:635-65-4
Gmelin:411033
HMDB:HMDB0000054
KEGG:C00486
KNApSAcK:C00029828
MetaCyc:BILIRUBIN
PDBeChem:BLR
PMID:12799017
PMID:18442622
PMID:23763371
PMID:23768684
PMID:30224965
PMID:8605219
PMID:9587403
Reaxys:74376
Wikipedia:Bilirubin
3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
bilirubin
chebi_ontology
1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid
2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid
2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione
Bilirubin
bilirubin(Z,Z)
bilirubin-IXalpha
CHEBI:16990
bilirubin IXalpha
Beilstein:74376
Beilstein
CAS:635-65-4
ChemIDplus
CAS:635-65-4
KEGG COMPOUND
Gmelin:411033
Gmelin
PMID:12799017
Europe PMC
PMID:18442622
Europe PMC
PMID:23763371
Europe PMC
PMID:23768684
Europe PMC
PMID:30224965
Europe PMC
PMID:8605219
Europe PMC
PMID:9587403
Europe PMC
Reaxys:74376
Reaxys
3,18-diethenyl-2,7,13,17-tetramethyl-1,19-dioxo-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
IUPAC
bilirubin
IUPAC
1,10,19,22,23,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinylbiline-8,12-dipropionic acid
ChemIDplus
2,17-diethenyl-1,10,19,22,23,24-hexahydro-3,7,13,18-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid
ChemIDplus
2,7,13,17-tetramethyl-1,19-dioxo-3,18-divinyl-1,10,19,22,23,24-hexahydro-21H-biline-8,12-dipropanoic acid
IUPAC
8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-3,18-divinylbiladiene-ac-1,19(21H,24H)-dione
JCBN
Bilirubin
KEGG_COMPOUND
bilirubin(Z,Z)
ChEBI
bilirubin-IXalpha
ChEBI
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
CHEBI:13302
CHEBI:21123
CHEBI:33698
CHEBI:4291
CAS:9007-49-2
KEGG:C00039
Deoxyribonucleic acid
deoxyribonucleic acids
chebi_ontology
(Deoxyribonucleotide)m
(Deoxyribonucleotide)n
(Deoxyribonucleotide)n+m
DNA
DNAn
DNAn+1
DNS
Desoxyribonukleinsaeure
deoxyribonucleic acids
desoxyribose nucleic acid
thymus nucleic acid
CHEBI:16991
deoxyribonucleic acid
CAS:9007-49-2
ChemIDplus
CAS:9007-49-2
KEGG COMPOUND
Deoxyribonucleic acid
KEGG_COMPOUND
deoxyribonucleic acids
IUPAC
(Deoxyribonucleotide)m
KEGG_COMPOUND
(Deoxyribonucleotide)n
KEGG_COMPOUND
(Deoxyribonucleotide)n+m
KEGG_COMPOUND
DNA
IUPAC
DNA
KEGG_COMPOUND
DNA
UniProt
DNAn
KEGG_COMPOUND
DNAn+1
KEGG_COMPOUND
DNS
ChEBI
Desoxyribonukleinsaeure
ChEBI
deoxyribonucleic acids
ChEBI
desoxyribose nucleic acid
ChemIDplus
thymus nucleic acid
ChEBI
A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H).
0
COR2
28.010
27.99491
[*]C([*])=O
CHEBI:13427
CHEBI:13646
CHEBI:24974
CHEBI:6127
CHEBI:8742
KEGG:C01450
Wikipedia:Ketone
Ketone
ketones
chebi_ontology
Keton
R-CO-R'
a ketone
cetone
ketones
CHEBI:17087
ketone
Ketone
KEGG_COMPOUND
ketones
IUPAC
Keton
ChEBI
R-CO-R'
KEGG_COMPOUND
a ketone
UniProt
cetone
ChEBI
ketones
ChEBI
A compound in which a carbohydrate component is covalently bound to a protein component.
CHEBI:14349
CHEBI:5481
CHEBI:5493
KEGG:C00326
Glycoprotein
glycoproteins
chebi_ontology
Glykoprotein
Glykoproteine
a glycoprotein
glicoproteina
glicoproteinas
glycoproteine
glycoproteines
CHEBI:17089
glycoprotein
Glycoprotein
KEGG_COMPOUND
glycoproteins
IUPAC
Glykoprotein
ChEBI
Glykoproteine
ChEBI
a glycoprotein
UniProt
glicoproteina
ChEBI
glicoproteinas
ChEBI
glycoproteine
ChEBI
glycoproteines
ChEBI
An aldohexose used as a source of energy and metabolic intermediate.
0
C6H12O6
180.15588
180.06339
CHEBI:14313
CHEBI:24277
CHEBI:33929
CHEBI:5418
CAS:50-99-7
KEGG:C00293
Wikipedia:Glucose
Glucose
gluco-hexose
glucose
chebi_ontology
DL-glucose
Glc
Glukose
CHEBI:17234
glucose
CAS:50-99-7
KEGG COMPOUND
Glucose
KEGG_COMPOUND
gluco-hexose
IUPAC
glucose
IUPAC
DL-glucose
ChEBI
Glc
JCBN
Glukose
ChEBI
Any substance that induces or promotes ferroptosis (a type of programmed cell death dependent on iron and characterized by the accumulation of lipid peroxides) in organisms.
PMID:31899616
PMID:32015325
PMID:33167414
PMID:34012798
Wikipedia:Ferroptosis
chebi_ontology
ferroptosis inducers
CHEBI:173085
ferroptosis inducer
PMID:31899616
Europe PMC
PMID:32015325
SUBMITTER
PMID:33167414
Europe PMC
PMID:34012798
Europe PMC
ferroptosis inducers
ChEBI
The carbon oxoanion resulting from the removal of a proton from carbonic acid.
-1
CHO3
InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
BVKZGUZCCUSVTD-UHFFFAOYSA-M
61.01684
60.99312
OC([O-])=O
CHEBI:13363
CHEBI:22863
CHEBI:40961
CHEBI:5589
Beilstein:3903504
CAS:71-52-3
Gmelin:49249
HMDB:HMDB0000595
KEGG:C00288
MetaCyc:HCO3
PDBeChem:BCT
PMID:17215880
PMID:17505962
PMID:18439416
PMID:28732801
PMID:29150416
PMID:29460248
PMID:29466234
PMID:4208463
Wikipedia:Bicarbonate
Hydrogencarbonate
hydrogen(trioxidocarbonate)(1-)
hydrogencarbonate
hydrogencarbonate(1-)
hydrogentrioxocarbonate(1-)
hydrogentrioxocarbonate(IV)
hydroxidodioxidocarbonate(1-)
chebi_ontology
Acid carbonate
BICARBONATE ION
Bicarbonate
HCO3(-)
HCO3-
[CO2(OH)](-)
hydrogen carbonate
CHEBI:17544
hydrogencarbonate
Beilstein:3903504
Beilstein
CAS:71-52-3
ChemIDplus
Gmelin:49249
Gmelin
PMID:17215880
Europe PMC
PMID:17505962
Europe PMC
PMID:18439416
Europe PMC
PMID:28732801
Europe PMC
PMID:29150416
Europe PMC
PMID:29460248
Europe PMC
PMID:29466234
Europe PMC
PMID:4208463
Europe PMC
Hydrogencarbonate
KEGG_COMPOUND
hydrogen(trioxidocarbonate)(1-)
IUPAC
hydrogencarbonate
IUPAC
hydrogencarbonate
UniProt
hydrogencarbonate(1-)
IUPAC
hydrogentrioxocarbonate(1-)
IUPAC
hydrogentrioxocarbonate(IV)
IUPAC
hydroxidodioxidocarbonate(1-)
IUPAC
Acid carbonate
KEGG_COMPOUND
BICARBONATE ION
PDBeChem
Bicarbonate
KEGG_COMPOUND
HCO3(-)
IUPAC
HCO3-
KEGG_COMPOUND
[CO2(OH)](-)
IUPAC
hydrogen carbonate
PDBeChem
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
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
CHEBI:14517
CHEBI:25054
CHEBI:6486
KEGG:C01356
Lipid
lipids
chebi_ontology
CHEBI:18059
lipid
Lipid
KEGG_COMPOUND
lipids
IUPAC
Any polysaccharide containing a substantial proportion of aminomonosaccharide residues.
CHEBI:14361
CHEBI:24398
CHEBI:5495
KEGG:C02545
Wikipedia:Glycosaminoglycan
Glycosaminoglycan
glycosaminoglycan
chebi_ontology
Glykosaminoglykan
glicosaminoglicano
glycosaminoglycane
glycosaminoglycans
CHEBI:18085
glycosaminoglycan
Glycosaminoglycan
KEGG_COMPOUND
glycosaminoglycan
IUPAC
Glykosaminoglykan
ChEBI
glicosaminoglicano
IUPAC
glycosaminoglycane
IUPAC
glycosaminoglycans
ChEBI
Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose).
CHEBI:14399
CHEBI:24590
CHEBI:5709
GlyGen:G70994MS
GlyTouCan:G70994MS
KEGG:C00738
Hexose
chebi_ontology
WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/
hexoses
CHEBI:18133
hexose
Hexose
KEGG_COMPOUND
WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/
GlyTouCan
hexoses
ChEBI
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
CHEBI:14864
CHEBI:26205
CHEBI:8322
KEGG:C00420
Polysaccharide
polysaccharides
chebi_ontology
Glycan
Glycane
Glykan
Glykane
glycans
polisacarido
polisacaridos
CHEBI:18154
polysaccharide
Polysaccharide
KEGG_COMPOUND
polysaccharides
IUPAC
Glycan
KEGG_COMPOUND
Glycane
ChEBI
Glykan
ChEBI
Glykane
ChEBI
glycans
IUPAC
polisacarido
ChEBI
polisacaridos
IUPAC
An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2.
0
C5H9NO4
InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)
WHUUTDBJXJRKMK-UHFFFAOYSA-N
147.12930
147.05316
NC(CCC(O)=O)C(O)=O
CHEBI:24314
CHEBI:5431
Beilstein:1723799
CAS:617-65-2
Gmelin:101971
KEGG:C00302
KEGG:D04341
KNApSAcK:C00001358
KNApSAcK:C00019577
PMID:15739367
PMID:17190852
PMID:24616376
PMID:24984001
Reaxys:1723799
Wikipedia:Glutamic_acid
2-aminopentanedioic acid
Glutamic acid
glutamic acid
chebi_ontology
2-Aminoglutaric acid
DL-Glutamic acid
DL-Glutaminic acid
E
Glu
Glutamate
Glutaminic acid
Glutaminsaeure
CHEBI:18237
glutamic acid
Beilstein:1723799
Beilstein
CAS:617-65-2
ChemIDplus
CAS:617-65-2
KEGG COMPOUND
CAS:617-65-2
NIST Chemistry WebBook
Gmelin:101971
Gmelin
PMID:15739367
Europe PMC
PMID:17190852
Europe PMC
PMID:24616376
Europe PMC
PMID:24984001
Europe PMC
Reaxys:1723799
Reaxys
2-aminopentanedioic acid
IUPAC
Glutamic acid
KEGG_COMPOUND
glutamic acid
IUPAC
2-Aminoglutaric acid
KEGG_COMPOUND
DL-Glutamic acid
KEGG_DRUG
DL-Glutaminic acid
KEGG_COMPOUND
E
ChEBI
Glu
ChEBI
Glutamate
KEGG_COMPOUND
Glutaminic acid
KEGG_COMPOUND
Glutaminsaeure
ChEBI
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
The R-enantiomer of noradrenaline.
0
C8H11NO3
InChI=1S/C8H11NO3/c9-4-8(12)5-1-2-6(10)7(11)3-5/h1-3,8,10-12H,4,9H2/t8-/m0/s1
SFLSHLFXELFNJZ-QMMMGPOBSA-N
169.17780
169.07389
NC[C@H](O)c1ccc(O)c(O)c1
CHEBI:1
CHEBI:14668
CHEBI:25592
CHEBI:258884
CHEBI:43725
Beilstein:2804840
Beilstein:4231961
CAS:51-41-2
DrugBank:DB00368
Drug_Central:1960
HMDB:HMDB0000216
KEGG:C00547
KEGG:D00076
KNApSAcK:C00001424
PDBeChem:LNR
Reaxys:2804840
Wikipedia:Norepinephrine
4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol
chebi_ontology
(-)-arterenol
(-)-noradrenaline
(-)-norepinephrine
(R)-(-)-norepinephrine
(R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol
(R)-norepinephrine
4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol
Arterenol
L-NOREPINEPHRINE
L-Noradrenaline
Noradrenaline
Norepinephrine
norepinefrina
norepinephrine
norepinephrinum
CHEBI:18357
(R)-noradrenaline
Beilstein:2804840
Beilstein
Beilstein:4231961
ChemIDplus
CAS:51-41-2
ChemIDplus
CAS:51-41-2
KEGG COMPOUND
Drug_Central:1960
DrugCentral
Reaxys:2804840
Reaxys
4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol
IUPAC
(-)-arterenol
ChemIDplus
(-)-noradrenaline
IUPHAR
(-)-norepinephrine
ChemIDplus
(R)-(-)-norepinephrine
ChemIDplus
(R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol
ChemIDplus
(R)-norepinephrine
ChemIDplus
4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol
KEGG_COMPOUND
Arterenol
KEGG_COMPOUND
L-NOREPINEPHRINE
PDBeChem
L-Noradrenaline
KEGG_COMPOUND
Noradrenaline
KEGG_COMPOUND
Norepinephrine
KEGG_COMPOUND
norepinefrina
ChEBI
norepinephrine
ChemIDplus
norepinephrine
WHO_MedNet
norepinephrinum
ChEBI
A phosphate ion that is the conjugate base of hydrogenphosphate.
-3
O4P
InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
NBIIXXVUZAFLBC-UHFFFAOYSA-K
94.97136
94.95507
[O-]P([O-])([O-])=O
CHEBI:14791
CHEBI:45024
CHEBI:7793
Beilstein:3903772
CAS:14265-44-2
Gmelin:1997
KEGG:C00009
PDBeChem:PO4
Reaxys:3903772
phosphate
tetraoxidophosphate(3-)
tetraoxophosphate(3-)
tetraoxophosphate(V)
chebi_ontology
Orthophosphate
PHOSPHATE ION
PO4(3-)
Phosphate
[PO4](3-)
CHEBI:18367
phosphate(3-)
Beilstein:3903772
Beilstein
CAS:14265-44-2
ChemIDplus
CAS:14265-44-2
KEGG COMPOUND
Gmelin:1997
Gmelin
PDBeChem:PO4
ChEBI
Reaxys:3903772
Reaxys
phosphate
IUPAC
tetraoxidophosphate(3-)
IUPAC
tetraoxophosphate(3-)
IUPAC
tetraoxophosphate(V)
IUPAC
Orthophosphate
KEGG_COMPOUND
PHOSPHATE ION
PDBeChem
PO4(3-)
IUPAC
Phosphate
KEGG_COMPOUND
[PO4](3-)
IUPAC
0
C24H42
InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18+,19+,20-,21+,22+,23+,24-/m1/s1
QSHQKIURKJITMZ-OBUPQJQESA-N
330.59028
330.32865
[H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC
Beilstein:2048472
5beta-cholane
chebi_ontology
CHEBI:20664
5beta-cholane
Beilstein:2048472
Beilstein
5beta-cholane
IUPAC
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
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
Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids.
Wikipedia:Alkaloid
Alkaloid
alkaloids
chebi_ontology
Alkaloide
alcaloide
alcaloides
CHEBI:22315
alkaloid
Alkaloid
ChEBI
alkaloids
IUPAC
Alkaloide
ChEBI
alcaloide
ChEBI
alcaloides
ChEBI
chebi_ontology
aminoglycans
CHEBI:22506
aminoglycan
aminoglycans
ChEBI
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 substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
chebi_ontology
antioxidants
antioxydant
antoxidant
CHEBI:22586
antioxidant
antioxidants
ChEBI
antioxydant
ChEBI
antoxidant
ChEBI
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
Basen
ChEBI
Nucleobase
KEGG_COMPOUND
bases
ChEBI
Base
ChEBI
base
ChEBI
base
IUPAC
Base1
KEGG_COMPOUND
Base2
KEGG_COMPOUND
chebi_ontology
benzopyrroles
CHEBI:22728
benzopyrrole
benzopyrroles
ChEBI
A sodium salt of the conjugate of any bile acid with either glycine or taurine.
KEGG:C01558
chebi_ontology
Bile acid
bile salts
CHEBI:22868
bile salt
Bile acid
KEGG_COMPOUND
bile salts
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
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
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
molecular entity
IUPAC
entidad molecular
IUPAC
entidades moleculares
IUPAC
entite moleculaire
IUPAC
molecular entities
IUPAC
molekulare Entitaet
ChEBI
chebi_ontology
Cyclopeptid
Zyklopeptid
cyclic peptides
peptide cyclique
peptido ciclico
CHEBI:23449
cyclic peptide
Cyclopeptid
ChEBI
Zyklopeptid
ChEBI
cyclic peptides
ChEBI
peptide cyclique
IUPAC
peptido ciclico
IUPAC
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
chebi_ontology
drugs
medicine
CHEBI:23888
drug
drugs
ChEBI
medicine
ChEBI
chebi_ontology
monoatomic cations
CHEBI:23906
monoatomic cation
monoatomic cations
ChEBI
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
An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class.
PMID:20716061
chebi_ontology
glutamine family amino acids
CHEBI:24318
glutamine family amino acid
PMID:20716061
Europe PMC
glutamine family amino acids
ChEBI
An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of glutamate--ammonia ligase (EC 6.3.1.2).
Wikipedia:Glutamine_synthetase
chebi_ontology
EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors
EC 6.3.1.2 inhibitor
EC 6.3.1.2 inhibitors
L-glutamate:ammonia ligase (ADP-forming) inhibitor
L-glutamate:ammonia ligase (ADP-forming) inhibitors
L-glutamine synthetase inhibitor
L-glutamine synthetase inhibitors
glutamate--ammonia ligase (EC 6.3.1.2) inhibitor
glutamate--ammonia ligase (EC 6.3.1.2) inhibitors
glutamate--ammonia ligase inhibitor
glutamate--ammonia ligase inhibitors
glutamine synthetase inhibitor
glutamine synthetase inhibitors
glutamylhydroxamic synthetase inhibitor
glutamylhydroxamic synthetase inhibitors
CHEBI:24319
EC 6.3.1.2 (glutamate--ammonia ligase) inhibitor
EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors
ChEBI
EC 6.3.1.2 inhibitor
ChEBI
EC 6.3.1.2 inhibitors
ChEBI
L-glutamate:ammonia ligase (ADP-forming) inhibitor
ChEBI
L-glutamate:ammonia ligase (ADP-forming) inhibitors
ChEBI
L-glutamine synthetase inhibitor
ChEBI
L-glutamine synthetase inhibitors
ChEBI
glutamate--ammonia ligase (EC 6.3.1.2) inhibitor
ChEBI
glutamate--ammonia ligase (EC 6.3.1.2) inhibitors
ChEBI
glutamate--ammonia ligase inhibitor
ChEBI
glutamate--ammonia ligase inhibitors
ChEBI
glutamine synthetase inhibitor
ChEBI
glutamine synthetase inhibitors
ChEBI
glutamylhydroxamic synthetase inhibitor
ChEBI
glutamylhydroxamic synthetase inhibitors
ChEBI
chebi_ontology
CHEBI:24384
glycogens
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chemical entity
chebi_ontology
CHEBI:24431
chemical entity
chemical entity
UniProt
A role played by the molecular entity or part thereof within a biological context.
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
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
A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond.
heterodetic cyclic peptide
chebi_ontology
heterodetic cyclic peptides
peptide cyclique heterodetique
peptido ciclico heterodetico
CHEBI:24533
heterodetic cyclic peptide
heterodetic cyclic peptide
IUPAC
heterodetic cyclic peptides
ChEBI
peptide cyclique heterodetique
IUPAC
peptido ciclico heterodetico
IUPAC
Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds.
chebi_ontology
endocrine
hormones
CHEBI:24621
hormone
endocrine
ChEBI
hormones
ChEBI
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
chebi_ontology
CHEBI:24651
hydroxides
Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position.
chebi_ontology
hydroxy-5beta-cholanic acids
CHEBI:24663
hydroxy-5beta-cholanic acid
hydroxy-5beta-cholanic acids
ChEBI
Any compound containing an indole skeleton.
chebi_ontology
CHEBI:24828
indoles
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
chebi_ontology
inorganic oxides
CHEBI:24836
inorganic oxide
inorganic oxides
ChEBI
A salt is an assembly of cations and anions.
salt
chebi_ontology
Salz
Salze
ionic compound
ionic compounds
sal
sales
salts
sel
sels
CHEBI:24866
salt
salt
IUPAC
Salz
ChEBI
Salze
ChEBI
ionic compound
ChEBI
ionic compounds
ChEBI
sal
ChEBI
sales
ChEBI
salts
ChEBI
sel
ChEBI
sels
ChEBI
chebi_ontology
monoatomic ions
CHEBI:24867
monoatomic ion
monoatomic ions
ChEBI
chebi_ontology
organic salts
organisches Salz
CHEBI:24868
organic salt
organic salts
ChEBI
organisches Salz
ChEBI
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
chebi_ontology
iron compounds
iron molecular entities
CHEBI:24873
iron molecular entity
iron molecular entity
ChEBI
iron compounds
ChEBI
iron molecular entities
ChEBI
Fe
55.845
55.93494
iron cation
chebi_ontology
Fe cation
iron cations
CHEBI:24875
iron cation
iron cation
IUPAC
Fe cation
UniProt
iron cations
ChEBI
chebi_ontology
CHEBI:25046
linear tetrapyrrole
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
chebi_ontology
a metal cation
metal cations
CHEBI:25213
metal cation
a metal cation
UniProt
metal cations
ChEBI
A molecule all atoms of which have the same atomic number.
chebi_ontology
homoatomic molecule
homoatomic molecules
CHEBI:25362
elemental molecule
homoatomic molecule
ChEBI
homoatomic molecules
ChEBI
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
A group of neurotransmitters and neuromodulators that contain one amino group that is connected to an aromatic ring by ethylene group (-CH2-CH2-). Monoamines are derived from the aromatic amino acids phenylalanine, tyrosine, histidine and tryptophan.
chebi_ontology
monamines
monoamines
CHEBI:25375
monoamine molecular messenger
monamines
ChEBI
monoamines
ChEBI
An oxoacid containing a single carboxy group.
chebi_ontology
monocarboxylic acids
CHEBI:25384
monocarboxylic acid
monocarboxylic acids
ChEBI
+1
0.00000
[*+]
chebi_ontology
monoatomic monocations
monovalent inorganic cations
CHEBI:25414
monoatomic monocation
monoatomic monocations
ChEBI
monovalent inorganic cations
ChEBI
An endogenous compound that is used to transmit information across the synapse between a neuron and another cell.
Wikipedia:Neurotransmitter
chebi_ontology
neurotransmitters
CHEBI:25512
neurotransmitter
neurotransmitters
ChEBI
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
Any organic ion with a net positive charge.
chebi_ontology
organic cations
CHEBI:25697
organic cation
organic cations
ChEBI
chebi_ontology
organic ions
CHEBI:25699
organic ion
organic ions
ChEBI
Compounds of the general formula SO3HOR where R is an organyl group
chebi_ontology
organic sulfates
CHEBI:25704
organic sulfate
organic sulfates
ChEBI
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
Any peptide with hormonal activity in animals, whether endocrine, neuroendocrine, or paracrine.
chebi_ontology
peptide hormones
polypeptide hormone
CHEBI:25905
peptide hormone
peptide hormones
ChEBI
polypeptide hormone
ChEBI
Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
phosphates
chebi_ontology
phosphates
CHEBI:26020
phosphate
phosphates
IUPAC
phosphates
ChEBI
A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom.
0
H3O4P
InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
NBIIXXVUZAFLBC-UHFFFAOYSA-N
97.99520
97.97690
[H]OP(=O)(O[H])O[H]
Beilstein:1921286
CAS:7664-38-2
Drug_Central:4478
Gmelin:2000
HMDB:HMDB0002142
KEGG:C00009
KEGG:D05467
KNApSAcK:C00007408
PMID:11455380
PMID:15630224
PMID:17439666
PMID:17518491
PMID:22282755
PMID:22333268
PMID:22381614
PMID:22401268
Reaxys:1921286
Wikipedia:Phosphoric_Acid
Phosphoric acid
phosphoric acid
tetraoxophosphoric acid
trihydrogen tetraoxophosphate(3-)
trihydroxidooxidophosphorus
chebi_ontology
H3PO4
Orthophosphoric acid
Phosphate
Phosphorsaeure
Phosphorsaeureloesungen
[PO(OH)3]
acide phosphorique
acidum phosphoricum
orthophosphoric acid
CHEBI:26078
phosphoric acid
Beilstein:1921286
Beilstein
CAS:7664-38-2
ChemIDplus
CAS:7664-38-2
KEGG COMPOUND
CAS:7664-38-2
NIST Chemistry WebBook
Drug_Central:4478
DrugCentral
Gmelin:2000
Gmelin
PMID:11455380
Europe PMC
PMID:15630224
Europe PMC
PMID:17439666
Europe PMC
PMID:17518491
Europe PMC
PMID:22282755
Europe PMC
PMID:22333268
Europe PMC
PMID:22381614
Europe PMC
PMID:22401268
Europe PMC
Reaxys:1921286
Reaxys
Phosphoric acid
KEGG_COMPOUND
phosphoric acid
IUPAC
tetraoxophosphoric acid
IUPAC
trihydrogen tetraoxophosphate(3-)
IUPAC
trihydroxidooxidophosphorus
IUPAC
H3PO4
IUPAC
Orthophosphoric acid
KEGG_COMPOUND
Phosphate
KEGG_COMPOUND
Phosphorsaeure
ChEBI
Phosphorsaeureloesungen
ChEBI
[PO(OH)3]
IUPAC
acide phosphorique
ChEBI
acidum phosphoricum
ChEBI
orthophosphoric acid
NIST_Chemistry_WebBook
chebi_ontology
CHEBI:26079
phosphoric acid derivative
chebi_ontology
phosphorus molecular entities
CHEBI:26082
phosphorus molecular entity
phosphorus molecular entities
ChEBI
Any amino acid whose side chain is capable of forming one or more hydrogen bonds.
0
C2H4NO2R
74.059
74.02420
OC(C(*)N)=O
CHEBI:8283
MetaCyc:Polar-amino-acids
PMID:12016058
polar amino acid
chebi_ontology
polar amino acids
polar amino-acid
polar amino-acids
CHEBI:26167
polar amino acid
PMID:12016058
Europe PMC
polar amino acid
ChEBI
polar amino acids
ChEBI
polar amino-acid
ChEBI
polar amino-acids
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
chebi_ontology
sodium compounds
sodium molecular entities
CHEBI:26712
sodium molecular entity
sodium compounds
ChEBI
sodium molecular entities
ChEBI
Any alkali metal salt having sodium(1+) as the cation.
chebi_ontology
Natriumsalz
Natriumsalze
sodium salts
CHEBI:26714
sodium salt
Natriumsalz
ChEBI
Natriumsalze
ChEBI
sodium salts
ChEBI
Any steroid that acts as hormone.
chebi_ontology
Steroidhormon
Steroidhormone
hormona esteroide
hormonas esteroideas
hormone steroide
hormones steroides
steroid hormones
CHEBI:26764
steroid hormone
Steroidhormon
ChEBI
Steroidhormone
ChEBI
hormona esteroide
ChEBI
hormonas esteroideas
ChEBI
hormone steroide
ChEBI
hormones steroides
ChEBI
steroid hormones
ChEBI
An ester of an alcohol and sulfuric acid.
0
O4SR2
96.06300
95.95173
[*]OS(=O)(=O)O[*]
chebi_ontology
sulfate ester
sulfuric acid ester
sulfuric acid esters
CHEBI:26819
sulfuric ester
sulfate ester
ChEBI
sulfuric acid ester
ChEBI
sulfuric acid esters
ChEBI
Salts and esters of sulfuric acid
sulfates
chebi_ontology
sulfuric acid derivative
sulphates
CHEBI:26820
sulfates
sulfates
ChEBI
sulfuric acid derivative
ChEBI
sulphates
ChEBI
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
sulfur
UniProt
sulphur
ChEBI
theion
IUPAC
sulfur molecular entity
chebi_ontology
sulfur molecular entities
CHEBI:26835
sulfur molecular entity
sulfur molecular entity
ChEBI
sulfur molecular entities
ChEBI
A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom.
0
H2O4S
InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)
QAOWNCQODCNURD-UHFFFAOYSA-N
98.07948
97.96738
[H]OS(=O)(=O)O[H]
CAS:7664-93-9
Gmelin:2122
KEGG:C00059
KEGG:D05963
KNApSAcK:C00007530
MolBase:4
PMID:13568755
PMID:16122922
PMID:19397353
PMID:22047659
PMID:22136045
PMID:22204399
PMID:22267186
PMID:22296037
PMID:22364556
PMID:22435616
PPDB:606
Reaxys:2037554
Wikipedia:Sulfuric_acid
Sulfuric acid
dihydrogen tetraoxosulfate
dihydroxidodioxidosulfur
hydrogen tetraoxosulfate(2-)
hydrogen tetraoxosulfate(VI)
sulfuric acid
tetraoxosulfuric acid
chebi_ontology
Acide sulfurique
Acido sulfurico
Acidum sulfuricum
H2SO4
Schwefelsaeureloesungen
[S(OH)2O2]
[SO2(OH)2]
sulphuric acid
CHEBI:26836
sulfuric acid
CAS:7664-93-9
ChemIDplus
CAS:7664-93-9
KEGG COMPOUND
CAS:7664-93-9
NIST Chemistry WebBook
Gmelin:2122
Gmelin
PMID:13568755
Europe PMC
PMID:16122922
Europe PMC
PMID:19397353
Europe PMC
PMID:22047659
Europe PMC
PMID:22136045
Europe PMC
PMID:22204399
Europe PMC
PMID:22267186
Europe PMC
PMID:22296037
Europe PMC
PMID:22364556
Europe PMC
PMID:22435616
Europe PMC
Reaxys:2037554
Reaxys
Sulfuric acid
KEGG_COMPOUND
dihydrogen tetraoxosulfate
IUPAC
dihydroxidodioxidosulfur
IUPAC
hydrogen tetraoxosulfate(2-)
IUPAC
hydrogen tetraoxosulfate(VI)
IUPAC
sulfuric acid
ChEBI
sulfuric acid
IUPAC
tetraoxosulfuric acid
IUPAC
Acide sulfurique
ChemIDplus
Acido sulfurico
ChemIDplus
Acidum sulfuricum
ChemIDplus
H2SO4
IUPAC
Schwefelsaeureloesungen
ChemIDplus
[S(OH)2O2]
MolBase
[SO2(OH)2]
IUPAC
sulphuric acid
MolBase
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
tetrapyrrole
tetrapyrroles
chebi_ontology
a tetrapyrrole
CHEBI:26932
tetrapyrrole
tetrapyrrole
IUPAC
tetrapyrroles
IUPAC
a tetrapyrrole
UniProt
Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions.
Wikipedia:Micronutrient
chebi_ontology
micronutrients
trace elements
CHEBI:27027
micronutrient
micronutrients
ChEBI
trace elements
ChEBI
An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
transition element
chebi_ontology
Uebergangselement
Uebergangsmetalle
metal de transicion
metal de transition
metales de transicion
metaux de transition
transition element
transition elements
transition metal
transition metals
CHEBI:27081
transition element atom
transition element
IUPAC
Uebergangselement
ChEBI
Uebergangsmetalle
ChEBI
metal de transicion
ChEBI
metal de transition
ChEBI
metales de transicion
ChEBI
metaux de transition
ChEBI
transition element
ChEBI
transition elements
ChEBI
transition metal
ChEBI
transition metals
ChEBI
Tryptamine and its substitution derivatives.
chebi_ontology
CHEBI:27162
tryptamines
chebi_ontology
heterobicyclic compounds
organic heterobicyclic compounds
CHEBI:27171
organic heterobicyclic compound
heterobicyclic compounds
ChEBI
organic heterobicyclic compounds
ChEBI
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
chebi_ontology
univalent acyl group
univalent carboacyl groups
univalent carboxylic acyl groups
CHEBI:27207
univalent carboacyl group
univalent acyl group
ChEBI
univalent carboacyl groups
ChEBI
univalent carboxylic acyl groups
ChEBI
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
zwitterion
zwitterions
chebi_ontology
compose zwitterionique
compuestos zwitterionicos
zwitteriones
zwitterionic compounds
CHEBI:27369
zwitterion
zwitterion
IUPAC
zwitterions
IUPAC
compose zwitterionique
IUPAC
compuestos zwitterionicos
IUPAC
zwitteriones
IUPAC
zwitterionic compounds
IUPAC
0
C
InChI=1S/C
OKTJSMMVPCPJKN-UHFFFAOYSA-N
12.01070
12.00000
[C]
CHEBI:23009
CHEBI:3399
CAS:7440-44-0
KEGG:C06265
WebElements:C
carbon
chebi_ontology
6C
C
Carbon
Kohlenstoff
carbon
carbone
carbonium
carbono
CHEBI:27594
carbon atom
CAS:7440-44-0
ChemIDplus
CAS:7440-44-0
KEGG COMPOUND
carbon
IUPAC
6C
IUPAC
C
IUPAC
C
KEGG_COMPOUND
Carbon
KEGG_COMPOUND
Kohlenstoff
ChEBI
carbon
ChEBI
carbone
ChEBI
carbonium
ChEBI
carbono
ChEBI
A polydisperse, highly branched glucan composed of chains of D-glucopyranose residues in alpha(1->4) glycosidic linkage, joined together by alpha(1->6) glycosidic linkages. A small number of alpha(1->3) glycosidic linkages and some cumulative alpha(1->6) links also may occur. The branches in glycogen typically contain 8 to 12 glucose residues.
CHEBI:24379
CHEBI:5466
CAS:9005-79-2
GlyGen:G99991IU
GlyTouCan:G99991IU
HMDB:HMDB0000757
KEGG:C00182
MetaCyc:CPD0-971
Wikipedia:Glycogen
Glycogen
chebi_ontology
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1
animal starch
liver starch
CHEBI:28087
glycogen
CAS:9005-79-2
ChemIDplus
CAS:9005-79-2
KEGG COMPOUND
Glycogen
KEGG_COMPOUND
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_b6-d1
GlyTouCan
animal starch
ChemIDplus
liver starch
ChemIDplus
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
0
CH3NO2
InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)
KXDHJXZQYSOELW-UHFFFAOYSA-N
61.04006
61.01638
NC(O)=O
CHEBI:22504
CHEBI:23002
CHEBI:3386
CHEBI:44573
Beilstein:1734754
CAS:463-77-4
DrugBank:DB04261
Gmelin:130345
KEGG:C01563
PDBeChem:OUT
Wikipedia:Carbamic_acid
CARBAMIC ACID
Carbamic acid
carbamic acid
chebi_ontology
Aminoameisensaeure
Aminoformic acid
Carbamate
Carbamidsaeure
CHEBI:28616
carbamic acid
Beilstein:1734754
Beilstein
CAS:463-77-4
ChemIDplus
CAS:463-77-4
KEGG COMPOUND
Gmelin:130345
Gmelin
CARBAMIC ACID
PDBeChem
Carbamic acid
KEGG_COMPOUND
carbamic acid
IUPAC
Aminoameisensaeure
ChEBI
Aminoformic acid
KEGG_COMPOUND
Carbamate
KEGG_COMPOUND
Carbamidsaeure
ChEBI
0
P
InChI=1S/P
OAICVXFJPJFONN-UHFFFAOYSA-N
30.97376
30.97376
[P]
CHEBI:26080
CHEBI:8168
CAS:7723-14-0
Gmelin:16235
KEGG:C06262
WebElements:P
phosphorus
chebi_ontology
15P
P
Phosphor
Phosphorus
fosforo
phosphore
phosphorus
CHEBI:28659
phosphorus atom
CAS:7723-14-0
ChemIDplus
CAS:7723-14-0
KEGG COMPOUND
Gmelin:16235
Gmelin
phosphorus
IUPAC
15P
IUPAC
P
IUPAC
P
KEGG_COMPOUND
Phosphor
ChEBI
Phosphorus
KEGG_COMPOUND
fosforo
ChEBI
phosphore
ChEBI
phosphorus
ChEBI
A primary amino compound that is the 5-hydroxy derivative of tryptamine.
0
C10H12N2O
InChI=1S/C10H12N2O/c11-4-3-7-6-12-10-2-1-8(13)5-9(7)10/h1-2,5-6,12-13H,3-4,11H2
QZAYGJVTTNCVMB-UHFFFAOYSA-N
176.215
176.09496
C1=CC(=CC=2C(=CNC12)CCN)O
CHEBI:1420
CHEBI:26652
CHEBI:49894
Beilstein:143524
CAS:50-67-9
Gmelin:1861995
HMDB:HMDB0000259
KEGG:C00780
KNApSAcK:C00001429
LINCS:LSM-6589
MetaCyc:SEROTONIN
PDBeChem:SRO
PMID:18593914
PMID:22770225
PMID:24136337
Reaxys:143524
Wikipedia:Serotonin
3-(2-aminoethyl)-1H-indol-5-ol
SEROTONIN
Serotonin
chebi_ontology
3-(2-Aminoethyl)-1H-indol-5-ol
5-HT
5-Hydroxytryptamine
Enteramine
serotonine
thrombocytin
thrombotonin
CHEBI:28790
serotonin
Beilstein:143524
Beilstein
CAS:50-67-9
ChemIDplus
CAS:50-67-9
KEGG COMPOUND
Gmelin:1861995
Gmelin
PMID:18593914
Europe PMC
PMID:22770225
Europe PMC
PMID:24136337
Europe PMC
Reaxys:143524
Reaxys
3-(2-aminoethyl)-1H-indol-5-ol
IUPAC
SEROTONIN
PDBeChem
Serotonin
KEGG_COMPOUND
3-(2-Aminoethyl)-1H-indol-5-ol
KEGG_COMPOUND
5-HT
IUPHAR
5-Hydroxytryptamine
KEGG_COMPOUND
Enteramine
KEGG_COMPOUND
serotonine
ChEBI
thrombocytin
ChemIDplus
thrombotonin
ChemIDplus
An onium cation obtained by protonation of ammonia.
+1
H4N
InChI=1S/H3N/h1H3/p+1
QGZKDVFQNNGYKY-UHFFFAOYSA-O
18.03850
18.03383
[H][N+]([H])([H])[H]
CHEBI:22534
CHEBI:49783
CHEBI:7435
CAS:14798-03-9
Gmelin:84
KEGG:C01342
MetaCyc:AMMONIUM
MolBase:929
PDBeChem:NH4
PMID:11319011
PMID:11341317
PMID:12096804
PMID:14512268
PMID:14879753
PMID:16345391
PMID:16903292
PMID:17392693
PMID:18515490
PMID:19199063
PMID:19596600
PMID:19682559
PMID:19716251
PMID:21993530
PMID:22265469
PMID:22524020
PMID:22562341
PMID:22631217
Reaxys:16093784
Wikipedia:Ammonium
ammonium
azanium
chebi_ontology
Ammonium(1+)
NH4(+)
NH4+
[NH4](+)
ammonium cation
ammonium ion
CHEBI:28938
ammonium
CAS:14798-03-9
ChemIDplus
CAS:14798-03-9
NIST Chemistry WebBook
Gmelin:84
Gmelin
PMID:11319011
Europe PMC
PMID:11341317
Europe PMC
PMID:12096804
Europe PMC
PMID:14512268
Europe PMC
PMID:14879753
Europe PMC
PMID:16345391
Europe PMC
PMID:16903292
Europe PMC
PMID:17392693
Europe PMC
PMID:18515490
Europe PMC
PMID:19199063
Europe PMC
PMID:19596600
Europe PMC
PMID:19682559
Europe PMC
PMID:19716251
Europe PMC
PMID:21993530
Europe PMC
PMID:22265469
Europe PMC
PMID:22524020
Europe PMC
PMID:22562341
Europe PMC
PMID:22631217
Europe PMC
Reaxys:16093784
Reaxys
ammonium
ChEBI
ammonium
IUPAC
azanium
IUPAC
Ammonium(1+)
ChemIDplus
NH4(+)
IUPAC
NH4(+)
UniProt
NH4+
KEGG_COMPOUND
[NH4](+)
MolBase
ammonium cation
ChemIDplus
ammonium ion
PDBeChem
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid.
-2
C2O4R
88.019
87.97966
[O-]C(=O)[*]C([O-])=O
CHEBI:13632
CHEBI:23688
CHEBI:23689
CHEBI:38711
dicarboxylic acid dianion
chebi_ontology
a dicarboxylate
dicarboxylate
dicarboxylates
dicarboxylic acid dianions
CHEBI:28965
dicarboxylic acid dianion
dicarboxylic acid dianion
ChEBI
a dicarboxylate
UniProt
dicarboxylate
ChEBI
dicarboxylates
ChEBI
dicarboxylic acid dianions
ChEBI
0
CH2O3
InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)
BVKZGUZCCUSVTD-UHFFFAOYSA-N
62.02478
62.00039
OC(O)=O
CHEBI:13351
CHEBI:23017
CHEBI:23744
CHEBI:3401
CAS:463-79-6
Gmelin:25554
KEGG:C01353
PDBeChem:CO3
Carbonic acid
carbonic acid
dihydroxidooxidocarbon
chebi_ontology
Dihydrogen carbonate
H2CO3
Koehlensaeure
[CO(OH)2]
CHEBI:28976
carbonic acid
CAS:463-79-6
ChemIDplus
CAS:463-79-6
KEGG COMPOUND
Gmelin:25554
Gmelin
Carbonic acid
KEGG_COMPOUND
carbonic acid
IUPAC
dihydroxidooxidocarbon
IUPAC
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