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Species

This class is initially intended to capture information about Alliance "core" model species, canonical species for each MOD member. The information in each record pertains to logistics of loading, processing, and displaying data and rendering Alliance pages for related entities.

classDiagram AuditedObject <|-- Species Species : abbreviation Species : common_names Species : created_by Species : data_provider Species : data_provider_cross_reference Species : date_created Species : date_updated Species : db_date_created Species : db_date_updated Species : display_name Species : full_name Species : genome_assembly Species : internal Species : obsolete Species : phylogenetic_order Species : taxon Species : updated_by

URI: alliance:Species

Parent Classes

Slots

Name Description
abbreviation The species abbreviation as used currently in Alliance stack; analogous to short_name in the agr_schemas species.yaml file
common_names The common name(s) for a species, such as "zebrafish", "fruit fly", or "rat"
created_by The individual that created the entity.
data_provider The organization (e.g. MOD) from which the data was sourced
data_provider_cross_reference CrossReference to the organization from which the data was sourced
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
display_name The display name of the species. Currently, these are HUMAN or the corresponding data provider MOD abbreviation, like RGD, MGI, etc. For Xenopus species these are XBXL or XBXT.
full_name The full Latin name of the species, like "Homo sapiens" or "Danio rerio"
genome_assembly The current canonical genome assembly used for the species
internal Classifies the entity as private (for internal use) or not (for public use).
obsolete Entity is no longer current.
phylogenetic_order The integer value assigned to a species to determine its relative ordering with respect to other Alliance species in various user interface displays and logical operations.
taxon The NCBI Taxonomy term ID for the species
updated_by The individual that last modified the entity.

Mappings

Mapping Type Mapped Value
self ['alliance:Species']
native ['alliance:Species']

LinkML Specification

Direct

name: Species
description: This class is initially intended to capture information about Alliance
  "core" model species, canonical species for each MOD member. The information in
  each record pertains to logistics of loading, processing, and displaying data and
  rendering Alliance pages for related entities.
notes:
- 'Intended to accommodate data in these locations: https://raw.githubusercontent.com/alliance-genome/agr_schemas/master/ingest/species/species.yaml
  https://github.com/alliance-genome/agr_java_software/blob/2fa8d334b92c23052451b6954bc4f125016782a2/agr_java_core/src/main/java/org/alliancegenome/neo4j/entity/SpeciesType.java'
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slots:
- taxon
- full_name
- display_name
- abbreviation
- genome_assembly
- common_names
- data_provider
- data_provider_cross_reference
- phylogenetic_order
slot_usage:
  taxon:
    name: taxon
    description: The NCBI Taxonomy term ID for the species
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  full_name:
    name: full_name
    description: The full Latin name of the species, like "Homo sapiens" or "Danio
      rerio"
    domain_of:
    - Species
    - Organization
  display_name:
    name: display_name
    description: The display name of the species. Currently, these are HUMAN or the
      corresponding data provider MOD abbreviation, like RGD, MGI, etc. For Xenopus
      species these are XBXL or XBXT.
    domain_of:
    - CrossReference
    - CrossReferenceDTO
    - Species
  abbreviation:
    name: abbreviation
    description: The species abbreviation as used currently in Alliance stack; analogous
      to short_name in the agr_schemas species.yaml file
    notes:
    - Examples are Hsa, Rno, Mmu, Xla, Xtr, Dre, Dme, Cel, Sce
    domain_of:
    - Species
    - VocabularyTerm
    - ECOTerm
    - Organization
  genome_assembly:
    name: genome_assembly
    description: The current canonical genome assembly used for the species
    domain_of:
    - AssemblyComponent
    - Species
    required: true
  common_names:
    name: common_names
    description: The common name(s) for a species, such as "zebrafish", "fruit fly",
      or "rat"
    domain_of:
    - Species

Induced

name: Species
description: This class is initially intended to capture information about Alliance
  "core" model species, canonical species for each MOD member. The information in
  each record pertains to logistics of loading, processing, and displaying data and
  rendering Alliance pages for related entities.
notes:
- 'Intended to accommodate data in these locations: https://raw.githubusercontent.com/alliance-genome/agr_schemas/master/ingest/species/species.yaml
  https://github.com/alliance-genome/agr_java_software/blob/2fa8d334b92c23052451b6954bc4f125016782a2/agr_java_core/src/main/java/org/alliancegenome/neo4j/entity/SpeciesType.java'
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: AuditedObject
slot_usage:
  taxon:
    name: taxon
    description: The NCBI Taxonomy term ID for the species
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: true
  full_name:
    name: full_name
    description: The full Latin name of the species, like "Homo sapiens" or "Danio
      rerio"
    domain_of:
    - Species
    - Organization
  display_name:
    name: display_name
    description: The display name of the species. Currently, these are HUMAN or the
      corresponding data provider MOD abbreviation, like RGD, MGI, etc. For Xenopus
      species these are XBXL or XBXT.
    domain_of:
    - CrossReference
    - CrossReferenceDTO
    - Species
  abbreviation:
    name: abbreviation
    description: The species abbreviation as used currently in Alliance stack; analogous
      to short_name in the agr_schemas species.yaml file
    notes:
    - Examples are Hsa, Rno, Mmu, Xla, Xtr, Dre, Dme, Cel, Sce
    domain_of:
    - Species
    - VocabularyTerm
    - ECOTerm
    - Organization
  genome_assembly:
    name: genome_assembly
    description: The current canonical genome assembly used for the species
    domain_of:
    - AssemblyComponent
    - Species
    required: true
  common_names:
    name: common_names
    description: The common name(s) for a species, such as "zebrafish", "fruit fly",
      or "rat"
    domain_of:
    - Species
attributes:
  taxon:
    name: taxon
    description: The NCBI Taxonomy term ID for the species
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: taxon
    owner: Species
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: true
  full_name:
    name: full_name
    description: The full Latin name of the species, like "Homo sapiens" or "Danio
      rerio"
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: full_name
    owner: Species
    domain_of:
    - Species
    - Organization
    range: string
  display_name:
    name: display_name
    description: The display name of the species. Currently, these are HUMAN or the
      corresponding data provider MOD abbreviation, like RGD, MGI, etc. For Xenopus
      species these are XBXL or XBXT.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: display_name
    owner: Species
    domain_of:
    - CrossReference
    - CrossReferenceDTO
    - Species
    range: string
    required: true
  abbreviation:
    name: abbreviation
    description: The species abbreviation as used currently in Alliance stack; analogous
      to short_name in the agr_schemas species.yaml file
    notes:
    - Examples are Hsa, Rno, Mmu, Xla, Xtr, Dre, Dme, Cel, Sce
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: abbreviation
    owner: Species
    domain_of:
    - Species
    - VocabularyTerm
    - ECOTerm
    - Organization
    range: string
  genome_assembly:
    name: genome_assembly
    description: The current canonical genome assembly used for the species
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AssemblyComponent
    multivalued: false
    alias: genome_assembly
    owner: Species
    domain_of:
    - AssemblyComponent
    - Species
    range: GenomeAssembly
    required: true
  common_names:
    name: common_names
    description: The common name(s) for a species, such as "zebrafish", "fruit fly",
      or "rat"
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Species
    multivalued: true
    alias: common_names
    owner: Species
    domain_of:
    - Species
    range: string
    required: false
  data_provider:
    name: data_provider
    description: The organization (e.g. MOD) from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider
    owner: Species
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: Organization
    required: true
  data_provider_cross_reference:
    name: data_provider_cross_reference
    description: CrossReference to the organization from which the data was sourced
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_cross_reference
    owner: Species
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  phylogenetic_order:
    name: phylogenetic_order
    description: The integer value assigned to a species to determine its relative
      ordering with respect to other Alliance species in various user interface displays
      and logical operations.
    notes:
    - In the agr_schemas repo species.yaml file, the phylogeneticOrder is given values
      like 10, 20, 30, 40 for the original Alliance species; Xenopus laevis is 46
      and Xenopus tropicalis is 45; In the SpeciesType.java file the species are simply
      numbered 1, 2, 3, 4, 5, etc.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Species
    multivalued: false
    alias: phylogenetic_order
    owner: Species
    domain_of:
    - Species
    range: integer
    required: true
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: Species
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: Species
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: Species
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean