Skip to content

Antibody

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

classDiagram Reagent <|-- Antibody Antibody : antibody_target_genes Antibody : antigen_taxon Antibody : clonality Antibody : created_by Antibody : cross_references Antibody : curie Antibody : data_provider Antibody : data_provider_cross_reference Antibody : date_created Antibody : date_updated Antibody : db_date_created Antibody : db_date_updated Antibody : generated_by Antibody : heavy_chain_isotype Antibody : internal Antibody : light_chain_isotype Antibody : manufactured_by Antibody : mod_internal_id Antibody : name Antibody : obsolete Antibody : original_reference Antibody : primary_external_id Antibody : references Antibody : related_notes Antibody : secondary_identifiers Antibody : taxon Antibody : unique_id Antibody : updated_by

URI: alliance:Antibody

Parent Classes

Slots

Name Description
antibody_target_genes The genes whose gene products are recognized by the antibody.
antigen_taxon Holds between an Antibody and the species from which the antigen originates (as represented by taxon).
clonality The clonality of the antibody: e.g., monoclonal.
created_by The individual that created the entity.
cross_references Holds between an object and its CrossReferences.
curie A unique identifier for the antibody: e.g., WBAntibody0000001.
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.
generated_by Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory.
heavy_chain_isotype The isotype of the antibody heavy chain: e.g., IgA.
internal Classifies the entity as private (for internal use) or not (for public use).
light_chain_isotype The isotype of the antibody light chain: e.g., i4.
manufactured_by Holds between a material entity and an Agent that has manufactured it: e.g., Molecular Probes.
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.
obsolete Entity is no longer current.
original_reference 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.
references holds between an object and a list of references
related_notes Holds between an object and a list of related Note objects.
secondary_identifiers None
taxon The species in which the antibody was raised: e.g., mouse, rabbit, guinea pig, goat, camel, etc.
unique_id A non-curie unique identifier for a thing.
updated_by The individual that last modified the entity.

Mappings

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

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • RGD

  • SGD

  • FB

  • MGI

  • WB

  • ZFIN

LinkML Specification

Direct

name: Antibody
id_prefixes:
- RGD
- SGD
- FB
- MGI
- WB
- ZFIN
description: 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
aliases:
- antibody
- antibodies
- antiserum
- antisera
is_a: Reagent
slots:
- name
- antigen_taxon
- clonality
- heavy_chain_isotype
- light_chain_isotype
- antibody_target_genes
- cross_references
- references
- original_reference
- related_notes
- taxon
- generated_by
- manufactured_by
slot_usage:
  curie:
    name: curie
    description: 'A unique identifier for the antibody: e.g., WBAntibody0000001.'
    notes:
    - As not all MODs have IDs (e.g., FB), some IDs will need to be minted at the
      Alliance. Does anyone use RRIDs as the 1o ID for antibody?
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  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:
    name: taxon
    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:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: false
  original_reference:
    name: original_reference
    description: The reference providing the original description of the antibody's
      generation.
    domain_of:
    - Antibody

Induced

name: Antibody
id_prefixes:
- RGD
- SGD
- FB
- MGI
- WB
- ZFIN
description: 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
aliases:
- antibody
- antibodies
- antiserum
- antisera
is_a: Reagent
slot_usage:
  curie:
    name: curie
    description: 'A unique identifier for the antibody: e.g., WBAntibody0000001.'
    notes:
    - As not all MODs have IDs (e.g., FB), some IDs will need to be minted at the
      Alliance. Does anyone use RRIDs as the 1o ID for antibody?
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
  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:
    name: taxon
    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:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    required: false
  original_reference:
    name: original_reference
    description: The reference providing the original description of the antibody's
      generation.
    domain_of:
    - Antibody
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: Antibody
    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:
    name: antigen_taxon
    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: Antibody
    multivalued: false
    alias: antigen_taxon
    owner: Antibody
    domain_of:
    - Antibody
    range: NCBITaxonTerm
    required: false
  clonality:
    name: clonality
    description: 'The clonality of the antibody: e.g., monoclonal.'
    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
    owner: Antibody
    domain_of:
    - Antibody
    range: VocabularyTerm
    required: true
  heavy_chain_isotype:
    name: heavy_chain_isotype
    description: 'The isotype of the antibody heavy chain: e.g., IgA.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Antibody
    multivalued: false
    alias: heavy_chain_isotype
    owner: Antibody
    domain_of:
    - Antibody
    range: VocabularyTerm
    required: false
  light_chain_isotype:
    name: light_chain_isotype
    description: 'The isotype of the antibody light chain: e.g., i4.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Antibody
    multivalued: false
    alias: light_chain_isotype
    owner: Antibody
    domain_of:
    - Antibody
    range: VocabularyTerm
    required: false
  antibody_target_genes:
    name: antibody_target_genes
    description: The genes whose gene products are recognized by the antibody.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Antibody
    multivalued: true
    alias: antibody_target_genes
    owner: Antibody
    domain_of:
    - Antibody
    range: Gene
    required: false
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: Antibody
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  references:
    name: references
    description: holds between an object and a list of references
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    singular_name: reference
    multivalued: true
    alias: references
    owner: Antibody
    domain_of:
    - Allele
    - SequenceTargetingReagent
    - Antibody
    - Construct
    - AffectedGenomicModel
    - Variant
    - HTPExpressionDatasetAnnotation
    range: Reference
  original_reference:
    name: original_reference
    description: The reference providing the original description of the antibody's
      generation.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    is_a: references
    multivalued: true
    alias: original_reference
    owner: Antibody
    domain_of:
    - Antibody
    range: Reference
  related_notes:
    name: related_notes
    description: Holds between an object and a list of related Note objects.
    notes:
    - The original name suggested for this slot was simply notes, but I think that
      label is reserved in LinkML for internal descriptions of objects, hence the
      related_notes label used here.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: related_notes
    owner: Antibody
    domain_of:
    - Allele
    - Antibody
    - ConstructComponentSlotAnnotation
    - ConstructGenomicEntityAssociation
    - Gene
    - GeneChangeEventSlotAnnotation
    - Annotation
    - Variant
    - HTPExpressionDatasetSampleAnnotation
    - ExpressionExperiment
    range: Note
  taxon:
    name: taxon
    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
    multivalued: false
    alias: taxon
    owner: Antibody
    domain_of:
    - Antibody
    - ConstructComponentSlotAnnotation
    - BiologicalEntity
    - Chromosome
    - Species
    - HTPExpressionDatasetSampleAnnotation
    - HTPExpressionDatasetSampleAnnotationDTO
    range: NCBITaxonTerm
    required: false
  generated_by:
    name: generated_by
    description: 'Holds between a material entity and an Agent that generated it:
      e.g., Thomas Blumenthal, Kornberg Laboratory.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: generated_by
    owner: Antibody
    domain_of:
    - Antibody
    range: Agent
    required: false
  manufactured_by:
    name: manufactured_by
    description: 'Holds between a material entity and an Agent that has manufactured
      it: e.g., Molecular Probes.'
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: manufactured_by
    owner: Antibody
    domain_of:
    - Antibody
    range: Agent
    required: false
  unique_id:
    name: unique_id
    description: A non-curie unique identifier for a thing.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: unique_id
    owner: Antibody
    domain_of:
    - Reagent
    - Exon
    - CodingSequence
    - Person
    - Annotation
    - ExperimentalCondition
    - ConditionRelation
    - ExpressionExperiment
    - GeneInteraction
    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: Antibody
    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: Antibody
    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
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: mod_internal_id
    owner: Antibody
    domain_of:
    - SubmittedObject
    - SubmittedObjectDTO
    - Annotation
    - AnnotationDTO
    range: string
  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: Antibody
    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: Antibody
    domain_of:
    - SubmittedObject
    - Chromosome
    - Species
    - Annotation
    - HTPExpressionDatasetAnnotation
    range: CrossReference
    required: false
  curie:
    name: curie
    description: 'A unique identifier for the antibody: e.g., WBAntibody0000001.'
    notes:
    - As not all MODs have IDs (e.g., FB), some IDs will need to be minted at the
      Alliance. Does anyone use RRIDs as the 1o ID for antibody?
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    alias: curie
    owner: Antibody
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
  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: Antibody
    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: Antibody
    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: Antibody
    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: Antibody
    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: Antibody
    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: Antibody
    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: Antibody
    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: Antibody
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean