a concept or class in an ontology, vocabulary or thesaurus
an ontology class that describes a functional aspect of a gene, gene prodoct or complex
A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities
An individual organism that has a patient role in some clinical context.
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.
A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes
a piece of information that typically describes some piece of biology or is used as support.
Class of evidence that supports an association
Any published piece of information. Can refer to a whole publication, or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web as well as journals.
A gene, gene product, small molecule or macromolecule (including protein complex)
May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part
A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
Any intermediate or product resulting from metabolism. Includes primary and secondary metabolites.
A subcellular location, cell type or gross anatomical part
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
Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
A genome is the sum of genetic material within a cell or virion.
An RNA synthesized on a DNA or RNA template by an RNA polymerase
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
A union of gene, 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.
a union of genes or gene products. Frequently an identifier for one will be used as proxy for another
The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules
A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA
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.
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
any grouping of multiple genes or gene products related by common descent
An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
A set of zero or more Alleles on a single instance of a Sequence[VMC]
An allele that varies in its sequence from what is considered the reference allele at that locus.
A drug exposure is an intake of a particular chemical substance
A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures'
a location that can be described in lat/long coordinates
a location that can be described in lat/long coordinates, for a particular time
Either an individual molecular activity, or a collection of causally connected molecular activities
An execution of a molecular function carried out by a gene product or macromolecular complex.
Activity or behavior of any independent integral living, organization or mechanical actor in the world
A series of actions conducted in a certain order or manner
a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question
One or more causally connected executions of molecular functions
Ensembl ID for gene, protein or transcript
connects a thing to a class representing a taxon
Refseq ID for gene, protein or transcript
Another drug that is known to interact with this drug in a way that impacts the effect of this drug or causes a risk to the patient. Note: disease interactions are typically captured as contraindications.
Genes or Proteins that are targeted by chemicals
GO molecular function enabled by the gene/protein.
GO biological process this gene/protein is involved in.
GO cellular component this gene/protein is involved in.
An interaction between a biological entity and a pathway
An interaction between a biological entity and a wikipathway
An interaction between a biological entity and a reactome pathway
holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it is used to treat
Specifying a cause of something in general. e.g in medicine , one of the causative agent(s) that are most directly responsible for the pathophysiologic process that eventually results in the occurrence.
holds between a therapeutic procedure or chemical substance and a disease or phenotypic feature that it might cause side effect
holds between a disease or phenotypic feature and a therapeutic process or chemical substance that is used to treat the condition
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.
holds between two molecular entities where the action or effect of one changes the amount of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the amount of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the amount of the other within a system of interest
holds between two molecular entities where the action or effect of one changes the activity of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the activity of the other within a system of interest
holds between two molecular entities where the action or effect of one is increased by the activity of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the activity of the other within a system of interest
holds between two molecular entities where the action or effect of one is decreased by the activity of the other within a system of interest
holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest
holds between two molecular entities where the action or effect of one changes the rate or quality of folding of the other
holds between two molecular entities where the action or effect of one increases the rate or quality of folding of the other
holds between two molecular entities where the action or effect of one decreases the rate or quality of folding of the other
holds between two molecular entities where the action or effect of one changes the localization of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the proper localization of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the proper localization of the other within a system of interest
holds between two molecular entities where the action or effect of one impacts the metabolic processing of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest
holds between two molecular entities where the action or effect of one leads changes in the molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
holds between two molecular entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
holds between two molecular entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)
holds between two molecular entities where the action or effect of one impacts the rate of chemical synthesis of the other
holds between two molecular entities where the action or effect of one increases the rate of chemical synthesis of the other
holds between two molecular entities where the action or effect of one decreases the rate of chemical synthesis of the other
holds between two molecular entities where the action or effect of one impacts the rate of degradation of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the rate of degradation of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the rate of degradation of the other within a system of interest
holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest
holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest
holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest
holds between two molecular entities where the action or effect of one impacts the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
holds between two molecular entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
holds between two molecular entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine, biological or pathological process) to the other
holds between a molecular entity and an mRNA where the action or effect of the molecular entity impacts the splicing of the mRNA
holds between a molecular entity and an mRNA where the action or effect of the molecular entity increases the proper splicing of the mRNA
holds between a molecular entity and an mRNA where the action or effect of the molecular entity decreases the proper splicing of the mRNA
holds between two molecular entities where the action or effect of one impacts the stability of the other within a system of interest
holds between two molecular entities where the action or effect of one increases the stability of the other within a system of interest
holds between two molecular entities where the action or effect of one decreases the stability of the other within a system of interest
holds between two molecular entities where the action or effect of one impacts the rate of transport of the other across some boundary in a system of interest
holds between two molecular entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest
holds between two molecular entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest
holds between two molecular entities where the action or effect of one impacts the rate of secretion of the other out of a cell, gland, or organ
holds between two molecular entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ
holds between two molecular entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ
holds between two molecular entities where the action or effect of one impacts the rate of uptake of the other into of a cell, gland, or organ
holds between two molecular entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ
holds between two molecular entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ
holds between a gene and a transcribed and/or translated product generated from it
holds between a gene and a gene transcript
holds between a gene or gene product and a protein structure
holds between two genes or gene products that are part of in the same biological pathway
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 genes or gene products that are expressed in the same cell type or population
holds between a gene and a disease or phenotypic feature that the gene or its alleles/products may influence, contribute to, or correlate with
holds between a disease or phenotypic feature and a measurable molecular entity that is used as an indicator of the presence or state of the disease or feature.
holds between a measurable molecular 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 gene or gene product and an anatomical entity in which it is expressed
holds between an anatomical entity and gene or gene product that is expressed there
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).
holds between two processes, where one completes before the other begins
holds between two classes where the domain class is a specialization of the range class