Genome Annotation Schema
The Genome Annotation schema is designed to represent types and relationships of an organism's annotated genome.
URI: https://identifiers.org/brain-bican/genome-annotation-schema
Name: genome-annotation-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 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 |
| 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. |
| 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. |
| 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). |
| 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 |
| 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. |
| 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 |
Slots
| Slot | Description |
|---|---|
| annotations | |
| attribute_name | The human-readable 'attribute name' can be set to a string which reflects its... |
| authority | The organization responsible for publishing the data |
| category | Name of the high level ontology class in which this entity is categorized |
| checksum_algorithm | The type of cryptographic hash function used to calculate the checksum value |
| content_url | |
| creation_date | date on which an entity was created |
| 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 |
| format | |
| full_name | a long-form human readable name for a thing |
| genome_annotations | |
| genome_assemblies | |
| 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 |
| 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 |
| iri | An IRI for an entity |
| license | |
| molecular_type | |
| name | A human-readable name for an attribute or entity |
| node_property | A grouping for any property that holds between a node and a value |
| provided_by | The value in this node property represents the knowledge provider that create... |
| reference_assembly | The reference genome assembly that this genome annotation was created from |
| referenced_in | The genome annotation that this gene annotation was referenced from |
| 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 |
| rights | |
| source_id | The authority specific identifier |
| strain | The genetic variant or subtype of a species or organism |
| symbol | Symbol for a particular thing |
| synonym | Alternate human-readable names for a thing |
| type | |
| value | The checksum value obtained from a specific cryotographic hash function |
| version | |
| xref | A database cross reference or alternative identifier for a NamedThing or edge... |
Enumerations
| Enumeration | Description |
|---|---|
| AuthorityType | |
| BioType | |
| DigestType |
Types
| Type | Description |
|---|---|
| BiologicalSequence | |
| Boolean | A binary (true or false) value |
| ChemicalFormulaValue | A chemical formula |
| 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 |
| FrequencyValue | |
| 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 |
| PercentageFrequencyValue | |
| PredicateType | A CURIE from the biolink related_to hierarchy |
| Quotient | |
| 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... |
| TimeType | |
| Unit | |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|
| ModelOrganismDatabase | Subset that is relevant for a typical Model Organism Database (MOD) |
| Samples | Sample/biosample datamodel |
| Testing | TBD |
| TranslatorMinimal | Minimum subset of translator work |