Biolink-Model A datamodel for life-sciences data.

The Biolink Model is a high-level data model designed to standardize types and relationships in biological knowledge graphs, covering entities like genes, diseases, chemical substances, organisms, genomics, phenotypes, and more. It is expressed as a YAML schema, which is then translated into various formats including OWL ontology, Python dataclasses, and JSON schema. The model divides into entities, associations, and slots, where entities represent nodes in a property graph, associations define edges with evidence and provenance, and slots are properties of nodes and edges. It also includes a comprehensive list of CURIE prefix mappings and provides guidelines for using the model with different graph representations like Neo4J and RDF. The goal of the Biolink Model is to provide a consistent framework for representing biological knowledge across various databases and formats.

Visualize Class Hierarchy

Visualize Predicate Hierarchy

Citing Biolink Model

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

Classes (nodes)

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

Class (node) Properties

View the Predicate Hierarchy Visualization

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

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 <>
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, expression, 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

Predicates

Property	Description	Inverse
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
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_of	None	has 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 an effect on the state or quality of another existing entity.	affected by
affects_likelihood_of	Holds between two entities where the presence or application of one alters the chance that the other will come to be.	likelihood affected by
affects_response_to	None	response affected by
ameliorates_condition	Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is able to ameliorate symptoms, stabilize progression, or cure the condition.	condition ameliorated by
amount_or_activity_decreased_by	None	decreases amount or activity of
amount_or_activity_increased_by	None	increases amount or activity of
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.	is assessed 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 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).	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 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.	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
beneficial_in_models_for	Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).	None
binds	A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.	symmetric
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
can_be_carried_out_by	None	capable of
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.	can be carried out by
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
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.	primarily composed of
condition_ameliorated_by	None	ameliorates condition
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
condition_exacerbated_by	None	exacerbates condition
condition_predisposed_by	None	predisposes to condition
condition_prevented_by	None	preventative for condition
consumed_by	None	consumes
consumes	None	consumed by
contains_process	None	occurs in
contraindicated_in	Holds between a substance, procedure, or activity and a medical condition or circumstance, where an authority has established that the substance, procedure, or activity should not be applied as an intervention in patients with the condition or circumstance because it can result in detrimental outcomes.	has contraindication
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
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_amount_or_activity_of	A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object.	amount or activity 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
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_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).	symmetric
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.	location of disease
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
exacerbates_condition	Holds between a substance, procedure, or activity and an existing medical condition (disease or phenotypic
feature) where the substance, procedure, or activity worsens some or all aspects of the condition.	condition 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
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
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.	symmetric
genetic_association	None	symmetric
genetic_neighborhood_of	holds between two genes located nearby one another on a chromosome.	symmetric
genetically_associated_with		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_component	None	active in
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_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.	adverse event 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_catalyst	None	catalyzes
has_chemical_role	A role is particular behaviour which a chemical entity may exhibit.	None
has_completed	holds between an entity and a process that the entity is capable of and has completed	completed by
has_contraindication	None	contraindicated in
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_member	Defines a mereological relation between a collection and an item.	member 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_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).	mode of inheritance 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_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.	is side effect 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_clinical_trials_for	Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).	None
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	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_preclinical_trials_for	Holds between an substance, procedure, or activity and a medical condition, and reports that a pre-clinical study has been performed specifically to test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).	None
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_amount_or_activity_of	A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object.	amount or activity 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
indirectly_physically_interacts_with	None	symmetric
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_assessed_by	None	assesses
is_diagnosed_by	None	diagnoses
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_side_effect_of	None	has side effect
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_affected_by	None	affects likelihood of
likelihood_associated_with		associated with likelihood 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
location_of_disease	None	disease has location
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
member_of	Defines a mereological relation between a item and a collection.	has member
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
missing_from	None	lacks part
mode_of_inheritance_of	None	has mode of inheritance
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
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
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	None	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
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_to_condition	Holds between two entities where the presence or application of one increases the chance that the other will come to be.	condition predisposed by
preventative_for_condition	Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to prevent it manifesting in the first place.	condition prevented by
primarily_composed_of	None	composed primarily of
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
promotes_condition	Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place.	None
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
regulated_by	None	regulates
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.	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
same_as	holds between two entities that are considered equivalent to each other	symmetric
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
studied_for_treatment_with	None	studied to treat
studied_to_treat	Holds between an substance, procedure, or activity and a medical condition, and reports that one or more scientific study has been performed to specifically test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).	studied for treatment with
subclass_of	holds between two classes where the domain class is a specialization of the range class	None
superclass_of	holds between two classes where the domain class is a super class of the range class	None
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
variant_part_of	None	has variant part
was_applied_to_treat	Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition.	None
xenologous_to	a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.	symmetric

Annotation (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_approval_status
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
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
max_research_phase	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
ClinicalApprovalStatusEnum	None
DirectionQualifierEnum	None
DrugAvailabilityEnum
DrugDeliveryEnum	None
DruggableGeneCategoryEnum	None
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
MaxResearchPhaseEnum	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