Class: OligonucleotideDetail

Structured attributes of a treatment that acts by base-pairing with a target RNA: its molecular mechanism, RNA target, splice exon (for splice-switching antisense oligonucleotides), backbone chemistry, targeting conjugate, and delivery platform. Attach via the oligonucleotide_details slot on a Treatment whose therapeutic_modality is ANTISENSE_OLIGONUCLEOTIDE or SIRNA. Single-stranded ASOs and double-stranded siRNAs share this class deliberately - they differ in effector (RNase H1 versus Argonaute-2) but are the same programmable platform, described by the same target, chemistry, and delivery attributes.

The carrier attributes here (delivery_platform, targeting_ligand, and the deprecated conjugation) predate the Treatment-level delivery_system block and are retained so entries authored before it continue to validate. New treatments record the carrier in delivery_system; this class keeps the mechanism, RNA target, exon, and backbone chemistry, which are genuinely specific to base-pairing therapeutics. just check-delivery-system reports entries still using the nested slots and gates on a value recorded in both places.

URI: dismech:class/OligonucleotideDetail

 classDiagram
    class OligonucleotideDetail
    click OligonucleotideDetail href "../../classes/OligonucleotideDetail/"
      OligonucleotideDetail : aso_chemistry





        OligonucleotideDetail --> "0..1" OligonucleotideChemistryEnum : aso_chemistry
        click OligonucleotideChemistryEnum href "../../enums/OligonucleotideChemistryEnum/"



      OligonucleotideDetail : aso_mechanism





        OligonucleotideDetail --> "0..1" OligonucleotideMechanismEnum : aso_mechanism
        click OligonucleotideMechanismEnum href "../../enums/OligonucleotideMechanismEnum/"



      OligonucleotideDetail : conjugation





        OligonucleotideDetail --> "0..1" TargetingLigandEnum : conjugation
        click TargetingLigandEnum href "../../enums/TargetingLigandEnum/"



      OligonucleotideDetail : delivery_platform





        OligonucleotideDetail --> "0..1" DeliveryPlatformEnum : delivery_platform
        click DeliveryPlatformEnum href "../../enums/DeliveryPlatformEnum/"



      OligonucleotideDetail : oligonucleotide_chemistry





        OligonucleotideDetail --> "0..1" OligonucleotideChemistryEnum : oligonucleotide_chemistry
        click OligonucleotideChemistryEnum href "../../enums/OligonucleotideChemistryEnum/"



      OligonucleotideDetail : oligonucleotide_mechanism





        OligonucleotideDetail --> "0..1" OligonucleotideMechanismEnum : oligonucleotide_mechanism
        click OligonucleotideMechanismEnum href "../../enums/OligonucleotideMechanismEnum/"



      OligonucleotideDetail : target_exon

      OligonucleotideDetail : target_gene





        OligonucleotideDetail --> "0..1" GeneDescriptor : target_gene
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      OligonucleotideDetail : target_transcript

      OligonucleotideDetail : targeting_ligand





        OligonucleotideDetail --> "0..1" TargetingLigandEnum : targeting_ligand
        click TargetingLigandEnum href "../../enums/TargetingLigandEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
oligonucleotide_mechanism	0..1 OligonucleotideMechanismEnum	Molecular mechanism of action of a therapeutic oligonucleotide	direct
target_gene	0..1 GeneDescriptor	The gene whose transcript a therapeutic oligonucleotide targets (bindable to ...	direct
target_transcript	0..1 String	The specific transcript, pre-mRNA element, or sequence motif targeted by a th...	direct
target_exon	0..1 String	The exon (or exons) modulated by a splice-switching antisense oligonucleotide...	direct
oligonucleotide_chemistry	0..1 OligonucleotideChemistryEnum	Backbone / sugar chemistry of a therapeutic oligonucleotide	direct
targeting_ligand	0..1 TargetingLigandEnum	Targeting ligand attached to the active agent, or to the carrier particle hol...	direct
conjugation	0..1 TargetingLigandEnum	Deprecated alias of targeting_ligand, retained so entries authored before the...	direct
delivery_platform	0..1 DeliveryPlatformEnum	How the active agent is carried to its target tissue - unformulated, ligand c...	direct
aso_mechanism	0..1 OligonucleotideMechanismEnum	Deprecated alias of oligonucleotide_mechanism	direct
aso_chemistry	0..1 OligonucleotideChemistryEnum	Deprecated alias of oligonucleotide_chemistry	direct

Usages

used by	used in	type	used
Treatment	oligonucleotide_details	range	OligonucleotideDetail
Treatment	aso_details	range	OligonucleotideDetail

Aliases

AntisenseOligonucleotideDetail

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type	Mapped Value
self	dismech:OligonucleotideDetail
native	dismech:OligonucleotideDetail

LinkML Source

Direct

name: OligonucleotideDetail
description: 'Structured attributes of a treatment that acts by base-pairing with
  a target RNA: its molecular mechanism, RNA target, splice exon (for splice-switching
  antisense oligonucleotides), backbone chemistry, targeting conjugate, and delivery
  platform. Attach via the oligonucleotide_details slot on a Treatment whose therapeutic_modality
  is ANTISENSE_OLIGONUCLEOTIDE or SIRNA. Single-stranded ASOs and double-stranded
  siRNAs share this class deliberately - they differ in effector (RNase H1 versus
  Argonaute-2) but are the same programmable platform, described by the same target,
  chemistry, and delivery attributes.

  The carrier attributes here (delivery_platform, targeting_ligand, and the deprecated
  conjugation) predate the Treatment-level delivery_system block and are retained
  so entries authored before it continue to validate. New treatments record the carrier
  in delivery_system; this class keeps the mechanism, RNA target, exon, and backbone
  chemistry, which are genuinely specific to base-pairing therapeutics. just check-delivery-system
  reports entries still using the nested slots and gates on a value recorded in both
  places.'
from_schema: https://w3id.org/monarch-initiative/dismech
aliases:
- AntisenseOligonucleotideDetail
slots:
- oligonucleotide_mechanism
- target_gene
- target_transcript
- target_exon
- oligonucleotide_chemistry
- targeting_ligand
- conjugation
- delivery_platform
- aso_mechanism
- aso_chemistry

Induced

name: OligonucleotideDetail
description: 'Structured attributes of a treatment that acts by base-pairing with
  a target RNA: its molecular mechanism, RNA target, splice exon (for splice-switching
  antisense oligonucleotides), backbone chemistry, targeting conjugate, and delivery
  platform. Attach via the oligonucleotide_details slot on a Treatment whose therapeutic_modality
  is ANTISENSE_OLIGONUCLEOTIDE or SIRNA. Single-stranded ASOs and double-stranded
  siRNAs share this class deliberately - they differ in effector (RNase H1 versus
  Argonaute-2) but are the same programmable platform, described by the same target,
  chemistry, and delivery attributes.

  The carrier attributes here (delivery_platform, targeting_ligand, and the deprecated
  conjugation) predate the Treatment-level delivery_system block and are retained
  so entries authored before it continue to validate. New treatments record the carrier
  in delivery_system; this class keeps the mechanism, RNA target, exon, and backbone
  chemistry, which are genuinely specific to base-pairing therapeutics. just check-delivery-system
  reports entries still using the nested slots and gates on a value recorded in both
  places.'
from_schema: https://w3id.org/monarch-initiative/dismech
aliases:
- AntisenseOligonucleotideDetail
attributes:
  oligonucleotide_mechanism:
    name: oligonucleotide_mechanism
    description: Molecular mechanism of action of a therapeutic oligonucleotide
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: oligonucleotide_mechanism
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: OligonucleotideMechanismEnum
  target_gene:
    name: target_gene
    description: The gene whose transcript a therapeutic oligonucleotide targets (bindable
      to HGNC).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_gene
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: GeneDescriptor
    inlined: true
  target_transcript:
    name: target_transcript
    description: The specific transcript, pre-mRNA element, or sequence motif targeted
      by a therapeutic oligonucleotide (e.g., a RefSeq/Ensembl transcript ID, "SMN2
      ISS-N1", or "APOB mRNA").
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_transcript
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: string
  target_exon:
    name: target_exon
    description: The exon (or exons) modulated by a splice-switching antisense oligonucleotide,
      expressed in human-readable form (e.g., "exon 51", "exon 7"). Not applicable
      to siRNA, which acts on mature mRNA rather than on splicing.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: target_exon
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: string
  oligonucleotide_chemistry:
    name: oligonucleotide_chemistry
    description: Backbone / sugar chemistry of a therapeutic oligonucleotide
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: oligonucleotide_chemistry
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: OligonucleotideChemistryEnum
  targeting_ligand:
    name: targeting_ligand
    description: 'Targeting ligand attached to the active agent, or to the carrier
      particle holding it, to direct uptake by a particular tissue or cell type. Orthogonal
      to delivery_platform: an unconjugated agent may still travel in a nanoparticle,
      and a nanoparticle may carry a ligand on its surface.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: targeting_ligand
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    - DeliverySystem
    range: TargetingLigandEnum
  conjugation:
    name: conjugation
    description: Deprecated alias of targeting_ligand, retained so entries authored
      before the slot was generalized continue to validate.
    deprecated: Renamed to targeting_ligand, which describes a ligand coupled to a
      carrier particle as well as one conjugated directly to an oligonucleotide. Existing
      entries carrying conjugation remain valid; do not populate it on new treatments.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: conjugation
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: TargetingLigandEnum
  delivery_platform:
    name: delivery_platform
    description: 'How the active agent is carried to its target tissue - unformulated,
      ligand conjugate, lipid nanoparticle, liposome, albumin-bound particle, viral
      vector. Orthogonal to targeting_ligand: an unconjugated agent may still be delivered
      in a nanoparticle. Prefer the Treatment-level delivery_system block, which carries
      this slot alongside the targeting detail; the copy nested in oligonucleotide_details
      predates it and stays valid.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: delivery_platform
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    - DeliverySystem
    range: DeliveryPlatformEnum
  aso_mechanism:
    name: aso_mechanism
    description: Deprecated alias of oligonucleotide_mechanism.
    deprecated: Renamed to oligonucleotide_mechanism.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: aso_mechanism
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: OligonucleotideMechanismEnum
  aso_chemistry:
    name: aso_chemistry
    description: Deprecated alias of oligonucleotide_chemistry.
    deprecated: Renamed to oligonucleotide_chemistry.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: aso_chemistry
    owner: OligonucleotideDetail
    domain_of:
    - OligonucleotideDetail
    range: OligonucleotideChemistryEnum