Library Generation Schema
The Library Generation schema is designed to represent types and relationships of samples and digital data assets generated during processes that generate multimodal genomic data.
URI: https://identifiers.org/brain-bican/library-generation-schema
Name: library-generation-schema
Classes
| Class | Description |
|---|---|
| Annotation | Biolink Model root class for entity annotations |
| QuantityValue | A value of an attribute that is quantitative and measurable, expressed as a c... |
| ChemicalEntityOrGeneOrGeneProduct | A union of chemical entities and children, and gene or gene product |
| Entity | Root Biolink Model class for all things and informational relationships, real... |
| Checksum | Checksum values associated with digital entities |
| DissectionRoiPolygon | A polygon annotated on a brain slab image delineating a region of interest (R... |
| NamedThing | a databased entity or concept/class |
| Activity | An activity is something that occurs over a period of time and acts upon or w... |
| Attribute | A property or characteristic of an entity |
| BiologicalEntity | |
| Gene | A region (or regions) that includes all of the sequence elements necessary to... |
| 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... |
| Dataset | an item that refers to a collection of data from a data source |
| DigitalAsset | |
| StudyResult | A collection of data items from a study that are about a particular study sub... |
| RelativeFrequencyAnalysisResult | A result of a relative frequency analysis |
| OrganismTaxon | A classification of a set of organisms |
| PhysicalEntity | An entity that has material reality (a |
| Donor | A person or organism that is the source of a biological sample for scientific... |
| MaterialSample | A sample is a limited quantity of something (e |
| AmplifiedCdna | A collection of cDNA molecules derived and amplified from an input barcoded c... |
| BarcodedCellSample | A collection of molecularly barcoded cells |
| BrainSlab | A thick flat piece of brain tissue obtained by slicing a whole brain, brain h... |
| DissociatedCellSample | A collection of dissociated cells or nuclei derived from dissociation of a ti... |
| EnrichedCellSample | A collection of enriched cells or nuclei after enrichment process, usually vi... |
| Library | A collection of fragmented and barcode-indexed DNA molecules for sequencing |
| LibraryAliquot | One library in the library pool |
| LibraryPool | A library pool is made up of library aliquots from multiple libraries |
| TissueSample | The final intact piece of tissue before cell or nuclei prep |
| 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 ... |
| CellBarcoding | The process of adding a molecular barcode to individual cells in a sample |
| CellDissociation | The process of generating dissociated cells from an input tissue sample |
| CellEnrichment | The process of enriching a dissociated cell sample by including or excluding ... |
| DissectionRoiDelineation | The process of outlining a region of interest on a brain slab image to guide ... |
| EnrichedCellSampleSplitting | The process of splitting an enriched cell sample into several portions |
| LibraryConstruction | The process of constructing a library from input material (such as amplified ... |
| LibraryPooling | The process of constructing of a libray pool by combining library aliquots fr... |
| TissueDissection | The process of dissecting a tissue sample from a brain slab guided by a disse... |
| VersionedNamedThing | An iteration of the biolink:NamedThing class that stores metadata about the o... |
| GenomicEntity | |
| MacromolecularMachineMixin | A union of gene locus, gene product, and macromolecular complex |
| GeneOrGeneProduct | A union of gene loci or gene products |
| OntologyClass | a concept or class in an ontology, vocabulary or thesaurus |
| TaxonomicRank | A descriptor for the rank within a taxonomic classification |
| PhysicalEssenceOrOccurrent | Either a physical or processual entity |
| Occurrent | A processual entity |
| ActivityAndBehavior | Activity or behavior of any independent integral living, organization or mech... |
| PhysicalEssence | Semantic mixin concept |
| ProvActivity | An activity is something that occurs over a period of time and acts upon or w... |
| ProvEntity | An entity is a physical, digital, conceptual, or other kind of thing with som... |
| SubjectOfInvestigation | An entity that has the role of being studied in an investigation, study, or e... |
| ThingWithTaxon | A mixin that can be used on any entity that can be taxonomically classified |
Slots
| Slot | Description |
|---|---|
| age_at_death_description | Text description of the age of death following typical scientific convention ... |
| age_at_death_reference_point | The reference point for an age interval; for example, birth or conception |
| age_at_death_unit | The unit used for representing the donor age from the reference point |
| age_at_death_value | The value representing the donor age from the reference point |
| amplified_cDNA_quantity_ng | Amount of cDNA produced after cDNA amplification measured in nanograms |
| amplified_cDNA_result | Pass or Fail result based on qualitative assessment of cDNA yield and size |
| annotates | The brain slab that was annotated by the delineation process |
| attribute_name | The human-readable 'attribute name' can be set to a string which reflects its... |
| average_size_bp | Average size of the library in terms of base pairs |
| biological_sex | Biological sex of donor at birth |
| category | Name of the high level ontology class in which this entity is categorized |
| cDNA_amplification_process_date | Date of cDNA amplification |
| cDNA_amplification_set | cDNA amplification set, containing multiple amplified_cDNA_names that were pr... |
| cell_barcoding_method | Standardized nomenclature to describe the general barcoding method used |
| cell_barcoding_process_date | Date of cell barcoding process |
| cell_dissociation_process_date | Date of cell dissociation process |
| cell_enrichment_process_date | Date of cell enrichment process |
| cell_prep_type | The type of cell preparation |
| checksum_algorithm | The type of cryptographic hash function used to calculate the checksum value |
| chembl_chirality | Tern indicating the chirality of the chemical entity |
| chembl_drug_warning | Text describing warnings for use of chemicals as therapeutics |
| chembl_prodrug | Flag indicating if a drug is a prodrug that is active only after being metabo... |
| concentration_nm | Concentration of library in terms of nM (nMol/L) |
| content_url | |
| creation_date | date on which an entity was created |
| data_type | The type of data in the file |
| deprecated | A boolean flag indicating that an entity is no longer considered current or v... |
| description | a human-readable description of an entity |
| digest | Stores checksum information |
| dissection_was_guided_by | The dissection ROI polygon that was used to guide the dissection |
| dissociated_cell_oligo_name | Name of cell source oligo used in cell plexing |
| enriched_cell_oligo_name | Name of cell source oligo used in cell plexing |
| enrichment_population | Actual percentage of cells as a result of using set of fluorescent marker lab... |
| equivalent_identifiers | A set of identifiers that are considered equivalent to the primary identifier... |
| format | |
| full_name | a long-form human readable name for a thing |
| has_attribute | connects any entity to an attribute |
| has_attribute_type | connects an attribute to a class that describes it |
| has_biological_sequence | connects a genomic feature to its sequence |
| has_numeric_value | connects a quantity value to a number |
| has_qualitative_value | connects an attribute to a value |
| has_quantitative_value | connects an attribute to a value |
| has_taxonomic_rank | |
| has_unit | connects a quantity value to a unit |
| histone_modification_marker | Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used i... |
| id | A unique identifier for an entity |
| in_taxon | connects an entity to its taxonomic classification |
| in_taxon_label | The human readable scientific name for the taxon of the entity |
| information_content | Information content (IC) value for a term, primarily from Automats |
| input_quantity | Number of enriched or dissociated cells/nuclei going into the barcoding proce... |
| input_quantity_ng | Amount of cDNA going into library construction in nanograms |
| iri | An IRI for an entity |
| library_construction_method | Standardized nomenclature to describe the specific library method used |
| library_construction_process_date | Date of library construction |
| library_construction_set | Library set, containing multiple library_names that were processed at the sam... |
| library_quantity_ng | Amount of library generated in terms of nanograms |
| library_result | Pass or Fail result based on qualitative assessment of library yield and size |
| license | |
| macromolecular_machine_mixin_name | genes are typically designated by a short symbol and a full name |
| name | A human-readable name for an attribute or entity |
| named_thing_category | Name of the high level ontology class in which this entity is categorized |
| node_property | A grouping for any property that holds between a node and a value |
| number_of_expected_cells | Expected number of cells/nuclei of a barcoded_cell_sample that will be barcod... |
| organism_taxon_has_taxonomic_rank | |
| pcr_cycles | Number of PCR cycles used during cDNA amplification for this cDNA |
| percent_cdna_longer_than_400bp | QC metric to measure mRNA degradation of cDNA |
| port_well | Specific position of the loaded port of the 10x chip |
| process_date | Date of library pooling process |
| provided_by | The value in this node property represents the knowledge provider that create... |
| quantity_fmol | Amount of library generated in terms of femtomoles |
| r1_r2_index | Name of the pair of library indexes used for sequencing |
| related_to | A relationship that is asserted between two named things |
| related_to_at_instance_level | Represents a relationship held between two instances of a data classes |
| revision_of | |
| rights | |
| species | Species of donor |
| structure | Structure of tissue sample |
| symbol | Symbol for a particular thing |
| synonym | Alternate human-readable names for a thing |
| tube_internal_label | Library Pool Tube local name |
| type | |
| used | Usage is the beginning of utilizing an entity by an activity |
| value | The checksum value obtained from a specific cryotographic hash function |
| version | |
| was_derived_from | A derivation is a transformation of an entity into another, an update of an e... |
| was_generated_by | Generation is the completion of production of a new entity by an activity |
| was_guided_by | The dissection ROI polygon which was used to guide the tissue dissection |
| xref | A database cross reference or alternative identifier for a NamedThing or edge... |
Enumerations
Types
| Type | Description |
|---|---|
| BiologicalSequence | |
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| IriType | An IRI |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| LabelType | A string that provides a human-readable name for an entity |
| NarrativeText | A string that provides a human-readable description of something |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| SymbolType | |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Unit | |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|
| Alignment | A subset of slots/attributes that are required for alignment |
| Analysis | A subset of slots/attributes that are required for analysis |
| Bican | A subset of classes that are associated with BICAN |
| LibraryGeneration | A subset of classes that are associated with library generation |
| ModelOrganismDatabase | Subset that is relevant for a typical Model Organism Database (MOD) |
| ProcessingElements | A subset of classes that are associated with processing |
| Samples | Sample/biosample datamodel |
| SequencingElements | A subset of classes that are associated with sequencing |
| Testing | TBD |
| TissueSpecimen | A subset of classes that are associated with tissue specimens |
| Tracking | A subset of slots/attributes that are required for tracking |
| TranslatorMinimal | Minimum subset of translator work |