| 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 |
| 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. |
| DissectionRoiPolygon |
A polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning. |
| NamedThing |
a databased entity or concept/class |
| 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. |
| Genome |
A genome is the sum of genetic material within a cell or virion. |
| 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. |
| 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. |
| PhysicalEntity |
An entity that has material reality (a.k.a. physical essence). |
| Donor |
A person or organism that is the source of a biological sample for scientific study. Many biological samples are generated from a single donor. |
| 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] |
| AmplifiedCdna |
A collection of cDNA molecules derived and amplified from an input barcoded cell sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods. |
| BarcodedCellSample |
A collection of molecularly barcoded cells. Input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples. The sequences of the molecular barcodes are revealed during alignment of the resulting fastq files for the barcoded cell sample. The barcoded cell sample name and the cell level molecular barcode together uniquely identify a single cell. |
| BrainSlab |
A thick flat piece of brain tissue obtained by slicing a whole brain, brain hemisphere or subdivision with a blade at regular interval. When multiple brain slabs are obtained from the slicing process, an ordinal is assigned to provide information about the relative positioning of the slabs. |
| DissociatedCellSample |
A collection of dissociated cells or nuclei derived from dissociation of a tissue sample. |
| EnrichedCellSample |
A collection of enriched cells or nuclei after enrichment process, usually via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied to dissociated cell sample. |
| Library |
A collection of fragmented and barcode-indexed DNA molecules for sequencing. An index or barcode is typically introduced to enable identification of library origin to allow libraries to be pooled together for sequencing. |
| LibraryAliquot |
One library in the library pool. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. The resulting demultiplexed fastq files will include the library aliquot name. A given library may produce multiple library aliquots, which is done in the case of resequencing. Each library aliquot will produce a set of fastq files. |
| LibraryPool |
A library pool is made up of library aliquots from multiple libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. |
| TissueSample |
The final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an region of interest polygon (ROI) associated with it. |
| Procedure |
A series of actions conducted in a certain order or manner |
| CdnaAmplification |
The process of creating a collection of cDNA molecules derived and amplified from an input barcoded cell sample. A large amount of cDNA is needed to have accurate and reliable sequencing detection of gene expression. This process generates multiple copies of each mRNA transcript (expressed gene) within each cell while retaining the cell's unique barcode from the barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods. |
| CellBarcoding |
The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples. |
| CellDissociation |
The process of generating dissociated cells from an input tissue sample. This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell dissociation samples at the cell barcoding step. |
| CellEnrichment |
The process of enriching a dissociated cell sample by including or excluding cells of different types based on an enrichment plan using techniques such as fluorescence-activated cell sorting (FACS). This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell enriched samples at the cell barcoding step. |
| DissectionRoiDelineation |
The process of outlining a region of interest on a brain slab image to guide the dissection and generation of a tissue sample. |
| EnrichedCellSampleSplitting |
The process of splitting an enriched cell sample into several portions. Each portion may be used by the same or different groups for different scientific studies. |
| LibraryConstruction |
The process of constructing a library from input material (such as amplified cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented into smaller pieces appropriate for sequencing and at the same time a library index barcode is incorporated to enable identification of library origin, allowing libraries to be pooled together for sequencing. |
| LibraryPooling |
The process of constructing of a libray pool by combining library aliquots from a set of input libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. |
| TissueDissection |
The process of dissecting a tissue sample from a brain slab guided by a dissection region of interest (ROI) delineation. |
| 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 |