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Biolink-Model: a data model for life-sciences data.

The Biolink Model is a high-level, open-source data model designed to standardize types and relationships in biological knowledge graphs, covering entities like genes, diseases, chemical substances, organisms, genomics, phenotypes, and more. Biolink Model can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates). The model provides class and edge attributes and associations that guide how entities should relate to one another. The goal of the Biolink Model is to provide a consistent framework for representing biological knowledge across various databases and formats. For more information, see: understanding the model

Classes (Visualization)

Class Description
AccessibleDnaRegion A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose
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 a piece of writing on a particular topic presented as a stand-alone section of a larger publication
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.
Bacterium A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.
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
CellularOrganism
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 A role played by the molecular entity or part thereof within a chemical context.
ChiSquaredAnalysisResult A result of a chi squared analysis.
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.
CommonDataElement A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)
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.
ConceptCountAnalysisResult A result of a concept count analysis.
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
DiagnosticAid A device or substance used to help diagnose disease or injury
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. 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.
DrugLabel a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc.
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.
Food A substance consumed by a living organism as a source of nutrition
FoodAdditive None
Fungus A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).
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
GeneticInheritance 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.
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.
Human A member of the the species Homo sapiens.
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.
Invertebrate An animal lacking a vertebral column. This group consists of 98% of all animal species.
JournalArticle an article, typically presenting results of research, that is published in an issue of a scientific journal.
LifeStage A stage of development or growth of an organism, including post-natal adult stages
LogOddsAnalysisResult A result of a log odds ratio analysis.
MacromolecularComplex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
Mammal A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex
MappingCollection A collection of deprecated mappings.
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]
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.
NucleosomeModification A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.
ObservedExpectedFrequencyAnalysisResult A result of a observed expected frequency analysis.
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
Patent a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
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.
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
Plant
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.
PosttranslationalModification A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.
PredicateMapping A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.
PreprintPublication a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal.
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. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).
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.
RegulatoryRegion A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene
RelationshipType An OWL property used as an edge label
RelativeFrequencyAnalysisResult A result of a relative frequency analysis.
RetrievalSource Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.
RNAProduct None
RNAProductIsoform Represents a protein that is a specific isoform of the canonical or reference RNA
SequenceVariant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
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
Study a detailed investigation and/or analysis
StudyPopulation A group of people banded together or treated as a group as participants in a research study.
StudyResult A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence.
StudyVariable a variable that is used as a measure in the investigation of a study
TaxonomicRank A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)
TextMiningResult A result of text mining.
Transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase.
TranscriptionFactorBindingSite A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription
Treatment A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures
Vertebrate A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.
Virus A virus is a microorganism that replicates itself as a microRNA and infects the host cell.
WebPage a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features.
Zygosity None

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
broad_synonym None
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
exact_synonym 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_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
in_taxon_label The human readable scientific name for the taxon of the entity.
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
narrow_synonym None
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.
related_synonym None
resource_id The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
resource_role The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.
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
upstream_resource_ids An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.
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

Predicates (Visualization)

Property Description
active_in None
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 None
acts_upstream_of None
acts_upstream_of_negative_effect None
acts_upstream_of_or_within None
acts_upstream_of_or_within_negative_effect None
acts_upstream_of_or_within_positive_effect None
acts_upstream_of_positive_effect None
adverse_event_of None
affected_by describes an entity of which the state or quality is affected by another existing entity.
affects describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.
affects_response_to None
affects_risk_for holds between two entities where exposure to one entity alters the chance of developing the other
ameliorates A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure, clinical intervention) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
amount_or_activity_decreased_by None
amount_or_activity_increased_by None
assesses The effect of a thing on a target was interrogated in some assay. A relationship between some perturbing agent (usually a chemical compound) and some target entity, where the affect of the perturbing agent on the target entity was interrogated in a particular assay. The target might be a particular protein, tissue, phenotype, whole organism, cell line, or other type of biological entity.
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 Infraction (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).
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.
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.
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 Infraction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI.
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.
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.
author an instance of one (co-)creator primarily responsible for a written work
binds A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.
biomarker_for holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
broad_match a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.
can_be_carried_out_by None
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.
catalyzes None
caused_by holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other
causes holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other
chemically_similar_to holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
close_match a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).
coexists_with holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
coexpressed_with holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.
colocalizes_with holds between two entities that are observed to be located in the same place.
completed_by None
composed_primarily_of x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
condition_associated_with_gene holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
consumed_by None
consumes None
contains_process None
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.
contributes_to holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other
contribution_from None
contributor None
correlated_with A relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated using a correlation analysis method.
decreased_amount_in None
decreased_likelihood_associated_with
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.
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
derives_from holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives_into holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
develops_from None
develops_into None
diagnoses a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.
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).
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.
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.
disrupted_by describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another.
disrupts describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
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).
enabled_by holds between a process and a physical entity, where the physical entity executes the process
enables holds between a physical entity and a process, where the physical entity executes the process
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.
exact_match holds between two entities that have strictly equivalent meanings, with a high degree of confidence
expressed_in holds between a gene or gene product and an anatomical entity in which it is expressed
expresses holds between an anatomical entity and gene or gene product that is expressed there
food_component_of holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)
gene_associated_with_condition holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
gene_product_of definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x
gene_fusion_with holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers.
genetic_association None
genetic_neighborhood_of holds between two genes located nearby one another on a chromosome.
genetically_associated_with
genetically_interacts_with holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.
has_active_component None
has_active_ingredient holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component
has_adverse_event An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment with a therapeutic agent. Adverse events may be caused by something other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or diseases temporally associated with the treatment, whether or not considered related to the treatment. Adverse events are unintended effects that occur when a medication is administered correctly.
has_author None
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
has_catalyst None
has_chemical_role A role is particular behaviour which a chemical entity may exhibit.
has_completed holds between an entity and a process that the entity is capable of and has completed
has_contraindication None
has_contributor None
has_decreased_amount None
has_editor None
has_excipient holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component
has_food_component holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)
has_frameshift_variant None
has_gene_product holds between a gene and a transcribed and/or translated product generated from it
has_increased_amount None
has_input holds between a process and a continuant, where the continuant is an input into the process
has_manifestation None
has_member Defines a mereological relation between a collection and an item.
has_metabolite holds between two molecular entities in which the second one is derived from the first one as a product of metabolism
has_missense_variant None
has_mode_of_inheritance Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).
has_molecular_consequence connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
has_nearby_variant None
has_negative_upstream_actor None
has_negative_upstream_or_within_actor None
has_non_coding_variant None
has_nonsense_variant None
has_not_completed holds between an entity and a process that the entity is capable of, but has not completed
has_nutrient one or more nutrients which are growth factors for a living organism
has_output holds between a process and a continuant, where the continuant is an output of the process
has_part holds between wholes and their parts (material entities or processes)
has_participant holds between a process and a continuant, where the continuant is somehow involved in the process
has_phenotype holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should translate into this predicate.
has_plasma_membrane_part Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
has_positive_upstream_actor None
has_positive_upstream_or_within_actor None
has_predisposing_factor None
has_provider None
has_publisher None
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.
has_sequence_variant None
has_side_effect An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of the medication.
has_splice_site_variant None
has_substrate None
has_synonymous_variant None
has_target None
has_upstream_actor None
has_upstream_or_within_actor None
has_variant_part holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it
homologous_to holds between two biological entities that have common evolutionary origin
in_cell_population_with holds between two genes or gene products that are expressed in the same cell type or population
in_complex_with holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
in_linkage_disequilibrium_with holds between two sequence variants, the presence of which are correlated in a population
in_pathway_with holds between two genes or gene products that are part of in the same biological pathway
in_taxon connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
increased_amount_of None
increased_likelihood_associated_with
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.
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
indirectly_physically_interacts_with None
interacts_with holds between any two entities that directly or indirectly interact with each other
is_active_ingredient_of holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component
is_ameliorated_by None
is_assessed_by None
is_diagnosed_by None
is_exacerbated_by None
is_excipient_of holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component
is_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.
is_input_of None
is_metabolite_of holds between two molecular entities in which the first one is derived from the second one as a product of metabolism
is_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.
is_molecular_consequence_of None
is_nearby_variant_of holds between a sequence variant and a gene sequence that the variant is genomically close to.
is_non_coding_variant_of holds between a sequence variant and a gene, where the variant does not affect the coding sequence
is_nonsense_variant_of holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon
is_output_of None
is_sequence_variant_of holds between a sequence variant and a nucleic acid entity
is_side_effect_of None
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.
is_substrate_of None
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
lacks_part None
likelihood_associated_with
located_in holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part)
location_of holds between material entity or site and a material entity that is located within it (but not considered a part of it)
location_of_disease None
manifestation_of that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
member_of Defines a mereological relation between a item and a collection.
mentioned_by refers to is a relation between one named thing and the information content entity that it makes reference to.
mentions refers to is a relation between one information content entity and the named thing that it makes reference to.
missing_from None
mode_of_inheritance_of None
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 None
narrow_match a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.
negatively_correlated_with A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other).
not_completed_by None
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)
occurs_in holds between a process and a material entity or site within which the process occurs
occurs_in_disease None
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.
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).
orthologous_to a homology relationship between entities (typically genes) that diverged after a speciation event.
overlaps holds between entities that overlap in their extents (materials or processes)
paralogous_to a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
part_of holds between parts and wholes (material entities or processes)
participates_in holds between a continuant and a process, where the continuant is somehow involved in the process
phenotype_of None
physically_interacts_with holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
plasma_membrane_part_of None
positively_correlated_with A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other).
preceded_by holds between two processes, where the other is completed before the one begins
precedes holds between two processes, where one completes before the other begins
predisposes holds between two entities where exposure to one entity increases the chance of developing the other
prevented_by holds between a potential outcome of which the likelihood was reduced by the application or use of an entity.
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.
primarily_composed_of None
produced_by None
produces holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
provider person, group, organization or project that provides a piece of information (e.g. a knowledge association).
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).
regulated_by None
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. Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or possibly one of the 'interacts with' predicates depending on the nature of the interaction.
related_condition None
related_to A relationship that is asserted between two named things
related_to_at_concept_level Represents a relationship held between terminology components that describe the conceptual model of a domain.
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.
resistance_associated_with None
response_affected_by holds between two chemical entities where the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) of one is affected by the action of the other.
response_decreased_by None
response_increased_by None
risk_affected_by None
same_as holds between two entities that are considered equivalent to each other
sensitivity_associated_with None
sequence_location_of None
similar_to holds between an entity and some other entity with similar features.
subclass_of holds between two classes where the domain class is a specialization of the range class
superclass_of holds between two classes where the domain class is a super class of the range class
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
taxon_of None
temporally_related_to holds between two entities with a temporal relationship
transcribed_from x is transcribed from y if and only if x is synthesized from template y
transcribed_to inverse of 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 inverse of translates to
treated_by holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition
treats holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat
variant_part_of None
xenologous_to a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.

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.
CausalGeneToDiseaseAssociation None
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)
ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect.
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 catalyst qualifier P
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.
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
CorrelatedGeneToDiseaseAssociation None
DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.
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.
GeneAffectsChemicalAssociation Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)
GeneAsAModelOfDiseaseAssociation None
GeneHasVariantThatContributesToDiseaseAssociation None
GeneToDiseaseAssociation None
GeneToDiseaseOrPhenotypicFeatureAssociation 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.
GeneToGeneFamilyAssociation Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships.
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

Association (edge) Properties

Property Description
adjusted_p_value The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.
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 sub-cellular location).
aspect_qualifier Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association.
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.
# TODO: add examples of values for this property.
association_slot any slot that relates an association to another entity
base_coordinate A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.
bonferonni_adjusted_p_value The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.
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.
concept_count_object The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association.
concept_count_subject The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association.
concept_pair_count The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association.
context_qualifier Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
dataset_count The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.
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.
evidence_count The number of evidence instances that are connected to an association.
expected_count The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent.
expression_site location in which gene or protein expression takes place. May be cell, tissue, or organ.
extraction_confidence_score 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.
FDA_adverse_event_level
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_supporting_study_result connects an association to an instance of supporting study result
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.
ln_ratio the natural log of the ratio of co-occurrence to expected
ln_ratio_confidence_interval The 99% confidence interval for the ln_ratio calculation (i.e. the range of values within which the true value has a 99% chance of falling)
log_odds_ratio The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group.
log_odds_ratio_95_ci The ninety-five percent confidence range in which the true log odds ratio for the sample population falls.
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_category Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
object_category_closure Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
object_closure Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
object_context_qualifier None
object_derivative_qualifier None
object_direction_qualifier None
object_form_or_variant_qualifier None
object_label_closure Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
object_location_in_text Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion
object_namespace Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
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. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to capture non-primary sources.
publications One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
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. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.
qualifier grouping slot for all qualifiers on an edge. useful for testing compliance with association classes
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)
relative_frequency_object The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records.
relative_frequency_object_confidence_interval The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling)
relative_frequency_subject The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the subject concept appears in these same records.
relative_frequency_subject_confidence_interval The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling)
semmed_agreement_count The number of times this concept has been asserted in the SemMedDB literature database.
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_category Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
subject_category_closure Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
subject_closure Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
subject_context_qualifier None
subject_derivative_qualifier None
subject_direction_qualifier None
subject_form_or_variant_qualifier None
subject_label_closure Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
subject_location_in_text Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion.
subject_namespace Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.
subject_part_qualifier None
support_graphs A list of knowledge graphs that support the existence of this node.
supporting_data_set A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data).
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_document_type The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result.
supporting_document_year The document year (typically the publication year) for the supporting document used in a Text Mining Result.
supporting_documents One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
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).
supporting_text The segment of text from a document that supports the mined assertion.
supporting_text_section_type The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text.
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.
total_sample_size The total number of patients or participants within a sample population.

Enumerations

Enumeration Description
CausalMechanismQualifierEnum None
ChemicalEntityDerivativeEnum None
ChemicalOrGeneOrGeneProductFormOrVariantEnum None
DirectionQualifierEnum None
DrugAvailabilityEnum
DrugDeliveryEnum None
DruggableGeneCategoryEnum None
FDAApprovalStatusEnum
FDAIDAAdverseEventEnum please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32
GeneOrGeneProductOrChemicalEntityAspectEnum None
GeneOrGeneProductOrChemicalPartQualifierEnum None
LogicalInterpretationEnum None
PhaseEnum phase
ReactionDirectionEnum None
ReactionSideEnum None
ResourceRoleEnum The role played by the information reource in serving as a source for an edge in a TRAPI message. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience.
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

Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ, The Biomedical Data Translator Consortium (2022). Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. Wiley; 2022 Jun 6; https://onlinelibrary.wiley.com/doi/10.1111/cts.13302