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AntibodyDTO

Ingest class for immunoglobulin proteins that bind specific molecule(s). Can be used experimentally for the purposes of detection or purification.

classDiagram ReagentDTO <|-- AntibodyDTO AntibodyDTO : antibody_target_gene_identifiers AntibodyDTO : antigen_taxon_curie AntibodyDTO : clonality_name AntibodyDTO : created_by_curie AntibodyDTO : cross_reference_dtos AntibodyDTO : data_provider_dto AntibodyDTO : date_created AntibodyDTO : date_updated AntibodyDTO : db_date_created AntibodyDTO : db_date_updated AntibodyDTO : generated_by_identifier AntibodyDTO : heavy_chain_isotype_name AntibodyDTO : internal AntibodyDTO : light_chain_isotype_name AntibodyDTO : manufactured_by_identifier AntibodyDTO : mod_internal_id AntibodyDTO : name AntibodyDTO : note_dtos AntibodyDTO : obsolete AntibodyDTO : original_reference_curie AntibodyDTO : primary_external_id AntibodyDTO : reference_curies AntibodyDTO : secondary_identifiers AntibodyDTO : taxon_curie AntibodyDTO : updated_by_curie

URI: alliance:AntibodyDTO

Parent Classes

Slots

Name Description
antibody_target_gene_identifiers Identifiers (curie/primary_external_id/mod_internal_id) of the genes whose gene products are recognized by the antibody.
antigen_taxon_curie Holds between an Antibody and the species from which the antigen originates (as represented by taxon).
clonality_name Name of the VocabularyTerm representing the clonality of the antibody: e.g., monoclonal. From the Antibody Clonality CV.
created_by_curie Curie of the Person object representing the individual that created the entity
cross_reference_dtos None
data_provider_dto Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site
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.
generated_by_identifier Identifier for Reagent generated_by field.
heavy_chain_isotype_name Name of the VocabularyTerm representing the isotype of the antibody heavy chain: e.g., IgA. From the Heavy Chain Isotope CV.
internal Classifies the entity as private (for internal use) or not (for public use).
light_chain_isotype_name Name of the VocabularyTerm representing the isotype of the antibody light chain: e.g., i4. From the Light Chain Isotope CV.
manufactured_by_identifier Identifier for Reagent manufactured_by field.
mod_internal_id The model organism database (MOD) internal identifier for the object
name Publicly displayed name of the antibody. It often includes the name of the antibody target: e.g., anti-WNT-4. It may also include the host species and antibody clonality.
note_dtos None
obsolete Entity is no longer current.
original_reference_curie The reference providing the original description of the antibody's generation.
primary_external_id The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity.
reference_curies External reference curies used for ingest
secondary_identifiers None
taxon_curie The species in which the antibody was raised: e.g., mouse, rabbit, guinea pig, goat, camel, etc.
updated_by_curie Curie of the Person object representing the individual that updated the entity

Mappings

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

LinkML Specification

Direct

name: AntibodyDTO
description: Ingest class for immunoglobulin proteins that bind specific molecule(s).
  Can be used experimentally for the purposes of detection or purification.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ReagentDTO
slots:
- name
- antigen_taxon_curie
- clonality_name
- heavy_chain_isotype_name
- light_chain_isotype_name
- antibody_target_gene_identifiers
- cross_reference_dtos
- reference_curies
- original_reference_curie
- note_dtos
- taxon_curie
- generated_by_identifier
- manufactured_by_identifier
slot_usage:
  name:
    name: name
    description: 'Publicly displayed name of the antibody. It often includes the name
      of the antibody target: e.g., anti-WNT-4. It may also include the host species
      and antibody clonality.'
    notes:
    - FB does not have names for antibodies, but would be easy to generate, so we
      may want to make this required.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    required: true
  taxon_curie:
    name: taxon_curie
    description: 'The species in which the antibody was raised: e.g., mouse, rabbit,
      guinea pig, goat, camel, etc.'
    notes:
    - FB does not have host taxon information for antibodies.
    domain_of:
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - BiologicalEntityDTO
    - ChromosomeDTO
    required: false
  original_reference_curie:
    name: original_reference_curie
    description: The reference providing the original description of the antibody's
      generation.
    domain_of:
    - AntibodyDTO

Induced

name: AntibodyDTO
description: Ingest class for immunoglobulin proteins that bind specific molecule(s).
  Can be used experimentally for the purposes of detection or purification.
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: ReagentDTO
slot_usage:
  name:
    name: name
    description: 'Publicly displayed name of the antibody. It often includes the name
      of the antibody target: e.g., anti-WNT-4. It may also include the host species
      and antibody clonality.'
    notes:
    - FB does not have names for antibodies, but would be easy to generate, so we
      may want to make this required.
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    required: true
  taxon_curie:
    name: taxon_curie
    description: 'The species in which the antibody was raised: e.g., mouse, rabbit,
      guinea pig, goat, camel, etc.'
    notes:
    - FB does not have host taxon information for antibodies.
    domain_of:
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - BiologicalEntityDTO
    - ChromosomeDTO
    required: false
  original_reference_curie:
    name: original_reference_curie
    description: The reference providing the original description of the antibody's
      generation.
    domain_of:
    - AntibodyDTO
attributes:
  name:
    name: name
    description: 'Publicly displayed name of the antibody. It often includes the name
      of the antibody target: e.g., anti-WNT-4. It may also include the host species
      and antibody clonality.'
    notes:
    - FB does not have names for antibodies, but would be easy to generate, so we
      may want to make this required.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: name
    owner: AntibodyDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    range: string
    required: true
  antigen_taxon_curie:
    name: antigen_taxon_curie
    description: Holds between an Antibody and the species from which the antigen
      originates (as represented by taxon).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AntibodyDTO
    alias: antigen_taxon_curie
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
  clonality_name:
    name: clonality_name
    description: 'Name of the VocabularyTerm representing the clonality of the antibody:
      e.g., monoclonal. From the Antibody Clonality CV.'
    notes:
    - I think this will be an antibody specific slot.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Antibody
    multivalued: false
    alias: clonality_name
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
    required: true
  heavy_chain_isotype_name:
    name: heavy_chain_isotype_name
    description: 'Name of the VocabularyTerm representing the isotype of the antibody
      heavy chain: e.g., IgA. From the Heavy Chain Isotope CV.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Antibody
    multivalued: false
    alias: heavy_chain_isotype_name
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
    required: false
  light_chain_isotype_name:
    name: light_chain_isotype_name
    description: 'Name of the VocabularyTerm representing the isotype of the antibody
      light chain: e.g., i4. From the Light Chain Isotope CV.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AntibodyDTO
    multivalued: false
    alias: light_chain_isotype_name
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
    required: false
  antibody_target_gene_identifiers:
    name: antibody_target_gene_identifiers
    description: Identifiers (curie/primary_external_id/mod_internal_id) of the genes
      whose gene products are recognized by the antibody.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AntibodyDTO
    multivalued: true
    alias: antibody_target_gene_identifiers
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
    required: false
  cross_reference_dtos:
    name: cross_reference_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: cross_reference_dtos
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    - GenomicEntityDTO
    - GenomeAssemblyDTO
    - ExternalDataBaseEntityDTO
    - GeneInteractionDTO
    range: CrossReferenceDTO
    inlined: true
    inlined_as_list: true
  reference_curies:
    name: reference_curies
    description: External reference curies used for ingest
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: reference_curies
    owner: AntibodyDTO
    domain_of:
    - AlleleDTO
    - SequenceTargetingReagentDTO
    - AntibodyDTO
    - ConstructDTO
    - AffectedGenomicModelDTO
    - HTPExpressionDatasetAnnotationDTO
    range: string
  original_reference_curie:
    name: original_reference_curie
    description: The reference providing the original description of the antibody's
      generation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: original_reference_curie
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
  note_dtos:
    name: note_dtos
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: note_dtos
    owner: AntibodyDTO
    domain_of:
    - VariantDTO
    - AlleleDTO
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - ConstructGenomicEntityAssociationDTO
    - GeneDTO
    - AnnotationDTO
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NoteDTO
    inlined: true
    inlined_as_list: true
  taxon_curie:
    name: taxon_curie
    description: 'The species in which the antibody was raised: e.g., mouse, rabbit,
      guinea pig, goat, camel, etc.'
    notes:
    - FB does not have host taxon information for antibodies.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: taxon_curie
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    - ConstructComponentSlotAnnotationDTO
    - BiologicalEntityDTO
    - ChromosomeDTO
    range: string
    required: false
  generated_by_identifier:
    name: generated_by_identifier
    description: Identifier for Reagent generated_by field.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ReagentDTO
    alias: generated_by_identifier
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
  manufactured_by_identifier:
    name: manufactured_by_identifier
    description: 'Identifier for Reagent manufactured_by field.  '
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: ReagentDTO
    alias: manufactured_by_identifier
    owner: AntibodyDTO
    domain_of:
    - AntibodyDTO
    range: string
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    multivalued: true
    alias: secondary_identifiers
    owner: AntibodyDTO
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
  primary_external_id:
    name: primary_external_id
    description: The primary external (non-Alliance) database identifier/curie for
      the object. Note that this may be an external (non-Alliance member) identifier
      for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance
      member's primary key for the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: primary_external_id
    owner: AntibodyDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Person
    - Annotation
    - AnnotationDTO
    range: string
  mod_internal_id:
    name: mod_internal_id
    description: The model organism database (MOD) internal identifier for the object
    notes:
    - This is required if primary_external_id is not submitted
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: AntibodyDTO
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  data_provider_dto:
    name: data_provider_dto
    description: Ingest object representing the organization (e.g. MOD) from which
      the data was sourced and a CrossReference to that organisation's site
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: data_provider_dto
    owner: AntibodyDTO
    domain_of:
    - SubmittedObjectDTO
    - ChromosomeDTO
    - AssemblyComponentDTO
    - AnnotationDTO
    range: DataProviderDTO
    required: true
    inlined: true
  created_by_curie:
    name: created_by_curie
    description: Curie of the Person object representing the individual that created
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: created_by_curie
    owner: AntibodyDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AntibodyDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by_curie:
    name: updated_by_curie
    description: Curie of the Person object representing the individual that updated
      the entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObjectDTO
    alias: updated_by_curie
    owner: AntibodyDTO
    domain_of:
    - AuditedObjectDTO
    range: string
  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: AntibodyDTO
    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: AntibodyDTO
    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: AntibodyDTO
    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: AntibodyDTO
    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: AntibodyDTO
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean