Genome Annotation Schema
The Genome Annotation Schema is designed to respresent all the genes from a given genome annotation.
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 c... |
| AnnotationCollection | |
| 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 |
| 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... |
| GeneAnnotation | Represents a single gene |
| Genome | A genome is the sum of genetic material within a cell or virion |
| GenomeAnnotation | Represents a genome annotation |
| GenomeAssembly | Represents a genome assembly |
| 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 |
| 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 |
| MaterialSample | A sample is a limited quantity of something (e |
| Procedure | A series of actions conducted in a certain order or manner |
| 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 |
| 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 |
|---|---|
| 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 |
| 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... |
| 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 |
| 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 |
| 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 |
| information_content | Information content (IC) value for a term, primarily from Automats |
| iri | An IRI for an entity |
| license | |
| macromolecular_machine_mixin_name | genes are typically designated by a short symbol and a full name |
| molecular_type | |
| 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 |
| organism_taxon_has_taxonomic_rank | |
| 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 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 |
| revision_of | |
| 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 |
| 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 |
|---|---|
| ModelOrganismDatabase | Subset that is relevant for a typical Model Organism Database (MOD) |
| Samples | Sample/biosample datamodel |
| Testing | TBD |
| TranslatorMinimal | Minimum subset of translator work |