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

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

Classes (Visualization)

Class	Description
AccessibleDnaRegion	A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose
Activity	An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.
AdministrativeEntity	An entity that is the byproduct of an administrative process.
AffinityMeasurement	The type of measurement describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity parameter is pIC50 and the affinity value is 8.6. The binary relation, if given, qualifies the affinity as greater than, less than, or equal.
Agent	person, group, organization or project that provides a piece of information (i.e. a knowledge association)
AnatomicalEntity	A part of a cellular organism at or above the granularity of a protein complex. This is a grouping class with three concrete subclasses that should be preferred when applicable: "biolink:Cell" for whole cells, "biolink:CellularComponent" for subcellular and intracellular structures (organelles, membranes, bacterial flagella, etc.), and "biolink:GrossAnatomcialStructure" for multicellular parts (tissues, organs, body parts). Excludes viral and other acellular biological entities.
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	The internally coordinated responses (actions or inactions) of organisms (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.
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	A heterogeneous substance that contains genomic material or is the product of a biological process.
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	An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
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	A section of a book that forms a discrete unit of a larger published work and may be independently authored or cited.
Case	An individual (human) organism that has a patient role in some clinical context.
Cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
CellLine	A cultured cell population that is genetically stable and homogeneous, sharing a common propagation history through successive passages in culture.
CellularComponent	A location in or around a cell
CellularOrganism	An organism that contains one or more cells belonging to the cellular lineages of life (Archaea, Bacteria, or Eukaryota), whose body consists of one or more cells. Distinguished from acellular biological entities such as viruses and viroids.
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	A medical procedure, treatment, or action taken by healthcare professionals to modify the course of a disease or condition.
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	A clinical trial is a research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.
CodingSequence	A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
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, 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 disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. 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.
DiseaseOrPhenotypicFeature	A disease or an individual phenotypic feature, grouped as a single class to accommodate source vocabularies and assertions that do not distinguish the two. Prefer the more specific subclasses disease or phenotypic feature when the distinction is known.
DiseaseOrPhenotypicFeatureExposure	A disease or phenotypic feature state, when viewed as an exposure, represented as a precondition, leading to or influencing an outcome,.
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.
Edge	A generic edge in a KGX-formatted knowledge graph, representing a directed relationship between a subject node and an object node qualified by a predicate. This class serves as the structural superclass for association in Biolink, providing the minimal KGX-compliant contract (subject, predicate, object, and associated metadata) that any biolink relationship participating in a knowledge graph must satisfy.
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	A system or entity in the natural environment that has the disposition to environ one or more material entities.
EnvironmentalFoodContaminant	Any unwanted chemical in food. The term includes agrochemicals and industrial chemicals that may contaminate foodstuffs during their production, transportation or storage.
EnvironmentalProcess	A process that occurs within or involves the components of an environmental system.
EpidemiologicalOutcome	An epidemiological outcome, such as societal disease burden, resulting from an exposure event.
Event	Something that happens at a given place and time.
Evidence	Dereferences detailed evidence that supports an association
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.
ExposureEvent	A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes
Food	A substance of plant, animal, or artificial origin consumed by a living organism to provide essential nutrients, energy, and support growth and the processes of life, or to satisfy other health needs or provide a social or organoleptic experience.
FoodAdditive	Any substance which is added to food to preserve or enhance its flavour and/or appearance.
Fungus	None
Gene	A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.
GeneFamily	any grouping of multiple genes or gene products related by common descent
GeneticInheritance	The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next.
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	An anatomical structure that has more than one cell as a part.
Haplotype	A set of zero or more Alleles on a single instance of a Sequence[VMC]
Hospitalization	The admission and care of a patient in a hospital for observation, diagnosis, or treatment.
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	None
IceesStudyResult	A study result that represents a result, from a supporting Study, which is specifically associated with an Integrated Clinical and Environmental Exposures Service (ICEES) knowledge assertion.
IndividualOrganism	An instance of an organism. For example, Charles Darwin, my pet cat.
InformationContentEntity	a piece of information that typically describes some topic of discourse or is used as support.
Invertebrate	None
JournalArticle	an article, typically presenting results of research, that is published in an issue of a scientific journal.
KnowledgeGraph	A knowledge graph is a structured representation of knowledge in the form of a graph, where nodes represent entities or concepts, and edges represent relationships between them. Knowledge graphs are used to organize and connect information from various sources, enabling better understanding, analysis, and reasoning about complex domains.
KnowledgeGraph	A container representing a knowledge graph serialized in KGX (Knowledge Graph Exchange) format. A KnowledgeGraph aggregates a collection of nodes (entities) and edges (relationships between entities) conforming to the KGX specification, enabling interoperable exchange of biomedical knowledge graphs across tools and systems in the Biolink ecosystem.
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	None
MappingCollection	An abstract container class that holds a set of predicate mappings. Serves as a top-level root for documents that enumerate how third-party or deprecated predicates should be rewritten to Biolink predicates and their associated qualifiers.
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	A small (~22 nucleotide) RNA molecule that is the endogenous transcript of a miRNA gene. Produced from precursor molecules that form hairpin structures, which are processed (typically via the Dicer pathway) to yield a single miRNA molecule. miRNAs function by triggering cleavage of target molecules or acting as translational repressors.
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
Node	A generic node in a KGX-formatted knowledge graph, representing a single entity or concept with a unique identifier. This class serves as the structural superclass for named thing in Biolink, providing the minimal KGX-compliant contract (identifier, category, etc.) that any biolink entity participating in a knowledge graph must satisfy.
NoncodingRNAProduct	An RNA transcript that does not encode for a protein rather the RNA molecule is the functional gene product.
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. 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.
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, represented as a precondition, leading to or influencing an 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.
PathologicalProcessOutcome	An outcome resulting from an exposure event which is the manifestation of a pathological process.
Pathway	A hierarchical ordering of connected molecular reactions (steps) that represent a specific biological process, such as signaling or metabolism.
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 often resulting from the interaction of its genotype with its molecular and physical environment.
PhenotypicQuality	A characteristic of a phenotype (e.g., weight, size, shape, color) that can be observed, measured, or compared across organisms or conditions.
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	A biological or chemical function within a living organism.
PlanetaryEntity	Any entity or process that exists at the level of the whole planet
Plant	None
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, altering its structure, activity, localization, or interactions.
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.
ProteinFamily	A set of proteins coding for diverse functions which, by virtue of their high degree of sequence similarity, are believed to have evolved from a single ancestral gene.
ProteinIsoform	Represents a protein that is a specific isoform of the canonical or reference protein.
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.
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	High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds typically synthesized by a DNA- or RNA-dependent RNA polymerase that constitutes the product of a gene. Distinct in emphasis from biolink:Transcript, which denotes the informational output of transcription at the gene-model level rather than the chemical species itself.
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.
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)
TextMiningStudyResult	A study result that represents information extracted from text using natural language processing techniques. This includes the extracted text, location offsets within the source document, confidence scores, and other metadata related to the text mining process.
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	None
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	An allelic state describing the degree of similarity between features at a single locus, specifically whether alleles at the same location on paired chromosomes are identical or different.

Class Properties

Property	Description
address	the particulars of the place where someone or an organization is situated. For now, this slot is a simple text "blob" containing all relevant details of the given location for fitness of purpose. For the moment, this "address" can include other contact details such as email and phone number(?).
affiliation	a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.
affinity	The numerical value describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the affinity is 8.6. Used in conjunction with the affinity parameter slot.
affinity_parameter	The type of parameter describing the strength of an affinity between two entities. For instance, if a chemical inhibits a protein with a pIC50 of 8.6, the 'affinity parameter' is pIC50. Used in conjunction with the 'affinity' slot, within an 'affinity measurement'.
aggregate_statistic	An abstract grouping for summary numerical measures (e.g. count, total, quotient, percentage, rate) computed over a set of observations or a reference population, used to describe a property of an aggregated entity rather than an individual instance.
animal_model_available_from	A resource (such as a model organism database) from which an animal model representing the given disease or phenotypic feature may be obtained.
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	The regulatory or commercial availability channel through which a drug or chemical entity can be obtained, drawn from DrugAvailabilityEnum.
broad_synonym	An alternate label for an entity whose meaning is broader (more general) than the primary label but is still useful as a lexical alternative.
chapter	chapter of a book
clinical_trial_age_range	The age range of a clinical trial as determined by clinicaltrials.gov
clinical_trial_age_stage	The age stage of a clinical trial as determined by clinicaltrials.gov (adult, child, older adult)
clinical_trial_brief_title	The brief title of a clinical trial as determined by clinicaltrials.gov
clinical_trial_conditions	connects a clinical trial to one or more conditions being studied in the trial
clinical_trial_enrollment	The enrollment number of a clinical trial as determined by clinicaltrials.gov
clinical_trial_enrollment_type	The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated)
clinical_trial_intervention_boxed_warning	A boolean flag indicating whether a clinical trial intervention has a boxed warning. A boxed warning is the strongest warning that the FDA requires on a prescription drug label. This property should be populated from DailyMed.
clinical_trial_intervention_model	The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null).
clinical_trial_interventions	connects a clinical trial to one or more interventions being tested in the trial
clinical_trial_overall_status	The overall status of a clinical trial as determined by clinicaltrials.gov
clinical_trial_phase	The phase that a clinical trials study represents
clinical_trial_primary_purpose	The primary purpose of a clinical trial as determined by clinicaltrials.gov. The most common values are TREATMENT and PREVENTION. Other possible values include BASIC_SCIENCE, SUPPORTIVE_CARE, DIAGNOSTIC, HEALTH_SERVICES_RESEARCH, SCREENING, DEVICE_FEASIBILITY, OTHER, and (null).
clinical_trial_start_date	The start date of a clinical trial as determined by clinicaltrials.gov
clinical_trial_tested_intervention	Records whether the clinical trials are testing the intervention.
clinical_trial_time_perspective	The time perspective of a clinical trial as determined by clinicaltrials.gov. The most common values are PROSPECTIVE, RETROSPECTIVE, CROSS_SECTIONAL, or OTHER (most common)..
created_with	An identifier (typically a URL or CURIE) of the software tool, service, or pipeline used to create the dataset.
creation_date	date on which an entity was created. This can be applied to nodes or edges
dataset_download_url	A URL from which the dataset itself may be directly downloaded specialised for the dataset domain.
distribution_download_url	A URL from which a specific distribution (serialization or format) of a dataset may be directly downloaded; corresponds to dcat:downloadURL specialised for the dataset distribution domain.
download_url	A URL from which the information content entity may be directly downloaded in its native serialization.
elevate_to_prediction	A boolean flag indicating whether a clinical trial finding should be elevated to a prediction.
exact_synonym	An alternate label for an entity that denotes exactly the same meaning as the primary label and is interchangeable with it in all contexts.
exposure_additional_condition	Additional conditions impacting an exposure event.
exposure_duration	Duration of an exposure event.
exposure_end_age	Ending stage of an exposure event.
exposure_magnitude	Magnitude of an exposure event, e.g, parts per million of a toxic chemical.
exposure_route	Route of exposure.
exposure_start_age	Starting age of an exposure event.
exposure_type	Type of exposure
exposure_vehicle	Type of an exposure event.
format	The file format, physical medium, or representational form of the information content entity; for digital resources typically a MIME type or format identifier. Corresponds to dct:format.
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	Links a dataset version to the underlying dataset that it is a version of.
has_device	connects an entity to one or more (medical) devices
has_distribution	Links a dataset version to one of its dataset distributions (a specific representation or serialization of the dataset).
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	An entity that interacts with an exposure stimulus during an exposure event.
has_route	the process that results in the stressor coming into direct contact with the receptor
has_stressor	An agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure_receptor during an exposure event.
has_taxonomic_rank	The taxonomic rank (e.g. species, genus, family, order, kingdom) assigned to an organism taxon.
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	The zygosity characterising a genotype or nucleic acid entity at a particular locus.
hgvs_nomenclature	HGVS syntax refers to the specific rules and conventions used by the Human Variant Nomenclature Committee to describe the location and change in DNA, RNA, and protein sequence variants. This slot is used to capture all the different forms of HGVS nomenclature that may be used to describe a sequence variant, including genomic, transcript, and protein HGVS expressions/nomenclatures and is thus multivalued.
in_taxon_label	The human readable scientific name for the taxon of the entity.
ingest_date	The date on which a dataset version was ingested into the local knowledge graph or downstream data system; a specialization of dct:issued for the ingestion context.
inheritance	Connects genetic inheritance to a disease or phenotypic feature, as a node property.
is_metabolite	indicates whether a molecular entity is a metabolite
is_supplement	A boolean or categorical flag indicating that a chemical mixture is marketed, formulated, or used as a dietary or nutritional supplement rather than as a conventional drug or food.
is_toxic	A boolean flag indicating whether a chemical entity is toxic under ordinary conditions of exposure.
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	A legal instrument under which the information content entity is made available, typically identified by a URL or CURIE pointing to a license document.
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	An alternate label for an entity whose meaning is narrower (more specific) than the primary label, for example naming a particular sub-type.
node_property	A grouping for any property that holds between a node and a value
number_of_cases	The number of cases in a study or clinical trial, primarily used in conversion of drug approval data.
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.
related_synonym	An alternate label that is related to the primary label but is neither exactly synonymous nor cleanly broader or narrower; useful as a lexical pointer but not for strict equivalence. Corresponds to oboInOwl:hasRelatedSynonym.
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	The date on which a dataset was retrieved or harvested from its original source, following pav:retrievedOn.
rights	A statement describing rights held in or over the information content entity, such as copyright, intellectual property, or access and usage rights.
source_logo	A URL referencing an image that serves as the visual logo of a data source.
source_record_urls	A URL linking to a specific web page or document provided by the source, that contains a record of the knowledge expressed in the Edge. If the knowledge is contained in more than one web page on an Information Resource's site, urls MAY be provided for each.
source_web_page	A URL of a web page that documents or serves as the landing page for a data source.
subsets	The set of ontology subsets a term belongs to (e.g. GO slim subsets, MONDO rare disease subset). Carries the values of oboInOwl:inSubset annotations from source ontologies through to downstream knowledge graphs.
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
taxon	A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology.
trade_name	A proprietary brand or trade name under which a chemical entity (typically a drug) is manufactured and marketed by a vendor.
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.
url	This slot holds a string representation of a URL for an external resource about the node it is present on. Unlike an 'xref' that is primarily represented by a CURIE, this slot is intended to hold a full URL that can be used to directly access a resource. When linking to an external resource that cannot be represented by a unique CURIE, this slot should be used. However, when the intent is to link to the default URI expansion of a CURIE related to the node it is present on, the xref slot should be used instead.
version	A label identifying a particular release or edition of a dataset or resource, typically following a versioning scheme such as a semantic version string or a release date.
version_of	Links a dataset version to the dataset summary of which it is a version, edition, or adaptation.
volume	volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication

Predicates (Visualization)

Property	Description
active_in	Holds between a gene or gene product and a cellular component in which it carries out its molecular function.
actively_involved_in	holds between a continuant and a process or function, where the continuant actively contributes to part or all of the process or function it realizes
actively_involves	None
acts_upstream_of	Holds between a gene or gene product and a biological process such that the molecular function of the gene product, by way of a chain of causally linked events, is upstream of and contributes to the execution of the process.
acts_upstream_of_negative_effect	Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a negative (inhibiting or decreasing) effect on the execution of the process.
acts_upstream_of_or_within	Holds between a gene or gene product and a biological process when the gene product either acts upstream of the process or participates in it; used when the more specific causal relationship is not known. Corresponds to RO:0002264.
acts_upstream_of_or_within_negative_effect	Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a negative (inhibiting or decreasing) effect on its execution. Corresponds to RO:0004033.
acts_upstream_of_or_within_positive_effect	Holds between a gene or gene product and a biological process when the gene product acts upstream of or within the process with a positive (activating or increasing) effect on its execution. Corresponds to RO:0004032.
acts_upstream_of_positive_effect	Holds between a gene or gene product and a biological process where the molecular function of the gene product is upstream of and has a positive (activating or increasing) effect on the execution of the process.
adverse_event_of	None
affected_by	describes an entity of which the state or quality is affected by another existing entity.
affects	Describes an entity that has an effect on the state or quality of another existing entity.
affects_likelihood_of	Holds between two entities where the presence or application of one alters the chance that the other will come to be.
affects_sensitivity_to	holds between two chemical entities or genes or gene products where the action of one affects the susceptibility/sensitivity of a biological entity or system to the other.
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.
amount_or_activity_decreased_by	None
amount_or_activity_increased_by	None
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.
associated_with	Expresses a relationship between two named things where the relationship is typically generated statistically (though not in all cases), and is weaker than its child, 'correlated with', but stronger than its parent, 'related to'. This relationship holds between two concepts represented by variables for which a statistical dependence is demonstrated. E.g. the statement “Atrial Fibrillation (Afib) is associated with Myocardial Infraction (MI)” asserts that having Afib is not statistically independent from whether a patient will also have MI. Note that in Translator associations, the subject and object concepts may map exactly to the statistical variables, or represent related entities for which the variables serve as proxies in an Association (e.g. diseases, chemical entities or processes).
associated_with_decreased_likelihood_of	Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable.
associated_with_increased_likelihood_of	Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable.
associated_with_likelihood_of	A a relationship that holds between two concepts represented by variables for which a statistical dependence is demonstrated, wherein the state or value of one variable predicts the future state or value of the other. E.g. the statement “An Atrial Fibrillation (Afib) diagnosis is associated with likelihood of a Myocardial Infraction (MI) diagnosis” asserts that the state of having Afib is associated with an increased or decreased likelihood that a patient will later exhibit MI.
associated_with_resistance_to	A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of resistance to treatment by the chemical.
associated_with_response_to	A statistical association used to indicate that the object of a statement using this predicate induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic, phenotypic, detrimental, resistant, etc. is captured in context, direction, and aspect qualifiers).
associated_with_sensitivity_to	A relation that holds between a named thing and a chemical that specifies that the change in the named thing is found to be associated with the degree of sensitivity to treatment by the chemical.
author	an instance of one (co-)creator primarily responsible for a written work
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).
binds	A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.
biomarker_for	holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
broad_match	a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.
can_be_carried_out_by	None
capable_of	holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function.
catalyzes	Holds between a macromolecular machine (typically an enzyme or ribozyme) and a biochemical reaction or process whose rate it accelerates, without itself being consumed, by lowering the activation energy.
caused_by	holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other
causes	holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other
chemically_similar_to	holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
close_match	a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives.
coexists_with	holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
coexpressed_with	holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.
colocalizes_with	holds between two entities that are observed to be located in the same place.
completed_by	None
composed_primarily_of	x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
condition_ameliorated_by	None
condition_associated_with_gene	holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
condition_exacerbated_by	None
condition_predisposed_by	None
condition_prevented_by	None
condition_promoted_by	None
consumed_by	None
consumes	Holds between a process and an entity that is taken in and depleted by the process; for example a metabolite consumed in a biochemical reaction.
contains_process	None
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.
contributes_to	holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other
contribution_from	None
contributor	Links an information content entity (such as a dataset, publication, or software artefact) to an agent responsible for making contributions to it. Used as an abstract grouping predicate over more specific contribution roles (author, editor, publisher, provider). Corresponds to dct:contributor.
correlated_with	A relationship that holds between two concepts represented by variables for which a statistical correlation is believed to exist, as demonstrated using a correlation analysis method.
decreased_amount_in	None
decreased_likelihood_associated_with
decreases_amount_or_activity_of	A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object.
decreases_sensitivity_to	holds between two chemical entities or genes or gene products where the action or effect of one decreases the susceptibility/sensitivity of a biological entity or system to the other
derives_from	holds between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives_into	holds between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
develops_from	Holds between two entities where the first develops, by one or more developmental processes, from the second; for example a cell type developing from a precursor cell type or a tissue developing from an embryonic primordium. Corresponds to RO:0002202.
develops_into	None
diagnoses	a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.
directly_physically_interacts_with	A causal mechanism mediated by a direct contact between the effector and target entities (this contact may be weak or strong, transient or stable).
disease_has_basis_in	A relation that holds between a disease and an entity where the state of the entity has contribution to the disease.
disease_has_location	A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
disrupted_by	describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another.
disrupts	describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
editor	editor of a compiled work such as a book or a periodical (newspaper or an academic journal). Note that in the case of publications which have a containing "published in" node property, the editor association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the editorial agent of the encompassing publication (e.g. only from the Book referenced by the 'published_in' property of a book chapter Publication node).
enabled_by	holds between a process and a physical entity, where the physical entity executes the process
enables	holds between a physical entity and a process, where the physical entity executes the process
exacerbates_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.
exact_match	holds between two entities that have strictly equivalent meanings, with a high degree of confidence
expressed_in	holds between a gene or gene product and an anatomical entity in which it is expressed
expresses	holds between an anatomical entity and gene or gene product that is expressed there
food_component_of	holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)
gene_associated_with_condition	holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
gene_product_of	definition x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of thatf process is either y or something that is ribosomally translated from x
gene_fusion_with	holds between two independent genes that have fused through translocation, interstitial deletion, or chromosomal inversion to form a new, hybrid gene. Fusion genes are often implicated in various neoplasms and cancers.
genetic_association	None
genetic_neighborhood_of	holds between two genes located nearby one another on a chromosome.
genetically_associated_with	A statistical association, observed in genetic studies, between a genetic entity such as a gene, locus, or variant and a phenotype, disease, or trait.
genetically_interacts_with	holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality.
has_active_component	None
has_active_ingredient	holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component
has_adverse_event	An untoward medical occurrence in a patient or clinical investigation subject that happens during treatment with a therapeutic agent. Adverse events may be caused by something other than the drug or therapy being given and may include abnormal laboratory finding, symptoms, or diseases temporally associated with the treatment, whether or not considered related to the treatment. Adverse events are unintended effects that occur when a medication is administered correctly.
has_author	None
has_biomarker	holds between a disease or phenotypic feature and a measurable chemical entity that is used as an indicator of the presence or state of the disease or feature.
# metabolite
has_catalyst	None
has_chemical_role	A role is particular behaviour which a chemical entity may exhibit.
has_completed	holds between an entity and a process that the entity is capable of and has completed
has_contraindication	None
has_contributor	None
has_decreased_amount	Holds between an entity and a component that is present at lower amount than in a reference state or sibling entity; used for comparative compositional statements.
has_editor	None
has_excipient	holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component
has_food_component	holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)
has_frameshift_variant	None
has_gene_product	holds between a gene and a transcribed and/or translated product generated from it
has_increased_amount	Holds between an entity and a component that is present at higher amount than in a reference state or sibling entity; used for comparative compositional statements.
has_input	holds between a process and a continuant, where the continuant is an input into the process
has_manifestation	None
has_member	Defines a mereological relation between a collection and an item.
has_metabolite	holds between two molecular entities in which the second one is derived from the first one as a product of metabolism
has_missense_variant	None
has_mode_of_inheritance	Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).
has_molecular_consequence	connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
has_nearby_variant	None
has_negative_upstream_actor	None
has_negative_upstream_or_within_actor	None
has_non_coding_variant	None
has_nonsense_variant	None
has_not_completed	holds between an entity and a process that the entity is capable of, but has not completed
has_nutrient	one or more nutrients which are growth factors for a living organism
has_output	holds between a process and a continuant, where the continuant is an output of the process
has_part	holds between wholes and their parts (material entities or processes)
has_participant	holds between a process and a continuant, where the continuant is somehow involved in the process
has_phenotype	holds between a biological entity and a phenotype, where a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). In SNOMEDCT, disorders with keyword 'characterized by' should translate into this predicate.
has_plasma_membrane_part	Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
has_positive_upstream_actor	None
has_positive_upstream_or_within_actor	None
has_provider	None
has_publisher	None
has_sequence_location	holds between two nucleic acid entities when the subject can be localized in sequence coordinates on the object. For example, between an exon and a chromosome/contig.
has_sequence_variant	None
has_side_effect	An unintended, but predictable, secondary effect shown to be correlated with a therapeutic agent, drug or treatment. Side effects happen at normal, recommended doses or treatments, and are unrelated to the intended purpose of the medication.
has_splice_site_variant	None
has_substrate	Holds between a biochemical reaction or catalytic process and a chemical entity that is acted upon (consumed or transformed) by that reaction.
has_synonymous_variant	None
has_target	None
has_upstream_actor	None
has_upstream_or_within_actor	None
has_variant_part	holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it
homologous_to	holds between two biological entities that have common evolutionary origin
in_cell_population_with	holds between two genes or gene products that are expressed in the same cell type or population
in_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).
in_complex_with	holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
in_linkage_disequilibrium_with	holds between two sequence variants, the presence of which are correlated in a population
in_pathway_with	holds between two genes or gene products that are part of in the same biological pathway
in_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).
in_taxon	connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
increased_amount_of	None
increased_likelihood_associated_with
increases_amount_or_activity_of	A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object.
increases_sensitivity_to	holds between two chemical entities or genes or gene products where the action or effect of one increases the susceptibility/sensitivity of a biological entity or system to the other
indirectly_physically_interacts_with	Holds between two entities that physically interact by way of one or more intermediary entities, rather than through direct physical contact.
interacts_with	holds between any two entities that directly or indirectly interact with each other
is_active_ingredient_of	holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component
is_chemical_role_of	Holds between a chemical role and a chemical entity that exhibits that role.
is_diagnosed_by	None
is_excipient_of	holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component
is_frameshift_variant_of	holds between a sequence variant and a gene, such the sequence variant causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.
is_input_of	None
is_metabolite_of	holds between two molecular entities in which the first one is derived from the second one as a product of metabolism
is_missense_variant_of	holds between a gene and a sequence variant, such the sequence variant results in a different amino acid sequence but where the length is preserved.
is_molecular_consequence_of	None
is_nearby_variant_of	holds between a sequence variant and a gene sequence that the variant is genomically close to.
is_non_coding_variant_of	holds between a sequence variant and a gene, where the variant does not affect the coding sequence
is_nonsense_variant_of	holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon
is_output_of	None
is_sequence_variant_of	holds between a sequence variant and a nucleic acid entity
is_side_effect_of	None
is_splice_site_variant_of	holds between a sequence variant and a gene, such the sequence variant is in the canonical splice site of one of the gene's exons.
is_substrate_of	None
is_synonymous_variant_of	holds between a sequence variant and a gene, such the sequence variant is in the coding sequence of the gene, but results in the same amino acid sequence
lacks_part	Holds between an entity and a component that is absent from it relative to a reference type; for example a cell type lacking a particular organelle or a protein lacking a particular domain. Corresponds to CL:lacks_part / PR:lacks_part.
likelihood_affected_by	None
likelihood_associated_with
located_in	holds between a material entity and a material entity or site within which it is located (but of which it is not considered a part)
location_of	holds between material entity or site and a material entity that is located within it (but not considered a part of it)
location_of_disease	None
manifestation_of	that part of a phenomenon which is directly observable or visibly expressed, or which gives evidence to the underlying process; used in SemMedDB for linking things like dysfunctions and processes to some disease or syndrome
member_of	Defines a mereological relation between a item and a collection.
mentioned_by	refers to is a relation between one named thing and the information content entity that it makes reference to.
mentions	refers to is a relation between one information content entity and the named thing that it makes reference to.
missing_from	None
mode_of_inheritance_of	None
model_of	holds between a thing and some other thing it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity.
models	None
models_demonstrating_benefits_for	None
narrow_match	a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.
negatively_correlated_with	A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move in opposite directions (i.e. increased in one or presence of one correlates with a decrease or absence of the other).
not_completed_by	None
nutrient_of	holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)
occurs_in	holds between a process and a material entity or site within which the process occurs
occurs_in_disease	None
occurs_together_in_literature_with	holds between two entities where their co-occurrence is correlated by counts of publications in which both occur, using some threshold of occurrence as defined by the edge provider.
opposite_of	x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). (This description is from RO. Needs to be rephrased).
orthologous_to	a homology relationship between entities (typically genes) that diverged after a speciation event.
overlaps	holds between entities that overlap in their extents (materials or processes)
paralogous_to	a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
part_of	holds between parts and wholes (material entities or processes)
participates_in	holds between a continuant and a process, where the continuant is somehow involved in the process
pharmacologically_interacts_with	holds between two pharmacologically active chemicals (typically drugs), where one alters the availability, efficacy, or toxicity of the other in the body when taken simultaneously - typically by altering how the body processes the chemical (pharmacokinetics) or how the chemical acts on the body (pharmacodynamics).
phenotype_of	None
physically_interacts_with	holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
plasma_membrane_part_of	None
positively_correlated_with	A relationship that holds between two concepts represented by variables for which a statistical correlation is demonstrated, wherein variable values move together in the same direction (i.e. increased in one or presence of one correlates with an increase or presence of the other).
preceded_by	holds between two processes, where the other is completed before the one begins
precedes	holds between two processes, where one completes before the other begins
predisposes_to_condition	Holds between two entities where the presence or application of one increases the chance that the other will come to be.
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.
primarily_composed_of	None
produced_by	None
produces	holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
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.
provider	person, group, organization or project that provides a piece of information.
publisher	organization or person responsible for publishing books, periodicals, podcasts, games or software. Note that in the case of publications which have a containing "published in" node property, the publisher association may not be attached directly to the embedded child publication, but only made in between the parent's publication node and the publisher agent of the encompassing publication (e.g. only from the Journal referenced by the 'published_in' property of an journal article Publication node).
regulated_by	None
regulates	A more specific form of affects, that implies the effect results from a biologically evolved control mechanism. Gene-affects-gene relationships will (almost) always involve regulation. Exogenous/environmental chemical-affects-gene relationships are not cases of regulation in this definition. Instead these would be captured using the 'affects' predicate, or possibly one of the 'interacts with' predicates depending on the nature of the interaction.
related_condition	Links a genotype or genetic variant to a condition (disease or phenotypic feature) that is associated with it.
related_to	A relationship that is asserted between two named things
related_to_at_concept_level	Represents a relationship held between terminology components that describe the conceptual model of a domain.
related_to_at_instance_level	Represents a relationship held between two instances of a data classes. Much like an assertion component, in an ABox, these represent facts associated with the conceptual model.
resistance_associated_with	None
response_associated_with	None
same_as	holds between two entities that are considered equivalent to each other
sensitivity_affected_by	None
sensitivity_associated_with	None
sensitivity_decreased_by	None
sensitivity_increased_by	None
sequence_location_of	None
similar_to	holds between an entity and some other entity with similar features.
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).
subclass_of	holds between two classes where the domain class is a specialization of the range class
subject_of_treatment_application_or_study_for_treatment_by	None
superclass_of	holds between two classes where the domain class is a super class of the range class
target_for	A gene is a target of a disease when its products are druggable and when a drug interaction with the gene product could have a therapeutic effect
taxon_of	None
temporally_related_to	holds between two entities with a temporal relationship
tested_by_clinical_trials_of	None
tested_by_preclinical_trials_of	None
transcribed_from	x is transcribed from y if and only if x is synthesized from template y
transcribed_to	inverse of transcribed from
translates_to	x (amino acid chain/polypeptide) is the ribosomal translation of y (transcript) if and only if a ribosome reads y (transcript) through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces x (amino acid chain/polypeptide)
translation_of	inverse of translates to
treated_by	None
treated_in_studies_by	None
treatment_applications_from	None
treats	Holds between an intervention (substance, procedure, or activity) and a medical condition (disease or phenotypic feature), and states that the intervention is, in some population(s), able to ameliorate, stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting in the first place. ‘Treats’ edges should be asserted (knowledge_level: assertion) only in cases where there is strong supporting evidence - i.e. in some population(s) the intervention is approved for the condition, passed phase 3 or in phase 4 trials for the condition, or is an otherwise established treatment in the medical community (e.g. a widely-accepted or formally recommended off-label use). In the absence of such evidence, weaker predicates should be used in asserted edges (e.g. ‘in clinical trials for’ or ‘beneficial in models of’). ‘Treats’ edges based on weaker or indirect forms of evidence can however be created as predictions (knowledge_level: prediction) and should point to the more foundational asserted edges that support them.
treats_or_applied_or_studied_to_treat	Holds between an substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to treat the condition, has been observed to be taken/prescribed in practice with the intent of treating the condition, or has been interrogated in a scientific study that hypothesized an ability to treat the condition (in humans or other biological systems/organisms).
variant_part_of	None
was_tested_for_effect_of	None
was_tested_for_effect_on	Reports that the subject was interrogated in an experiment to determine how it may affect the object. 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.
xenologous_to	a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.

Qualifiers (Visualization)

Property	Description
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.
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
context_qualifier	Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
derivative_qualifier	A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’.
direction_qualifier	Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.
disease_context_qualifier	A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
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
object_activity_qualifier	None
object_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. This qualifier specifies a change in the object of an association (aka: statement).
object_context_qualifier	A qualifier describing the context in which the object of an association holds.
object_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’. This qualifier is for the object of an association (or statement).
object_direction_qualifier	Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).
object_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’. This qualifier specifies a change in the object of an association (aka: statement).
object_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). This qualifier is for the object of an association (or statement).
object_process_qualifier	None
object_specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
onset_qualifier	a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.
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).
population_context_qualifier	a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
process_qualifier	Restricts the biological process within which the core concept (or qualified core concept) participates.
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. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats 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
response_context_qualifier	a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
response_target_context_qualifier	a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)
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.
specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
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.
statement_qualifier	A property that qualifies the entirety of the statement made in an association. It applies to both a fully qualified subject and a fully qualified object as well as the predicate and qualified predicate in an association.
subject_activity_qualifier	None
subject_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. This qualifier specifies a change in the subject of an association (aka: statement).
subject_context_qualifier	A qualifier describing the context in which the subject of an association holds.
subject_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’. This qualifier is for the subject of an association (or statement).
subject_direction_qualifier	Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).
subject_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’. This qualifier specifies a change in the subject of an association (aka: statement).
subject_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). This qualifier is for the subject of an association (or statement).
subject_process_qualifier	None
subject_specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
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.

Associations

Association	Description
AnatomicalEntityHasPartAnatomicalEntityAssociation	A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is has the object entity as a part (the expected predicate is "biolink:has_part" or suitable predicate slots inheriting from it, i.e., "biolink:has_plasma_membrane_part", "biolink:has_variant_part", etc.). This includes relationships between cells and cellular components, between issues and cells, whole organisms and tissues.
AnatomicalEntityPartOfAnatomicalEntityAssociation	A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood, that is, the subject is a part of the object entity (the expected predicate is "biolink:part_of" or suitable predicate slots inheriting from it, i.e., "biolink:plasma_membrane_part_of", "biolink:variant_part_of", etc.). This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms.
AnatomicalEntityToAnatomicalEntityAssociation	An abstract parent class for associations between two anatomical entities, such as part-of, develops-from, or other mereological and ontogenic relationships.
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.
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.
BiologicalProcessOrActivityToAnatomicalEntityAssociation	An association between a biological process or activity and an anatomical entity.
BiologicalProcessOrActivityToBiologicalProcessOrActivityAssociation	Classification relationship between biological processes or activities (e.g. coupling of two molecular activities; assignment of molecular activity to a pathway; implicating a pathway in a biological process; etc.)
BiologicalProcessOrActivityToGeneOrGeneProductOrGeneFamilyAssociation	Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family.
CaseToDiseaseAssociation	An association between a Case (patient) and a Disease
CaseToGeneAssociation	Association between a Case and a Gene (e.g., indicating a gene of interest for the case)
CaseToPhenotypicFeatureAssociation	An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.
CaseToVariantAssociation	Association between a Case and a Genetic Variant
CausalGeneToDiseaseAssociation	An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease.
CellLineAsAModelOfDiseaseAssociation	An association in which a cell line - typically derived from an organismal entity with a disease state - serves as a model for that disease in experimental settings.
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.
ChemicalAffectsBiologicalEntityAssociation	Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)
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
ChemicalEntityToBiologicalProcessAssociation	An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process.
ChemicalEntityToChemicalDerivationAssociation	A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P
ChemicalEntityToChemicalEntityAssociation	A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.
ChemicalEntityToDiseaseOrPhenotypicFeatureAssociation	An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.
ChemicalEntityToPathwayAssociation	An interaction between a chemical entity and a biological process or pathway.
ChemicalGeneInteractionAssociation	describes an 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)
ChemicalOrDrugOrTreatmentAdverseEventAssociation	This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an untoward medical occurrence that happens during treatment, whether or not considered related to the treatment.
ChemicalOrDrugOrTreatmentSideEffectAssociation	This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is an unintended, but predictable, secondary effect of the treatment.
ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation	This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the chemical or treatment is used to treat, or is being studied to treat, the disease or phenotypic feature.
ContributorAssociation	Any association between an entity (such as a publication) and various agents that contribute to its realisation
CorrelatedGeneToDiseaseAssociation	An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score.
DiseaseAssociatedWithResponseToChemicalEntityAssociation	A statistical association between a disease and a chemical entity where the chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes in a patient, cell line, or any model system.
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	An association between a gene (or gene product) and a disease in which the gene is classified by its druggability (e.g., via the IDG/Pharos target development-level tiers).
EntityToDiseaseAssociation	An association between any entity and a disease, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.
EntityToPhenotypicFeatureAssociation	An association between any entity and a phenotypic feature, capturing clinical context such as approval status, research phase, FDA regulatory approvals, and number of cases.
ExonToTranscriptRelationship	A transcript is formed from multiple exons
ExposureEventToOutcomeAssociation	An association between an exposure event and an outcome.
ExposureEventToPhenotypicFeatureAssociation	Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.
FunctionalAssociation	An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed.
GeneAffectsChemicalAssociation	Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)
GeneAsAModelOfDiseaseAssociation	An association in which a gene (e.g., a model-organism ortholog of a known disease gene) serves as a model of a human disease - for example, because mutants of the gene recapitulate core features of the disease.
GeneFamilyToGeneOrGeneProductOrGeneFamilyAssociation	Relationship between a gene family and a contained gene or gene product or gene family.
GeneHasVariantThatContributesToDiseaseAssociation	A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution.
GeneOrGeneProductOrGeneFamilyToAnatomicalEntityAssociation	An association between a gene or gene product or gene family and an anatomical entity.
GeneOrGeneProductOrGeneFamilyToBiologicalProcessOrActivityAssociation	Relationship between a gene or gene product or gene family to a specified biological process or activity (e.g. molecular activity, biological process or pathway).
GeneRegulatesGeneAssociation	Describes a regulatory relationship between two genes or gene products.
GeneToDiseaseAssociation	An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.
GeneToExpressionSiteAssociation	An association between a gene and a gene expression site, possibly qualified by stage/timing info.
GeneToGeneAssociation	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	A functional association between a gene (or gene product or macromolecular complex) and a Gene Ontology (GO) term describing the molecular function, biological process, or cellular component in which it participates.
GeneToPathwayAssociation	An interaction between a gene or gene product and a biological process or pathway.
GeneToPhenotypicFeatureAssociation	An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature.
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	An association in which a genotype serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.
GenotypeToDiseaseAssociation	An association between a genotype and a disease, in which the genotype (typically a combination of alleles at one or more loci) is linked to the disease state.
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).
MacromolecularMachineHasSubstrateAssociation	Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein.
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	An association in which the subject entity is linked to the likelihood of the object entity occurring, manifesting, or being observed. Subject and object may each be qualified by aspect and context, and the association may be further qualified by a population context.
OrganismTaxonToEnvironmentAssociation	An abstract association between an organism taxon and an environmental context (e.g., a habitat, biome, or ecological setting) in which the taxon occurs.
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	An association between two individual organisms (e.g., symbiosis, parasitism, predation, or other inter-organism relationships).
OrganismalEntityAsAModelOfDiseaseAssociation	An association in which an organismal entity (e.g., a strain or breed) serves as a model of a disease, either because it has a natural predisposition to the disease or was bred or engineered specifically to recapitulate it.
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
PhenotypicFeatureToDiseaseAssociation	An association between a phenotypic feature (sign or symptom) and a disease, where the phenotypic feature is a manifestation or clinical indicator of the disease.
PhenotypicFeatureToPhenotypicFeatureAssociation	Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
PopulationToPopulationAssociation	An association between a two populations
ProcessRegulatesProcessAssociation	Describes a regulatory relationship between two genes or gene products.
ReactionToCatalystAssociation	A specialization of reaction-to-participant association in which the participant is a gene or gene product (e.g., an enzyme) that catalyses the reaction.
ReactionToParticipantAssociation	An association between a biochemical reaction and a participating molecular entity, qualified by the stoichiometry, the side (reactant vs. product) on which the participant appears, and the direction of the reaction.
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	An association between two organism taxa, capturing ecological or evolutionary relationships between the taxa (e.g., a host-pathogen relationship or shared habitat).
TranscriptToGeneRelationship	A gene is a collection of transcripts
VariantAsAModelOfDiseaseAssociation	An association in which a sequence variant serves as a model of a disease, recapitulating features relevant for studying the disease outside of a patient who carries it.
VariantToDiseaseAssociation	An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state.
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	An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype.
VariantToPopulationAssociation	An association between a variant and a population, where the variant has particular frequency in the population

Association 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<.
agent_type	Describes the high-level category of agent who originally generated a statement of knowledge or other type of information.
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.
allelic_requirement	The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance.
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
chi_squared_dof	Degrees of freedom (dof) in a chi-squared test referring to the number of values in the final calculation of a statistic that are free to vary
chi_squared_p	The chi-square p-value tells you the probability that the observed differences (or associations) in your data occurred by random chance, assuming the null hypothesis is true.
chi_squared_statistic	The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis.
clinical_approval_status	The clinical approval status of a chemical entity for treating a specific disease or condition, as captured in the context of the association between the chemical and the disease.
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 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.
disease_context_qualifier	A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
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	The level or severity grade of an adverse event as classified by FDA adverse-event terminology, drawn from FDAIDAAdverseEventEnum; used on adverse-event associations.
fisher_exact_odds_ratio	The Fisher Exact Test is used to determine whether there is a non-random association between two categorical variables in a 2×2 contingency table, especially when sample sizes are small. The odds ratio (OR) quantifies the strength of that association.
OR = 1 implies No association
OR > 1 implies Positive association (Group A more likely to have Outcome 1)
OR < 1 implies Negative association (Group A less likely to have Outcome 1)
fisher_exact_p	The Fisher exact p-value tells you the probability of observing a table as extreme as (or more extreme than) your actual data, assuming that the null hypothesis of independence is true. It's most commonly used for 2×2 contingency tables, especially when sample sizes are small or expected counts are low.
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_affinity	Set of measurements documenting the strength of chemical entity to gene or gene product interactions.
has_confidence_level	connects an association to a qualitative term denoting the level of confidence
has_confidence_score	connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about.
has_evidence	Connects an association to detailed information providing supporting evidence.
has_evidence_of_type	Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology.
has_study_results	Connects an study to instances of its study result
has_supporting_studies	Studies that produced information used as evidence to generate the knowledge expressed in an Association.
interacting_molecules_category	None
interbase_coordinate	A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge.
knowledge_level	Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
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 natural logarithm of the odds ratio (OR), or the ratio of the odds of an event Y occurring in an exposed group versus the odds of an 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. To calculate the 95% confidence interval (CI) for a log odds ratio (a pair of numbers), you need the standard error (SE) of the log odds ratio. This interval helps you understand the precision of your estimate and whether the association is statistically significant.
logical_interpretation	None
max_research_phase	The maximum research phase reached for a specific chemical-disease pair, indicating the highest clinical trial phase achieved for the chemical entity's investigation as a treatment for the associated disease or condition.
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_activity_qualifier	None
object_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. This qualifier specifies a change in the object of an association (aka: statement).
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	A qualifier describing the context in which the object of an association holds.
object_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’. This qualifier is for the object of an association (or statement).
object_direction_qualifier	Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).
object_feature_name	Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease
object_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’. This qualifier specifies a change in the object of an association (aka: statement).
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	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). This qualifier is for the object of an association (or statement).
object_process_qualifier	None
object_specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
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).
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	Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats
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.
process_qualifier	Restricts the biological process within which the core concept (or qualified core concept) participates.
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. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats 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	Indicates whether a chemical reaction is stoichiometrically balanced, i.e. whether the conservation of atoms (and charge) holds between the reactants and the products.
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)
response_context_qualifier	a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
response_target_context_qualifier	a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)
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.
sources	A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org).
specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
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	A property that qualifies the entirety of the statement made in an association. It applies to both a fully qualified subject and a fully qualified object as well as the predicate and qualified predicate in an association.
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_activity_qualifier	None
subject_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. This qualifier specifies a change in the subject of an association (aka: statement).
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	A qualifier describing the context in which the subject of an association holds.
subject_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’. This qualifier is for the subject of an association (or statement).
subject_direction_qualifier	Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement).
subject_feature_name	Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene
subject_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’. This qualifier specifies a change in the subject of an association (aka: statement).
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	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). This qualifier is for the subject of an association (or statement).
subject_process_qualifier	None
subject_specialization_qualifier	A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier.
support_graphs	A list of knowledge graphs that support the existence of this association.
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.
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, 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_types	Type(s) of methods that were 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.
z_score	A measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.

Enumerations

Enumeration	Description
AffinityParameterEnum	The types of parameters that can be used to describe the affinity between two entities, characteristically chemicals and proteins. The values are generally stated as the negative base 10 logarithm of the raw measurements.
AgentTypeEnum	An enumeration of agent types responsible for generating a statement of knowledge, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values distinguish human (manual) agents from automated agents (including data analysis pipelines, computational models, text-mining agents, image-processing agents) and mixed cases such as manual validation of automated output.
ApprovalStatusEnum	An enumeration of regulatory and development milestones for a drug or therapeutic, spanning discovery, preclinical research, FDA clinical trial phases (1-4), special review designations (e.g., fast track, breakthrough therapy, priority review), regular FDA approval, and post-approval withdrawal.
BinaryRelationEnum	Mathematical binary relation qualifiers of a value in its context.
CausalMechanismQualifierEnum	An enumeration used as a qualifier to specify the causal or pharmacologic mechanism by which an effect is exerted in an association (e.g., agonism, antagonism, inverse agonism, allosteric modulation, activation, inhibition, and their competitive or partial variants).
ChemicalEntityDerivativeEnum	An enumeration of relationships by which one chemical entity is derived from another, e.g., a metabolite produced from a parent compound.
ChemicalOrGeneOrGeneProductFormOrVariantEnum	An enumeration used as a qualifier to indicate a specific form or variant of a chemical, gene, or gene product involved in an association (e.g., modified form, loss-of-function variant, gain-of-function variant, dominant-negative variant, polymorphic form, SNP form, mutant form, or analog form).
ClinicalApprovalStatusEnum	An enumeration describing whether a chemical or therapy is approved for use in treating a specific condition (e.g., FDA-approved for a condition, not approved, off-label use, or withdrawn following approval).
ClinicalTrialAgeStageEnum	Enumeration of age stages or populations commonly used in clinical trials to categorize participant demographics and target populations.
ClinicalTrialStatusEnum	Enumeration of clinical trial statuses indicating the recruitment state, availability, or regulatory status of a clinical study or intervention.
DirectionQualifierEnum	An enumeration of values that qualify a change or effect by its direction, i.e., whether the referenced quantity or activity is increased (including up-regulated) or decreased (including down-regulated).
DrugAvailabilityEnum	An enumeration describing how a drug or chemical entity may be obtained, distinguishing products that are available over the counter from those that require a prescription.
DrugDeliveryEnum	An enumeration of routes by which a drug is administered or delivered to a patient, including inhalation, oral, transdermal absorption, and various forms of injection (intravenous, subcutaneous, intramuscular).
DruggableGeneCategoryEnum	An enumeration of druggability categories for gene targets as defined by the IDG (Illuminating the Druggable Genome) / Pharos target development level classification: Tclin (targets of approved drugs), Tchem (targets with potent bioactives), Tbio (targets with biological knowledge), and Tdark (poorly characterized targets).
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	An enumeration used as a qualifier to indicate the specific aspect of a gene, gene product, or chemical entity that is affected or measured in an association. Values cover activity and abundance (expression, synthesis, degradation, stability, localization, transport), molecular interactions, and a wide range of molecular modifications such as phosphorylation, methylation, acetylation, ubiquitination, and other post-translational or chemical modifications.
GeneOrGeneProductOrChemicalPartQualifierEnum	An enumeration used as a qualifier to indicate a particular structural or functional part of a gene, gene product, or chemical (e.g., 3' UTR, 5' UTR, poly-A tail, promoter, enhancer, exon, or intron).
GeneToDiseasePredicateEnum	Enumeration of predicates permissible for use in gene to disease associations. This constrains the relationship types that can be used between genes and diseases.
GeneToPhenotypicFeaturePredicateEnum	Enumeration of predicates permissible for use in gene to phenotypic feature associations. This constrains the relationship types that can be used between genes and phenotypic features.
KnowledgeLevelEnum	An enumeration characterizing the type of knowledge expressed in a statement and the kind of evidence and reasoning that supports it, as defined by the Translator Knowledge Level / Agent Type (KL/AT) standard. Values include knowledge assertion, logical entailment, prediction, statistical association, text co-occurrence, direct observation, and not-provided.
LogicalInterpretationEnum	An enumeration of logical interpretations that can be applied to a triple to indicate whether the relation should be read as existential on both sides (some-some), universal-existential (all-some), or its inverse (inverse all-some).
PhaseEnum	phase
ReactionDirectionEnum	An enumeration of possible directions for a biochemical reaction, indicating whether it proceeds left-to-right, right-to-left, is bidirectional (reversible), or has no net direction.
ReactionSideEnum	An enumeration indicating on which side of a biochemical reaction a participant appears - the left-hand (reactant/substrate) side or the right-hand (product) side, as written.
ResearchPhaseEnum	An enumeration of research phases describing the stage of investigation for a drug or therapy, spanning preclinical research through clinical trial phases 1 through 4 (including phase 1/2 and phase 2/3 combinations).
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.
ResponseEnum	A response to a treatment or intervention
ResponseTargetEnum	The target of a treatment or intervention
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

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