| Annotation |
Biolink Model root class for entity annotations. |
| QuantityValue |
A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value |
| AnnotationCollection |
None |
| ChemicalEntityOrGeneOrGeneProduct |
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. |
| Entity |
Root Biolink Model class for all things and informational relationships, real or imagined. |
| Checksum |
Checksum values associated with digital entities. |
| NamedThing |
a databased entity or concept/class |
| Abbreviation |
Maps an abbreviation string to its decoded meaning. Optionally the abbreviation can be link to one or more entities it denotes. |
| Activity |
An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. |
| Attribute |
A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material. |
| BiologicalEntity |
None |
| Gene |
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. |
| GeneAnnotation |
An annotation describing the location, boundaries, and functions of individual genes within a genome annotation. |
| Genome |
A genome is the sum of genetic material within a cell or virion. |
| GenomeAnnotation |
Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types. |
| CellSpecimen |
( defined as in BERS) |
| CellTypeSet |
A grouping of cell type taxons. The grouping may represent a specific taxonomic level (rank) or cell type neighborhood. |
| CellTypeTaxon |
A cell type taxon is a node in a taxonomy. Taxons represents a unit of cell type classification and is defined by a set of clusters. Taxons may be organized into a heirarchy and levels. Taxons at higher levels represents broader cell type classes and partitioned into more specific types at lower levels. Additionally, taxons may be organized into neighborhoods or related groups. |
| CellTypeTaxonomy |
A cell type taxonomy is a systematic classification of cell types and their heirarchical relationships and groupings. A taxonomy may include concepts such as heirarchical taxonomic levels or (potentially overlapping) neighborhoods. |
| Cluster |
One specific cluster from the set of clusters determined by a clustering process. A cluster is defined by set of observations which has been grouped together based on similarities or patterns. |
| ClusterSet |
The output of a clustering process where input observations are organized or classified into a set of clusters based on similarities or patterns. |
| ColorPalette |
A schematic set of display colors that can be applied to individual components of the associated entity set (for example, a taxonomy). |
| DisplayColor |
One element of a color palette representing the association between a color and entity, |
| GenomeAssembly |
Genome assembly to contain version and label information |
| InformationContentEntity |
a piece of information that typically describes some topic of discourse or is used as support. |
| Dataset |
an item that refers to a collection of data from a data source. |
| MatrixFile |
A digital file containing the representation of full or partial data matrix. |
| ObservationMatrix |
A matrix (potentially virtual) of observations. Each row represents a specific observation or measurements on specific sample (such as a cell) over a set of variables or features. Each column represents the set of measurements (such as gene expression) of a specific variable (such as gene) over all samples. |
| ObservationRow |
One specific row of the observation matrix representing a set of measurements preformed on a sample over a set of variables or features. |
| OrganismTaxon |
A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies. |
| ParcellationTerm |
( defined in AnSRS ) |
| PhysicalEntity |
An entity that has material reality (a.k.a. physical essence). |
| MaterialSample |
A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] |
| Procedure |
A series of actions conducted in a certain order or manner |
| CellTypeTaxonomyCreationProcess |
The process of organizing cells or clusters into a systematic classification of cell types and their heirarchical relationships and groupings. |
| ClusteringProcess |
The process of organizing and classifying observations into groups or clusters based on similarities or patterns. |
| ObservationMatrixCreationProcess |
The process of aggregating data to create an observation matrix (potentially virtual) for the purpose of dissemination or performing an analysis (such as clustering). |
| GenomicEntity |
None |
| MacromolecularMachineMixin |
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. |
| GeneOrGeneProduct |
A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another |
| OntologyClass |
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. |
| TaxonomicRank |
A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) |
| PhysicalEssenceOrOccurrent |
Either a physical or processual entity. |
| Occurrent |
A processual entity. |
| ActivityAndBehavior |
Activity or behavior of any independent integral living, organization or mechanical actor in the world |
| PhysicalEssence |
Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge. |
| ProvActivity |
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. |
| ProvEntity |
An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary. |
| SubjectOfInvestigation |
An entity that has the role of being studied in an investigation, study, or experiment |
| ThingWithTaxon |
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 |