Biolink_Model schema
Entity and association taxonomy and datamodel for life-sciences data
Classes
- AbstractEntity - Any thing that is not a process or a physical mass-bearing entity
- Attribute - A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.
- BiologicalSex
- GenotypicSex - An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.
- PhenotypicSex - An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.
- ClinicalModifier - Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects
- FrequencyValue - describes the frequency of occurrence of an event or condition
- Onset - The age group in which manifestations appear
- SeverityValue - describes the severity of a phenotypic feature or disease
- Zygosity
- QuantityValue - A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value
- Association - A typed association between two entities, supported by evidence
- AnatomicalEntityToAnatomicalEntityAssociation
- AnatomicalEntityToAnatomicalEntityOntogenicAssociation - A relationship between two anatomical entities where the relationship is ontogenic, i.e the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship
- AnatomicalEntityToAnatomicalEntityPartOfAssociation - A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms
- CaseToPhenotypicFeatureAssociation - An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype
- CaseToThingAssociation - An abstract association for use where the case is the subject
- CellLineToDiseaseOrPhenotypicFeatureAssociation - An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype
- CellLineToThingAssociation - An relationship between a cell line and another entity
- ChemicalToChemicalAssociation - A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.
- ChemicalToChemicalDerivationAssociation - A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction:
- ChemicalToDiseaseOrPhenotypicFeatureAssociation - An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype
- ChemicalToGeneAssociation - An interaction between a chemical entity and a gene or gene product
- ChemicalToPathwayAssociation - An interaction between a chemical entity and a biological process or pathway
- ChemicalToThingAssociation - An interaction between a chemical entity and another entity
- DiseaseOrPhenotypicFeatureAssociationToThingAssociation
- DiseaseToPhenotypicFeatureAssociation - An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way
- DiseaseToThingAssociation
- EntityToPhenotypicFeatureAssociation
- EnvironmentToPhenotypicFeatureAssociation - Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype
- FunctionalAssociation - An association between a macromolecular machine (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed
- GeneToGoTermAssociation
- MacromolecularMachineToBiologicalProcessAssociation - A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it
- MacromolecularMachineToCellularComponentAssociation - A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component
- MacromolecularMachineToMolecularActivityAssociation - A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution
- GeneRegulatoryRelationship - A regulatory relationship between two genes
- GeneToDiseaseAssociation
- GeneToExpressionSiteAssociation - An association between a gene and an expression site, possibly qualified by stage/timing info.
- GeneToGeneAssociation - abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.
- GeneToGeneHomologyAssociation - A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)
- PairwiseGeneToGeneInteraction - An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)
- GeneToPhenotypicFeatureAssociation
- GeneToThingAssociation
- GenomicSequenceLocalization - A relationship between a sequence feature and an entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig
- GenotypeToGeneAssociation - Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality
- GenotypeToGenotypePartAssociation - Any association between one genotype and a genotypic entity that is a sub-component of it
- GenotypeToPhenotypicFeatureAssociation - Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
- GenotypeToThingAssociation
- GenotypeToVariantAssociation - Any association between a genotype and a sequence variant.
- MaterialSampleDerivationAssociation - An association between a material sample and the material entity it is derived from
- MaterialSampleToDiseaseOrPhenotypicFeatureAssociation - An association between a material sample and a disease or phenotype
- MaterialSampleToThingAssociation - An association between a material sample and something
- PairwiseInteractionAssociation - An interaction at the molecular level between two physical entities
- PopulationToPopulationAssociation - An association between a two populations
- SequenceFeatureRelationship - For example, a particular exon is part of a particular transcript or gene
- SequenceVariantModulatesTreatmentAssociation - An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.
- ThingToDiseaseOrPhenotypicFeatureAssociation
- VariantToDiseaseAssociation
- VariantToPhenotypicFeatureAssociation
- VariantToPopulationAssociation - An association between a variant and a population, where the variant has particular frequency in the population
- VariantToThingAssociation
- NamedThing - a databased entity or concept/class
- AdministrativeEntity
- Provider - person, group, organization or project that provides a piece of information
- BiologicalEntity
- BiologicalProcessOrActivity - Either an individual molecular activity, or a collection of causally connected molecular activities
- BiologicalProcess - One or more causally connected executions of molecular functions
- MolecularActivity - An execution of a molecular function carried out by a gene product or macromolecular complex.
- DiseaseOrPhenotypicFeature - Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
- Environment - A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes
- DrugExposure - A drug exposure is an intake of a particular chemical substance
- Treatment - A treatment is targeted at a disease or phenotype and may involve multiple drug ‘exposures’
- MolecularEntity - A gene, gene product, small molecule or macromolecule (including protein complex)
- ChemicalSubstance - May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
- Carbohydrate
- Drug - A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
- Metabolite - Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.
- GeneFamily - any grouping of multiple genes or gene products related by common descent
- GenomicEntity - an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
- CodingSequence
- Exon - A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
- Genome - A genome is the sum of genetic material within a cell or virion.
- Genotype - An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
- Haplotype - A set of zero or more Alleles on a single instance of a Sequence[VMC]
- MacromolecularMachine - A union of gene, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.
- GeneOrGeneProduct - a union of genes or gene products. Frequently an identifier for one will be used as proxy for another
- Gene
- GeneProduct - The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules
- RNAProduct
- GeneProductIsoform - This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.
- Protein - A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
- ProteinIsoform - Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
- MacromolecularComplex
- SequenceVariant - An allele that varies in its sequence from what is considered the reference allele at that locus.
- Transcript - An RNA synthesized on a DNA or RNA template by an RNA polymerase
- OrganismalEntity - A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities
- AnatomicalEntity - A subcellular location, cell type or gross anatomical part
- CellLine
- IndividualOrganism
- Case - An individual organism that has a patient role in some clinical context.
- LifeStage - A stage of development or growth of an organism, including post-natal adult stages
- PopulationOfIndividualOrganisms - A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes [Alliance for Genome Resources]
- ClinicalEntity - Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
- DataFile
- DataSet
- Device - A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
- InformationContentEntity - a piece of information that typically describes some piece of biology or is used as support.
- ConfidenceLevel - Level of confidence in a statement
- EvidenceType - Class of evidence that supports an association
- Publication - Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.
- MaterialSample - A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]
- Occurrent - A processual entity
- ActivityAndBehavior - Activity or behavior of any independent integral living, organization or mechanical actor in the world
- Phenomenon - a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
- Procedure - A series of actions conducted in a certain order or manner
- OntologyClass - a concept or class in an ontology, vocabulary or thesaurus
- PhysicalEntity - An entity that has physical properties such as mass, volume, or charge
- PlanetaryEntity - Any entity or process that exists at the level of the whole planet
Mixins
Slots
- association slot - any slot that relates an association to another entity
- association type - connects an association to the type of association (e.g. gene to phenotype)
- change is catalyzed by - hyperedge connecting an association between two causally connected entities (for example, two chemical entities, or a chemical entity in that changes location) and the gene product, gene, or complex that enables or catalyzes the change.
- clinical modifier qualifier - Used to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects
- edge label - A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.
- frequency qualifier - a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
- has confidence level - connects an association to a qualitative term denoting the level of confidence
- has evidence - connects an association to an instance of supporting evidence
- negated - if set to true, then the association is negated i.e. is not true
- object - connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
- onset qualifier - a qualifier used in a phenotypic association to state when the phenotype appears is in the subject
- provided by - connects an association to the agent (person, organization or group) that provided it
- publications - connects an association to publications supporting the association
- qualifiers - connects an association to qualifiers that modify or qualify the meaning of that association
- quantifier qualifier - A measurable quantity for the object of the association
- relation - the relationship type by which a subject is connected to an object in an association
- sequence variant qualifier - a qualifier used in an association where the variant
- 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.
- stage qualifier - stage at which expression takes place
- subject - connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
- drug
- has attribute - connects any named thing to an attribute
- has attribute type - connects an attribute to a class that describes it
- has exposure parts
- has numeric value - connects a quantity value to a number
- has qualitative value - connects an attribute to a value
- has quantitative value - connects an attribute to a value
- has unit - connects a quantity value to a unit
- interacting molecules category
- node property - A grouping for any property that holds between a node and a value
- related to - A relationship that is asserted between two named things
- 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 abundance of - holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest
- decreases abundance of - holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest
- increases abundance of - holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest
- affects activity of - holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest
- decreases activity of - holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest
- increases activity of - holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest
- affects degradation of - holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest
- decreases degradation of - holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest
- increases degradation of - holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest
- affects expression of - holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest
- decreases expression of - holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest
- increases expression of - holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest
- affects folding of - holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other
- decreases folding of - holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other
- increases folding of - holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other
- affects localization of - holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest
- decreases localization of - holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest
- increases localization of - holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest
- affects metabolic processing of - holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest
- decreases metabolic processing of - holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest
- increases metabolic processing of - holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest
- affects molecular modification of - holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
- decreases molecular modification of - holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
- increases molecular modification of - holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
- affects mutation rate of - holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest
- decreases mutation rate of - holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest
- increases mutation rate of - holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest
- affects response to - holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
- decreases response to - holds between two molecular 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, biological or pathological process) to the other
- increases response to - holds between two molecular 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, biological or pathological process) to the other
- affects secretion of - holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ
- decreases secretion of - holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ
- increases secretion of - holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ
- affects splicing of - holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA
- decreases splicing of - holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA
- increases splicing of - holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA
- affects stability of - holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest
- decreases stability of - holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest
- increases stability of - holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest
- affects synthesis of - holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other
- decreases synthesis of - holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other
- increases synthesis of - holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other
- affects transport of - holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest
- decreases transport of - holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest
- increases transport of - holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest
- affects uptake of - holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ
- decreases uptake of - holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ
- increases uptake of - holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ
- disrupts - describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
- regulates
- treats - holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat
- affects risk for - holds between two entities where exposure to one entity alters the chance of developing the other
- 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 substance, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.
- 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.
- 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
- contributes to - holds between two entities where the occurrence, existence, or activity of one causes or contributes to 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
- correlated with - holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.
- biomarker for - holds between a measurable molecular 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.
- has biomarker
- 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
- 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
- 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
- has gene product - holds between a gene and a transcribed and/or translated product generated from it
- has molecular consequence - connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
- has participant - holds between a process and a continuant, where the continuant is somehow involved in the process
- enabled by - holds between a process and a physical entity, where the physical entity executes the process
- has input - holds between a process and a continuant, where the continuant is an input into the process
- has output - holds between a process and a continuant, where the continuant is an output of 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).
- homologous to - holds between two biological entities that have common evolutionary origin
- orthologous to - a homology relationship between entities (typically genes) that diverged after a speciation event.
- paralogous to - a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
- xenologous to - a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
- in taxon - connects a thing to a class representing a taxon
- interacts with - holds between any two entities that directly or indirectly interact with each other
- 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.
- physically interacts with - holds between two entities that make physical contact as part of some interaction
- 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 - used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
- model of - holds between an entity and some other entity it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
- occurs in - holds between a process and a material entity or site within which the process occurs
- overlaps - holds between entties that overlap in their extents (materials or processes)
- has part - holds between wholes and their parts (material entities or processes)
- part of - holds between parts and wholes (material entities or processes)
- participates in - holds between a continuant and a process, where the continuant is somehow involved in the process
- 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
- 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.
- precedes - holds between two processes, where one completes before the other begins
- produces - holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
- same as - holds between two entities that are considered equivalent to each other
- subclass of - holds between two classes where the domain class is a specialization of the range class
- treated by - holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is used to treat the condition
Types
Built in
- Bool
- ElementIdentifier
- NCName
- NodeIdentifier
- URI
- URIorCURIE
- XSDDate
- XSDDateTime
- XSDTime
- float
- int
- str
Defined