| 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 |
Represents a single gene. Includes metadata about the gene, such as its molecular type and the genome annotation it was referenced from. |
| Genome |
A genome is the sum of genetic material within a cell or virion. |
| GenomeAnnotation |
Represents a genome annotation. Includes metadata about the genome, such as its version and reference assembly. |
| 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 |
Represents a genome assembly. A genome assembly is a computational representation of a genome sequence. |
| 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 |
A parcellation term is an individual term within a specific parcellation terminology describing a single anatomical entity by a persistent identifier, name, symbol and description. A parcellation term is a unique and exclusive member of a versioned release parcellation terminology. Although term identifiers must be unique within the context of one versioned release of a parcellation terminology, they can be reused in different parcellation terminology versions enabling the representation of terminology updates and modifications over time. |
| ParcellationTermSet |
A parcellation term set is the set of parcellation terms within a specific parcellation terminology. A parcellation term set belongs to one and only one parcellation terminology and each parcellation term in a parcellation terminology belongs to one and only one term set. If the parcellation terminology is a taxonomy, parcellation term sets can be used to represent taxonomic ranks. For consistency, if the terminology does not have the notion of taxonomic ranks, all terms are grouped into a single parcellation term set. |
| 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). |
| VersionedNamedThing |
An iteration of the biolink:NamedThing class that stores metadata about the object's version. |
| AnatomicalAnnotationSet |
An anatomical annotation set is a versioned release of a set of anatomical annotations anchored in the same anatomical space that divides the space into distinct segments following some annotation criteria or parcellation scheme. For example, the anatomical annotation set of 3D image based reference atlases (e.g. Allen Mouse CCF) can be expressed as a set of label indices of single multi-valued image annotations or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499) |
| AnatomicalSpace |
An anatomical space is versioned release of a mathematical space with a defined mapping between the anatomical axes and the mathematical axes. An anatomical space may be defined by a reference image chosen as the biological reference for an anatomical structure of interest derived from a single or multiple specimens (ref: ILX:0777106, RRID:SCR_023499) |
| ImageDataset |
An image dataset is versioned release of a multidimensional regular grid of measurements and metadata required for a morphological representation of an entity such as an anatomical structure (ref: OBI_0003327, RRID:SCR_006266) |
| ParcellationAtlas |
A parcellation atlas is a versioned release reference used to guide experiments or deal with the spatial relationship between objects or the location of objects within the context of some anatomical structure. An atlas is minimally defined by a notion of space (either implicit or explicit) and an annotation set. Reference atlases usually have additional parts that make them more useful in certain situations, such as a well defined coordinate system, delineations indicating the boundaries of various regions or cell populations, landmarks, and labels and names to make it easier to communicate about well known and useful locations (ref: ILX:0777109, RRID:SCR_023499). |
| ParcellationColorScheme |
A parcellation color scheme is a versioned release color palette that can be used to visualize a parcellation terminology or its related parcellation annotation. A parcellation terminology may have zero or more parcellation color schemes and each color scheme is in context of a specific parcellation terminology, where each parcellation term is assigned a hex color value. A parcellation color scheme is defined as a part of one and only one parcellation terminology. |
| ParcellationTerminology |
A parcellation terminology is a versioned release set of terms that can be used to label annotations in an atlas, providing human readability and context and allowing communication about brain locations and structural properties. Typically, a terminology is a set of descriptive anatomical terms following a specific naming convention and/or approach to organization scheme. The terminology may be a flat list of controlled vocabulary, a taxonomy and partonomy, or an ontology (ref: ILX:0777107, RRID:SCR_023499) |
| 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) |
| ParcellationAnnotation |
A parcellation annotation defines a specific segment of an anatomical space denoted by an internal identifier and is a unique and exclusive member of a versioned release anatomical annotation set. For example, in the case where the anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF), a specific annotation corresponds to a specific label index (internal identifier) in the mask. |
| ParcellationAnnotationTermMap |
The parcellation annotation term map table defines the relationship between parcellation annotations and parcellation terms. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to. A parcellation term can be spatially parameterized by the union of one or more parcellation annotations within a versioned release of an anatomical annotation set. For example, annotations defining individual cortical layers in cortical region R (R1, R2/3, R4, etc) can be combined to define the parent region R. |
| ParcellationColorAssignment |
The parcellation color assignment associates hex color value to a parcellation term within a versioned release of a color scheme. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to. |
| 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 |