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Class: ProteinLigandAssayResult

Description: The type of study result describing the strength of interaction affinity - or enzymatic interaction - between a ligand and a target protein. Measured binding or enzymatic assay values are generally stated as the negative base 10 logarithm of the raw measurements. For instance (i.e., in a molecular interaction database like BindingDb) if a ligand inhibits a target protein with a pIC50 of 8.6, then the affinity parameter is pIC50 and the affinity value is 8.6.
classDiagram class ProteinLigandAssayResult StudyResult <|-- ProteinLigandAssayResult ProteinLigandAssayResult : broad_synonym ProteinLigandAssayResult : category ProteinLigandAssayResult : deprecated ProteinLigandAssayResult : description ProteinLigandAssayResult : equivalent_identifiers ProteinLigandAssayResult : exact_synonym ProteinLigandAssayResult : full_name ProteinLigandAssayResult : has_attribute ProteinLigandAssayResult --|> Attribute : has_attribute ProteinLigandAssayResult : id ProteinLigandAssayResult : information_content ProteinLigandAssayResult : iri ProteinLigandAssayResult : name ProteinLigandAssayResult : narrow_synonym ProteinLigandAssayResult : pAC50 ProteinLigandAssayResult --|> QuantityValue : pAC50 ProteinLigandAssayResult : pEC50 ProteinLigandAssayResult --|> QuantityValue : pEC50 ProteinLigandAssayResult : pIC50 ProteinLigandAssayResult --|> QuantityValue : pIC50 ProteinLigandAssayResult : pKd ProteinLigandAssayResult --|> QuantityValue : pKd ProteinLigandAssayResult : pKi ProteinLigandAssayResult --|> QuantityValue : pKi ProteinLigandAssayResult : pKoff ProteinLigandAssayResult --|> QuantityValue : pKoff ProteinLigandAssayResult : pKon ProteinLigandAssayResult --|> QuantityValue : pKon ProteinLigandAssayResult : provided_by ProteinLigandAssayResult : pXC50 ProteinLigandAssayResult --|> QuantityValue : pXC50 ProteinLigandAssayResult : related_synonym ProteinLigandAssayResult : synonym ProteinLigandAssayResult : taxon ProteinLigandAssayResult : type ProteinLigandAssayResult : xref

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
pKd:
Negative base 10 logarithm of the equilibrium dissociation constant (KD) which is a measure of the binding affinity and is defined as the ratio of koff to kon. 		0..1
QuantityValue		 direct
pKi:
Negative base 10 logarithm of the equilibrium binding affinity for a ligand that reduces the activity of its binding partner. Ki represents the concentration at which the inhibitor ligand occupies 50% of the receptor sites when no competing ligand is present 		0..1
QuantityValue		 direct
pIC50:
Negative base 10 logarithm of the the inhibitory concentration 50% (IC50) measures the concentration needed to block or inhibit a biological response. 		0..1
QuantityValue		 direct
pEC50:
Negative base 10 logarithm of the molar concentration of a chemical that produces a 50% excitation of a function 		0..1
QuantityValue		 direct
pAC50:
pAC50 is a base 10 negative logarithmic measure of potency for an activating (agonist) interaction between a molecule (such as a drug or ligand) and a biological target (such as a receptor or enzyme), where AC50 is the concentration (in molar units) of a compound that produces 50% of its maximal activation in a functional assay. 		0..1
QuantityValue		 direct
pXC50:
In the context of molecular interactions and drug discovery, pXC50 is a generic, base 10 negative logarithmic measure of compound potency that unifies different types of half‑maximal concentration values into a single notation, where XC50 means “the concentration at which 50% of the maximal effect is observed”, and X is a placeholder for the type of effect being measured (e.g., inhibition or activation). The X in pXC50 is intentionally generic and can represent different assay endpoints. 		0..1
QuantityValue		 direct
pKon:
Negative base 10 logarithm of the association rate constant (Kon) describes the rate at which molecules bind to each other. 		0..1
QuantityValue		 direct
pKoff:
Negative base 10 logarithm of the dissociation rate constant (koff) describes the rate at which they dissociate. 		0..1
QuantityValue		 direct
provided_by:
The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph. 		*
String		 NamedThing
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. 		*
Uriorcurie		 NamedThing
full_name:
a long-form human readable name for a thing 		0..1
LabelType		 NamedThing
synonym:
Alternate human-readable names for a thing 		*
LabelType		 NamedThing
exact_synonym:
An alternate label for an entity that denotes exactly the same meaning as the primary label and is interchangeable with it in all contexts. 		*
LabelType		 NamedThing
broad_synonym:
An alternate label for an entity whose meaning is broader (more general) than the primary label but is still useful as a lexical alternative. 		*
LabelType		 NamedThing
narrow_synonym:
An alternate label for an entity whose meaning is narrower (more specific) than the primary label, for example naming a particular sub-type. 		*
LabelType		 NamedThing
related_synonym:
An alternate label that is related to the primary label but is neither exactly synonymous nor cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. Corresponds to oboInOwl:hasRelatedSynonym. 		*
LabelType		 NamedThing
equivalent_identifiers:
A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources. 		*
Uriorcurie		 NamedThing
information_content:
Information content (IC) value for a term, primarily from Automats. 		0..1
Float		 NamedThing
taxon:
A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology. 		0..1
Uriorcurie		 NamedThing
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing} 		1..*
Uriorcurie		 Entity
type:
An rdf:type property asserting that an entity is an instance of a particular class. In Biolink the value is typically used to indicate the most specific category of which the entity is an instance. 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

LinkML Source

name: protein ligand assay result
description: The type of study result describing the strength of interaction affinity
  - or enzymatic interaction - between a ligand and a target protein. Measured binding
  or enzymatic assay values are generally stated as the negative base 10 logarithm
  of the raw measurements. For instance (i.e., in a molecular interaction database
  like BindingDb) if a ligand inhibits a target protein with a pIC50 of 8.6, then
  the affinity parameter is pIC50 and the affinity value is 8.6.
from_schema: https://w3id.org/biolink/vocab/
is_a: study result
slots:
- pKd
- pKi
- pIC50
- pEC50
- pAC50
- pXC50
- pKon
- pKoff