Entity and association taxonomy and datamodel for life-sciences data
An outcome resulting from an exposure event which is the manifestation of human behavior.
Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype.
An edge in a KGX graph, will be superclass for association
An epidemiological outcome, such as societal disease burden, resulting from an exposure event.
An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization.
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.
A knowledge graph represented in KGX format
An outcome of death from resulting from an exposure event.
A node in a KGX graph, will be superclass for named thing
An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure.
An outcome resulting from an exposure event which is the manifestation of a pathological process.
An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event
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.
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.
A causal mechanism mediated by the direct contact between effector and target chemical or biomolecular entity, which form a stable physical interaction.
A role played by the chemical entity or part thereof within a biological context.
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<.
A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives.
holds between two entities where the occurrence, existence, or activity of one is caused by the occurrence or generation of the other
A union of chemical entities and children, and drug or treatment.
A role played by the chemical entity or part thereof within a chemical context.
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.
the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.
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.
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)..
holds between any two genes or gene products, in which both are generally expressed within a single defined experimental context.
holds between two entities that are observed to be located in the same place.
The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association.
The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association.
The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association.
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
A score defined by DGIdb that quantifies the gene-interaction specificity of a given drug - representing the ratio of average known gene partners for all drugs to the known partners for the given drug. See https://dgidb.org/about/overview/interaction-score.
A score defined by DGIdb that quantifies the drug-interaction specificity of a given gene - representing the ratio of average known drug partners for all genes to the known partners for the given gene. See https://dgidb.org/about/overview/interaction-score.
describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another.
The position at which the subject genomic entity ends on the chromosome or other entity to which it is located on.
The number of evidence instances that are connected to an association.
A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives.
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.
holds between an anatomical entity and gene or gene product that is expressed there
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.
holds between two genes located nearby one another on a chromosome.
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
description of chemical compound based on element symbols
connects an association to a qualitative term denoting the level of confidence
one or more molecular entities within a chemical mixture
holds between a gene and a transcribed and/or translated product generated from it
5 prime UTR premature start codon gain variant
the organism or organism part being exposed
the process that results in the stressor coming into direct contact with the receptor
the process or entity that the receptor is being exposed to
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
holds between two genes or gene products that are expressed in the same cell type or population
holds between two genes or gene products that are part of (or code for products that are part of) in the same macromolecular complex
holds between two sequence variants, the presence of which are correlated in a population
holds between two genes or gene products that are part of in the same biological pathway
A score defined by MI / IntAct that represents the degree of confidence in the existence of a particular interaction by assessing the annotation of that specific interaction in a standards-compliant dataset. The score given to an interaction will increase as the number of experimental evidences supporting that interaction increases. Experimental evidences contribute more highly to the final score than evidences derived by predictive algorithms or literature text-mining methods. Range is 0-1, with higher scores indicated more confidence. See here for details: https://www.ebi.ac.uk/intact/documentation/user-guide#interaction_scoring.
holds between a molecular entity and a drug, in which the former is a part of the latter, and is a biologically active component
holds between a molecular entity and a drug in which the former is a part of the latter, and is a biologically inactive component
holds between two molecular entities in which the first one is derived from the second one as a product of metabolism
The CHEBI ID represents a role rather than a predicate
the natural log of the ratio of co-occurrence to expected
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)
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.
Defines a mereological relation between a item and a collection.
refers to is a relation between one named thing and the information content entity that it makes reference to.
A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives.
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).
holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)
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.
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).
a homology relationship between entities (typically genes) that diverged after a speciation event.
a homology relationship that holds between entities (typically genes) that diverged after a duplication event.
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).
holds between two processes, where the other is completed before the one begins
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)
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)
holds between two entities that are considered equivalent to each other
The number of times this concept has been asserted in the SemMedDB literature database.
a qualifier used in an association with the variant
a qualifier used in a phenotypic association to state how severe the phenotype is in the subject
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).
holds between two classes where the domain class is a super class of the range class
A list of knowledge graphs that support the existence of this association.
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).
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).
For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The "primary knowledge source" for this edge is "infores:icees-asthma". A "supporting data source" for this KP- generated knowledge is "infores:unc-cdw-health." The "aggregator knowledge source" for this data is "infores:aragorn-ara"
One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria).
A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.).
The date range over which data was collected in a study that provided evidence for an Association.
A uri or curie pointing to information about the methodology used to generate data supporting an Association.
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).
The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study).
more commonly used for gene symbols in yeast
a constraint of a time interval placed upon the truth value of an association.
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.
a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor.
Biolink Model root class for entity annotations.
An interaction between a chemical entity and another entity
entity to feature or gene qualifiers mixin
Qualifiers for entity to gene associations.
entity to feature or variant qualifiers mixin
Qualifiers for entity to variant associations.
A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease
acts upstream of or within negative effect
acts upstream of or within positive effect
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.
This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing disease, and excludes interventions that prevent/reduce risk of developing a condition in the future.
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.
This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here).
Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is less probable.
Expresses a relationship between two named things where the relationship is typically generated statistically and the state or fact of something is more probable.
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.
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.
an instance of one (co-)creator primarily responsible for a written work
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).
This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) .
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.
holds between a physical entity and process or function, where the continuant alone has the ability to carry out the process or function.
holds between two entities where the occurrence, existence, or activity of one causes the occurrence or generation of the other
a list of terms from different schemas or terminology systems that have a semantically similar but not strictly equivalent, broader, or narrower meaning. Such terms often describe the same general concept from different ontological perspectives (e.g. drug as a type of chemical entity versus drug as a type of role borne by a chemical entity).
x composed_primarily_of_y if:more than half of the mass of x is made from parts of y.
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.
This predicate relates the intervention with a specific disease, phenotype, or other medical circumstance that puts patients at high risk for detrimental outcomes. This may be a different condition from the one that the drug would be used to treat (e.g. pseudoephedrine is contraindicated in people with high-blood pressure as a treatment for nasal congestion), a biological state (e.g. isotretinoin is contraindicated in people who are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated in people taking warfarin as a preventative treatment for stroke).
The total number of instances (e.g., number of patients, number of rows, etc) in a dataset/cohort.
A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object.
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 (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
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
a relationship that identifies the nature of (an illness or other problem) by examination of the symptoms.
A causal mechanism mediated by a direct contact between the effector and target entities (this contact may be weak or strong, transient or stable).
A relation that holds between a disease and an entity where the state of the entity has contribution to the disease.
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
describes a relationship where one entity degrades or interferes with the structure, function, or occurrence of another.
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).
holds between a physical entity and a process, where the physical entity executes the process
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.
holds between a gene or gene product and an anatomical entity in which it is expressed
holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
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
holds between a drug and a molecular entity in which the latter is a part of the former, and is a biologically active component
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.
holds between an entity and a process that the entity is capable of and has completed
holds between a drug and a molecular entities in which the latter is a part of the former, and is a biologically inactive component
Defines a mereological relation between a collection and an item.
holds between two molecular entities in which the second one is derived from the first one as a product of metabolism
Relates a disease or phenotypic feature to its observed genetic segregation and assumed associated underlying DNA manifestation (i.e. autosomal, sex or mitochondrial chromosome).
connects a sequence variant to a class describing the molecular consequence. E.g. SO:0001583
holds between an entity and a process that the entity is capable of, but has not completed
one or more nutrients which are growth factors for a living organism
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.
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.
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.
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.
Side effects are listed on drug labels. There can be positive side effects, while adverse events are always negative. Aeolus, Sider are both resources that provide side effects.
holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it
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).
This predicate should be used when a source reports a clinical trial where the intervention is being or was interrogated, regardless of the phase of the trial, or its ultimate outcome. Information about phase and outcome can be capture using other modeling elements.
A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object.
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 (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other
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.
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.
holds between a sequence variant and a gene sequence that the variant is genomically close to.
holds between a sequence variant and a gene, where the variant does not affect the coding sequence
holds between a sequence variant and a gene, such the sequence variant results in a premature stop codon
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.
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
holds between material entity or site and a material entity that is located within it (but not considered a part of it)
refers to is a relation between one information content entity and the named thing that it makes reference to.
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.
holds between a process and a material entity or site within which the process occurs
holds between two processes, where one completes before the other begins
Holds between two entities where the presence or application of one increases the chance that the other will come to be.
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.
holds between a material entity and a product that is generated through the intentional actions or functioning of the material entity
person, group, organization or project that provides a piece of information (e.g. a knowledge association).
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).
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.
The RO definition of 'directly regulates the activity of' is an exact_mapping here because it describes genetic regulation from the point of view of one genetic entity regulating another, as opposed to "RO:0002211" which describes process to process regulation.
holds between two classes where the domain class is a specialization of the range class
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
x is transcribed from y if and only if x is synthesized from template y
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)
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.
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
anatomical entity to anatomical entity ontogenic association
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.
anatomical entity to anatomical entity part of association
A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms
A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.
behavior to behavioral feature association
An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior.
A behavioral exposure is a factor relating to behavior impacting an individual.
biological process or activity to anatomical entity association
An association between a biological process or activity and an anatomical entity.
biological process or activity to biological process or activity association
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.)
biological process or activity to gene or gene product or gene family association
Relationship between a biological processor activity (e.g. molecular activity, biological process or pathway) to gene or gene product or gene family.
An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses).
This class may rarely be instantiated except if use cases of a given knowledge graph support its utility.
An association between a Case (patient) and a Disease
Association between a Case and a Gene (e.g., indicating a gene of interest for the case)
An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype.
Association between a Case and a Genetic Variant
cell line as a model of disease association
An relationship between a cell line and another entity
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.)
chemical entity assesses named thing association
chemical entity or gene or gene product regulates gene association
A regulatory relationship between two genes
chemical entity to biological process association
An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process.
chemical entity to chemical derivation association
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
chemical entity to disease or phenotypic feature association
An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype.
An interaction between a chemical entity and a biological process or pathway.
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)
chemical or drug or treatment side effect disease or phenotypic feature association
This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect.
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.
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.
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.
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)
A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug.
A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry.
Any association between an entity (such as a publication) and various agents that contribute to its realisation
disease associated with response to chemical entity association
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.
A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer.
disease or phenotypic feature to genetic inheritance association
An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance.
disease or phenotypic feature to location association
An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site.
An association between an exposure event and a disease.
disease to phenotypic feature association
An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way.
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.
An interaction between a drug and another entity
An interaction between a drug and a gene or gene product.
drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome.
entity to exposure event association mixin
An association between some entity and an exposure event.
An association between some entity and an outcome
entity to phenotypic feature association
Something that happens at a given place and time.
A transcript is formed from multiple exons
An association between an exposure event and an outcome.
exposure event to phenotypic feature association
Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype.
feature or disease qualifiers to entity mixin
Qualifiers for disease or phenotype to entity associations.
A substance consumed by a living organism as a source of nutrition
A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds).
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.)
gene family to gene or gene product or gene family association
Relationship between a gene family and a contained gene or gene product or gene family.
gene has variant that contributes to disease association
gene or gene product or gene family to anatomical entity association
An association between a gene or gene product or gene family and an anatomical entity.
gene or gene product or gene family to biological process or activity association
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).
Describes a regulatory relationship between two genes or gene products.
An association between a gene and a gene expression site, possibly qualified by stage/timing info.
TBD: introduce subclasses for distinction between wild-type and experimental conditions?
Indicates that two genes are co-expressed, generally under the same conditions.
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.
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)
A gene is transcribed and potentially translated to a gene product
An interaction between a gene or gene product and a biological process or pathway.
A genome is the sum of genetic material within a cell or virion.
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 as a model of disease association
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
Any association between one genotype and a genotypic entity that is a sub-component of it
genotype to phenotypic feature association
Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
Any association between a genotype and a sequence variant.
An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes.
A geographic exposure is a factor relating to geographic proximity to some impactful entity.
a location that can be described in lat/long coordinates, for a particular time
A set of zero or more Alleles on a single instance of a Sequence[VMC]
A member of the the species Homo sapiens.
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.
information content entity to named thing association
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).
An animal lacking a vertebral column. This group consists of 98% of all animal species.
an article, typically presenting results of research, that is published in an issue of a scientific journal.
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.
macromolecular machine to biological process association
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.
macromolecular machine to cellular component association
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.
macromolecular machine to molecular activity association
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.
An association between a material sample and the material entity from which it is derived.
material sample to disease or phenotypic feature association
An association between a material sample and a disease or phenotype.
material sample to entity association mixin
An association between a material sample and something.
molecular activity to chemical entity association
Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples
molecular activity to molecular activity association
molecular activity to pathway association
Association that holds the relationship between a reaction and the pathway it participates in.
named thing associated with likelihood of named thing association
A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences.
A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A.
observed expected frequency analysis result
A result of a observed expected frequency analysis.
organism taxon to environment association
organism taxon to organism taxon interaction
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
organism taxon to organism taxon specialization
A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo
organismal entity as a model of disease association
An interaction at the molecular level between two physical entities
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.
An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome.
An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.
A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease.
a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
phenotypic feature to disease association
phenotypic feature to phenotypic feature association
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.
An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present.
An association between a two populations
A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination.
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.
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.
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.
A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain.
Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/
Represents a protein that is a specific isoform of the canonical or reference RNA
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.
A result of a relative frequency analysis.
sequence variant modulates treatment association
An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used.
An alternate way to model the same information could be via a qualifier
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.
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).
SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist
A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty).
a variable that is used as a measure in the investigation of a study
A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)
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.
A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription
variant as a model of disease association
An association between a variant and expression of a gene (i.e. e-QTL)
variant to phenotypic feature association
An association between a variant and a population, where the variant has particular frequency in the population
A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column.
A virus is a microorganism that replicates itself as a microRNA and infects the host cell.
a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features.
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
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.
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.
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.
for good examples of aspects in the gene-> chemical space, please see the GeneOrGeneProductOrChemicalEntityAspectEnum (below) which lists many aspects that can be used to qualify the gene making the full subject a different ontological type. the qualifier ‘expression’ combines with a core concept of ‘Gene X’ to express the composed concept ‘expression of Gene X’ (Gene → Biological Process) the qualifier ‘exposure’ combines with a core concept of ‘Chemical X’ to express the composed concept ‘exposure to Chemical X’ (Chemical → Exposure Process) the qualifier ‘activity’ combines with a core concept of ‘PPARG’ to express the concept ‘activity of PPARG’ (Gene → function/activity) the qualifier ‘emergency Department Visit’ combines with a core concept of ‘Disease X’ to express the concept ‘Emergency Department visits for Disease X’ (Disease → Clinical Event) the qualifier ‘infection’ combines with a core concept of ‘Giardia’ to express the concept ‘Infection with Giardia’ (Taxon → Biological / Pathological Process) the qualifier ‘severity’ combines with a core concept of ‘DILI’ to express the concept ‘the severity level of DILI’ (Disease → (intrinsic) Characteristic/Quality) the qualifier ‘abundance’ combines with a core concept of ‘BRCA2’ to express the concept ‘abundance of BRCA2’ (Gene → (extrinsic) characteristic/quality)
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.
A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.
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.
The age stage of a clinical trial as determined by clinicaltrials.gov (adult, child, older adult)
connects a clinical trial to one or more conditions being studied in the trial
connects a clinical trial to one or more interventions being tested in the trial
holds between two entities where the occurrence, existence, or activity of one contributes to the occurrence or generation of the other
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’.
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
Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree.
the qualifier ‘increased’ combines with a core concept of ‘Gene X’ and an aspect of ‘expression’ to express the composed concept ‘increased expression of Gene X’ the qualifier ‘decreased’ combines with a core concept of ‘Protein X’ and an aspect of ‘abundance’ to express the composed concept ‘decreased abundance of Protein X’
A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources.
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’.
please see the ChemicalOrGeneOrGeneProductFormOrVariantEnum (below) for examples of 'form or variant qualifier' terms in the gene->chemical association space. the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘Mutated forms of Gene X’. the qualifier ‘late stage’ combines with a core concept of ‘Disease X’ to express the more specific concept ‘Late Stage forms of Disease X’ the qualifier ‘recombinant’ combines with a core concept of ‘FLT1 Gene’ to express the composed concept ‘Recombinant forms of the FLT1 gene’ the qualifier ‘chemical analog’ combines with a core concept of ‘Ditiocarb’ to express the composed concept ‘analog forms of Ditiocarb’
Co-occurrence of a certain allele of a genetic marker and the phenotype of interest in the same individuals at above-chance level
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.
A role is particular behaviour which a chemical entity may exhibit.
We expect primarily to use CHEBI chemical roles here; however, we are looking for a mapping between CHEBI And ATC codes to support this slot.
connects an entity to one or more (medical) devices
holds between food and one or more chemical entities composing it, irrespective of nutritional value (i.e. could also be a contaminant or additive)
connects an entity associated with one or more genes
connects an entity to one or more (medical) procedures
Connects an study to instances of its study result
Studies that produced information used as evidence to generate the knowledge expressed in an Association.
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.
For more information, please see: https://hgvs-nomenclature.org/stable/background/simple/ and examples: https://hgvs-nomenclature.org/stable/recommendations/summary/.
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).
A position in interbase coordinates. Interbase coordinates start at position 0 instead of position 1. This is applied to a sequence localization edge.
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)
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.
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
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.
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.
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.
Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion
holds between entities that overlap in their extents (materials or processes)
page number of source referenced for statement or publication
defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail).
holds between two entities that make physical contact as part of some interaction. does not imply a causal relationship.
A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.
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.
Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
The notion of a ‘Publication’ is considered broadly to include any document made available for public consumption. It covers journal issues, individual articles, and books - and also things like article pre-prints, white papers, patents, drug labels, web pages, protocol documents, etc.
A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.
holds between an entity and some other entity with similar features.
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.
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).
Note that source retrieval provenance concerns the mechanical retrieval and transformation of data between web accessible information systems. It does not trace the source of knowledge back to specific publications or data sets. And it is not concerned with the reasoning, inference or analysis activities that generate knowledge in the first place (this is instead covered by 'knowledge level' and 'agent type' properties).
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.
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.
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.
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.
Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion.
The segment of text from a document that supports the mined assertion.
holds between two entities with a temporal relationship
An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.
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.
a piece of writing on a particular topic presented as a stand-alone section of a larger publication
A phenotypic feature which is behavioral in nature.
An individual (human) organism that has a patient role in some clinical context.
cell line to disease or phenotypic feature association
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.
chemical affects biological entity association
Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)
chemical entity or protein or polypeptide
A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
chemical entity to entity association mixin
A chemical exposure is an intake of a particular chemical entity.
chemical or drug or treatment to disease or phenotypic feature association
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 a secondary undesirable effect.
The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual
Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects
disease or phenotypic feature to entity association mixin
A drug exposure is an intake of a particular drug.
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.
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.
Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs.
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.
TODO decide no how to model pathogenicity
a location that can be described in lat/long coordinates
A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex
A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.
describes a characteristic of an organismal entity.
An association between an organism taxon and another entity
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)
phenotypic feature to entity association mixin
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.
An association between a sequence feature and a nucleic acid entity it is localized to.
describes the severity of a phenotypic feature or disease
Attributes relating to a socioeconomic manifestation
A group of people banded together or treated as a group as participants in a research study.
A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures
An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)
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(?).
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 (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other.
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information.
Note that this property indicates the type of agent who produced a final statement of knowledge, which is often different from the agent oragents who produced information used as evidence to support generation of this knowledge. For example, if a human curator concludes that a particular gene variant causes a medical condition - based on their interpretation of information produced by computational modeling tools, automated data analysis pipelines, and robotic laboratory assay systems - the agent_type for this statement is 'manual agent' - despite all of the evidence being created by automated agents. But if any of these systems is programmed to generate knowledge statements directly and without human assistance, the statement would be attributed to an 'automated_agent'.
The allele configuration of a particular gene or variant required for the expression of a disease or phenotype in a specific patient or instance.
This edge property may be used by associations between Genes or SequenceVariants and DiseaseOrPhenotypicFeatures to provide the inheritance pattern and genetic context of the relationship. Terms from the HP mode of inheritance sub-ontology (HP:0000005) should be used in the value of this slot. This slot differs from the predicate "has_mode_of_inheritance", in that the predicate is used to link a disease or phenotype with its general inheritance pattern (how it is typically transmitted from one generation to the next, regardless of the specific genetic variant that is present in an individual or instance).
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.
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.
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).
subject: NCBIGene:2064 # HER2 subject_aspect: Amplification predicate: associated with response to object: CHEBI:10035 # Trastuzumab response_type_qualifier: therapeutic_sensitivity response_direction_qualifer: increased response_target_qualifier: human patient disease_context_qualifier: MONDO:0007254 # breast cancer subject: MONDO:0007254 predicate: associated with response to qualified_predicate: associated with object: CHEBI:10035 # Trastuzumab response_context_qualifier: therapeutic_sensitivity
Text indicating the availability type of the chemical entity.
Text describing black box warnings for use of chemicals as therapeutics.
Tern indicating the chirality of the chemical entity.
Text describing warnings for use of chemicals as therapeutics.
Flag indicating if a chemical entity is a natural product.
Flag indicating if a drug is a prodrug that is active only after being metabolized by the body.
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
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.
The chi-squared statistic measures how much observed data deviate from expected values under the null hypothesis.
The age range of a clinical trial as determined by clinicaltrials.gov
The brief title of a clinical trial as determined by clinicaltrials.gov
The enrollment number of a clinical trial as determined by clinicaltrials.gov
The enrollment type of a clinical trial as determined by clinicaltrials.gov (actual, anticipated, or estimated)
The intervention model of a clinical trial as determined by clinicaltrials.gov. The most common values are SINGLE_GROUP, PARALLEL, CROSSOVER, FACTORIAL, and (null).
The overall status of a clinical trial as determined by clinicaltrials.gov
The phase that a clinical trials study represents
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).
The start date of a clinical trial as determined by clinicaltrials.gov
Records whether the clinical trials are testing the intervention.
A boolean flag indicating that an entity is no longer considered current or valid.
a human-readable description of an entity
An agglomeration of drug regulatory status worldwide. Not specific to FDA.
A boolean flag indicating whether a clinical trial finding should be elevated to a prediction.
The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.
Additional conditions impacting an exposure event.
Magnitude of an exposure event, e.g, parts per million of a toxic chemical.
location in which gene or protein expression takes place. May be cell, tissue, or organ.
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.
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)
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.
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
a long-form human readable name for a thing
The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens.
The biological sex of the entity (e.g., male or female) regarding a case description from a phenopacket
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.
connects an entity with one or more gene or gene products
equivalent to has quotient multiplied by 100
Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
holds between two biological entities that have common evolutionary origin
typically used to describe homology relationships between genes or gene products
The human readable scientific name for the taxon of the entity.
Information content (IC) value for a term, primarily from Automats.
Connects genetic inheritance to a disease or phenotypic feature, as a node property.
holds between any two entities that directly or indirectly interact with each other
please use a more specific child predicate of interacts with, either physically interacts with or genetically interacts with.
indicates whether a molecular entity is a metabolite
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.
The notion of a 'level' of knowledge can in one sense relate to the strength of a statement - i.e. how confident we are that it says something true about our domain of discourse. Here, we can generally consider Assertions to be stronger than Entailments to be stronger than Predictions. But in another sense, 'level' of knowledge can refer to the scope or specificity of what a statement expresses - on a spectrum from context-specific results of a data analysis, to generalized assertions of knowledge or fact. Here, Statistical Associations and Observations represent more foundational statements that are only slightly removed from the data on which they are based (the former reporting the direct results of an analysis in terms of correlations between variables in the data, and the latter describing phenomena that were observed/reported to have occurred).
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.
The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.
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.
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.
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.
Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease
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.
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.
used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.
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.
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.
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.
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.
For example: a single ChemicalToGene Edge originally curated by ClinicalTrials.org, is aggregated by ChEMBL, then incorporated into the MolePro KP, then sent via TRAPI message to the ARAGORN ARA, and finally sent to the NCATS ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> MolePro --retrieved_from--> ChEMBL --retrieved_from--> ClinicalTrials.gov The "primary knowledge source" for this edge is "infores:clinical-trials-gov". "infores:chembl" and "infores:molecular_data_provider" are listed in the "aggregator knowledge source" property.
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.
the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)
the side of a reaction being modeled (ie: left or right)
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.
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.
a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material, etc.)
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).
the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.
The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).
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).
Predicates in this hierarchy are used in practice when a source reports performance of a study, but there is not sufficient evidence or demonstrated efficacy against the condition to warrant creating a ‘treats’ assertion edge. Note however that a 'studied to treat' edge may be used as evidence to support creation of a separate 'treats' prediction edge.
Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene
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.
The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result.
The document year (typically the publication year) for the supporting document used in a Text Mining Result.
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.
A property that indicates the taxonomic classification of an entity. Values for this slot should be from the NCBITaxon ontology.
Note there is also a predicate 'in taxon' that can be used to instantiate an edge between a taxon entity and a thing with taxon entity. This is an acceptable practice for KG construction, but for many applications it is more convenient to use this property slot to directly annotate the taxon on the entity itself.
The total number of patients or participants within a sample population.
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.
date on which an entity was updated. This can be applied to nodes or edges
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.
Activity or behavior of any independent integral living, organization or mechanical actor in the world
anatomical entity to anatomical entity association
chemical entity to chemical entity association
A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another.
A role played by the molecular entity or part thereof within a chemical context.
A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
A device or substance used to help diagnose disease or injury
entity to feature or disease qualifiers mixin
Qualifiers for entity to disease or phenotype associations.
Class of evidence that supports an association
Numbers that identify specific drug applications. Each drug can have multiple approval numbers (for example, as seen with ranitidine having both ANADA200536 and ANDA200536).
any grouping of multiple genes or gene products related by common descent
A union of gene family or gene loci or gene products, useful to define the association between a gene or gene product or gene family and some other general class of entity (e.g. biological process or anatomical entity)
gene to disease or phenotypic feature association
NCIT:R176 refers to the inverse relationship
for use in describing the affect that the loss of function of a gene can have on exacerbating or ameliorating a symptom/phenotype
if the relationship of the statement using this predicate is statistical in nature, please use `associated with likelihood` or one of its children.
macromolecular machine to entity association mixin
an association which has a macromolecular machine mixin as a subject
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]
organism taxon to organism taxon association
A relationship between two organism taxon nodes
A pathological (abnormal) structure or process.
A series of actions conducted in a certain order or manner
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
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<.
Holds between two entities where the presence or application of one alters the chance that the other will come to be.
- This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)
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.
holds between two entities that are co-located in the same aggregate object, process, or spatio-temporal region
A list of associations between two entities.
holds between two entities that have strictly equivalent meanings, with a high degree of confidence
connects an association to an instance of supporting evidence
connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
A list of entities that can be a subject or object of an association
connects an association to qualifiers that modify or qualify the meaning of that association
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.
a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.
An abstract association for use where the case is the subject
an item that holds distribution level information about a dataset.
an item that holds summary level information about a dataset.
This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms.
abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.
An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576
A stage of development or growth of an organism, including post-natal adult stages
Any entity or process that exists at the level of the whole planet
A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value
For example, a particular exon is part of a particular transcript or gene
Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
This is a grouping for predicates relating entities to their associated contributors realizing them
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.
holds between parts and wholes (material entities or processes)
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.
Attributes relating to a clinical manifestation
an item that holds version level information about a dataset.
entity to disease or phenotypic feature association mixin
Qualifier for frequency type associations
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.
any grouping of multiple genes or gene products
This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease
The age group in which (disease) symptom manifestations appear.
This class is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. This should be the primary use case for this class.
An entity that has material reality (a.k.a. physical essence).
a detailed investigation and/or analysis
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.
These 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). Note also that this predicate can be used in the absence of a direct statistical analysis, if there is other evidence suggesting that a correlation is likely to exist.
date on which an entity was created. This can be applied to nodes or edges
A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score.
A score defined by DGIdb that is used to rank interaction record results in DGIdb, which combines their evidence score (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity score. See https://dgidb.org/about/overview/interaction-score.
A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
holds between a process and a physical entity, where the physical entity executes the process
connects an attribute to a class that describes it
holds between wholes and their parts (material entities or processes)
total number of things in a particular reference set
An IRI for an entity. This is determined by the id using expansion rules.
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 of a newspaper, a scientific journal or magazine for reference purpose
if set to true, then the association is negated i.e. is not true
The number of cases in a study or clinical trial, primarily used in conversion of drug approval data.
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).
holds between a continuant and a process, where the continuant is somehow involved in the process
a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.
CURIE identifier of a broader publication context within which the publication may be placed, e.g. a specified book or journal.
A measurable quantity for the object of the association
A relationship that is asserted between two named things
a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.
stage during which gene or protein expression of takes place.
subject of treatment application or study for treatment by
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.
Note that these concrete 'supporting study metadata' slots are used only when a more normalized model that leverages the 'supporting studdies' slot and 'Study' class to link to and describe the Study itself are not possible or preferred, such that this study metadata must be captured directly on the edge.
This is an abstract slot that groups a set of concrete slots used to directly attach to an association information about a study that produced evidence used to generate the knowledge expressed in the edge.
A chemical mixture is a chemical entity composed of two or more molecular entities.
The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules.
The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc.
A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.
An execution of a molecular function carried out by a gene product or macromolecular complex.
A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes
describes an entity of which the state or quality is affected by another existing entity.
Describes an entity that has an effect on the state or quality of another existing entity.
Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or may not come into existence.
number of things with a particular property
holds between a process and a continuant, where the continuant is an output of the process
holds between a process and a continuant, where the continuant is somehow involved in the process
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).
This predicate is helpful both as a grouping predicate to aid in searching for broader senses of treating a condition, and as a catch-all for representing sources that are not clear about the sense of treats that is being reported. For example, text-mined statements concerning treatments for disease are based on sentences that can report treatment in any of these different senses and thus require a broader predicate such as this to safely report statement semantics.
an item that refers to a collection of data from a data source.
holds between a process and a continuant, where the continuant is an input into the process
gene product sequence variation encoded by gene mutant
holds between a sequence variant and a nucleic acid entity
Represents a relationship held between terminology components that describe the conceptual model of a domain.
Alternate human-readable names for a thing
A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
The CHEBI ID represents a role rather than a substance
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
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.
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
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).
connects a genomic feature to its sequence
a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.
This is in Biolink to support HP ontology annotations which use "onset" (with terms from HP) as an annotation on a disease to phenotypic feature association. Please only use it for this purpose. If the intent is to describe the onset of a disease in the context of a treatment, use object_aspect_qualifier and object_direction_qualifier to capture "delayed onset" or "exacerbated onset" slot.
volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication
entity to phenotypic feature association mixin
An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes.
A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment.
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.
mixin class for any association whose object (target node) is a disease
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.
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.
The data/metadata included in a Study Result object are typically a subset of data from a larger study data set, that are selected by a curator because they may be useful as evidence for deriving knowledge about a specific focus of the study. The notion of a 'study' here is defined broadly to include any research activity at any scale that is aimed at generating knowledge or hypotheses. This may include a single assay or computational analyses, or a larger scale clinical trial or experimental research investigation.
A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities
An entity that has the role of being studied in an investigation, study, or experiment
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).
Anatomical context values can be any term from UBERON. For example, the context qualifier ‘cerebral cortext’ combines with a core concept of ‘neuron’ to express the composed concept ‘neuron in the cerebral cortext’. The species_context_qualifier applies taxonomic context, e.g. species-specific molecular activity. Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs.
A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')
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).
defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).
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).
defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).
Root Biolink Model class for all things and informational relationships, real or imagined.
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.
person, group, organization or project that provides a piece of information (i.e. a knowledge association)
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.
Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
A human-readable name for an attribute or entity.
A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
grouping slot for all qualifiers on an edge. useful for testing compliance with association classes
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).
Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
A molecular entity is a chemical entity composed of individual or covalently bonded atoms.
a piece of information that typically describes some topic of discourse or is used as support.
A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.
Ontology CURIEs are expected as values here, the examples below are intended to help clarify the content of the CURIEs.
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).
One or more causally connected executions of molecular functions
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.
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
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.
Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP).
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
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).
A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.
This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)
A subcellular location, cell type or gross anatomical part
A chemical entity is a physical entity that pertains to chemistry or biochemistry.
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).
Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.
to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)
A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.
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).
A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another
Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature.
a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc
any slot that relates an association to another entity
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.
A grouping for any property that holds between a node and a value
A typed association between two entities, supported by evidence
This is roughly the model used by biolink and ontobio at the moment
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.
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
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}
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.
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.