Class: translator_minimal

Minimum subset of translator work

URI: biolink:translator_minimal

Classes

ChemicalEntity - A chemical entity is a physical entity that pertains to chemistry or biochemistry.
ChemicalMixture - A chemical mixture is a chemical entity composed of two or more molecular entities.
ComplexMolecularMixture - A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.
Disease - A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
Gene - A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
MolecularEntity - A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
MolecularMixture - A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.
NucleicAcidEntity - A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included.
SmallMolecule - A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion).

Mixins

Slots

actively involved in - holds between a continuant and a process or function, where the continuant actively contributes to part or all of the process or function it realizes
actively involves
affects - describes an entity that has a direct affect on the state or quality of another existing entity. Use of the ‘affects’ predicate implies that the affected entity already exists, unlike predicates such as ‘affects risk for’ and ‘prevents, where the outcome is something that may or may not come to be.
affects response to
affects risk for - holds between two entities where exposure to one entity alters the chance of developing the other
id - A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
name - A human-readable name for an attribute or entity.
anatomical context qualifier - A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).
aspect qualifier - Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an ‘affects’ association.
category - Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
biomarker for - holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
broad match - a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.
capable of - holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function.
causal mechanism qualifier - A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. ‘agonism’, ‘inhibition’, ‘allosteric modulation’, ‘channel blocker’)
caused by - holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other
causes - holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other
object aspect qualifier
object context qualifier
object direction qualifier
object form or variant qualifier
object part qualifier
species context qualifier - A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.
subject aspect qualifier
subject context qualifier
subject derivative qualifier
subject direction qualifier
subject form or variant qualifier
subject part qualifier
chemically similar to - holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
close match - a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).
coexists with - holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
colocalizes with - holds between two entities that are observed to be located in the same place.
composed primarily of - x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
condition associated with gene - holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
context qualifier - Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
contributes to - holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other
contribution from
correlated with - A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method.
decreases response to - holds between two chemical entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
derivative qualifier - A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’.
derives from - holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives into - holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
description - a human-readable description of an entity
direction qualifier - Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.
disrupts - describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
enabled by - holds between a process and a physical entity, where the physical entity executes the process
enables - holds between a physical entity and a process, where the physical entity executes the process
exact match - holds between two entities that have strictly equivalent meanings, with a high degree of confidence
expressed in - holds between a gene or gene product and an anatomical entity in which it is expressed
expresses - holds between an anatomical entity and gene or gene product that is expressed there
food component of - holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)
form or variant qualifier - A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’.
frequency qualifier - a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
gene associated with condition - holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
gene product of - definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x
stage qualifier - stage during which gene or protein expression of takes place.
gene_fusion_with - holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers.
genetic_neighborhood_of - holds between two genes located nearby one another on a chromosome.
genetically associated with
genetically interacts with - holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.
has active ingredient - holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component
has biomarker - holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature.
has excipient - holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component
has food component - holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)
has gene product - holds between a gene and a transcribed and/or translated product generated from it
has input - holds between a process and a continuant, where the continuant is an input into the process
has member - Defines a mereological relation between a collection and an item.
has metabolite - holds between two molecular entities in which the second one is derived from the first one as a product of metabolism
has mode of inheritance - Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).
has nutrient - one or more nutrients which are growth factors for a living organism
has output - holds between a process and a continuant, where the continuant is an output of the process
has part - holds between wholes and their parts (material entities or processes)
has participant - holds between a process and a continuant, where the continuant is somehow involved in the process
has phenotype - holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword ‘characterized by’ should translate into this predicate.
has plasma membrane part - 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.
has predisposing factor
homologous to - holds between two biological entities that have common evolutionary origin
in cell population with - holds between two genes or gene products that are expressed in the same cell type or population
in complex with - holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
in pathway with - holds between two genes or gene products that are part of in the same biological pathway
in taxon - connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
in taxon label - The human readable scientific name for the taxon of the entity.
increases response to - holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
interacts with - holds between any two entities that directly or indirectly interact with each other
iri - An IRI for an entity. This is determined by the id using expansion rules.
is active ingredient of - holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component
is exacerbated by
is excipient of - holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component
is input of
is metabolite of - holds between two molecular entities in which the first one is derived from the second one as a product of metabolism
is output of
located in - holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part)
location of - holds between material entity or site and a material entity that is located within it (but not considered a part of it)
manifestation of - that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
member of - Defines a mereological relation between a item and a collection.
model of - holds between a thing and some other thing it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
narrow match - a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.
negatively correlated with - A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other).
nutrient of
object derivative qualifier
occurs in - holds between a process and a material entity or site within which the process occurs
occurs together in literature with - holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider.
onset qualifier - a qualifier used in a phenotypic association to state when the phenotype appears is in the subject
orthologous to - a homology relationship between entities (typically genes) that diverged after a speciation event.
overlaps - holds between entities that overlap in their extents (materials or processes)
paralogous to - a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
part of - holds between parts and wholes (material entities or processes)
part qualifier - defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. ‘ESR1 transcript’ q: polyA tail).
participates in - holds between a continuant and a process, where the continuant is somehow involved in the process
physically interacts with - holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
positively correlated with - A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other).
preceded by - holds between two processes, where the other is completed before the one begins
precedes - holds between two processes, where one completes before the other begins
predisposes - holds between two entities where exposure to one entity increases the chance of developing the other
prevents - holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.
produces - holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
qualifier - grouping slot for all qualifiers on an edge. useful for testing compliance with association classes
resource id - The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
resource role - The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one ‘primary’ source, and may have any number of ‘aggregator’ or ‘supporting data’ sources.
response affected by - holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other.
response decreased by
response increased by
retrieval source ids - A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
same as - holds between two entities that are considered equivalent to each other
severity qualifier - a qualifier used in a phenotypic association to state how severe the phenotype is in the subject
sex qualifier - a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.
similar to - holds between an entity and some other entity with similar features.
statement qualifier
subclass of - holds between two classes where the domain class is a specialization of the range class
superclass of - holds between two classes where the domain class is a super class of the range class
support graphs - A list of knowledge graphs that support the existence of this node.
synonym - Alternate human-readable names for a thing
treated by - holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition
treats - holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat
xenologous to - a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
xref - A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.

Types

Enums

ResourceRoleEnum - The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one ‘primary’ source, and may have any number of ‘aggregator’ or ‘supporting data’ sources. This enumeration is found in Biolink Model, but is repeated here for convenience.