A formal ontology of phenotypes observed in fission yeast.
Fission Yeast Phenotype Ontology (FYPO)
OBO-Edit 2.3.1
12:05:2020 14:21
fission_yeast_phenotype
1.2
midori
svn version: $Revision: 303 $
2022-05-16
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
has obsolescence reason
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
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
Term not to be used for direct annotation
Term not to be used for direct manual annotation
http://purl.org/dc/elements/1.1/creator
uberon
dc-creator
true
dc-creator
creator
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/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
Used in FYPO to identify phenotypes that are always observed in the context of another, usually larger-scale, phenotype.
BFO:0000050
BrendaTissueOBO
external
fission_yeast_phenotype
protein
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/
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
Used in FYPO to link phenotypes that are collections of features to phenotypes representing the features.
BFO:0000051
chebi_ontology
external
fission_yeast_phenotype
protein
quality
uberon
has_part
false
has_part
has part
has part
has_part
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X).
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
external
uberon
preceded_by
preceded_by
preceded by
preceded by
preceded_by
is preceded by
SIO:000249
takes place after
Allen:precedes
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
external
uberon
precedes
precedes
precedes
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Used in FYPO to identify a location, usually a cellular component or cell type, within which a phenotype is observed or relevant.
BFO:0000066
external
fission_yeast_phenotype
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
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer.
cjm
2009-07-31T02:15:46Z
BSPO:0000096
uberon
anterior_to
anterior_to
anterior_to
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer.
http://orcid.org/0000-0002-6601-2165
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:0000097
uberon
distal_to
distal_to
distal_to
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
http://orcid.org/0000-0002-6601-2165
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000098
uberon
dorsal_to
dorsal_to
dorsal_to
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
http://orcid.org/0000-0002-6601-2165
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
BSPO:0000099
caudal_to
uberon
posterior_to
posterior_to
posterior_to
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
http://orcid.org/0000-0002-6601-2165
x proximal_to y iff x is closer to the point of attachment with the body than y.
BSPO:0000100
uberon
proximal_to
proximal_to
proximal_to
x proximal_to y iff x is closer to the point of attachment with the body than y.
http://orcid.org/0000-0002-6601-2165
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000102
uberon
ventral_to
ventral_to
ventral_to
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
http://orcid.org/0000-0002-6601-2165
BSPO:0000107
uberon
deep_to
deep_to
deep_to
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:0000120
uberon
in_left_side_of
in_left_side_of
in_left_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
BSPO:PATO_mtg_2009
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:0000121
uberon
in_right_side_of
in_right_side_of
in_right_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
BSPO:PATO_mtg_2009
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in_posterior_side_of
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:PATO_mtg_2009
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:0000123
uberon
in_anterior_side_of
in_anterior_side_of
in_anterior_side_of
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
BSPO:PATO_mtg_2009
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure.
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure.
https://orcid.org/0000-0002-6601-2165
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y.
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y.
https://orcid.org/0000-0002-6601-2165
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
http://orcid.org/0000-0002-6601-2165
Identifies a process, cell cycle stage or life stage during which a phenotype that affects an occurrent, i.e. a biological process or molecular function, is observed or relevant.
GOREL:0000001
fission_yeast_phenotype
happens_during
happens_during
happens_during
Identifies a process, cell cycle stage or life stage during which a phenotype is observed or relevant.
GOREL:0000002
fission_yeast_phenotype
during
during
during
Identifies a process, cell cycle stage or life stage during which a phenotype that affects a continuant, such as a cellular component or the level of a substance, is observed or relevant.
GOREL:0000032
fission_yeast_phenotype
exists_during
exists_during
exists_during
This relation is not constrained with respect to whether the place where an event occurs completely surrounds, or is adjacent to, the location indicated. Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin. Used in FYPO to identify a position where a phenotype is observed or relevant, usually a DNA or RNA sequence feature specified by a SO ID.
GOREL:0000501
fission_yeast_phenotype
occurs_at
occurs_at
occurs_at
GOREL:0002003
external
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
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
inheres in
this fragility inheres in this vase
this fragility is a characteristic of this vase
this red color inheres in this apple
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
Used in FYPO as described in PATO best practices; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps).
RO:0000052
fission_yeast_phenotype
inheres_in
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
inheres in
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
external
uberon
bearer_of
bearer_of
bearer of
bearer of
has characteristic
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
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
protein
uberon
has_quality
false
has_quality
has quality
has quality
has_quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
chebi_ontology
has_role
false
false
has_role
has role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
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/
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
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/
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
Used in FYPO to indicate where a physical quality phenotype is observed.
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
fission_yeast_phenotype
protein
uberon
located_in
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
RO:0002000
uberon
boundary_of
boundary_of
2D boundary of
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.
David Osumi-Sutherland
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
David Osumi-Sutherland
http://www.ncbi.nlm.nih.gov/pubmed/22402613
RO:0002005
nerve supply
uberon
innervated_by
innervated_by
http://code.google.com/p/obo-relations/issues/detail?id=6
innervated_by
innervated_by
nerve supply
FMA:85999
X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000
David Osumi-Sutherland
RO:0002007
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.
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 relationship that holds between a process that regulates a transport process and the entity transported by that process.
David Osumi-Sutherland
regulates transport 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
Relation between occurrents, shares start and end boundaries.
David Osumi-Sutherland
RO:0002082
coincides_with
is_equal_to
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
Relation between occurrents, shares start and end boundaries.
Allen:is_equal_to
https://orcid.org/0000-0002-6601-2165
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
David Osumi-Sutherland
di
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y).
David Osumi-Sutherland
starts_at_end_of
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
external
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
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
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
RO:0002092
external
happens_during
happens_during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
happens during
David Osumi-Sutherland
o
overlaps
RO:0002093
external
ends_during
ends_during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
ends_during
Relation between a neuron and an anatomical structure that its soma is part of.
David Osumi-Sutherland
<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
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.
Alexander Diehl
Chris Mungall
Lindsay Cowell
<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
x overlaps y if and only if there exists some z such that x has part z and z part of y
BFO_0000051 some (BFO_0000050 some ?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.
David Osumi-Sutherland
<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
http://code.google.com/p/obo-relations/issues/detail?id=6
innervates
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
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'
S only_in_taxon T iff: S SubClassOf in_taxon only T.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
uberon
only_in_taxon
only_in_taxon
only in taxon
only_in_taxon
S only_in_taxon T iff: S SubClassOf in_taxon only T.
PMID:20973947
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-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).
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
RO:0002176
uberon
connects
connects
connects
connects
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-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
attaches_to_part_of
true
true
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
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
arterial supply of
uberon
supplies
supplies
source: FMA
supplies
supplies
arterial supply of
FMA:86003
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
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
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
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
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
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
develops_into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
Chris Mungall
David Osumi-Sutherland
has developmental precursor
FBbt
RO:0002207
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
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO: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.
Chris Mungall
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
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y.
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded_by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y.
https://orcid.org/0000-0002-6601-2165
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary.
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
external
uberon
adjacent_to
adjacent_to
adjacent to
adjacent to
adjacent_to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
inverse of surrounded by
inverse of surrounded_by.
Chris Mungall
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
inverse of surrounded_by.
https://orcid.org/0000-0002-6601-2165
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
inverse of starts with
Chris Mungall
Allen
RO:0002223
uberon
starts
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
https://orcid.org/0000-0002-6601-2165
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
Chris Mungall
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
Chris Mungall
EHDAA2
Jonathan Bard, EHDAA2
RO:0002226
uberon
develops_in
develops_in
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
develops_in
Relation between occurrents, shares an end boundary with.
inverse of ends with
Chris Mungall
RO:0002229
finishes
uberon
ends
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
https://orcid.org/0000-0002-6601-2165
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
Chris Mungall
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
Chris Mungall
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.
Chris Mungall
consumes
RO:0002233
external
has_input
has_input
has input
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
Chris Mungall
produces
RO:0002234
external
has_output
has_output
has output
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
developmentally_contributes_to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
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
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
developmentally_induced_by
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
GO:0001759
Inverse of developmentally induced by
Chris Mungall
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
RO:0002258
uberon
developmentally_preceded_by
developmentally_preceded_by
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
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
Chris Mungall
replaces
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally replaces
developmentally_replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
Chris Mungall
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
Chris Mungall
RO:0002295
external
results_in_developmental_progression_of
results_in_developmental_progression_of
results in developmental progression of
results in developmental progression of
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.
Chris Mungall
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)
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002297
external
results_in_formation_of
results_in_formation_of
results in formation of
results in formation of
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.
Chris Mungall
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.
Chris Mungall
GOC:mtg_berkeley_2013
RO:0002299
external
results_in_maturation_of
results_in_maturation_of
results in maturation of
results in maturation of
cjm
RO:0002304
external
causally_upstream_of,_positive_effect
causally_upstream_of,_positive_effect
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
cjm
RO:0002305
external
causally_upstream_of,_negative_effect
causally_upstream_of,_negative_effect
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
causally upstream of, negative effect
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
Chris Mungall
regulates localization of
RO:0002313
external
transports_or_maintains_localization_of
transports_or_maintains_localization_of
transports or maintains localization of
transports or maintains localization of
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
Chris Mungall
inheres in part of
Used in FYPO as described in MP/HP logical definition best practices for processes, and in an analogous manner for cell/cell part structure; identifies an entity that displays a quality in an entity-quality logical definition. Used only in logical definitions (aka xps).
RO:0002314
fission_yeast_phenotype
inheres_in_part_of
inheres_in_part_of
characteristic of part of
inheres in 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
Chris Mungall
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
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
part of structure that is capable of
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
Chris Mungall
actively involved in
enables part of
involved in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
Chris Mungall
regulates levels of (process to entity)
RO:0002332
external
regulates_levels_of
regulates_levels_of
regulates levels of
regulates levels of
inverse of enables
Chris Mungall
enabled by
inverse of regulates
Chris Mungall
regulated by (processual)
RO:0002334
external
regulated_by
regulated_by
regulated by
regulated by
inverse of negatively regulates
Chris Mungall
RO:0002335
external
negatively_regulated_by
negatively_regulated_by
negatively regulated by
negatively regulated by
inverse of positively regulates
Chris Mungall
RO:0002336
external
positively_regulated_by
positively_regulated_by
positively regulated by
positively regulated by
A relationship that holds via some process of localization
Chris Mungall
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.
Chris Mungall
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.
Chris Mungall
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
Chris Mungall
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.
Chris Mungall
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'
Chris Mungall
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)
Chris Mungall
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
RO:0002350
uberon
member_of
member_of
member of
member of
has member is a mereological relation between a collection and an item.
SIO
RO:0002351
uberon
has_member
has_member
has member
has member
inverse of has input
Chris Mungall
RO:0002352
uberon
input_of
input_of
input of
input of
inverse of has output
Chris Mungall
RO:0002353
external
protein
uberon
output_of
false
output_of
output of
output of
output_of
Chris Mungall
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
Chris Mungall
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_to
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.
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.
Chris Mungall
Wikipedia:Insertion_(anatomy)
RO:0002373
uberon
has_muscle_insertion
has_muscle_insertion
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
has muscle insertion
has_muscle_insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
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)
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.
Chris Mungall
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.
Chris Mungall
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
drains into
tributary_of
tributary_of
tributary of
tributary_of
http://en.wikipedia.org/wiki/Tributary
drains into
dbpowl:drainsTo
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
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
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
Chris Mungall
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).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y.
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
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
Chris Mungall
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y.
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
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
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y.
Chris Mungall
RO:0002388
uberon
has_potential_to_directly_develop_into
has_potential_to_directly_develop_into
has potential to directly develop into
has potential to directly develop into
inverse of upstream of
Chris Mungall
RO:0002404
external
causally_downstream_of
causally_downstream_of
causally downstream of
causally downstream of
Chris Mungall
RO:0002405
external
immediately_causally_downstream_of
immediately_causally_downstream_of
immediately causally downstream of
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
RO:0002411
external
causally_upstream_of
causally_upstream_of
causally upstream of
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
RO:0002412
external
immediately_causally_upstream_of
immediately_causally_upstream_of
immediately causally upstream of
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
RO:0002418
external
affects
causally_upstream_of_or_within
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
RO:0002427
external
causally_downstream_of_or_within
causally_downstream_of_or_within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
Chris Mungall
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/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.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y.
Chris Mungall
RO:0002473
uberon
composed_primarily_of
composed_primarily_of
composed primarily of
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Chris Mungall
is ubiquitination
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
Chris Mungall
RO:0002488
begins_to_exist_during
uberon
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
https://orcid.org/0000-0002-6601-2165
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
Chris Mungall
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
https://orcid.org/0000-0002-6601-2165
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
Chris Mungall
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence overlaps
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
Chris Mungall
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).
Chris Mungall
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
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
Chris Mungall
RO:0002493
uberon
existence_ends_with
existence_ends_with
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
https://orcid.org/0000-0002-6601-2165
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
Chris Mungall
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
Chris Mungall
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
https://orcid.org/0000-0002-6601-2165
immediately transforms from
SIO:000658
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
Chris Mungall
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.
Chris Mungall
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
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.
Chris Mungall
Relation binding a relational quality or disposition to the relevant type of entity. Used in FYPO as described in PATO best practices; identifies abolished GO processes; identifies substances affected by phenotypes.
RO:0002503
fission_yeast_phenotype
towards
towards
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
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
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.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
Chris Mungall
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 sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
http://orcid.org/0000-0002-6601-2165
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
Chris Mungall
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
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
inverse of branching part of
Chris Mungall
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
Chris Mungall
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
Chris Mungall
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
A relation that holds between an attribute or a qualifier and another attribute.
Chris Mungall
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
Used in FYPO as described in PATO best practices; placeholder relation to indicate normality/abnormality.
RO:0002573
fission_yeast_phenotype
qualifier
qualifier
has modifier
qualifier
inverse of has skeleton
Chris Mungall
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
results in breakdown of
RO:0002588
external
results_in_assembly_of
results_in_assembly_of
results in assembly of
results_in_assembly_of
RO:0002590
external
results_in_disassembly_of
results_in_disassembly_of
results in disassembly of
results_in_disassembly_of
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
RO:0002592
external
results_in_organization_of
results_in_organization_of
results in organization of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
RO:0002608
external
process_has_causal_agent
process_has_causal_agent
process has causal agent
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
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.
Melissa Haendel
RO:0003001
external
uberon
produced_by
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.
cjm
2018-12-13T11:26:17Z
RO:0004007
external
has_primary_input_or_output
has_primary_input_or_output
has primary input or output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
cjm
2018-12-13T11:26:32Z
RO:0004008
external
has_primary_output
has_primary_output
has primary output
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
GOC:cjm
GOC:dph
GOC:kva
GOC:pt
PMID:27812932
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
cjm
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.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
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
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
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
A diagnostic testing device utilizes a specimen.
X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.
Asiyah Lin
https://orcid.org/0000-0001-9625-1899 Bill Duncan
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
2021-11-08
2021-11-08T12:00:00Z
utilizes
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
p has anatomical participant c iff p has participant c, and c is an anatomical entity
cjm
2018-09-26T01:08:58Z
results in changes to anatomical or cellular structure
chebi_ontology
has_functional_parent
false
false
has functional parent
chebi_ontology
has_parent_hydride
false
false
has parent hydride
chebi_ontology
is_conjugate_acid_of
true
false
is conjugate acid of
chebi_ontology
is_conjugate_base_of
true
false
is conjugate base of
chebi_ontology
is_enantiomer_of
true
false
is enantiomer of
chebi_ontology
is_substituent_group_from
false
false
is substituent group from
chebi_ontology
is_tautomer_of
true
is tautomer 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
p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues.
Def comes from gorel file. Used in FYPO where one phenotype (p) always results in an additional phenotype (c) as a consequence. There may be other ways to get phenotype (c).
fission_yeast_phenotype
has_output
has_output
p has output c if either: p has direct output c or p has output input c. Implies that if p happens, c always ensues.
GOC:curators
Inverse of has_output. Relation between a structure and a process that forms it, or between one process and a preceding process; A output_of B used where B has_output A isn't always true. Implies that process B is the only way to get output. Used in FYPO where one phenotype (c) always results when another phenotype (p) is present. Phenotype (p) may have other consequences in addition to phenotype (c).
formation results from
fission_yeast_phenotype
output_of
output_of
formation results from
PomBase:mah
Used in FYPO when a phenotype is observed after another event, usually a GO biological process, has ended, and where there isn't a suitable process to use with a during relation.
fission_yeast_phenotype
preceded_by
preceded_by
Used in FYPO when a phenotype is observed before another event, usually a GO biological process, begins, and where there isn't a suitable process to use with a during relation.
fission_yeast_phenotype
precedes
precedes
protein
has_gene_template
false
has_gene_template
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
sequence
adjacent_to
adjacent_to
A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.
PMID:20226267
SO:ke
sequence
derives_from
derives_from
Inverse of part_of.
sequence
has_part
Example: operon has_part gene.
has_part
Inverse of part_of.
http://precedings.nature.com/documents/3495/version/1
sequence
has_quality
The relationship between a feature and an attribute.
has_quality
sequence
member_of
A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
member_of
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
kareneilbeck
2010-10-14T01:33:15Z
sequence
overlaps
Example: coding_exon overlaps CDS.
overlaps
X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.
PMID:20226267
X part_of Y if X is a subregion of Y.
sequence
part_of
Example: amino_acid part_of polypeptide.
part_of
X part_of Y if X is a subregion of Y.
http://precedings.nature.com/documents/3495/version/1
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 is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
uberon
distally_connected_to
distally connected to
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
extends_fibers_into
extends_fibers_into
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s.
add to RO
uberon
indirectly_supplies
indirectly_supplies
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
Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
uberon
synapsed_by
synapsed by
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern
uberon
transitively_connected_to
transitively_connected to
.
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
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
bfo
BFO:0000019
quality
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
bfo
BFO:0000030
object
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
bfo
BFO:0000040
material entity
material entity
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
BrendaTissueOBO
BTO:0000000
tissues, cell types and enzyme sources
A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.
curators:mgr
BrendaTissueOBO
BTO:0000001
culture condition:-induced cell
BrendaTissueOBO
BTO:0000002
culture condition:1,4-dichlorobenzene-grown cell
Cells taken from a living organism and grown under controlled conditions (in culture). Methods used to maintain cell lines or strains.
BrendaTissueOBO
BTO:0000214
cell culture
Cells taken from a living organism and grown under controlled conditions (in culture). Methods used to maintain cell lines or strains.
Glossary_of_Fermentation_&_Cell_Culture_Terms:http://www.nbsc.com/files/papers/bp0600_gloss_36-44.pdf
BrendaTissueOBO
BTO:0000216
culture condition
A substance, either solid or liquid, used for the cultivation, isolation, identification, or storage of microorganisms.
BrendaTissueOBO
growth medium
medium
nutrient medium
BTO:0000316
Added as synonym to culture fluid.
culture medium
true
A substance, either solid or liquid, used for the cultivation, isolation, identification, or storage of microorganisms.
Biology-Online_Dictionary:http://www.biology-online.org/dictionary/
BrendaTissueOBO
BTO:0001479
culture condition:-grown cell
Other sources of an enzyme as cell culture or commercial preparation, not related to a specific tissue.
BrendaTissueOBO
BTO:0001490
other source
Other sources of an enzyme as cell culture or commercial preparation, not related to a specific tissue.
curators:mgr
anatomical entity
connected anatomical structure
material anatomical entity
biological entity
A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species.
0
C12H12N2O3
InChI=1S/C12H12N2O3/c1-3-14-6-9(12(16)17)10(15)8-5-4-7(2)13-11(8)14/h4-6H,3H2,1-2H3,(H,16,17)
MHWLWQUZZRMNGJ-UHFFFAOYSA-N
232.23530
232.08479
CCn1cc(C(O)=O)c(=O)c2ccc(C)nc12
CHEBI:7456
CAS:389-08-2
DrugBank:DB00779
Drug_Central:1875
KEGG:C05079
KEGG:D00183
LINCS:LSM-5590
PDBeChem:NIX
PMID:11321869
PMID:12002106
PMID:12399485
PMID:12702698
PMID:14107587
PMID:16107187
PMID:16423473
PMID:16667857
PMID:16803589
PMID:17132068
PMID:17631104
PMID:18788798
PMID:19071706
PMID:28166217
Patent:BE612258
Patent:US3590036
Reaxys:750515
VSDB:1880
Wikipedia:Nalidixic_Acid
1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid
NALIDIXIC ACID
Nalidixic acid
chebi_ontology
1,4-dihydro-1-ethyl-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid
1-Aethyl-7-methyl-1,8-naphthyridin-4-on-3-karbonsaeure
1-Ethyl-7-methyl-4-oxo-1,4-dihydro-[1,8]naphthyridine-3-carboxylic acid
1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid
1-ethyl-7-methyl-1,4-dihydro-1,8-naphthyridin-4-one-3-carboxylic acid
3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one
acide nalidixique
acido nalidixico
acidum nalidixicum
nalidixic acid
CHEBI:100147
nalidixic acid
CAS:389-08-2
ChemIDplus
CAS:389-08-2
KEGG COMPOUND
Drug_Central:1875
DrugCentral
PMID:11321869
Europe PMC
PMID:12002106
Europe PMC
PMID:12399485
Europe PMC
PMID:12702698
Europe PMC
PMID:14107587
Europe PMC
PMID:16107187
Europe PMC
PMID:16423473
Europe PMC
PMID:16667857
Europe PMC
PMID:16803589
Europe PMC
PMID:17132068
Europe PMC
PMID:17631104
Europe PMC
PMID:18788798
Europe PMC
PMID:19071706
Europe PMC
PMID:28166217
Europe PMC
Reaxys:750515
Reaxys
1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid
IUPAC
NALIDIXIC ACID
ChEMBL
Nalidixic acid
KEGG_COMPOUND
1,4-dihydro-1-ethyl-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid
ChemIDplus
1-Aethyl-7-methyl-1,8-naphthyridin-4-on-3-karbonsaeure
ChemIDplus
1-Ethyl-7-methyl-4-oxo-1,4-dihydro-[1,8]naphthyridine-3-carboxylic acid
ChEMBL
1-ethyl-1,4-dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxylic acid
ChemIDplus
1-ethyl-7-methyl-1,4-dihydro-1,8-naphthyridin-4-one-3-carboxylic acid
ChemIDplus
3-carboxy-1-ethyl-7-methyl-1,8-naphthyridin-4-one
ChemIDplus
acide nalidixique
ChemIDplus
acido nalidixico
ChemIDplus
acidum nalidixicum
ChemIDplus
nalidixic acid
ChemIDplus
A macrolide comprising a fourteen-membered lactone fused to 1,3-dihydroxybenzene; a potent estrogenic metabolite produced by some Giberella species.
0
C18H22O5
InChI=1S/C18H22O5/c1-12-6-5-9-14(19)8-4-2-3-7-13-10-15(20)11-16(21)17(13)18(22)23-12/h3,7,10-12,20-21H,2,4-6,8-9H2,1H3/b7-3+/t12-/m0/s1
MBMQEIFVQACCCH-QBODLPLBSA-N
318.36430
318.14672
C[C@H]1CCCC(=O)CCC\C=C\c2cc(O)cc(O)c2C(=O)O1
CAS:17924-92-4
KEGG:C09981
KNApSAcK:C00003025
LIPID_MAPS_instance:LMPK04000016
PMID:17339071
PMID:18027362
PMID:18221829
PMID:18280460
PMID:18692541
PMID:20654554
Reaxys:4875541
(3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione
chebi_ontology
(-)-Zearalenone
(10S)-Zearalenone
(S)-(-)-Zearalenone
(S)-Zearalenone
(S-(E))-3,4,5,6,9,10-Hexahydro-14,16-dihydroxy-3-methyl-1H-2-benzoxacyclotetradecin-1,7(8H)-dione
6-(10-Hydroxy-6-oxo-trans-1-undecenyl)-beta-resorcylic acid lactone
trans-Zearalenone
CHEBI:10106
zearalenone
CAS:17924-92-4
ChemIDplus
CAS:17924-92-4
KEGG COMPOUND
LIPID_MAPS_instance:LMPK04000016
LIPID MAPS
PMID:17339071
Europe PMC
PMID:18027362
Europe PMC
PMID:18221829
Europe PMC
PMID:18280460
Europe PMC
PMID:18692541
Europe PMC
PMID:20654554
Europe PMC
Reaxys:4875541
Reaxys
(3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione
IUPAC
(-)-Zearalenone
ChemIDplus
(10S)-Zearalenone
ChemIDplus
(S)-(-)-Zearalenone
ChemIDplus
(S)-Zearalenone
ChemIDplus
(S-(E))-3,4,5,6,9,10-Hexahydro-14,16-dihydroxy-3-methyl-1H-2-benzoxacyclotetradecin-1,7(8H)-dione
ChemIDplus
6-(10-Hydroxy-6-oxo-trans-1-undecenyl)-beta-resorcylic acid lactone
ChemIDplus
trans-Zearalenone
ChemIDplus
A naphthol carrying a hydroxy group at position 2.
0
C10H8O
InChI=1S/C10H8O/c11-10-6-5-8-3-1-2-4-9(8)7-10/h1-7,11H
JWAZRIHNYRIHIV-UHFFFAOYSA-N
144.173
144.05751
OC1=CC2=CC=CC=C2C=C1
Beilstein:742134
CAS:135-19-3
Drug_Central:3370
FooDB:FDB000877
Gmelin:27395
HMDB:HMDB0012322
KEGG:C11713
MetaCyc:CPD-8131
PDBeChem:03V
PMID:13386410
PMID:14751800
PMID:18515997
PMID:18856458
PMID:20260560
PMID:22069470
PMID:22740618
PMID:23344974
PMID:29987264
PMID:30572877
PMID:30828382
PMID:32206945
PMID:33862438
PMID:34033865
Reaxys:742134
Wikipedia:2-Naphthol
2-Naphthol
2-naphthol
naphthalen-2-ol
chebi_ontology
2-Naftol
2-hydroxynaphthalene
2-naftolo
2-naphthalenol
2-naphtol
Antioxygene BN
Azogen Developer A
C.I. Azoic Coupling Component 1
C.I. Developer 5
Developer A
Developer AMS
Developer BN
Isonaphthol
beta-Naftol
beta-Naphthol
beta-Naphtol
beta-hydroxynaphthalene
beta-naftolo
beta-naphthol
beta-naphthyl alcohol
beta-naphthyl hydroxide
CHEBI:10432
2-naphthol
Beilstein:742134
Beilstein
CAS:135-19-3
ChemIDplus
CAS:135-19-3
KEGG COMPOUND
CAS:135-19-3
NIST Chemistry WebBook
Drug_Central:3370
DrugCentral
Gmelin:27395
Gmelin
PMID:13386410
Europe PMC
PMID:14751800
Europe PMC
PMID:18515997
Europe PMC
PMID:18856458
Europe PMC
PMID:20260560
Europe PMC
PMID:22069470
Europe PMC
PMID:22740618
Europe PMC
PMID:23344974
Europe PMC
PMID:29987264
Europe PMC
PMID:30572877
Europe PMC
PMID:30828382
Europe PMC
PMID:32206945
Europe PMC
PMID:33862438
Europe PMC
PMID:34033865
Europe PMC
Reaxys:742134
Reaxys
2-Naphthol
KEGG_COMPOUND
2-naphthol
UniProt
naphthalen-2-ol
IUPAC
2-Naftol
ChemIDplus
2-hydroxynaphthalene
HMDB
2-naftolo
ChemIDplus
2-naphthalenol
NIST_Chemistry_WebBook
2-naphtol
ChemIDplus
Antioxygene BN
HMDB
Azogen Developer A
HMDB
C.I. Azoic Coupling Component 1
ChemIDplus
C.I. Developer 5
ChemIDplus
Developer A
ChemIDplus
Developer AMS
ChemIDplus
Developer BN
ChemIDplus
Isonaphthol
ChemIDplus
beta-Naftol
ChemIDplus
beta-Naphthol
KEGG_COMPOUND
beta-Naphtol
ChemIDplus
beta-hydroxynaphthalene
ChemIDplus
beta-hydroxynaphthalene
NIST_Chemistry_WebBook
beta-naftolo
ChemIDplus
beta-naphthol
NIST_Chemistry_WebBook
beta-naphthyl alcohol
ChemIDplus
beta-naphthyl hydroxide
ChemIDplus
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
0
C6H12O6
InChI=1S/C6H12O6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-12H/t1-,2-,3+,4+,5-,6-
CDAISMWEOUEBRE-CDRYSYESSA-N
180.15588
180.06339
O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1O
CHEBI:26614
Beilstein:2206312
CAS:488-59-5
Gmelin:561300
KEGG:C06153
PMID:24352657
Reaxys:2206312
scyllo-Inositol
scyllo-inositol
chebi_ontology
(1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol
1,3,5/2,4,6-cyclohexanehexol
Cocositol
Quercinitol
Scyllitol
CHEBI:10642
scyllo-inositol
Beilstein:2206312
Beilstein
CAS:488-59-5
ChemIDplus
CAS:488-59-5
KEGG COMPOUND
CAS:488-59-5
NIST Chemistry WebBook
Gmelin:561300
Gmelin
PMID:24352657
Europe PMC
Reaxys:2206312
Reaxys
scyllo-Inositol
KEGG_COMPOUND
scyllo-inositol
IUPAC
scyllo-inositol
UniProt
(1r,2r,3r,4r,5r,6r)-cyclohexane-1,2,3,4,5,6-hexol
IUPAC
1,3,5/2,4,6-cyclohexanehexol
IUPAC
Cocositol
NIST_Chemistry_WebBook
Quercinitol
ChemIDplus
Scyllitol
ChemIDplus
An organophosphate oxoanion that is the trianion of (R)-5-phosphopantothenic acid arising from deprotonation of the carboxy and phosphate OH groups; major species at pH 7.3
-3
C9H15NO8P
InChI=1S/C9H18NO8P/c1-9(2,5-18-19(15,16)17)7(13)8(14)10-4-3-6(11)12/h7,13H,3-5H2,1-2H3,(H,10,14)(H,11,12)(H2,15,16,17)/p-3/t7-/m0/s1
XHFVGHPGDLDEQO-ZETCQYMHSA-K
296.19110
296.05517
CC(C)(COP([O-])([O-])=O)[C@@H](O)C(=O)NCCC([O-])=O
3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonatooxy)butanamido]propanoate
chebi_ontology
(R)-4'-phosphopantothenate
CHEBI:10986
(R)-4'-phosphonatopantothenate(3-)
3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonatooxy)butanamido]propanoate
IUPAC
(R)-4'-phosphopantothenate
UniProt
A glycerophosphocholine having an unspecified O-acyl substituent at the 1-position of the glycerol fragment.
+1
C9H20NO7PR
285.232
285.09774
C[N+](C)(C)CCOP(O)(=O)OCC(O)COC([*])=O
CHEBI:53029
chebi_ontology
1-O-acylglycerophosphocholines
2-lysophosphatidylcholine
CHEBI:11230
1-acylglycerophosphocholine(1+)
1-O-acylglycerophosphocholines
ChEBI
2-lysophosphatidylcholine
ChEBI
A glycerophosphocholine having an unspecified acyl group attached at the 2-position.
+1
C9H20NO7PR
285.23140
285.09774
C[N+](C)(C)CCOP(O)(=O)OCC(CO)OC([*])=O
PMID:15913955
chebi_ontology
2-acylglycerophosphocholines
LPC
CHEBI:11502
2-acylglycerophosphocholine
PMID:15913955
Europe PMC
2-acylglycerophosphocholines
ChEBI
LPC
ChEBI
A member of the class of 3-(3,4-substituted-phenyl)-1,1-dimethylureas that is urea in which both of the hydrogens attached to one nitrogen are substituted by methyl groups, and one of the hydrogens attached to the other nitrogen is substituted by a 3,4-dichlorophenyl group.
0
C9H10Cl2N2O
InChI=1S/C9H10Cl2N2O/c1-13(2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14)
XMTQQYYKAHVGBJ-UHFFFAOYSA-N
233.09500
232.01702
CN(C)C(=O)Nc1ccc(Cl)c(Cl)c1
CAS:330-54-1
KEGG:C18428
LINCS:LSM-25609
MetaCyc:CPD-16775
PMID:10866370
PMID:17142046
PMID:17449247
PMID:23081760
PMID:33400299
PPDB:260
Patent:CN103120180
Patent:CN103125511
Patent:US2768971
Pesticides:diuron
Reaxys:2215168
Wikipedia:Diuron
3-(3,4-dichlorophenyl)-1,1-dimethylurea
diuron
chebi_ontology
1,1-dimethyl-3-(3,4-dichlorophenyl)urea
1-(3,4-dichlorophenyl)-3,3-dimethylurea
1-(3,4-dichlorophenyl)-3,3-dimethyluree
3-(3,4-Dichlor-phenyl)-1,1-dimethyl-harnstoff
3-(3,4-Dichloro-phenyl)-1,1-dimethyl-urea
DCMU
N'-(3,4-dichlorophenyl)-N,N-dimethylurea
N,N,-dimethyl-N'-(3,4-dichlorophenyl)urea
N-(3,4-dichlorophenyl)-N',N'-dimethylurea
CHEBI:116509
diuron
CAS:330-54-1
ChemIDplus
CAS:330-54-1
KEGG COMPOUND
CAS:330-54-1
NIST Chemistry WebBook
PMID:10866370
ChEMBL
PMID:17142046
ChEMBL
PMID:17449247
ChEMBL
PMID:23081760
Europe PMC
PMID:33400299
Europe PMC
Pesticides:diuron
Alan Wood's Pesticides
Reaxys:2215168
Reaxys
3-(3,4-dichlorophenyl)-1,1-dimethylurea
IUPAC
diuron
UniProt
1,1-dimethyl-3-(3,4-dichlorophenyl)urea
ChemIDplus
1-(3,4-dichlorophenyl)-3,3-dimethylurea
ChemIDplus
1-(3,4-dichlorophenyl)-3,3-dimethyluree
ChemIDplus
3-(3,4-Dichlor-phenyl)-1,1-dimethyl-harnstoff
ChemIDplus
3-(3,4-Dichloro-phenyl)-1,1-dimethyl-urea
ChEMBL
DCMU
ChEBI
N'-(3,4-dichlorophenyl)-N,N-dimethylurea
ChemIDplus
N,N,-dimethyl-N'-(3,4-dichlorophenyl)urea
ChemIDplus
N-(3,4-dichlorophenyl)-N',N'-dimethylurea
ChemIDplus
An alpha,omega dicarboxyacyl-CoA that results from the formal condensation of the thiol group of coenzyme A with one of the carboxy groups of 3-hydroxy-3-methylglutaric acid.
0
C27H44N7O20P3S
InChI=1S/C27H44N7O20P3S/c1-26(2,21(40)24(41)30-5-4-15(35)29-6-7-58-17(38)9-27(3,42)8-16(36)37)11-51-57(48,49)54-56(46,47)50-10-14-20(53-55(43,44)45)19(39)25(52-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,19-21,25,39-40,42H,4-11H2,1-3H3,(H,29,35)(H,30,41)(H,36,37)(H,46,47)(H,48,49)(H2,28,31,32)(H2,43,44,45)/t14-,19-,20-,21+,25-,27?/m1/s1
CABVTRNMFUVUDM-SJBCKIPMSA-N
911.66072
911.15747
CC(O)(CC(O)=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12
PMID:20640529
PMID:9160173
3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxy-3-hydroxy-3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate}
chebi_ontology
(4-carboxy-3-hydroxy-3-methylbutanoyl)-CoA
(4-carboxy-3-hydroxy-3-methylbutanoyl)-coenzyme A
3-hydroxy-3-methylglutaryl-coenzyme A
CHEBI:11814
3-hydroxy-3-methylglutaryl-CoA
PMID:20640529
Europe PMC
PMID:9160173
Europe PMC
3'-phosphoadenosine 5'-{3-[(3R)-4-{[3-({2-[(4-carboxy-3-hydroxy-3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl] dihydrogen diphosphate}
IUPAC
(4-carboxy-3-hydroxy-3-methylbutanoyl)-CoA
ChEBI
(4-carboxy-3-hydroxy-3-methylbutanoyl)-coenzyme A
ChEBI
3-hydroxy-3-methylglutaryl-coenzyme A
ChEBI
A ribose diphosphate carrying an additional phosphate group at position 5.
chebi_ontology
CHEBI:12164
5-phosphoribosyl diphosphate
-1
C9H17NO8P
InChI=1S/C9H18NO8P/c1-9(2,5-18-19(15,16)17)7(13)8(14)10-4-3-6(11)12/h7,13H,3-5H2,1-2H3,(H,10,14)(H,11,12)(H2,15,16,17)/p-1/t7-/m0/s1
XHFVGHPGDLDEQO-ZETCQYMHSA-M
298.20698
298.06973
CC(C)(COP(O)(O)=O)[C@@H](O)C(=O)NCCC([O-])=O
3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanamido]propanoate
chebi_ontology
CHEBI:12886
(R)-4'-phosphopantothenate(1-)
3-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanamido]propanoate
IUPAC
0
C6H12O6
180.15588
180.06339
D-galacto-hexose
D-galactose
chebi_ontology
D-Gal
CHEBI:12936
D-galactose
D-galacto-hexose
IUPAC
D-galactose
IUPAC
D-Gal
JCBN
An antagonist that interferes with the action of the calcium-binding messenger protein calmodulin.
PMID:26717596
chebi_ontology
CHEBI:130181
calmodulin antagonist
PMID:26717596
Europe PMC
A disaccharide formed by a (1<->1)-glycosidic bond between two hexopyranose units.
hexopyranosyl hexopyranoside
chebi_ontology
CHEBI:131401
hexopyranosyl hexopyranoside
hexopyranosyl hexopyranoside
IUPAC
A pyridinium ion obtained by protonation of the ring nitrogen of pyridoxal.
+1
C8H10NO3
InChI=1S/C8H9NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,4,10,12H,3H2,1H3/p+1
RADKZDMFGJYCBB-UHFFFAOYSA-O
168.170
168.06552
C1(O)=C(C)[NH+]=CC(CO)=C1C([H])=O
4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium
chebi_ontology
pyridoxal cation
CHEBI:131530
pyridoxal(1+)
4-formyl-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium
IUPAC
pyridoxal cation
ChEBI
A pyridinium ion obtained by protonation of both nitrogens of pyridoxamine.
+2
C8H14N2O2
InChI=1S/C8H12N2O2/c1-5-8(12)7(2-9)6(4-11)3-10-5/h3,11-12H,2,4,9H2,1H3/p+2
NHZMQXZHNVQTQA-UHFFFAOYSA-P
170.209
170.10443
C1(O)=C(C)[NH+]=CC(CO)=C1C[NH3+]
4-(azaniumylmethyl)-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium
chebi_ontology
pyridoxamine cation
pyridoxamine dication
CHEBI:131533
pyridoxamine(2+)
4-(azaniumylmethyl)-3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-1-ium
IUPAC
pyridoxamine cation
ChEBI
pyridoxamine dication
ChEBI
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
chebi_ontology
Mycoplasma genitalium metabolites
CHEBI:131604
Mycoplasma genitalium metabolite
Mycoplasma genitalium metabolites
ChEBI
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a dicarboxylic acid monoester.
chebi_ontology
CHEBI:131605
dicarboxylic acid monoester(1-)
An echinocandin initially isolated as a very minor bioactive fermentation product of Glarea lozoyensis (originally known as Zalerion arboricola). Subsequent random mutagenesis work and optimisation of the fermentation medium permitted the industrial production of pneumocandin B0, which is used as the starting point for the synthesis of the antifungal drug caspofungin.
0
C50H80N8O17
InChI=1S/C50H80N8O17/c1-5-25(2)20-26(3)12-10-8-6-7-9-11-13-37(66)52-31-22-35(64)46(71)56-48(73)41-33(62)18-19-57(41)50(75)39(34(63)23-36(51)65)54-47(72)40(43(68)42(67)28-14-16-29(60)17-15-28)55-45(70)32-21-30(61)24-58(32)49(74)38(27(4)59)53-44(31)69/h14-17,25-27,30-35,38-43,46,59-64,67-68,71H,5-13,18-24H2,1-4H3,(H2,51,65)(H,52,66)(H,53,69)(H,54,72)(H,55,70)(H,56,73)/t25-,26+,27+,30+,31-,32-,33-,34+,35+,38-,39-,40-,41-,42-,43-,46+/m0/s1
DQXPFAADCTZLNL-FXDJFZINSA-N
1065.216
1064.56414
[C@@]12(N(C[C@@H](C1)O)C([C@H]([C@@H](C)O)NC(=O)[C@](C[C@H]([C@@H](O)NC([C@@H]3[C@H](CCN3C([C@H]([C@@H](CC(N)=O)O)NC(=O)[C@H]([C@@H]([C@H](C4=CC=C(C=C4)O)O)O)NC2=O)=O)O)=O)O)(NC(CCCCCCCC[C@H](C[C@H](CC)C)C)=O)[H])=O)[H]
CAS:135575-42-7
PMID:24086376
PMID:24270605
PMID:25527531
Reaxys:9316734
Wikipedia:Pneumocandin_Bo
(10R,12S)-N-{(2R,6S,9S,11R,12R,14aS,15S,20S,23S,25aS)-20-[(1R)-3-amino-1-hydroxy-3-oxopropyl]-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,12,15-tetrahydroxy-6-[(1R)-1-hydroxyethyl]-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-10,12-dimethyltetradecanamide
chebi_ontology
L 688,786
L-688,786
L-688786
pneumocandin B(0)
pneumocardin B(0)
CHEBI:131609
pneumocandin B0
CAS:135575-42-7
ChemIDplus
PMID:24086376
Europe PMC
PMID:24270605
Europe PMC
PMID:25527531
Europe PMC
Reaxys:9316734
Reaxys
(10R,12S)-N-{(2R,6S,9S,11R,12R,14aS,15S,20S,23S,25aS)-20-[(1R)-3-amino-1-hydroxy-3-oxopropyl]-23-[(1S,2S)-1,2-dihydroxy-2-(4-hydroxyphenyl)ethyl]-2,11,12,15-tetrahydroxy-6-[(1R)-1-hydroxyethyl]-5,8,14,19,22,25-hexaoxotetracosahydro-1H-dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13,16]hexaazacyclohenicosin-9-yl}-10,12-dimethyltetradecanamide
IUPAC
L 688,786
ChemIDplus
L-688,786
ChemIDplus
L-688786
ChemIDplus
pneumocandin B(0)
ChemIDplus
pneumocardin B(0)
ChemIDplus
A 2-acyl-sn-glycero-3-phosphocholine in which the acyl group is specified as tertadecanoyl (myristoyl).
0
C22H46NO7P
InChI=1S/C22H46NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-22(25)30-21(19-24)20-29-31(26,27)28-18-17-23(2,3)4/h21,24H,5-20H2,1-4H3/t21-/m1/s1
IGZPHNNYPPAPLA-OAQYLSRUSA-N
467.578
467.30119
OC[C@@H](OC(CCCCCCCCCCCCC)=O)COP(=O)([O-])OCC[N+](C)(C)C
LIPID_MAPS_instance:LMGP01050073
PMID:21510612
PMID:26860358
Reaxys:9670780
(2R)-3-hydroxy-2-(tetradecanoyloxy)propyl 2-(trimethylazaniumyl)ethyl phosphate
2-tetradecanoyl-sn-glycero-3-phosphocholine
chebi_ontology
2-myristoyl-sn-glycero-3-phosphocholine
PC(0:0/14:0)
CHEBI:131738
2-tetradecanoyl-sn-glycero-3-phosphocholine
LIPID_MAPS_instance:LMGP01050073
LIPID MAPS
PMID:21510612
Europe PMC
PMID:26860358
Europe PMC
Reaxys:9670780
Reaxys
(2R)-3-hydroxy-2-(tetradecanoyloxy)propyl 2-(trimethylazaniumyl)ethyl phosphate
IUPAC
2-tetradecanoyl-sn-glycero-3-phosphocholine
UniProt
2-myristoyl-sn-glycero-3-phosphocholine
ChEBI
PC(0:0/14:0)
LIPID_MAPS
Any monounsaturated fatty acid carrying one or more hydroxy substituents.
chebi_ontology
hydroxy MUFA
hydroxy monounsaturated fatty acids
CHEBI:131869
hydroxy monounsaturated fatty acid
hydroxy MUFA
SUBMITTER
hydroxy monounsaturated fatty acids
ChEBI
Any monounsaturated fatty acid anion carrying one or more hydroxy substituents.
chebi_ontology
hydroxy MUFA anion
hydroxy MUFA anions
hydroxy monounsaturated fatty acid anions
CHEBI:131870
hydroxy monounsaturated fatty acid anion
hydroxy MUFA anion
SUBMITTER
hydroxy MUFA anions
ChEBI
hydroxy monounsaturated fatty acid anions
ChEBI
Any polyunsaturated fatty acid anion carrying one or more hydroxy substituents.
-1
CHO3R
61.017
60.99257
O*C([O-])=O
chebi_ontology
a hydroxy polyunsaturated fatty acid
hydroxy PUFA
hydroxy polyunsaturated fatty acid anions
CHEBI:131871
hydroxy polyunsaturated fatty acid anion
a hydroxy polyunsaturated fatty acid
UniProt
hydroxy PUFA
SUBMITTER
hydroxy polyunsaturated fatty acid anions
ChEBI
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 lysophosphatidylcholine 20:1 in which the acyl group is located at position 1.
0
C28H56NO7P
549.722
549.37944
[C@@H](COC(=O)*)(COP(OCC[N+](C)(C)C)(=O)[O-])O
chebi_ontology
1-eicosenoyl-GPC
1-eicosenoyl-GPC (20:1)
1-eicosenoyl-sn-glycero-3-phosphocholine
GPC(20:1)
GPC(20:1/0:0)
LPC(20:1/0:0)
PC(20:1/0:0)
lysophosphatidylcholine (20:1/0:0)
CHEBI:131982
1-icosenoyl-sn-glycero-3-phosphocholine
1-eicosenoyl-GPC
ChEBI
1-eicosenoyl-GPC (20:1)
ChEBI
1-eicosenoyl-sn-glycero-3-phosphocholine
ChEBI
GPC(20:1)
ChEBI
GPC(20:1/0:0)
ChEBI
LPC(20:1/0:0)
ChEBI
PC(20:1/0:0)
ChEBI
lysophosphatidylcholine (20:1/0:0)
ChEBI
Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives.
0
C6O2R4
104.063
103.98983
O=C1C(*)=C(*)C(=O)C(*)=C1*
chebi_ontology
a quinone
p-benzoquinones
para-benzoquinones
CHEBI:132124
1,4-benzoquinones
a quinone
UniProt
p-benzoquinones
ChEBI
para-benzoquinones
ChEBI
Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group.
chebi_ontology
hydroxyquinones
CHEBI:132130
hydroxyquinone
hydroxyquinones
ChEBI
A naphthoquinone in which the oxo groups of the quinone moiety are at positions 1 and 4 of the parent naphthalene ring.
chebi_ontology
CHEBI:132142
1,4-naphthoquinones
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 naphthoquinone in which the naphthaoquinone moiety is substituted by at least one hydroxy group.
Wikipedia:Hydroxynaphthoquinone
chebi_ontology
hydroxynaphthoquinones
CHEBI:132155
hydroxynaphthoquinone
hydroxynaphthoquinones
ChEBI
Any member of the class of 1,4-naphthoquinones in which the naphthoquinone moiety is substituted by at least one hydroxy group.
chebi_ontology
hydroxy-1,4-naphthoquinones
CHEBI:132157
hydroxy-1,4-naphthoquinone
hydroxy-1,4-naphthoquinones
ChEBI
A citrate anion obtained by deprotonation of the three carboxy groups as well as the hydroxy group of citric acid.
-4
C6H4O7
InChI=1S/C6H7O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h1-2H2,(H,7,8)(H,9,10)(H,11,12)/q-1/p-3
KSXLKRAZYZIYCZ-UHFFFAOYSA-K
188.092
187.99790
C(=O)([O-])C(CC(=O)[O-])(CC(=O)[O-])[O-]
Chemspider:34552020
2-oxidopropane-1,2,3-tricarboxylate
chebi_ontology
2-oxido-1,2,3-propanetricarboxylate
citric acid tetraanion
CHEBI:132362
citrate(4-)
2-oxidopropane-1,2,3-tricarboxylate
IUPAC
2-oxido-1,2,3-propanetricarboxylate
ChEBI
citric acid tetraanion
ChEBI
A reagent that lightens or whitens a substrate through chemical reaction. Bleaching reactions usually involve oxidative or reductive processes that degrade colour systems. Bleaching can occur by destroying one or more of the double bonds in the conjugated chain, by cleaving the conjugated chain, or by oxidation of one of the other moieties in the conjugated chain. Their reactivity results in many bleaches having strong bactericidal, disinfecting, and sterilising properties.
Wikipedia:Bleach
chebi_ontology
CHEBI:132717
bleaching agent
chebi_ontology
CHEBI:132943
aspartate
An octadecenoate in which the double bond is at C-9.
-1
C18H33O2
InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1
ZQPPMHVWECSIRJ-UHFFFAOYSA-M
281.454
281.24860
C(=CCCCCCCCC)CCCCCCCC(=O)[O-]
octadec-9-enoate
chebi_ontology
9-octadecenoate
C18:1, n-9(1-)
Delta(9)-octadecenoate
CHEBI:132944
octadec-9-enoate
octadec-9-enoate
IUPAC
9-octadecenoate
ChEBI
C18:1, n-9(1-)
ChEBI
Delta(9)-octadecenoate
ChEBI
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of maleic acid.
chebi_ontology
maleate anion
maleate anions
maleates
maleic acid anion
maleic acid anions
CHEBI:132951
maleate
maleate anion
ChEBI
maleate anions
ChEBI
maleates
ChEBI
maleic acid anion
ChEBI
maleic acid anions
ChEBI
A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of suberic acid.
chebi_ontology
octanedioic acid anion
octanedioic acid anions
suberate anion
suberate anions
suberates
suberic acid anion
suberic acid anions
CHEBI:132953
suberate
octanedioic acid anion
ChEBI
octanedioic acid anions
ChEBI
suberate anion
ChEBI
suberate anions
ChEBI
suberates
ChEBI
suberic acid anion
ChEBI
suberic acid anions
ChEBI
A drug that makes increases the sensitivity of tumour cells to radiation therapy.
PMID:12520460
Wikipedia:Radiosensitizer
chebi_ontology
radiosensitiser
radiosensitisers
radiosensitising agent
radiosensitising agents
radiosensitizer
radiosensitizers
radiosensitizing agents
CHEBI:132992
radiosensitizing agent
PMID:12520460
Europe PMC
radiosensitiser
ChEBI
radiosensitisers
ChEBI
radiosensitising agent
ChEBI
radiosensitising agents
ChEBI
radiosensitizer
ChEBI
radiosensitizers
ChEBI
radiosensitizing agents
ChEBI
A dipeptide obtained by formal condensation of the gamma-carboxy group of glutamic acid with the amino group of 2-aminobutyric acid.
0
C9H16N2O5
InChI=1S/C9H16N2O5/c1-2-6(9(15)16)11-7(12)4-3-5(10)8(13)14/h5-6H,2-4,10H2,1H3,(H,11,12)(H,13,14)(H,15,16)
FUZOZPRKGAXGOB-UHFFFAOYSA-N
232.234
232.10592
NC(C(O)=O)CCC(=O)NC(C(=O)O)CC
Reaxys:25853400
N-(1-carboxypropyl)glutamine
chebi_ontology
gamma-glutamyl-2-aminobutyric acid
CHEBI:133092
gamma-Glu-Abu
Reaxys:25853400
Reaxys
N-(1-carboxypropyl)glutamine
IUPAC
gamma-glutamyl-2-aminobutyric acid
ChEBI
A peptide anion that is the conjugate base of gamma-Glu-Abu, obtained by removal of protons from the two carboxy groups as well as protonation of the amino group; major species at pH 7.3.
-1
C9H15N2O5
InChI=1S/C9H16N2O5/c1-2-6(9(15)16)11-7(12)4-3-5(10)8(13)14/h5-6H,2-4,10H2,1H3,(H,11,12)(H,13,14)(H,15,16)/p-1
FUZOZPRKGAXGOB-UHFFFAOYSA-M
231.226
231.09865
[NH3+]C(C([O-])=O)CCC(=O)NC(C(=O)[O-])CC
2-azaniumyl-5-[(1-carboxylatopropyl)amino]-5-oxopentanoate
chebi_ontology
gamma-glutamyl-2-aminobutyrate
CHEBI:133093
gamma-Glu-Abu(1-)
2-azaniumyl-5-[(1-carboxylatopropyl)amino]-5-oxopentanoate
IUPAC
gamma-glutamyl-2-aminobutyrate
ChEBI
An oxaspiro compound in which a carbon atom of an epoxide ring is the only common member of two rings.
chebi_ontology
spiro-epoxides
spiroepoxide
spiroepoxides
CHEBI:133131
spiro-epoxide
spiro-epoxides
ChEBI
spiroepoxide
ChEBI
spiroepoxides
ChEBI
Any organic heteroolycyclic compound whose skeleton two ortho-fused chromene rings, and their derivatives.
chebi_ontology
chromenochromenes
CHEBI:133135
chromenochromene
chromenochromenes
ChEBI
An acyl-CoA oxoanion obtained by deprotonation of the phosphate, diphosphate and carboxy groups of any omega-carboxyacyl-CoA; major species at pH 7.3.
-5
C23H31N7O19P3SR
834.516
834.06083
[C@@H]1(N2C3=C(C(=NC=N3)N)N=C2)O[C@H](COP(OP(OCC(C)([C@H](C(NCCC(NCCSC(=O)*C([O-])=O)=O)=O)O)C)(=O)[O-])(=O)[O-])[C@H]([C@H]1O)OP([O-])([O-])=O
chebi_ontology
omega-dicarboxyl-CoA
CHEBI:133241
omega-carboxyacyl-CoA(5-)
omega-dicarboxyl-CoA
UniProt
A dicarboxylic acid dianion that results from the removal of a proton from both of the carboxylic acid groups of any 3-hydroxydicarboxylic acid.
-2
C4H4O5R
132.072
132.00587
C(*C(CC(=O)[O-])O)([O-])=O
chebi_ontology
3-hydroxydicarboxylic acid dianion(2-)
a 3-hydroxy dicarboxylic acid
CHEBI:133251
3-hydroxydicarboxylate(2-)
3-hydroxydicarboxylic acid dianion(2-)
SUBMITTER
a 3-hydroxy dicarboxylic acid
UniProt
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid that contains no carbon-carbon double bonds.
-2
C2O4R
88.019
87.97966
[O-]C(*C([O-])=O)=O
chebi_ontology
a saturated dicarboxylic acid
saturated dicarboxylate(2-)
CHEBI:133291
saturated dicarboxylic acid dianion(2-)
a saturated dicarboxylic acid
UniProt
saturated dicarboxylate(2-)
SUBMITTER
A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of any oxo dicarboxylic acid.
chebi_ontology
oxo dicarboxylic acid
oxo dicarboxylic acid dianions
CHEBI:133294
oxo dicarboxylic acid dianion
oxo dicarboxylic acid
UniProt
oxo dicarboxylic acid dianions
ChEBI
An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-lysine; major species at pH 7.3.
0
C6H14N2O2
InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1
KDXKERNSBIXSRK-YFKPBYRVSA-N
146.188
146.10553
[O-]C([C@H](CCCCN)[NH3+])=O
(2S)-6-amino-2-azaniumylhexanoate
chebi_ontology
L-lysine
Lys
lysine zwitterion
CHEBI:133538
L-lysine zwitterion
(2S)-6-amino-2-azaniumylhexanoate
IUPAC
L-lysine
ChEBI
Lys
ChEBI
lysine zwitterion
ChEBI
A tricarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of citric acid.
chebi_ontology
citrate
citrate anions
CHEBI:133748
citrate anion
citrate
ChEBI
citrate anions
ChEBI
A phosphonium ylide that is 2-(triphenylphosphoranylidene)acetamide in which the nitrogen has been converted to the corresponding carbamoyl derivative. By targeting the beta-subunit of fatty acid synthase, it inhibits nuclear envelope expansion and nuclear elongation during the closed mitosis of fission yeast.
0
C21H19N2O2P
InChI=1S/C21H19N2O2P/c22-21(25)23-20(24)16-26(17-10-4-1-5-11-17,18-12-6-2-7-13-18)19-14-8-3-9-15-19/h1-16H,(H3,22,23,24,25)
HIFJFZSMVLIPEA-UHFFFAOYSA-N
362.362
362.11841
P(=CC(NC(N)=O)=O)(C=1C=CC=CC1)(C=2C=CC=CC2)C=3C=CC=CC3
CAS:53296-08-5
PMID:26869222
Reaxys:2765280
2-(triphenyl-lambda(5)-phosphanylidene)acetamide
N-carbamoyl-2-(triphenylphosphoranylidene)acetamide
chebi_ontology
triphenylphosphonium(carbamoylcarbamoyl)methylylid
ureidocarbomethylentriphenylphosphoniumylid
CHEBI:133750
Cutin-1
CAS:53296-08-5
ChEBI
PMID:26869222
Europe PMC
Reaxys:2765280
Reaxys
2-(triphenyl-lambda(5)-phosphanylidene)acetamide
IUPAC
N-carbamoyl-2-(triphenylphosphoranylidene)acetamide
IUPAC
triphenylphosphonium(carbamoylcarbamoyl)methylylid
ChEBI
ureidocarbomethylentriphenylphosphoniumylid
ChEBI
Any member of the class of ureas in which at least one of the nitrogens of the urea moiety is substituted by a phenyl or substituted phenyl group.
chebi_ontology
CHEBI:134043
phenylureas
Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.
Wikipedia:Volatile_organic_compound
chebi_ontology
VOC
VOCs
volatile organic compounds
CHEBI:134179
volatile organic compound
VOC
ChEBI
VOCs
ChEBI
volatile organic compounds
ChEBI
An alkanesulfonate in which the carbon at position 1 is attached to R, which can represent hydrogens, a carbon chain, or other groups.
-1
CH2O3SR
94.091
93.97246
C(S([O-])(=O)=O)*
CHEBI:22318
MetaCyc:Alkanesulfonates
chebi_ontology
alkanesulfonate oxoanions
alkanesulfonates
an alkanesulfonate
CHEBI:134249
alkanesulfonate oxoanion
alkanesulfonate oxoanions
ChEBI
alkanesulfonates
ChEBI
an alkanesulfonate
UniProt
An alpha-amino-acid cation obtained by protonation of the imidazole ring of ergothioneine. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.).
+1
C9H16N3O2S
InChI=1S/C9H15N3O2S/c1-12(2,3)7(8(13)14)4-6-5-10-9(15)11-6/h5,7H,4H2,1-3H3,(H2-,10,11,13,14,15)/p+1/t7-/m0/s1
SSISHJJTAXXQAX-ZETCQYMHSA-O
230.309
230.09577
C=1([NH+]=C(NC1)S)C[C@@H](C(=O)[O-])[N+](C)(C)C
(2S)-3-(2-sulfanylidene-2,3-dihydro-1H-imidazol-3-ium-4-yl)-2-(trimethylazaniumyl)propanoate
chebi_ontology
ergothioneine
ergothioneine cation
CHEBI:134344
ergothioneine(1+)
(2S)-3-(2-sulfanylidene-2,3-dihydro-1H-imidazol-3-ium-4-yl)-2-(trimethylazaniumyl)propanoate
IUPAC
ergothioneine
UniProt
ergothioneine cation
ChEBI
An alcohol where the hydroxy group is attached to a saturated carbon atom adjacent to a double bond (R groups may be H, organyl, etc.).
0
C3HOR5
53.040
53.00274
C(C(=C(*)*)*)(O)(*)*
chebi_ontology
allylic alcohols
CHEBI:134361
allylic alcohol
allylic alcohols
ChEBI
An aliphatic alcohol where the hydroxy carbon is beta to a double bond.
0
C4HOR7
65.050
65.00274
C(=C(*)*)(C(C(O)(*)*)(*)*)*
chebi_ontology
homoallylic alcohols
CHEBI:134362
homoallylic alcohol
homoallylic alcohols
ChEBI
An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to two hydrogens.
0
C3H3OR3
55.055
55.01839
C(C(=C(*)*)*)(O)([H])[H]
chebi_ontology
primary allylic alcohols
CHEBI:134394
primary allylic alcohol
primary allylic alcohols
ChEBI
An allylic alcohol in which the carbon atom that links the double bond to the hydroxy group is also attached to one other carbon and one hydrogen.
0
C3H2OR4
54.047
54.01056
C(C(=C(*)*)*)(O)([H])*
chebi_ontology
secondary allylic alcohols
CHEBI:134396
secondary allylic alcohol
secondary allylic alcohols
ChEBI
A furonaphthodioxole that is 4'-demethyldeoxypodophyllotoxin which is substituted at position 4 of the C-ring by a 2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl group. While structurally related to etoposide, TOP-53 is significantly more toxic to non-small cell lung cancer cells, more active at generating chromosomal breaks, and displays improved cellular uptake and pharmacokinetics in animal lung tissues.
0
C28H36N2O7
InChI=1S/C28H36N2O7/c1-29(2)8-9-30(3)7-6-17-18-12-21-22(37-15-36-21)13-19(18)25(26-20(17)14-35-28(26)32)16-10-23(33-4)27(31)24(11-16)34-5/h10-13,17,20,25-26,31H,6-9,14-15H2,1-5H3/t17-,20-,25-,26+/m1/s1
KLCCMMSKRMSMKI-QVNMXXJYSA-N
512.596
512.25225
C12=CC3=C(C=C1[C@H]([C@@]4([C@@]([C@@H]2CCN(CCN(C)C)C)(COC4=O)[H])[H])C=5C=C(C(=C(C5)OC)O)OC)OCO3
CAS:148262-19-5
PMID:11106259
PMID:11170388
PMID:12081147
PMID:15892669
PMID:15992351
PMID:24827545
PMID:8665518
PMID:9106054
Reaxys:6377812
(5R,5aR,8aR,9S)-9-(2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl)-5-(4-hydroxy-3,5-dimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one
chebi_ontology
4'-demethyl-4beta-(2-{N-[2-(N',N'-dimethylamino)ethyl]-N-methylamino}ethyl)-4-desoxypodophyllotoxin
TOP 53
CHEBI:134547
TOP-53
CAS:148262-19-5
ChemIDplus
PMID:11106259
Europe PMC
PMID:11170388
Europe PMC
PMID:12081147
Europe PMC
PMID:15892669
Europe PMC
PMID:15992351
Europe PMC
PMID:24827545
Europe PMC
PMID:8665518
Europe PMC
PMID:9106054
Europe PMC
Reaxys:6377812
Reaxys
(5R,5aR,8aR,9S)-9-(2-{[2-(dimethylamino)ethyl](methyl)amino}ethyl)-5-(4-hydroxy-3,5-dimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one
IUPAC
4'-demethyl-4beta-(2-{N-[2-(N',N'-dimethylamino)ethyl]-N-methylamino}ethyl)-4-desoxypodophyllotoxin
ChEBI
TOP 53
ChEBI
A UDP-amino sugar having alpha-D-glucosamine as the amino-sugar component.
0
C15H25N3O16P2
InChI=1S/C15H25N3O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4,16H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9-,10-,11-,12-,13-,14-/m1/s1
CYKLRRKFBPBYEI-NQQHDEILSA-N
565.31700
565.07101
N[C@H]1[C@@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n2ccc(=O)[nH]c2=O)O[C@H](CO)[C@@H](O)[C@@H]1O
KEGG:C02200
uridine 5'-[3-(2-amino-2-deoxyglucopyranosyl) dihydrogen diphosphate]
chebi_ontology
UDPglucosamine
CHEBI:13497
UDP-alpha-D-glucosamine
uridine 5'-[3-(2-amino-2-deoxyglucopyranosyl) dihydrogen diphosphate]
IUPAC
UDPglucosamine
KEGG_COMPOUND
A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent.
glycols
chebi_ontology
Glykol
CHEBI:13643
glycol
glycols
IUPAC
Glykol
ChEBI
A non-proteinogenic amino acid derivative resulting from reaction of homocysteine at the amino group, the carboxy group, or the side-chain amino group, or from the replacement of any hydrogen of homocysteine by a heteroatom. The definition normally excludes peptides containing homocysteine residues.
chebi_ontology
homocysteine derivatives
CHEBI:136505
homocysteine derivative
homocysteine derivatives
ChEBI
Organonitrogen compounds that have the general structure R(1)(R(2))C=N(O)OH (R(1),R(2) = H, organyl). They are tautomers of C-nitro compounds.
0
CHNO2R2
59.024
59.00073
C(*)(=[N+](O)[O-])*
chebi_ontology
aci-nitro compounds
oxime N-oxide
oxime N-oxides
CHEBI:136622
aci-nitro compound
aci-nitro compounds
ChEBI
oxime N-oxide
ChEBI
oxime N-oxides
ChEBI
A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent.
PMID:26449612
chebi_ontology
pro-agents
proagent
proagents
CHEBI:136859
pro-agent
PMID:26449612
Europe PMC
pro-agents
ChEBI
proagent
ChEBI
proagents
ChEBI
An organic cation obtained by protonation of any secondary amino compound; major species at pH 7.3.
+1
H2NR2
16.023
16.01872
*[NH+](*)[H]
MetaCyc:Secondary-Amines
chebi_ontology
a secondary amine
secondary amine(1+)
CHEBI:137419
secondary ammonium ion
a secondary amine
UniProt
secondary amine(1+)
ChEBI
An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of 11beta-hydroxysteroid dehydrogenase (EC 1.1.1.146).
chebi_ontology
11beta-hydroxy steroid dehydrogenase inhibitor
11beta-hydroxy steroid dehydrogenase inhibitors
11beta-hydroxysteroid dehydrogenase inhibitor
11beta-hydroxysteroid dehydrogenase inhibitors
11beta-hydroxysteroid dehydrogenase type 1 inhibitor
11beta-hydroxysteroid dehydrogenase type 1 inhibitors
11beta-hydroxysteroid:NADP(+) 11-oxidoreductase inhibitor
11beta-hydroxysteroid:NADP(+) 11-oxidoreductase inhibitors
EC 1.1.1.146 (11beta-hydroxysteroid dehydrogenase) inhibitors
EC 1.1.1.146 inhibitor
EC 1.1.1.146 inhibitors
beta-hydroxysteroid dehydrogenase inhibitor
beta-hydroxysteroid dehydrogenase inhibitors
corticosteroid 11-reductase inhibitor
corticosteroid 11-reductase inhibitors
corticosteroid 11beta-dehydrogenase inhibitor
corticosteroid 11beta-dehydrogenase inhibitors
dehydrogenase, 11beta-hydroxy steroid inhibitor
dehydrogenase, 11beta-hydroxy steroid inhibitors
CHEBI:137626
EC 1.1.1.146 (11beta-hydroxysteroid dehydrogenase) inhibitor
11beta-hydroxy steroid dehydrogenase inhibitor
ChEBI
11beta-hydroxy steroid dehydrogenase inhibitors
ChEBI
11beta-hydroxysteroid dehydrogenase inhibitor
ChEBI
11beta-hydroxysteroid dehydrogenase inhibitors
ChEBI
11beta-hydroxysteroid dehydrogenase type 1 inhibitor
ChEBI
11beta-hydroxysteroid dehydrogenase type 1 inhibitors
ChEBI
11beta-hydroxysteroid:NADP(+) 11-oxidoreductase inhibitor
ChEBI
11beta-hydroxysteroid:NADP(+) 11-oxidoreductase inhibitors
ChEBI
EC 1.1.1.146 (11beta-hydroxysteroid dehydrogenase) inhibitors
ChEBI
EC 1.1.1.146 inhibitor
ChEBI
EC 1.1.1.146 inhibitors
ChEBI
beta-hydroxysteroid dehydrogenase inhibitor
ChEBI
beta-hydroxysteroid dehydrogenase inhibitors
ChEBI
corticosteroid 11-reductase inhibitor
ChEBI
corticosteroid 11-reductase inhibitors
ChEBI
corticosteroid 11beta-dehydrogenase inhibitor
ChEBI
corticosteroid 11beta-dehydrogenase inhibitors
ChEBI
dehydrogenase, 11beta-hydroxy steroid inhibitor
ChEBI
dehydrogenase, 11beta-hydroxy steroid inhibitors
ChEBI
An atom of an element that exhibits properties that are between those of metals and nonmetals, or that has a mixture of them. The term generally includes boron, silicon, germanium, arsenic, antimony, and tellurium, while carbon, aluminium, selenium, polonium, and astatine are less commonly included.
Wikipedia:Metalloid
chebi_ontology
metalloid
metalloids
CHEBI:137980
metalloid atom
metalloid
ChEBI
metalloids
ChEBI
An organic cation obtained by protonation of the amino group of any tertiary amino compound.
+1
HNR3
15.015
15.01090
[NH+](*)(*)*
chebi_ontology
a tertiary amine
tertiary amine(1+)
tertiary ammonium ions
CHEBI:137982
tertiary ammonium ion
a tertiary amine
UniProt
tertiary amine(1+)
ChEBI
tertiary ammonium ions
ChEBI
Any compound that can disrupt the functions of the endocrine (hormone) system
PMID:27929035
PMID:28356401
PMID:28526231
Wikipedia:Endocrine_disruptor
chebi_ontology
endocrine disrupting chemical
endocrine disrupting chemicals
endocrine disrupting compound
endocrine disrupting compounds
endocrine disruptors
endocrine-disrupting chemical
endocrine-disrupting chemicals
hormonally active agent
hormonally active agents
CHEBI:138015
endocrine disruptor
PMID:27929035
Europe PMC
PMID:28356401
Europe PMC
PMID:28526231
Europe PMC
endocrine disrupting chemical
ChEBI
endocrine disrupting chemicals
ChEBI
endocrine disrupting compound
ChEBI
endocrine disrupting compounds
ChEBI
endocrine disruptors
ChEBI
endocrine-disrupting chemical
ChEBI
endocrine-disrupting chemicals
ChEBI
hormonally active agent
ChEBI
hormonally active agents
ChEBI
Any steroid carrying a 14alpha-methyl substituent.
0
C20H33R
273.477
273.25823
C12C([C@]3(C(C(CC3)*)(C)CC1)C)CCC4C2(CCCC4)C
MetaCyc:14-alpha-methylsteroids
chebi_ontology
a 14alpha-methyl steroid
CHEBI:138029
14alpha-methyl steroid
MetaCyc:14-alpha-methylsteroids
SUBMITTER
a 14alpha-methyl steroid
UniProt
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
A 2-acyl-sn-glycero-3-phospho-D-myo-inositol that has palmitoleoyl as the acyl group.
0
C25H47O12P
InChI=1S/C25H47O12P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(27)36-18(16-26)17-35-38(33,34)37-25-23(31)21(29)20(28)22(30)24(25)32/h7-8,18,20-26,28-32H,2-6,9-17H2,1H3,(H,33,34)/b8-7-/t18-,20-,21-,22+,23-,24-,25-/m1/s1
PEWKZKILLSBVNX-YUCDOUPMSA-N
570.608
570.28051
[C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O)O)O)O)OP(OC[C@@H](CO)OC(CCCCCCC/C=C\CCCCCC)=O)(=O)O)O
PMID:28667014
(2R)-1-hydroxy-3-[(hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl)oxy]propan-2-yl (9Z)-hexadec-9-enoate
chebi_ontology
2-(9Z-hexadecenoyl)-glycero-3-phospho-(1'-myo-inositol)
2-(9Z-hexadecenoyl)-sn-glycero-3-phospho-D-myo-inositol
CHEBI:138108
2-palmitoleoyl-sn-glycero-3-phospho-D-myo-inositol
PMID:28667014
Europe PMC
(2R)-1-hydroxy-3-[(hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl)oxy]propan-2-yl (9Z)-hexadec-9-enoate
IUPAC
2-(9Z-hexadecenoyl)-glycero-3-phospho-(1'-myo-inositol)
ChEBI
2-(9Z-hexadecenoyl)-sn-glycero-3-phospho-D-myo-inositol
ChEBI
Any pathway inhibitor that acts on the carotenoid biosynthesis pathway.
chebi_ontology
carotenogenesis inhibitor
carotenogenesis inhibitors
carotenoid biosynthesis inhibitors
carotenoid-biosynthesis inhibitor
carotenoid-biosynthesis inhibitors
CHEBI:138208
carotenoid biosynthesis inhibitor
carotenogenesis inhibitor
ChEBI
carotenogenesis inhibitors
ChEBI
carotenoid biosynthesis inhibitors
ChEBI
carotenoid-biosynthesis inhibitor
ChEBI
carotenoid-biosynthesis inhibitors
ChEBI
A nucleoside 5'-monophosphate(2-) obtained by deprotonation of the phospohate OH groups of any pyrimidine ribonucleoside 5'-monophosphate; major species at pH 7.3.
-2
C9H8N2O7PR4
287.143
287.00691
N1([C@@H]2O[C@H](COP([O-])(=O)[O-])[C@H]([C@H]2O)O)C(=C(C(=NC1=*)*)*)*
CHEBI:140282
chebi_ontology
a pyrimidine ribonucleoside 5'-phosphate
CHEBI:138238
pyrimidine ribonucleoside 5'-monophosphate(2-)
a pyrimidine ribonucleoside 5'-phosphate
UniProt
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
Any compound that induces the process of autophagy (the self-digestion of one or more components of a cell through the action of enzymes originating within the same cell).
chebi_ontology
autophagocytosis inducer
autophagocytosis inducers
autophagy inducers
CHEBI:138880
autophagy inducer
autophagocytosis inducer
ChEBI
autophagocytosis inducers
ChEBI
autophagy inducers
ChEBI
An N-acylsphingoid obtained by formal condensation of the carboxy group of any fatty acid with the amino group of any dihydrosphingoid base.
0
C5H9NO3R2
131.130
131.05824
OC[C@@H]([C@H](O)C*)NC(=O)*
chebi_ontology
N-acyldihydrosphingoid
N-acyldihydrosphingoids
a dihydroceramide
dihydroceramides
CHEBI:139048
dihydroceramide
N-acyldihydrosphingoid
ChEBI
N-acyldihydrosphingoids
ChEBI
a dihydroceramide
UniProt
dihydroceramides
ChEBI
A member of the class of imidazoles that is 1,3-dihydroimidazole-2-thione and its derivatives by substitution.
0
C3N2SR4
96.112
95.97822
N1(C(N(C(=C1*)*)*)=S)*
chebi_ontology
CHEBI:139340
1,3-dihydroimidazole-2-thiones
Any molecular entity in which the isotopic ratio of nuclides for at least one element deviates measurably from that occurring in nature. The term includes both isotopically substituted compounds (in which essentially all the molecules of the compound have only the indicated nuclide(s) at each designated position) and isotopically labeled compounds (a formal mixture of an isotopically unmodified compound with one or more analogous isotopically substituted compound(s).
chebi_ontology
isotopically modified compounds
CHEBI:139358
isotopically modified compound
isotopically modified compounds
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 alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety.
PMID:15326516
PMID:19908854
PMID:20382022
PMID:23295224
chebi_ontology
alpha-hydroxy ketones
alpha-hydroxy-ketone
alpha-hydroxy-ketones
alpha-hydroxyketone
alpha-hydroxyketones
CHEBI:139588
alpha-hydroxy ketone
PMID:15326516
Europe PMC
PMID:19908854
Europe PMC
PMID:20382022
Europe PMC
PMID:23295224
Europe PMC
alpha-hydroxy ketones
ChEBI
alpha-hydroxy-ketone
ChEBI
alpha-hydroxy-ketones
ChEBI
alpha-hydroxyketone
ChEBI
alpha-hydroxyketones
ChEBI
An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a -CH2 (methylene) group.
0
C2H3O2R
59.044
59.01330
*C(C(O)([H])[H])=O
chebi_ontology
primary alpha-hydroxy ketones
primary alpha-hydroxy-ketone
primary alpha-hydroxy-ketones
primary alpha-hydroxyketone
primary alpha-hydroxyketones
CHEBI:139590
primary alpha-hydroxy ketone
primary alpha-hydroxy ketones
ChEBI
primary alpha-hydroxy-ketone
ChEBI
primary alpha-hydroxy-ketones
ChEBI
primary alpha-hydroxyketone
ChEBI
primary alpha-hydroxyketones
ChEBI
An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups.
0
C2HO2R3
57.028
56.99765
C(C(=O)*)(O)(*)*
chebi_ontology
tertiary alpha-hydroxy ketones
tertiary alpha-hydroxy-ketone
tertiary alpha-hydroxy-ketones
tertiary alpha-hydroxyketone
tertiary alpha-hydroxyketones
CHEBI:139592
tertiary alpha-hydroxy ketone
tertiary alpha-hydroxy ketones
ChEBI
tertiary alpha-hydroxy-ketone
ChEBI
tertiary alpha-hydroxy-ketones
ChEBI
tertiary alpha-hydroxyketone
ChEBI
tertiary alpha-hydroxyketones
ChEBI
A carboxamide resulting from the formal condensation of a carboxylic acid with ammonia; formula RC(=O)NH2.
0
CH2NOR
44.033
44.01364
N(C(*)=O)([H])[H]
chebi_ontology
primary carboxamides
CHEBI:140324
primary carboxamide
primary carboxamides
ChEBI
A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1).
0
CHNOR2
43.025
43.00581
N(C(*)=O)(*)[H]
chebi_ontology
secondary carboxamides
CHEBI:140325
secondary carboxamide
secondary carboxamides
ChEBI
Any polyunsaturated fatty acid carrying one or more hydroxy substituents.
chebi_ontology
CHEBI:140345
hydroxy polyunsaturated fatty acid
A nucleotide-sugar oxoanion obtained by deprotonation of the phosphate OH groups of any UDP-monosaccharide. This compound class represents generic and unspecified UDP-sugars.
-2
C9H11N2O12P2R
401.138
400.97872
[C@@H]1(N2C(NC(C=C2)=O)=O)O[C@H](COP(OP([O-])(O*)=O)([O-])=O)[C@H]([C@H]1O)O
MetaCyc:UDP-sugar
chebi_ontology
UDP-sugar(2-)
a UDP-monosaccharide
CHEBI:140359
UDP-monosaccharide(2-)
MetaCyc:UDP-sugar
SUBMITTER
UDP-sugar(2-)
ChEBI
a UDP-monosaccharide
UniProt
Any saturated fatty acid containing 4 carbons.
0
CHO2R
45.017
44.99765
*C(O)=O
chebi_ontology
CHEBI:140601
fatty acid 4:0
Any plant metabolite that is produced by Arabidopsis thaliana.
Wikipedia:Arabidopsis_thaliana
chebi_ontology
Arabidopsis thaliana metabolites
CHEBI:140602
Arabidopsis thaliana metabolite
Arabidopsis thaliana metabolites
ChEBI
A primary ammonium ion resulting from the protonation of the amino group of L-tyrosinal.
+1
C9H12NO2
InChI=1S/C9H11NO2/c10-8(6-11)5-7-1-3-9(12)4-2-7/h1-4,6,8,12H,5,10H2/p+1/t8-/m0/s1
DXGAIOIQACHYRK-QMMMGPOBSA-O
166.197
166.08626
O=C[C@@H]([NH3+])CC=1C=CC(=CC1)O
MetaCyc:CPD-21526
PMID:23281040
(2S)-1-(4-hydroxyphenyl)-3-oxopropan-2-aminium
chebi_ontology
(2S)-1-(p-hydroxyphenyl)-3-oxopropan-2-aminium
L-tyrosinal
CHEBI:141668
L-tyrosinal(1+)
PMID:23281040
SUBMITTER
(2S)-1-(4-hydroxyphenyl)-3-oxopropan-2-aminium
IUPAC
(2S)-1-(p-hydroxyphenyl)-3-oxopropan-2-aminium
ChEBI
L-tyrosinal
UniProt
Any carbobycyclic compound that is an hexahydronaphthalene or a compound obtained from an hexahydronaphthalene by formal substitution of one or more hydrogens.
chebi_ontology
CHEBI:142348
hexahydronaphthalenes
A purine ribonucleoside that is a purine derivative attached to a beta-D-ribofuranosyl residue at position 9 via a glycosidic (N-glycosyl) linkage.
0
C10H11N4O4R2
251.219
251.07803
C1(=*)NC(=NC2=C1N=CN2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)*
chebi_ontology
a purine D-ribonucleoside
CHEBI:142355
purines D-ribonucleoside
a purine D-ribonucleoside
UniProt
A purine derivative attached to a beta-D-2'-deoxy-ribofuranosyl residue at position 9 via a glycosidic (N-glycosyl) linkage.
0
C10H11N4O3R2
235.220
235.08312
C1(=*)NC(=NC2=C1N=CN2[C@@H]3O[C@H](CO)[C@@H](O)C3)*
chebi_ontology
a purine 2'-deoxy-D-ribonucleoside
CHEBI:142361
purines 2'-deoxy-D-ribonucleoside
a purine 2'-deoxy-D-ribonucleoside
UniProt
A organic ion resulting from the deprotonation of the hydroxy group of any oxime.
-1
CNO
42.017
41.99799
C(*)(=N[O-])*
oxime anion
chebi_ontology
oximate
oximates
oxime anions
CHEBI:142513
oxime anion
oxime anion
ChEBI
oximate
ChEBI
oximates
ChEBI
oxime anions
ChEBI
A benzoate ester resulting from the formal condensation of the carboxy group of vanillic acid with the hydroxy group of (-)-borneol. A metabolite isolated from Ferula dissecta.
0
C18H24O4
InChI=1S/C18H24O4/c1-17(2)12-7-8-18(17,3)15(10-12)22-16(20)11-5-6-13(19)14(9-11)21-4/h5-6,9,12,15,19H,7-8,10H2,1-4H3/t12-,15+,18+/m0/s1
KTOAGBIQQPGNIR-WBHUJUFNSA-N
304.381
304.16746
C(C1=CC(=C(C=C1)O)OC)(=O)O[C@@H]2C[C@@]3(CC[C@]2(C3(C)C)C)[H]
PMID:20350297
PMID:21589808
PMID:23521895
PMID:29900664
PMID:29912155
Reaxys:26876325
(1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl 4-hydroxy-3-methoxybenzoate
tschimganine
chebi_ontology
chimganin
tschimganin
CHEBI:142517
tschimganine
PMID:20350297
Europe PMC
PMID:21589808
Europe PMC
PMID:23521895
Europe PMC
PMID:29900664
Europe PMC
PMID:29912155
Europe PMC
Reaxys:26876325
Reaxys
(1S,2R,4S)-1,7,7-trimethylbicyclo[2.2.1]heptan-2-yl 4-hydroxy-3-methoxybenzoate
IUPAC
tschimganine
ChEBI
chimganin
ChEBI
tschimganin
ChEBI
A triazinoindole that is 5H-[1,2,4]triazino[5,6-b]indole which is substituted at position 3 by a (2-methylprop-2-en-1-yl)thio group. A potent inhibitor of midasin which is an essential protein for eukaryotic ribosome biogenesis.
0
C13H12N4S
InChI=1S/C13H12N4S/c1-8(2)7-18-13-15-12-11(16-17-13)9-5-3-4-6-10(9)14-12/h3-6H,1,7H2,2H3,(H,14,15,17)
LPCWHNSRTRBKBO-UHFFFAOYSA-N
256.328
256.07827
C12=CC=CC=C1NC3=C2N=NC(=N3)SCC(C)=C
CAS:328023-11-6
PMID:27667686
PMID:30318141
3-[(2-methylprop-2-en-1-yl)thio]-5H-[1,2,4]triazino[5,6-b]indole
ribozinoindole-1
chebi_ontology
3-((2-methylallyl)thio)-5H-[1,2,4]triazino[5,6-b]indole
3-(2-methylprop-2-enylsulfanyl)-5H-[1,2,4]triazino[5,6-b]indole
3-[(2-methyl-2-propenyl)sulfanyl]-5H-[1,2,4]triazino[5,6-b]indole
Rbin-1
CHEBI:142676
ribozinoindole-1
CAS:328023-11-6
ChEBI
PMID:27667686
Europe PMC
PMID:30318141
Europe PMC
3-[(2-methylprop-2-en-1-yl)thio]-5H-[1,2,4]triazino[5,6-b]indole
IUPAC
ribozinoindole-1
ChEBI
3-((2-methylallyl)thio)-5H-[1,2,4]triazino[5,6-b]indole
ChEBI
3-(2-methylprop-2-enylsulfanyl)-5H-[1,2,4]triazino[5,6-b]indole
ChEBI
3-[(2-methyl-2-propenyl)sulfanyl]-5H-[1,2,4]triazino[5,6-b]indole
ChEBI
Rbin-1
ChEBI
Any heterotricyclic compound whose skeleton consists of an indole fused to a triazine ring.
triazinoindole
chebi_ontology
triazinoindoles
CHEBI:142677
triazinoindole
triazinoindole
ChEBI
triazinoindoles
ChEBI
An organic anion arising from deprotonation of the hydroxy group of an enol.
-1
C2OR3
40.021
39.99491
[O-]C(=C(*)*)*
chebi_ontology
enolate anion
enolate anions
enolates
CHEBI:142839
enolate
enolate anion
ChEBI
enolate anions
ChEBI
enolates
ChEBI
A polar amino acid zwitterion restulting from the transfer of a proton from the carboxy group to the alpha-amino group of D-histidine. The major species at pH 7.3.
0
C6H9N3O2
InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m1/s1
HNDVDQJCIGZPNO-RXMQYKEDSA-N
155.155
155.06948
C=1(N=CNC1)C[C@H](C(=O)[O-])[NH3+]
MetaCyc:CPD-12151
PMID:27230378
(2R)-2-ammonio-3-(1H-imidazol-4-yl)propanoate
(2R)-2-azaniumyl-3-(1H-imidazol-4-yl)propanoate
chebi_ontology
D-histidine
CHEBI:142967
D-histidine zwitterion
PMID:27230378
SUBMITTER
(2R)-2-ammonio-3-(1H-imidazol-4-yl)propanoate
IUPAC
(2R)-2-azaniumyl-3-(1H-imidazol-4-yl)propanoate
IUPAC
D-histidine
UniProt
A D-alpha-amino acid zwitterion arising from the transfer of a proton from the carboxy to the amino group of D-leucine; major species at pH 7.3.
0
C6H13NO2
InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1
ROHFNLRQFUQHCH-RXMQYKEDSA-N
131.173
131.09463
[O-]C([C@@H](CC(C)C)[NH3+])=O
MetaCyc:CPD-12150
PMID:24419381
(2R)-2-azaniumyl-4-methylpentanoate
chebi_ontology
D-leu
D-leucine
CHEBI:143079
D-leucine zwitterion
PMID:24419381
SUBMITTER
(2R)-2-azaniumyl-4-methylpentanoate
IUPAC
D-leu
SUBMITTER
D-leucine
UniProt
A D-alpha-amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of D-homoserine; major species at pH 7.3.
0
C4H9NO3
InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m1/s1
UKAUYVFTDYCKQA-GSVOUGTGSA-N
119.119
119.05824
C([C@H](C([O-])=O)[NH3+])CO
MetaCyc:CPD-12255
PMID:24419381
(2R)-2-azaniumyl-4-hydroxybutanoate
chebi_ontology
D-homoserine
CHEBI:143081
D-homoserine zwitterion
PMID:24419381
SUBMITTER
(2R)-2-azaniumyl-4-hydroxybutanoate
IUPAC
D-homoserine
UniProt
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
0
C10H17NO8R2
279.244
279.09542
[C@H]([C@@H](*)O)(NC(=O)*)CO[C@@H]1O[C@@H]([C@@H]([C@@H]([C@H]1O)O)O)CO
PMID:10748143
PMID:3921539
chebi_ontology
beta-D-Gal-(1<->1')-Cer
beta-D-GalCer
beta-D-galactosyl-N-acyl sphingoid base
beta-galactocerebroside
CHEBI:143593
beta-galactosylceramide
PMID:10748143
SUBMITTER
PMID:3921539
SUBMITTER
beta-D-Gal-(1<->1')-Cer
UniProt
beta-D-GalCer
SUBMITTER
beta-D-galactosyl-N-acyl sphingoid base
SUBMITTER
beta-galactocerebroside
SUBMITTER
A phosphatidylinositol where R1 can be an alkyl or an acyl chain and 2R2 is an acyl chain.
-1
C10H16O12PR2
359.201
359.03794
[C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O)O)O)O)OP(OC[C@H](CO*)OC(=O)*)(=O)[O-])O
PMID:9463366
chebi_ontology
1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol)
CHEBI:143813
1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol)(1-)
PMID:9463366
SUBMITTER
1-radyl,2-acyl-sn-glycero-3-phospho-(1D-myo-2-acyl-inositol)
UniProt
0
C21H17N2O7R5
409.370
409.10358
C12=C(C=C(C(=C1C(C=3[C@]([C@@H]([C@]4([C@@H](C([O-])=C(C([C@@]4(O)C3O)=O)C(N)=O)[NH+](C)C)[H])*)(C2(*)*)[H])=O)O)*)*
chebi_ontology
a tetracycline
CHEBI:144644
a tetracycline zwittterion
a tetracycline
UniProt
A peptide anion obtained by deprotonation of both carboxy groups and protonation of the glutamyl amino group of S-nitrosoglutathione; major species at pH 7.3.
-1
C10H15N4O7S
InChI=1S/C10H16N4O7S/c11-5(10(19)20)1-2-7(15)13-6(4-22-14-21)9(18)12-3-8(16)17/h5-6H,1-4,11H2,(H,12,18)(H,13,15)(H,16,17)(H,19,20)/p-1/t5-,6-/m0/s1
HYHSBSXUHZOYLX-WDSKDSINSA-M
335.310
335.06669
[NH3+][C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)[O-])C(=O)[O-]
MetaCyc:S-NITROSOGLUTATHIONE
(2S)-2-ammonio-5-{[(2S)-1-[(carboxylatomethyl)amino]-3-(nitrosothio)-1-oxopropan-2-yl]amino}-5-oxopentanoate
chebi_ontology
(2S)-2-azaniumyl-5-{[(2R)-1-[(carboxylatomethyl)amino]-3-(nitrososulfanyl)-1-oxopropan-2-yl]amino}-5-oxopentanoate
GSNO(1-)
L-gamma-glutamyl-S-nitroso-L-cysteinylglycine(1-)
S-nitrosoglutathione
CHEBI:145544
S-nitrosoglutathione(1-)
(2S)-2-ammonio-5-{[(2S)-1-[(carboxylatomethyl)amino]-3-(nitrosothio)-1-oxopropan-2-yl]amino}-5-oxopentanoate
IUPAC
(2S)-2-azaniumyl-5-{[(2R)-1-[(carboxylatomethyl)amino]-3-(nitrososulfanyl)-1-oxopropan-2-yl]amino}-5-oxopentanoate
IUPAC
GSNO(1-)
ChEBI
L-gamma-glutamyl-S-nitroso-L-cysteinylglycine(1-)
ChEBI
S-nitrosoglutathione
UniProt
Any nitroso compound in which a carbon atom of an organyl group is attached to the sulfur atom of a nitrosothio group: R-S-N=O.
0
NOSR
62.072
61.97006
*SN=O
chebi_ontology
S-nitrosothiol compound
S-nitrosothiols
SNO compound
nitrosothio compounds
CHEBI:145545
nitrosothio compound
S-nitrosothiol compound
ChEBI
S-nitrosothiols
SUBMITTER
SNO compound
SUBMITTER
nitrosothio compounds
ChEBI
Macrolides (macrocyclic lactones) in which the macrocyclic ring contains more than one ester linkage. Macropolylides include macrodiolides, macrotriolides, macrotetrolides and macropentolides, each containing di-, tri-, tetra-, and penta- ester linkages, respectively, in one macrocyclic ring. Macrocyclic lactones containing nitrogen in their skeletons (azamacrolides and macrolide lactams) and also containing oxazole or thiazole in their skeletons are known in nature.
chebi_ontology
macropolylides
CHEBI:145555
macropolylide
macropolylides
ChEBI
A macropolylide which contains two ester linkages in one macrocyclic ring.
PMID:17446696
PMID:29624065
PMID:29671776
PMID:31247219
chebi_ontology
macrodiolides
CHEBI:145556
macrodiolide
PMID:17446696
Europe PMC
PMID:29624065
Europe PMC
PMID:29671776
Europe PMC
PMID:31247219
Europe PMC
macrodiolides
ChEBI
A macrolide in which the macrocyclic lactone ring includes an amide group.
PMID:11678663
PMID:12227772
PMID:15248618
PMID:17378533
PMID:31226284
chebi_ontology
macrolide lactams
CHEBI:145565
macrolide lactam
PMID:11678663
Europe PMC
PMID:12227772
Europe PMC
PMID:15248618
Europe PMC
PMID:17378533
Europe PMC
PMID:31226284
Europe PMC
macrolide lactams
ChEBI
A branched-chain saturated fatty acid anion resulting from the deprotonation of the carboxy group of (S)-2-methylbutanoic acid. The major species at pH 7.3.
-1
C5H9O2
InChI=1S/C5H10O2/c1-3-4(2)5(6)7/h4H,3H2,1-2H3,(H,6,7)/p-1/t4-/m0/s1
WLAMNBDJUVNPJU-BYPYZUCNSA-M
101.126
101.06080
[O-]C([C@H](CC)C)=O
PMID:16819884
(2S)-2-methylbutanoate
(S)-2-methylbutanoate
chebi_ontology
(2S)-2-methylbutyrate
(2S)-2-methylbutyric acid anion
(S)-2-methylbutyrate
(S)-alpha-methylbutyrate
CHEBI:145932
(S)-2-methylbutanoate
PMID:16819884
Europe PMC
(2S)-2-methylbutanoate
IUPAC
(S)-2-methylbutanoate
UniProt
(2S)-2-methylbutyrate
ChEBI
(2S)-2-methylbutyric acid anion
ChEBI
(S)-2-methylbutyrate
ChEBI
(S)-alpha-methylbutyrate
ChEBI
A cardiovascular drug that prevents atherosclerosis (a disease in which the inside of an artery narrows due to the build up of plaque). Compare with antiatherogenic agent.
antiatherosclerotic agent
chebi_ontology
anti-atherosclerotic agent
anti-atherosclerotic agents
anti-atherosclerotic drug
anti-atherosclerotic drugs
antiatherosclerotic agents
antiatherosclerotic drug
antiatherosclerotic drugs
CHEBI:145947
antiatherosclerotic agent
antiatherosclerotic agent
ChEBI
anti-atherosclerotic agent
ChEBI
anti-atherosclerotic agents
ChEBI
anti-atherosclerotic drug
ChEBI
anti-atherosclerotic drugs
ChEBI
antiatherosclerotic agents
ChEBI
antiatherosclerotic drug
ChEBI
antiatherosclerotic drugs
ChEBI
An EC 3.4.22.* (cysteine endopeptidase) inhibitor that interferes with the action of SARS coronavirus main proteinase (EC 3.4.22.69).
Wikipedia:C30_Endopeptidase
chebi_ontology
3C-like protease inhibitor
3C-like protease inhibitors
3cLpro inhibitor
3cLpro inhibitors
EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitors
EC 3.4.22.69 inhibitor
EC 3.4.22.69 inhibitors
Mpro inhibitor
Mpro inhibitors
SARS 3C-like protease inhibitor
SARS 3C-like protease inhibitors
SARS coronavirus 3CL protease inhibitor
SARS coronavirus 3CL protease inhibitors
SARS coronavirus main peptidase inhibitor
SARS coronavirus main peptidase inhibitors
SARS coronavirus main protease inhibitor
SARS coronavirus main protease inhibitors
SARS coronavirus main proteinase inhibitor
SARS coronavirus main proteinase inhibitors
SARS-CoV 3CLpro enzyme inhibitor
SARS-CoV 3CLpro enzyme inhibitors
SARS-CoV Mpro inhibitor
SARS-CoV Mpro inhibitors
SARS-CoV main protease inhibitor
SARS-CoV main protease inhibitors
coronavirus 3C-like protease inhibitor
coronavirus 3C-like protease inhibitors
severe acute respiratory syndrome coronavirus main protease inhibitor
severe acute respiratory syndrome coronavirus main protease inhibitors
CHEBI:147285
EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor
3C-like protease inhibitor
ChEBI
3C-like protease inhibitors
ChEBI
3cLpro inhibitor
ChEBI
3cLpro inhibitors
ChEBI
EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitors
ChEBI
EC 3.4.22.69 inhibitor
ChEBI
EC 3.4.22.69 inhibitors
ChEBI
Mpro inhibitor
ChEBI
Mpro inhibitors
ChEBI
SARS 3C-like protease inhibitor
ChEBI
SARS 3C-like protease inhibitors
ChEBI
SARS coronavirus 3CL protease inhibitor
ChEBI
SARS coronavirus 3CL protease inhibitors
ChEBI
SARS coronavirus main peptidase inhibitor
ChEBI
SARS coronavirus main peptidase inhibitors
ChEBI
SARS coronavirus main protease inhibitor
ChEBI
SARS coronavirus main protease inhibitors
ChEBI
SARS coronavirus main proteinase inhibitor
ChEBI
SARS coronavirus main proteinase inhibitors
ChEBI
SARS-CoV 3CLpro enzyme inhibitor
ChEBI
SARS-CoV 3CLpro enzyme inhibitors
ChEBI
SARS-CoV Mpro inhibitor
ChEBI
SARS-CoV Mpro inhibitors
ChEBI
SARS-CoV main protease inhibitor
ChEBI
SARS-CoV main protease inhibitors
ChEBI
coronavirus 3C-like protease inhibitor
ChEBI
coronavirus 3C-like protease inhibitors
ChEBI
severe acute respiratory syndrome coronavirus main protease inhibitor
ChEBI
severe acute respiratory syndrome coronavirus main protease inhibitors
ChEBI
A phosphatidylinositol anion where the inositol is either not phosphorylated or phosphorylated at position 4 and/or position 5; major species at pH 7.3.
-1
C11H14O13PR4
385.195
385.01720
[C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O*)O*)O)O)OP(OC[C@@H](COC(=O)*)OC(=O)*)(=O)[O-])O
chebi_ontology
1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol anion derivative
a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol derivative
CHEBI:147334
1-phosphatidyl-1D-myo-inositol anion derivative
a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol derivative
UniProt
1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol anion derivative
SUBMITTER
A phosphatidylinositol anion where the inositol is phosphorylated at position 3 and either phosphorylated or not at position 4 and/or position 5; major species at pH 7.3.
-3
C11H13O16P2R4
463.159
462.96788
[C@@H]1([C@@H]([C@@H]([C@@H]([C@H]([C@@H]1O*)O*)OP(=O)([O-])[O-])O)OP(OC[C@@H](COC(=O)*)OC(=O)*)(=O)[O-])O
chebi_ontology
1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate anion derivative
a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate derivative
CHEBI:147335
1-phosphatidyl-1D-myo-inositol-3-phosphate anion derivative
1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate anion derivative
SUBMITTER
a 1,2-diacyl-sn-glycero-3-phospho-1D-myo-inositol-3-phosphate derivative
UniProt
Any agent that induces nausea and vomiting.
chebi_ontology
emetics
CHEBI:149552
emetic
emetics
ChEBI
Any antiviral agent which inhibits the activity of coronaviruses.
Wikipedia:Coronavirus
anticoronaviral agent
chebi_ontology
anti-coronaviral agent
anti-coronaviral agents
anti-coronavirus agent
anti-coronavirus agents
anticoronaviral agents
anticoronaviral drug
anticoronaviral drugs
anticoronavirus agent
anticoronavirus agents
anticoronviral agent
anticoronviral agents
CHEBI:149553
anticoronaviral agent
anticoronaviral agent
ChEBI
anti-coronaviral agent
ChEBI
anti-coronaviral agents
ChEBI
anti-coronavirus agent
ChEBI
anti-coronavirus agents
ChEBI
anticoronaviral agents
ChEBI
anticoronaviral drug
ChEBI
anticoronaviral drugs
ChEBI
anticoronavirus agent
ChEBI
anticoronavirus agents
ChEBI
anticoronviral agent
ChEBI
anticoronviral agents
ChEBI
A divalent inorganic anion obtained by removal of both protons from selenic acid.
-2
O4Se
InChI=1S/H2O4Se/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
QYHFIVBSNOWOCQ-UHFFFAOYSA-L
142.95760
143.89728
[O-][Se]([O-])(=O)=O
CAS:14124-68-6
PDBeChem:SE4
Selenate
selenate
tetraoxidoselenate(2-)
chebi_ontology
SELENATE ION
[SeO4](2-)
CHEBI:15075
selenate
CAS:14124-68-6
ChemIDplus
Selenate
ChemIDplus
selenate
IUPAC
selenate
UniProt
tetraoxidoselenate(2-)
IUPAC
SELENATE ION
PDBeChem
[SeO4](2-)
IUPAC
A divalent inorganic anion obtained by removal of both protons from hydrogen sulfide.
-2
S
InChI=1S/S/q-2
UCKMPCXJQFINFW-UHFFFAOYSA-N
32.06600
31.97317
[S--]
CAS:18496-25-8
UM-BBD_compID:c0569
sulfanediide
sulfide(2-)
chebi_ontology
S(2-)
Sulfide
sulphide
CHEBI:15138
sulfide(2-)
CAS:18496-25-8
ChemIDplus
UM-BBD_compID:c0569
UM-BBD
sulfanediide
IUPAC
sulfide(2-)
IUPAC
S(2-)
IUPAC
Sulfide
ChemIDplus
sulphide
ChEBI
A purine nucleobase found in humans and other organisms.
0
C5H4N4O2
152.111
152.03343
ECMDB:ECMDB00292
KNApSAcK:C00019660
PMID:1557408
PMID:24629268
PMID:9007687
YMDB:YMDB00263
xanthine
chebi_ontology
2,6-dioxopurine
2,6-dioxopurines
xanthines
CHEBI:15318
xanthine
PMID:1557408
Europe PMC
PMID:24629268
Europe PMC
PMID:9007687
Europe PMC
xanthine
ChEBI
2,6-dioxopurine
ChEBI
2,6-dioxopurines
ChEBI
xanthines
ChEBI
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
The aldehyde formed from acetic acid by reduction of the carboxy group. It is the most abundant carcinogen in tobacco smoke.
0
C2H4O
InChI=1S/C2H4O/c1-2-3/h2H,1H3
IKHGUXGNUITLKF-UHFFFAOYSA-N
44.05256
44.02621
[H]C(C)=O
CHEBI:13703
CHEBI:22158
CHEBI:2383
CHEBI:40533
Beilstein:505984
CAS:75-07-0
Gmelin:779
HMDB:HMDB0000990
KEGG:C00084
KNApSAcK:C00007392
LINCS:LSM-37193
PDBeChem:ACE
PMID:11058591
PMID:110589
PMID:11087437
PMID:11290854
PMID:15239123
PMID:15833031
PMID:16404561
PMID:16485909
PMID:18001279
PMID:19396661
PMID:2233695
PMID:24282063
PMID:24326678
PMID:24503565
PMID:4239189
PMID:5526694
PMID:6036728
PMID:7163973
PMID:9171333
Reaxys:505984
UM-BBD_compID:c0160
Wikipedia:Acetaldehyde
ACETALDEHYDE
Acetaldehyde
acetaldehyde
chebi_ontology
Acetaldehyd
Azetaldehyd
Ethanal
acetaldehydes
acetic aldehyde
ethyl aldehyde
CHEBI:15343
acetaldehyde
Beilstein:505984
Beilstein
CAS:75-07-0
ChemIDplus
CAS:75-07-0
KEGG COMPOUND
CAS:75-07-0
NIST Chemistry WebBook
Gmelin:779
Gmelin
PMID:11058591
Europe PMC
PMID:110589
Europe PMC
PMID:11087437
Europe PMC
PMID:11290854
Europe PMC
PMID:15239123
Europe PMC
PMID:15833031
Europe PMC
PMID:16404561
Europe PMC
PMID:16485909
Europe PMC
PMID:18001279
Europe PMC
PMID:19396661
Europe PMC
PMID:2233695
Europe PMC
PMID:24282063
Europe PMC
PMID:24326678
Europe PMC
PMID:24503565
Europe PMC
PMID:4239189
Europe PMC
PMID:5526694
Europe PMC
PMID:6036728
Europe PMC
PMID:7163973
Europe PMC
PMID:9171333
Europe PMC
Reaxys:505984
Reaxys
UM-BBD_compID:c0160
UM-BBD
ACETALDEHYDE
PDBeChem
Acetaldehyde
KEGG_COMPOUND
acetaldehyde
IUPAC
acetaldehyde
UniProt
Acetaldehyd
NIST_Chemistry_WebBook
Azetaldehyd
ChEBI
Ethanal
KEGG_COMPOUND
acetaldehydes
ChEBI
acetic aldehyde
NIST_Chemistry_WebBook
ethyl aldehyde
NIST_Chemistry_WebBook
A thiol comprising a panthothenate unit in phosphoric anhydride linkage with a 3',5'-adenosine diphosphate unit; and an aminoethanethiol unit.
0
C21H36N7O16P3S
InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
767.53540
767.11521
CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS
CHEBI:13294
CHEBI:13295
CHEBI:13298
CHEBI:23355
CHEBI:3771
CHEBI:41597
CHEBI:41631
CHEBI:741566
Beilstein:77809
CAS:85-61-0
DrugBank:DB01992
KEGG:C00010
KNApSAcK:C00007258
PDBeChem:COA
PDBeChem:COZ
PMID:11923312
PMID:13025483
PMID:15014152
PMID:15893380
PMID:18407920
PMID:19666462
PMID:20351285
PMID:2981478
PMID:7310833
Wikipedia:Coenzyme_A
3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate}
COENZYME A
Coenzyme A
chebi_ontology
3'-phosphoadenosine-(5')diphospho(4')pantatheine
CoA
CoA-SH
CoASH
Coenzym A
HSCoA
Koenzym A
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate
CHEBI:15346
coenzyme A
Beilstein:77809
Beilstein
CAS:85-61-0
ChemIDplus
CAS:85-61-0
KEGG COMPOUND
PMID:11923312
Europe PMC
PMID:13025483
Europe PMC
PMID:15014152
Europe PMC
PMID:15893380
Europe PMC
PMID:18407920
Europe PMC
PMID:19666462
Europe PMC
PMID:20351285
Europe PMC
PMID:2981478
Europe PMC
PMID:7310833
ChEMBL
3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)butyl] dihydrogen diphosphate}
IUPAC
COENZYME A
PDBeChem
Coenzyme A
KEGG_COMPOUND
3'-phosphoadenosine-(5')diphospho(4')pantatheine
ChEBI
CoA
KEGG_COMPOUND
CoA-SH
KEGG_COMPOUND
CoASH
ChEBI
Coenzym A
ChEBI
HSCoA
ChEBI
Koenzym A
ChEBI
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-4-({3-oxo-3-[(2-sulfanylethyl)amino]propyl}amino)-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate
ChEBI
An acyl-CoA having acetyl as its S-acetyl component.
0
C23H38N7O17P3S
InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
ZSLZBFCDCINBPY-ZSJPKINUSA-N
809.57208
809.12577
CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)n1cnc2c(N)ncnc12
CHEBI:13712
CHEBI:22192
CHEBI:2408
CHEBI:40470
CAS:72-89-9
ECMDB:ECMDB01206
HMDB:HMDB0001206
KEGG:C00024
KNApSAcK:C00007259
PDBeChem:ACO
PMID:12527305
PMID:12739170
PMID:15247244
PMID:16101314
PMID:16667687
PMID:16708165
PMID:17189273
PMID:17242360
PMID:17631502
PMID:18613815
PMID:19356710
PMID:19596230
PMID:19914586
PMID:3950616
Reaxys:78145
UM-BBD_compID:c0031
Wikipedia:Acetyl-CoA
YMDB:YMDB00312
3'-phosphoadenosine 5'-(3-{(3R)-4-[(3-{[2-(acetylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} dihydrogen diphosphate)
Acetyl-CoA
chebi_ontology
AcCoA
Acetyl coenzyme A
S-acetyl-CoA
S-acetyl-coenzyme A
CHEBI:15351
acetyl-CoA
CAS:72-89-9
ChemIDplus
CAS:72-89-9
KEGG COMPOUND
PMID:12527305
Europe PMC
PMID:12739170
Europe PMC
PMID:15247244
Europe PMC
PMID:16101314
Europe PMC
PMID:16667687
Europe PMC
PMID:16708165
Europe PMC
PMID:17189273
Europe PMC
PMID:17242360
Europe PMC
PMID:17631502
Europe PMC
PMID:18613815
Europe PMC
PMID:19356710
Europe PMC
PMID:19596230
Europe PMC
PMID:19914586
Europe PMC
PMID:3950616
Europe PMC
Reaxys:78145
Reaxys
UM-BBD_compID:c0031
UM-BBD
3'-phosphoadenosine 5'-(3-{(3R)-4-[(3-{[2-(acetylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} dihydrogen diphosphate)
IUPAC
Acetyl-CoA
KEGG_COMPOUND
AcCoA
ChEBI
Acetyl coenzyme A
KEGG_COMPOUND
S-acetyl-CoA
ChEBI
S-acetyl-coenzyme A
ChEBI
A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function.
+1
C5H14NO
InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1
OEYIOHPDSNJKLS-UHFFFAOYSA-N
104.17080
104.10699
C[N+](C)(C)CCO
CHEBI:13985
CHEBI:23212
CHEBI:3665
CHEBI:41524
Beilstein:1736748
CAS:62-49-7
DrugBank:DB00122
Drug_Central:3097
ECMDB:ECMDB00097
Gmelin:324597
HMDB:HMDB0000097
KEGG:C00114
KEGG:D07690
KNApSAcK:C00007298
MetaCyc:CHOLINE
PDBeChem:CHT
PMID:10930630
PMID:12826235
PMID:12946691
PMID:14972364
PMID:16210714
PMID:17087106
PMID:17283071
PMID:17344490
PMID:18204095
PMID:18230680
PMID:18786517
PMID:18786520
PMID:19246089
PMID:20038853
PMID:20446114
PMID:22770225
PMID:22961562
PMID:23095202
PMID:23616508
PMID:23637565
PMID:23733158
PMID:6420466
PMID:7590654
PMID:9517478
Reaxys:1736748
Wikipedia:Choline
YMDB:YMDB00227
2-hydroxy-N,N,N-trimethylethanaminium
Choline
choline
chebi_ontology
Bilineurine
CHOLINE ION
N,N,N-trimethylethanol-ammonium
N-trimethylethanolamine
trimethylethanolamine
CHEBI:15354
choline
Beilstein:1736748
Beilstein
CAS:62-49-7
ChemIDplus
CAS:62-49-7
KEGG COMPOUND
Drug_Central:3097
DrugCentral
Gmelin:324597
Gmelin
PMID:10930630
Europe PMC
PMID:12826235
Europe PMC
PMID:12946691
Europe PMC
PMID:14972364
Europe PMC
PMID:16210714
Europe PMC
PMID:17087106
Europe PMC
PMID:17283071
Europe PMC
PMID:17344490
Europe PMC
PMID:18204095
Europe PMC
PMID:18230680
Europe PMC
PMID:18786517
Europe PMC
PMID:18786520
Europe PMC
PMID:19246089
Europe PMC
PMID:20038853
Europe PMC
PMID:20446114
Europe PMC
PMID:22770225
Europe PMC
PMID:22961562
Europe PMC
PMID:23095202
Europe PMC
PMID:23616508
Europe PMC
PMID:23637565
Europe PMC
PMID:23733158
Europe PMC
PMID:6420466
Europe PMC
PMID:7590654
Europe PMC
PMID:9517478
Europe PMC
Reaxys:1736748
Reaxys
2-hydroxy-N,N,N-trimethylethanaminium
IUPAC
Choline
KEGG_COMPOUND
choline
UniProt
Bilineurine
KEGG_COMPOUND
CHOLINE ION
PDBeChem
N,N,N-trimethylethanol-ammonium
ChEBI
N-trimethylethanolamine
ChEBI
trimethylethanolamine
ChEBI
A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3.
0
C3H7NO2S
InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)
XUJNEKJLAYXESH-UHFFFAOYSA-N
121.15922
121.01975
NC(CS)C(O)=O
CHEBI:14061
CHEBI:23508
CHEBI:4050
Beilstein:1721406
CAS:3374-22-9
Gmelin:2933
KEGG:C00736
KNApSAcK:C00001351
KNApSAcK:C00007323
PMID:17439666
PMID:25181601
Reaxys:1721406
Wikipedia:Cysteine
Cysteine
cysteine
chebi_ontology
2-Amino-3-mercaptopropionic acid
2-amino-3-mercaptopropanoic acid
2-amino-3-sulfanylpropanoic acid
C
Cys
Cystein
Hcys
Zystein
cisteina
CHEBI:15356
cysteine
Beilstein:1721406
Beilstein
CAS:3374-22-9
ChemIDplus
CAS:3374-22-9
KEGG COMPOUND
CAS:3374-22-9
NIST Chemistry WebBook
Gmelin:2933
Gmelin
PMID:17439666
Europe PMC
PMID:25181601
Europe PMC
Reaxys:1721406
Reaxys
Cysteine
KEGG_COMPOUND
cysteine
ChEBI
cysteine
IUPAC
2-Amino-3-mercaptopropionic acid
KEGG_COMPOUND
2-amino-3-mercaptopropanoic acid
JCBN
2-amino-3-sulfanylpropanoic acid
IUPAC
C
ChEBI
Cys
ChEBI
Cystein
ChEBI
Hcys
IUPAC
Zystein
ChEBI
cisteina
ChEBI
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