Biolink-Model
Entity and association taxonomy and datamodel for life-sciences data
URI: https://w3id.org/biolink/biolink-model
Classes (nodes)
| Class | Description |
|---|---|
| Activity | An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. |
| AdministrativeEntity | None |
| Agent | person, group, organization or project that provides a piece of information (i.e. a knowledge association) |
| AnatomicalEntity | A subcellular location, cell type or gross anatomical part |
| Annotation | Biolink Model root class for entity annotations. |
| Article | None |
| 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. |
| Behavior | None |
| BehavioralExposure | A behavioral exposure is a factor relating to behavior impacting an individual. |
| BehavioralFeature | A phenotypic feature which is behavioral in nature. |
| BehavioralOutcome | An outcome resulting from an exposure event which is the manifestation of human behavior. |
| BiologicalEntity | None |
| BiologicalProcess | One or more causally connected executions of molecular functions |
| BiologicalProcessOrActivity | Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system. |
| BiologicalSex | None |
| BioticExposure | An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). |
| Book | This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. |
| BookChapter | None |
| Case | An individual (human) organism that has a patient role in some clinical context. |
| Cell | None |
| CellLine | None |
| CellularComponent | A location in or around a cell |
| ChemicalEntity | A chemical entity is a physical entity that pertains to chemistry or biochemistry. |
| ChemicalExposure | A chemical exposure is an intake of a particular chemical entity. |
| ChemicalMixture | A chemical mixture is a chemical entity composed of two or more molecular entities. |
| ChemicalRole | None |
| ClinicalAttribute | Attributes relating to a clinical manifestation |
| ClinicalCourse | The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual |
| ClinicalEntity | Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities |
| ClinicalFinding | this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations. |
| ClinicalIntervention | None |
| ClinicalMeasurement | A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot. |
| ClinicalModifier | Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects |
| ClinicalTrial | None |
| CodingSequence | None |
| Cohort | A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time. |
| ComplexChemicalExposure | A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. |
| ComplexMolecularMixture | A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry. |
| ConfidenceLevel | Level of confidence in a statement |
| Dataset | an item that refers to a collection of data from a data source. |
| DatasetDistribution | an item that holds distribution level information about a dataset. |
| DatasetSummary | an item that holds summary level information about a dataset. |
| DatasetVersion | an item that holds version level information about a dataset. |
| Device | A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment |
| 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. |
| 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. distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature. |
| DiseaseOrPhenotypicFeatureExposure | A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer. |
| DiseaseOrPhenotypicFeatureOutcome | Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype. |
| Drug | A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease |
| DrugExposure | A drug exposure is an intake of a particular drug. |
| DrugToGeneInteractionExposure | drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome. |
| Entity | Root Biolink Model class for all things and informational relationships, real or imagined. |
| EnvironmentalExposure | A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants. |
| EnvironmentalFeature | None |
| EnvironmentalFoodContaminant | None |
| EnvironmentalProcess | None |
| EpidemiologicalOutcome | An epidemiological outcome, such as societal disease burden, resulting from an exposure event. |
| Event | Something that happens at a given place and time. |
| EvidenceType | Class of evidence that supports an association |
| Exon | A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. |
| ExposureEventToEntityAssociationMixin | None |
| Food | A substance consumed by a living organism as a source of nutrition |
| FoodAdditive | None |
| 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. |
| GeneFamily | any grouping of multiple genes or gene products related by common descent |
| GeneOntologyClass | None |
| Genome | A genome is the sum of genetic material within a cell or virion. |
| GenomicBackgroundExposure | A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome. |
| Genotype | An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background |
| GenotypicSex | An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes. |
| GeographicExposure | A geographic exposure is a factor relating to geographic proximity to some impactful entity. |
| GeographicLocation | a location that can be described in lat/long coordinates |
| GeographicLocationAtTime | a location that can be described in lat/long coordinates, for a particular time |
| GrossAnatomicalStructure | None |
| Haplotype | A set of zero or more Alleles on a single instance of a Sequence[VMC] |
| Hospitalization | None |
| HospitalizationOutcome | An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization. |
| IndividualOrganism | An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576 |
| InformationContentEntity | a piece of information that typically describes some topic of discourse or is used as support. |
| InformationResource | A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb. |
| Inheritance | The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc. |
| LifeStage | A stage of development or growth of an organism, including post-natal adult stages |
| Macronutrient | None |
| 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] |
| Micronutrient | None |
| MicroRNA | None |
| MolecularActivity | An execution of a molecular function carried out by a gene product or macromolecular complex. |
| 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. |
| MortalityOutcome | An outcome of death from resulting from an exposure event. |
| NamedThing | a databased entity or concept/class |
| NoncodingRNAProduct | None |
| 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. |
| NucleicAcidSequenceMotif | A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences. |
| Nutrient | None |
| Onset | The age group in which (disease) symptom manifestations appear |
| OrganismAttribute | describes a characteristic of an organismal entity. |
| OrganismTaxon | A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies. |
| OrganismalEntity | A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities |
| PathologicalAnatomicalExposure | An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome. |
| PathologicalAnatomicalOutcome | An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure. |
| PathologicalAnatomicalStructure | An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. |
| PathologicalProcess | A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level. |
| PathologicalProcessExposure | A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease. |
| PathologicalProcessOutcome | An outcome resulting from an exposure event which is the manifestation of a pathological process. |
| Pathway | None |
| Phenomenon | a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question |
| PhenotypicFeature | A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment. A combination of entity and quality that makes up a phenotyping statement. |
| PhenotypicQuality | A property of a phenotype |
| PhenotypicSex | An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. |
| PhysicalEntity | An entity that has material reality (a.k.a. physical essence). |
| PhysiologicalProcess | None |
| PlanetaryEntity | Any entity or process that exists at the level of the whole planet |
| Polypeptide | A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule. |
| 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. |
| Procedure | A series of actions conducted in a certain order or manner |
| ProcessedMaterial | A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing. |
| Protein | A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA |
| ProteinDomain | A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain. |
| ProteinFamily | None |
| 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/ |
| Publication | Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (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 printed materials, either directly or in one of the Publication Biolink category subclasses. |
| QuantityValue | A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value |
| ReagentTargetedGene | A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. |
| RelationshipType | An OWL property used as an edge label |
| RNAProduct | None |
| RNAProductIsoform | Represents a protein that is a specific isoform of the canonical or reference RNA |
| SequenceVariant | An allele that varies in its sequence from what is considered the reference allele at that locus. |
| Serial | This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. |
| SeverityValue | describes the severity of a phenotypic feature or disease |
| SiRNA | A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. |
| 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). |
| Snv | SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist |
| SocioeconomicAttribute | Attributes relating to a socioeconomic manifestation |
| SocioeconomicExposure | A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty). |
| SocioeconomicOutcome | An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event |
| StudyPopulation | A group of people banded together or treated as a group as participants in a research study. |
| TaxonomicRank | A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) |
| Transcript | An RNA synthesized on a DNA or RNA template by an RNA polymerase. |
| Treatment | A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures |
| UnclassifiedOntologyClass | None |
| Vitamin | None |
| Zygosity | None |
Class (node) Properties
| Property | Description |
|---|---|
| address | the particulars of the place where someone or an organization is situated. For now, this slot is a simple text "blob" containing all relevant details of the given location for fitness of purpose. For the moment, this "address" can include other contact details such as email and phone number(?). |
| affiliation | a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations. |
| aggregate_statistic | None |
| animal_model_available_from | |
| authors | connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication. |
| available_from | |
| chapter | chapter of a book |
| created_with | None |
| creation_date | date on which an entity was created. This can be applied to nodes or edges |
| dataset_download_url | None |
| distribution_download_url | None |
| download_url | None |
| format | None |
| full_name | a long-form human readable name for a thing |
| has_biological_sequence | connects a genomic feature to its sequence |
| has_chemical_formula | description of chemical compound based on element symbols |
| has_chemical_role | A role is particular behaviour which a material entity may exhibit. |
| has_constituent | one or more molecular entities within a chemical mixture |
| has_count | number of things with a particular property |
| has_dataset | None |
| has_device | connects an entity to one or more (medical) devices |
| has_distribution | None |
| has_drug | connects an entity to one or more drugs |
| has_gene | connects an entity associated with one or more genes |
| has_gene_or_gene_product | connects an entity with one or more gene or gene products |
| has_percentage | equivalent to has quotient multiplied by 100 |
| has_procedure | connects an entity to one or more (medical) procedures |
| has_quotient | None |
| has_receptor | the organism or organism part being exposed |
| has_route | the process that results in the stressor coming into direct contact with the receptor |
| has_stressor | the process or entity that the receptor is being exposed to |
| has_taxonomic_rank | None |
| has_topic | Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred. See https://github.com/biolink/biolink-model/issues/238 |
| has_total | total number of things in a particular reference set |
| has_zygosity | None |
| ingest_date | None |
| is_metabolite | indicates whether a molecular entity is a metabolite |
| is_supplement | |
| is_toxic | |
| iso_abbreviation | Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself. |
| issue | issue of a newspaper, a scientific journal or magazine for reference purpose |
| keywords | keywords tagging a publication |
| latitude | latitude |
| license | None |
| longitude | longitude |
| max_tolerated_dose | The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD. |
| mesh_terms | mesh terms tagging a publication |
| node_property | A grouping for any property that holds between a node and a value |
| pages | page number of source referenced for statement or publication |
| 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. |
| published_in | CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal. |
| retrieved_on | None |
| rights | None |
| source_logo | None |
| source_web_page | None |
| summary | executive summary of a publication |
| symbol | Symbol for a particular thing |
| synonym | Alternate human-readable names for a thing |
| systematic_synonym | more commonly used for gene symbols in yeast |
| trade_name | |
| update_date | date on which an entity was updated. This can be applied to nodes or edges |
| version | None |
| version_of | None |
| volume | volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication |
| xref | Alternate CURIEs for a thing |
Associations (edges)
| Association | Description |
|---|---|
| AnatomicalEntityToAnatomicalEntityAssociation | None |
| 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 |
| Association | A typed association between two entities, supported by evidence |
| BehaviorToBehavioralFeatureAssociation | An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior. |
| CaseToPhenotypicFeatureAssociation | An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype. |
| CellLineAsAModelOfDiseaseAssociation | None |
| 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. |
| ChemicalAffectsGeneAssociation | Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity, localization, processing, expression, etc.) |
| ChemicalEntityAssessesNamedThingAssociation | None |
| ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation | A regulatory relationship between two genes |
| ChemicalGeneInteractionAssociation | describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction) |
| 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: |
| IF | |
| R has-input C1 AND | |
| R has-output C2 AND | |
| R enabled-by P AND | |
| R type Reaction | |
| THEN | |
| C1 derives-into C2 < |
|
| 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. |
| ContributorAssociation | Any association between an entity (such as a publication) and various agents that contribute to its realisation |
| DiseaseOrPhenotypicFeatureToLocationAssociation | An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site. |
| DiseaseToExposureEventAssociation | An association between an exposure event and a disease. |
| DiseaseToPhenotypicFeatureAssociation | An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way. |
| DrugToGeneAssociation | An interaction between a drug and a gene or gene product. |
| DruggableGeneToDiseaseAssociation | None |
| EntityToDiseaseAssociation | None |
| EntityToPhenotypicFeatureAssociation | None |
| ExonToTranscriptRelationship | A transcript is formed from multiple exons |
| ExposureEventToOutcomeAssociation | An association between an exposure event and an outcome. |
| ExposureEventToPhenotypicFeatureAssociation | Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype. |
| FunctionalAssociation | An association between a macromolecular machine mixin (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. |
| GeneAsAModelOfDiseaseAssociation | None |
| GeneHasVariantThatContributesToDiseaseAssociation | None |
| GeneRegulatoryRelationship | A regulatory relationship between two genes |
| GeneToDiseaseAssociation | None |
| GeneToExpressionSiteAssociation | An association between a gene and a gene 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. |
| GeneToGeneCoexpressionAssociation | Indicates that two genes are co-expressed, generally under the same conditions. |
| 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) |
| GeneToGeneProductRelationship | A gene is transcribed and potentially translated to a gene product |
| GeneToGoTermAssociation | None |
| GeneToPathwayAssociation | An interaction between a gene or gene product and a biological process or pathway. |
| GeneToPhenotypicFeatureAssociation | None |
| GenomicSequenceLocalization | A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig. |
| GenotypeAsAModelOfDiseaseAssociation | None |
| GenotypeToDiseaseAssociation | None |
| 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 |
| GenotypeToVariantAssociation | Any association between a genotype and a sequence variant. |
| InformationContentEntityToNamedThingAssociation | association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property). |
| 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. |
| MaterialSampleDerivationAssociation | An association between a material sample and the material entity from which it is derived. |
| MaterialSampleToDiseaseOrPhenotypicFeatureAssociation | An association between a material sample and a disease or phenotype. |
| MolecularActivityToChemicalEntityAssociation | Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples |
| MolecularActivityToMolecularActivityAssociation | Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples |
| MolecularActivityToPathwayAssociation | Association that holds the relationship between a reaction and the pathway it participates in. |
| NamedThingAssociatedWithLikelihoodOfNamedThingAssociation | |
| OrganismTaxonToEnvironmentAssociation | None |
| OrganismTaxonToOrganismTaxonAssociation | A relationship between two organism taxon nodes |
| OrganismTaxonToOrganismTaxonInteraction | An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens |
| OrganismTaxonToOrganismTaxonSpecialization | A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo |
| OrganismToOrganismAssociation | None |
| OrganismalEntityAsAModelOfDiseaseAssociation | None |
| 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) |
| PairwiseMolecularInteraction | An interaction at the molecular level between two physical entities |
| PopulationToPopulationAssociation | An association between a two populations |
| ReactionToCatalystAssociation | None |
| ReactionToParticipantAssociation | None |
| SequenceAssociation | An association between a sequence feature and a nucleic acid entity it is localized to. |
| 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. |
| TaxonToTaxonAssociation | None |
| TranscriptToGeneRelationship | A gene is a collection of transcripts |
| VariantAsAModelOfDiseaseAssociation | None |
| VariantToDiseaseAssociation | None |
| VariantToGeneAssociation | An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium) |
| VariantToGeneExpressionAssociation | An association between a variant and expression of a gene (i.e. e-QTL) |
| VariantToPhenotypicFeatureAssociation | None |
| VariantToPopulationAssociation | An association between a variant and a population, where the variant has particular frequency in the population |
Predicates
| Property | Description | Inverse |
|---|---|---|
| abundance_affected_by | None | affects abundance of |
| abundance_decreased_by | None | decreases abundance of |
| abundance_increased_by | None | increases abundance of |
| active_in | None | has active component |
| 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 |
| actively_involves | None | actively involved in |
| activity_affected_by | holds between two chemical or gene/gene product where the action or effect of one is changed by the activity of the other within a system of interest | affects activity of |
| activity_decreased_by | None | decreases activity of |
| activity_increased_by | None | increases activity of |
| acts_upstream_of | None | has upstream actor |
| acts_upstream_of_negative_effect | None | has negative upstream actor |
| acts_upstream_of_or_within | None | has upstream or within actor |
| acts_upstream_of_or_within_negative_effect | None | has negative upstream or within actor |
| acts_upstream_of_or_within_positive_effect | None | has positive upstream or within actor |
| acts_upstream_of_positive_effect | None | has positive upstream actor |
| adverse_event_caused_by | None | causes adverse event |
| affected_by | describes an entity of which the state or quality is affected by another existing entity. | affects |
| 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. | affected by |
| affects_abundance_of | holds between two chemical or gene/gene product entities where the action or effect of one changes the amount of the other within a system of interest | abundance affected by |
| affects_activity_of | holds between two chemical or gene/gene product where the action or effect of one changes the activity of the other within a system of interest | activity affected by |
| affects_degradation_of | holds between two chemical entities where the action or effect of one impacts the rate of degradation of the other within a system of interest, where chemical degradation is defined act or process of simplifying or breaking down a molecule into smaller parts, either naturally or artificially (Oxford English Dictionary, UK, 1995) | degradation affected by |
| affects_expression_in | Holds between a variant and an anatomical entity where the expression of the variant is located in. | None |
| affects_expression_of | holds between a named thing (most often a chemical or gene/gene product, but can also be used to link an environmental affect on expression) and a nucleic acid entity where the action or effect of one changes the level of expression of the other within a system of interest | expression affected by |
| affects_folding_of | holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one changes the rate or quality of folding of the other | folding affected by |
| affects_localization_of | holds between two chemical or gene/gene product entities where the action or effect of one changes the localization of the other within a system of interest | localization affected by |
| affects_metabolic_processing_of | holds between two chemical or gene/gene product entities where the action or effect of one impacts the metabolic processing of the other within a system of interest | metabolic processing affected by |
| affects_molecular_modification_of | holds between two chemical or gene/gene product 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) | molecular modification affected by |
| affects_mutation_rate_of | holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity impacts the rate of mutation of the nucleic acid entity within a system of interest | mutation rate affected by |
| affects_response_to | None | response affected by |
| affects_risk_for | holds between two entities where exposure to one entity alters the chance of developing the other | risk affected by |
| affects_secretion_of | holds between two chemical or gene/gene product entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ | secretion affected by |
| affects_splicing_of | holds between a chemical entity and an mRNA where the action or effect of the chemical entity impacts the splicing of the mRNA | splicing affected by |
| affects_stability_of | holds between two entities where the action or effect of one impacts the stability of the other within a system of interest | stability affected by |
| affects_synthesis_of | holds between two chemical entities where the action or effect of one impacts the rate of chemical synthesis of the other | synthesis affected by |
| affects_transport_of | holds between two chemical or gene/gene product entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest | transport affected by |
| affects_uptake_of | holds between two chemical or gene/gene product entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ | uptake affected by |
| ameliorates | A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. | is ameliorated by |
| associated_with | Expresses a relationship between two named things where the relationship is typically generated statistically (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, 'related to'. This relationship holds between two concepts represented by variables for which a statistical dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial Infarction (MI)” asserts that having Afib is not statistically independent from whether a patient will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes). | symmetric |
| associated_with_decreased_likelihood_of | Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable. | decreased likelihood associated with |
| associated_with_increased_likelihood_of | Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable. | increased likelihood associated with |
| associated_with_likelihood_of | A a relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated, wherein the state or value of one variable predicts the future state or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated with likelihood of a Myocardial Infarction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI. | likelihood associated with |
| associated_with_resistance_to | A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of resistance to treatment by the chemical. | resistance associated with |
| associated_with_sensitivity_to | A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of sensitivity to treatment by the chemical. | sensitivity associated with |
| author | an instance of one (co-)creator primarily responsible for a written work | has author |
| binds | A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction. | None |
| 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. | has biomarker |
| 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. | narrow match |
| 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. | has capability |
| catalyzes | None | has catalyst |
| 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 |
| causes | holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other | caused by |
| causes_adverse_event | holds between a drug and a disease or phenotype that can be caused by the drug | adverse event caused by |
| chemically_interacts_with | None | symmetric |
| 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. | symmetric |
| 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). | symmetric |
| coexists_with | holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region | symmetric |
| coexpressed_with | holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context. | symmetric |
| colocalizes_with | holds between two entities that are observed to be located in the same place. | symmetric |
| completed_by | None | has completed |
| composed_primarily_of | x composed_primarily_of_y if:more than half of the mass of x is made from parts of y. | None |
| 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 | gene associated with condition |
| consumed_by | None | consumes |
| consumes | None | consumed by |
| contains_process | None | occurs in |
| contraindicated_for | Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug. | has contraindication |
| 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 | contribution from |
| contribution_from | None | contributes to |
| contributor | None | has contributor |
| correlated_with | A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method. | symmetric |
| decreased_amount_in | None | has decreased amount |
| decreased_likelihood_associated_with | associated with decreased likelihood of | |
| decreases_abundance_of | holds between two chemical or gene/gene product where the action or effect of one decreases the amount of the other within a system of interest | abundance decreased by |
| decreases_activity_of | holds between two chemical or gene/gene product where the action or effect of one decreases the activity of the other within a system of interest | activity decreased by |
| decreases_amount_or_activity_of | A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object. | None |
| decreases_degradation_of | holds between two chemical entities where the action or effect of one decreases the rate of degradation of the other within a system of interest | degradation decreased by |
| decreases_expression_of | holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one decreases the level of expression of the other within a system of interest | expression decreased by |
| decreases_folding_of | holds between a chemical or gene or gene product entity and a nucleic acid entity where the action or effect of one decreases the rate or quality of folding of the other | folding decreased by |
| decreases_localization_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the proper localization of the other within a system of interest | localization decreased by |
| decreases_metabolic_processing_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest | metabolic processing decreased by |
| decreases_molecular_interaction | indicates that the source decreases the molecular interaction between the target and some other chemical entity | molecular interaction decreased by |
| decreases_molecular_modification_of | holds between two chemical 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) | molecular modification decreased by |
| decreases_mutation_rate_of | holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest | mutation rate decreased by |
| 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 | response decreased by |
| decreases_secretion_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ | secretion decreased by |
| decreases_splicing_of | holds between a chemical entity and an mRNA where the action or effect of the chemical entity decreases the proper splicing of the mRNA | splicing decreased by |
| decreases_stability_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the stability of the other within a system of interest | stability decreased by |
| decreases_synthesis_of | holds between two chemical entities where the action or effect of one decreases the rate of chemical synthesis of the other | synthesis decreased by |
| decreases_transport_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest | transport decreased by |
| decreases_uptake_of | holds between two chemical or gene/gene product entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ | uptake decreased by |
| degradation_affected_by | None | affects degradation of |
| degradation_decreased_by | None | decreases degradation of |
| degradation_increased_by | None | increases degradation of |
| 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 |
| 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 | derives from |
| develops_from | None | develops into |
| develops_into | None | develops from |
| diagnoses | a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms. | is diagnosed by |
| directly_interacts_with | Holds between chemical entities that physically and directly interact with each other | symmetric |
| directly_physically_interacts_with | A causal mechanism mediated by a direct contact between the effector and target entities (this contact may be weak or strong, transient or stable). | None |
| disease_has_basis_in | A relation that holds between a disease and an entity where the state of the entity has contribution to the disease. | occurs in disease |
| disease_has_location | A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. | None |
| disrupted_by | describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another. | disrupts |
| disrupts | describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another. | disrupted by |
| editor | editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing "published in" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node). | has editor |
| enabled_by | holds between a process and a physical entity, where the physical entity executes the process | enables |
| enables | holds between a physical entity and a process, where the physical entity executes the process | enabled by |
| entity_negatively_regulated_by_entity | None | entity negatively regulates entity |
| entity_negatively_regulates_entity | None | entity negatively regulated by entity |
| entity_positively_regulated_by_entity | None | entity positively regulates entity |
| entity_positively_regulates_entity | None | entity positively regulated by entity |
| entity_regulated_by_entity | None | entity regulates entity |
| entity_regulates_entity | None | entity regulated by entity |
| exacerbates | A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. | is exacerbated by |
| exact_match | holds between two entities that have strictly equivalent meanings, with a high degree of confidence | symmetric |
| expressed_in | holds between a gene or gene product and an anatomical entity in which it is expressed | expresses |
| expresses | holds between an anatomical entity and gene or gene product that is expressed there | expressed in |
| expression_affected_by | None | affects expression of |
| expression_decreased_by | None | decreases expression of |
| expression_increased_by | None | increases expression of |
| folding_affected_by | None | affects folding of |
| folding_decreased_by | None | decreases folding of |
| folding_increased_by | None | increases folding of |
| 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) | has food component |
| 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 | condition associated with gene |
| 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 | has gene product |
| genetic_association | Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level | symmetric |
| 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. | symmetric |
| 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 | is active ingredient of |
| has_author | None | author |
| 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. # metabolite | biomarker for |
| has_capability | None | capable of |
| has_catalyst | None | catalyzes |
| has_completed | holds between an entity and a process that the entity is capable of and has completed | completed by |
| has_contraindication | None | contraindicated for |
| has_contributor | None | contributor |
| has_decreased_amount | None | decreased amount in |
| has_editor | None | editor |
| 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 | is excipient of |
| 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) | food component of |
| has_frameshift_variant | None | is frameshift variant of |
| has_gene_product | holds between a gene and a transcribed and/or translated product generated from it | gene product of |
| has_increased_amount | None | increased amount of |
| has_input | holds between a process and a continuant, where the continuant is an input into the process | is input of |
| has_manifestation | None | manifestation of |
| has_metabolite | holds between two molecular entities in which the second one is derived from the first one as a product of metabolism | is metabolite of |
| has_missense_variant | None | is missense variant of |
| has_molecular_consequence | connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583 | is molecular consequence of |
| has_nearby_variant | None | is nearby variant of |
| has_negative_upstream_actor | None | acts upstream of negative effect |
| has_negative_upstream_or_within_actor | None | acts upstream of or within negative effect |
| has_non_coding_variant | None | is non coding variant of |
| has_nonsense_variant | None | is nonsense variant of |
| has_not_completed | holds between an entity and a process that the entity is capable of, but has not completed | not completed by |
| has_nutrient | one or more nutrients which are growth factors for a living organism | nutrient of |
| has_output | holds between a process and a continuant, where the continuant is an output of the process | is output of |
| has_part | holds between wholes and their parts (material entities or processes) | part of |
| has_participant | holds between a process and a continuant, where the continuant is somehow involved in the process | participates in |
| 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. | phenotype of |
| 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. | plasma membrane part of |
| has_positive_upstream_actor | None | acts upstream of positive effect |
| has_positive_upstream_or_within_actor | None | acts upstream of or within positive effect |
| has_provider | None | provider |
| has_publisher | None | publisher |
| has_sequence_location | holds between two nucleic acid entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig. | sequence location of |
| has_sequence_variant | None | is sequence variant of |
| has_splice_site_variant | None | is splice site variant of |
| has_substrate | None | is substrate of |
| has_synonymous_variant | None | is synonymous variant of |
| has_target | None | target for |
| has_upstream_actor | None | acts upstream of |
| has_upstream_or_within_actor | None | acts upstream of or within |
| has_variant_part | holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it | variant part of |
| homologous_to | holds between two biological entities that have common evolutionary origin | symmetric |
| in_cell_population_with | holds between two genes or gene products that are expressed in the same cell type or population | symmetric |
| 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 mixin | symmetric |
| in_linkage_disequilibrium_with | holds between two sequence variants, the presence of which are correlated in a population | symmetric |
| in_pathway_with | holds between two genes or gene products that are part of in the same biological pathway | symmetric |
| in_taxon | connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' | taxon of |
| increased_amount_of | None | has increased amount |
| increased_likelihood_associated_with | associated with increased likelihood of | |
| increases_abundance_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the amount of the other within a system of interest | abundance increased by |
| increases_activity_of | holds between two chemical or gene/gene product where the action or effect of one increases the activity of the other within a system of interest | activity increased by |
| increases_amount_or_activity_of | A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object. | None |
| increases_degradation_of | holds between two chemical entities where the action or effect of one increases the rate of degradation of the other within a system of interest | degradation increased by |
| increases_expression_of | holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one increases the level of expression of the other within a system of interest | expression increased by |
| increases_folding_of | holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one increases the rate or quality of folding of the other | folding increased by |
| increases_localization_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the proper localization of the other within a system of interest | localization increased by |
| increases_metabolic_processing_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest | metabolic processing increased by |
| increases_molecular_interaction | indicates that the source increases the molecular interaction between the target and some other chemical entity | molecular interaction increased by |
| increases_molecular_modification_of | holds between two chemical or gene/gene product 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) | molecular modification increased by |
| increases_mutation_rate_of | holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest | mutation rate increased by |
| 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 | response increased by |
| increases_secretion_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ | secretion increased by |
| increases_splicing_of | holds between a chemical entity and an mRNA where the action or effect of the chemical entity increases the proper splicing of the mRNA | splicing increased by |
| increases_stability_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the stability of the other within a system of interest | stability increased by |
| increases_synthesis_of | holds between two chemical entities where the action or effect of one increases the rate of chemical synthesis of the other | synthesis increased by |
| increases_transport_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest | transport increased by |
| increases_uptake_of | holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ | uptake increased by |
| indirectly_phsyically_interacts_with | None | None |
| interacts_with | holds between any two entities that directly or indirectly interact with each other | symmetric |
| 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 | has active ingredient |
| is_ameliorated_by | None | ameliorates |
| is_diagnosed_by | None | diagnoses |
| is_exacerbated_by | None | exacerbates |
| 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 | has excipient |
| is_frameshift_variant_of | holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. | has frameshift variant |
| is_input_of | None | has input |
| is_metabolite_of | holds between two molecular entities in which the first one is derived from the second one as a product of metabolism | has metabolite |
| is_missense_variant_of | holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved. | has missense variant |
| is_molecular_consequence_of | None | has molecular consequence |
| is_nearby_variant_of | holds between a sequence variant and a gene sequence that the variant is genomically close to. | has nearby variant |
| is_non_coding_variant_of | holds between a sequence variant and a gene, where the variant does not affect the coding sequence | has non coding variant |
| is_nonsense_variant_of | holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon | has nonsense variant |
| is_output_of | None | has output |
| is_sequence_variant_of | holds between a sequence variant and a nucleic acid entity | has sequence variant |
| is_splice_site_variant_of | holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons. | has splice site variant |
| is_substrate_of | None | has substrate |
| is_synonymous_variant_of | holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence | has synonymous variant |
| lacks_part | None | missing from |
| likelihood_associated_with | associated with likelihood of | |
| localization_affected_by | None | affects localization of |
| localization_decreased_by | None | decreases localization of |
| localization_increased_by | None | increases localization 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 |
| location_of | holds between material entity or site and a material entity that is located within it (but not considered a part of it) | located in |
| 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 | has manifestation |
| mentioned_by | refers to is a relation between one named thing and the information content entity that it makes reference to. | mentions |
| mentions | refers to is a relation between one information content entity and the named thing that it makes reference to. | mentioned by |
| metabolic_processing_affected_by | None | affects metabolic processing of |
| metabolic_processing_decreased_by | None | decreases metabolic processing of |
| metabolic_processing_increased_by | None | increases metabolic processing of |
| missing_from | None | lacks part |
| 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. | models |
| models | None | model of |
| molecular_interaction_decreased_by | None | decreases molecular interaction |
| molecular_interaction_increased_by | None | increases molecular interaction |
| molecular_modification_affected_by | None | affects molecular modification of |
| molecular_modification_decreased_by | None | decreases molecular modification of |
| molecular_modification_increased_by | None | increases molecular modification of |
| molecularly_interacts_with | None | symmetric |
| mutation_rate_affected_by | None | affects mutation rate of |
| mutation_rate_decreased_by | None | decreases mutation rate of |
| mutation_rate_increased_by | None | increases mutation rate of |
| 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. | broad match |
| 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). | symmetric |
| negatively_regulates | None | negatively regulated by |
| not_completed_by | None | has not completed |
| nutrient_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) | has nutrient |
| occurs_in | holds between a process and a material entity or site within which the process occurs | contains process |
| occurs_in_disease | None | disease has basis in |
| 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. | symmetric |
| opposite_of | x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased). | symmetric |
| orthologous_to | a homology relationship between entities (typically genes) that diverged after a speciation event. | symmetric |
| overlaps | holds between entities that overlap in their extents (materials or processes) | symmetric |
| paralogous_to | a homology relationship that holds between entities (typically genes) that diverged after a duplication event. | symmetric |
| part_of | holds between parts and wholes (material entities or processes) | has part |
| participates_in | holds between a continuant and a process, where the continuant is somehow involved in the process | has participant |
| phenotype_of | holds between a phenotype and a biological entity, 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). | has phenotype |
| physically_interacts_with | holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship. | symmetric |
| plasma_membrane_part_of | None | has plasma membrane part |
| 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). | symmetric |
| positively_regulates | None | positively regulated by |
| preceded_by | holds between two processes, where the other is completed before the one begins | precedes |
| precedes | holds between two processes, where one completes before the other begins | preceded by |
| predisposes | holds between two entities where exposure to one entity increases the chance of developing the other | has predisposing factor |
| prevented_by | holds between a potential outcome of which the likelihood was reduced by the application or use of an entity. | prevents |
| 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. | prevented by |
| process_negatively_regulated_by_process | None | process negatively regulates process |
| process_negatively_regulates_process | None | process negatively regulated by process |
| process_positively_regulated_by_process | None | process positively regulates process |
| process_positively_regulates_process | None | process positively regulated by process |
| process_regulated_by_process | None | process regulates process |
| process_regulates_process | None | process regulated by process |
| produced_by | None | produces |
| produces | holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity | produced by |
| provider | person, group, organization or project that provides a piece of information (e.g. a knowledge association). | has provider |
| publisher | organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing "published in" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node). | has publisher |
| regulates | A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. Gene-affects-gene relationships will (almost) always involve regulation. Chemical-affects-gene relationships may in some cases be considered regulation (if the chemical is some endogenously produced signaling molecule created to execute a certain function/activity), but exogenous/environmental chemical-affects-gene relationships are usually not cases of regulation. | regulated by |
| related_condition | None | symmetric |
| related_to | A relationship that is asserted between two named things | symmetric |
| related_to_at_concept_level | Represents a relationship held between terminology components that describe the conceptual model of a domain. | symmetric |
| related_to_at_instance_level | Represents a relationship held between two instances of a data classes. Much like an assertion component, in an ABox, these represent facts associated with the conceptual model. | symmetric |
| resistance_associated_with | None | associated with resistance to |
| 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. | affects response to |
| response_decreased_by | None | decreases response to |
| response_increased_by | None | increases response to |
| risk_affected_by | None | affects risk for |
| same_as | holds between two entities that are considered equivalent to each other | symmetric |
| secretion_affected_by | None | affects secretion of |
| secretion_decreased_by | None | decreases secretion of |
| secretion_increased_by | None | increases secretion of |
| sensitivity_associated_with | None | associated with sensitivity to |
| sequence_location_of | None | has sequence location |
| similar_to | holds between an entity and some other entity with similar features. | symmetric |
| splicing_affected_by | None | affects splicing of |
| splicing_decreased_by | None | decreases splicing of |
| splicing_increased_by | None | increases splicing of |
| stability_affected_by | None | affects stability of |
| stability_decreased_by | None | decreases stability of |
| stability_increased_by | None | increases stability of |
| subclass_of | holds between two classes where the domain class is a specialization of the range class | superclass of |
| superclass_of | holds between two classes where the domain class is a super class of the range class | subclass of |
| synthesis_affected_by | None | affects synthesis of |
| synthesis_decreased_by | None | decreases synthesis of |
| synthesis_increased_by | None | increases synthesis of |
| target_for | A gene is a target of a disease when its products are druggable and when a drug interaction with the gene product could have a therapeutic effect | has target |
| taxon_of | None | in taxon |
| temporally_related_to | holds between two entities with a temporal relationship | symmetric |
| transcribed_from | x is transcribed from y if and only if x is synthesized from template y | transcribed to |
| transcribed_to | inverse of transcribed from | transcribed from |
| translates_to | x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide) | translation of |
| translation_of | inverse of translates to | translates to |
| transport_affected_by | None | affects transport of |
| transport_decreased_by | None | decreases transport of |
| transport_increased_by | None | increases transport of |
| treated_by | holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition | treats |
| treats | holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat | treated by |
| uptake_affected_by | None | affects uptake of |
| uptake_decreased_by | None | decreases uptake of |
| uptake_increased_by | None | increases uptake of |
| variant_part_of | None | has variant part |
| xenologous_to | a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor. | symmetric |
Annotation (edge) Properties
| Property | Description |
|---|---|
| aggregator_knowledge_source | An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form. |
| 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 subcellular 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. |
| associated_environmental_context | An attribute that can be applied to an association where the association holds between two entities located or occurring in a particular environment. For example, two microbial taxa may interact in the context of a human gut; a disease may give rise to a particular phenotype in a particular environmental exposure. |
| association_slot | any slot that relates an association to another entity |
| association_type | connects an association to the category of association (e.g. gene to phenotype) |
| base_coordinate | A position in the base coordinate system. Base coordinates start at position 1 instead of position 0. |
| catalyst_qualifier | a qualifier that connects 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. |
| 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') |
| chi_squared_statistic | represents the chi-squared statistic computed from observations |
| clinical_modifier_qualifier | the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals. |
| context_qualifier | Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs. |
| 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’. |
| direction_qualifier | Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. |
| end_coordinate | The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on. |
| end_interbase_coordinate | The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on. |
| expression_site | location in which gene or protein expression takes place. May be cell, tissue, or organ. |
| FDA_approval_status | |
| 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 |
| genome_build | The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens. |
| 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 |
| has_population_context | a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. |
| has_temporal_context | a constraint of time placed upon the truth value of an association. |
| interacting_molecules_category | None |
| interbase_coordinate | A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge. |
| knowledge_source | An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property. |
| logical_interpretation | None |
| mechanism_of_action | a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes the mechanism of action for a result. |
| 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. |
| object_aspect_qualifier | None |
| object_context_qualifier | None |
| object_derivative_qualifier | None |
| object_direction_qualifier | None |
| object_form_or_variant_qualifier | None |
| object_part_qualifier | None |
| onset_qualifier | a qualifier used in a phenotypic association to state when the phenotype appears is in the subject |
| original_object | used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. |
| original_predicate | used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. |
| original_subject | used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. |
| p_value | A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. |
| 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). |
| phase | The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2. |
| phenotypic_state | in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX. |
| population_context_qualifier | a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association. |
| predicate | A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. |
| primary_knowledge_source | The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source). |
| publications | connects an association to publications supporting the association |
| qualified_predicate | predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading |
| 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 |
| reaction_balanced | None |
| reaction_direction | the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.) |
| reaction_side | the side of a reaction being modeled (ie: left or right) |
| sequence_localization_attribute | An attribute that can be applied to a genome sequence localization edge. These edges connect a nucleic acid entity such as an exon to an entity such as a chromosome. Edge properties are used to ascribe specific positional information and other metadata to the localization. In pragmatic terms this can be thought of as columns in a GFF3 line. |
| sequence_variant_qualifier | a qualifier used in an association with 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. |
| species_context_qualifier | A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place. |
| stage_qualifier | stage during which gene or protein expression of takes place. |
| start_coordinate | The position at which the subject genomic entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 1). |
| start_interbase_coordinate | The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0). |
| statement_qualifier | |
| stoichiometry | the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers. |
| strand | The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand). |
| 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. |
| subject_aspect_qualifier | None |
| subject_context_qualifier | None |
| subject_derivative_qualifier | None |
| subject_direction_qualifier | None |
| subject_form_or_variant_qualifier | None |
| subject_part_qualifier | None |
| supporting_data_source | An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data). |
| supporting_study_cohort | A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria). |
| supporting_study_context | A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.). |
| supporting_study_date_range | The date range over which data was collected in a study that provided evidence for an Association. |
| supporting_study_metadata | Information about a study used to generate information used as evidence to support the knowledge expressed in an Association. In practice, data creators should use one of the more specific subtypes of this property. |
| supporting_study_method_description | A uri or curie pointing to information about the methodology used to generate data supporting an Association. |
| supporting_study_method_type | A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis). |
| supporting_study_size | The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study). |
| temporal_context_qualifier | a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier. |
| temporal_interval_qualifier | a constraint of a time interval placed upon the truth value of an association. |
Enumerations
| Enumeration | Description |
|---|---|
| AnatomicalContextQualifierEnum | None |
| CausalMechanismQualifierEnum | None |
| ChemicalEntityDerivativeEnum | None |
| ChemicalOrGeneOrGeneProductFormEnum | None |
| DirectionQualifierEnum | None |
| DrugAvailabilityEnum | |
| DrugDeliveryEnum | None |
| DruggableGeneCategoryEnum | None |
| FDAApprovalStatusEnum | |
| GeneOrGeneProductOrChemicalEntityAspectEnum | None |
| GeneOrGeneProductOrChemicalPartQualifierEnum | None |
| LogicalInterpretationEnum | None |
| PhaseEnum | phase |
| ReactionDirectionEnum | None |
| ReactionSideEnum | None |
| SequenceEnum | type of sequence |
| StrandEnum | strand |
Subsets
| Subset | Description |
|---|---|
| ModelOrganismDatabase | Subset that is relevant for a typical Model Organism Database (MOD) |
| Samples | Sample/biosample datamodel |
| Testing | TBD |
| TranslatorMinimal | Minimum subset of translator work |