Class: SampleNucleicAcidAssociation

M:N link between Sample and NucleicAcid. A sample may hold several strands - the two strands of a duplex, a guide RNA with its target DNA, a primer with its template - and one strand turns up in many samples. What changes from preparation to preparation lives here: the role, the copy number, the form the strand takes (single, duplex, hairpin, quadruplex), how it was made, the modifications it carries, and the mass actually measured.

URI: lambda:SampleNucleicAcidAssociation

classDiagram class SampleNucleicAcidAssociation click SampleNucleicAcidAssociation href "../SampleNucleicAcidAssociation/" SampleNucleicAcidAssociation : chain_ids SampleNucleicAcidAssociation : copy_number SampleNucleicAcidAssociation : modifications SampleNucleicAcidAssociation : nucleic_acid_id SampleNucleicAcidAssociation --> "1" NucleicAcid : nucleic_acid_id click NucleicAcid href "../NucleicAcid/" SampleNucleicAcidAssociation : observed_molecular_weight SampleNucleicAcidAssociation --> "0..1" QuantityValue : observed_molecular_weight click QuantityValue href "../QuantityValue/" SampleNucleicAcidAssociation : residue_range SampleNucleicAcidAssociation : role SampleNucleicAcidAssociation --> "0..1" SampleNucleicAcidRoleEnum : role click SampleNucleicAcidRoleEnum href "../SampleNucleicAcidRoleEnum/" SampleNucleicAcidAssociation : sample_id SampleNucleicAcidAssociation --> "1" Sample : sample_id click Sample href "../Sample/" SampleNucleicAcidAssociation : sequence_coverage SampleNucleicAcidAssociation : source_method SampleNucleicAcidAssociation --> "0..1" NucleicAcidSourceEnum : source_method click NucleicAcidSourceEnum href "../NucleicAcidSourceEnum/" SampleNucleicAcidAssociation : structural_form SampleNucleicAcidAssociation --> "0..1" NucleicAcidFormEnum : structural_form click NucleicAcidFormEnum href "../NucleicAcidFormEnum/"

Slots

Name	Cardinality and Range	Description	Inheritance
sample_id	1 Sample	Reference to the sample	direct
nucleic_acid_id	1 NucleicAcid	Reference to the nucleic acid	direct
role	0..1 SampleNucleicAcidRoleEnum	Part this nucleic acid plays in the sample	direct
copy_number	0..1 Integer	Copies of this strand per assembly in the sample: 2 for a self-complementary ...	direct
residue_range	0..1 String	Nucleotides of the reference sequence present in this sample (e	direct
sequence_coverage	0..1 Float	Fraction of the reference sequence present in this sample (range: 0-1)	direct
chain_ids	* String	Chain identifiers this strand occupies in the deposited structure, where the ...	direct
structural_form	0..1 NucleicAcidFormEnum	Form the strand takes in this sample: single-stranded, paired in a duplex, fo...	direct
source_method	0..1 NucleicAcidSourceEnum	How this strand was made for this preparation: chemical synthesis, in vitro t...	direct
modifications	* String	Modifications carried by this strand in this sample: fluorophore or biotin la...	direct
observed_molecular_weight	0..1 QuantityValue	Mass as measured for this preparation (mass spectrometry, SEC-MALS, SAXS), ty...	direct

Usages

used by	used in	type	used
Dataset	sample_nucleic_acid_associations	range	SampleNucleicAcidAssociation

Comments

A SampleComponent row of type nucleic_acid for the same sample and strand is the inventory entry and the handle a SampleComponentInteraction points at; this association is the per-preparation detail. A dataset that records no interactions may carry this row alone. Where role or copy_number is set on both, they must agree.

Identifier and Mapping Information

Schema Source

from schema: http://w3id.org/lambda/

Mappings

Mapping Type	Mapped Value
self	lambda:SampleNucleicAcidAssociation
native	lambda:SampleNucleicAcidAssociation
related	IHMCIF:_ihm_struct_assembly_details, IHMCIF:_ihm_entity_poly_segment

LinkML Source

Direct

name: SampleNucleicAcidAssociation
description: 'M:N link between Sample and NucleicAcid. A sample may hold several strands
  - the two strands of a duplex, a guide RNA with its target DNA, a primer with its
  template - and one strand turns up in many samples. What changes from preparation
  to preparation lives here: the role, the copy number, the form the strand takes
  (single, duplex, hairpin, quadruplex), how it was made, the modifications it carries,
  and the mass actually measured.'
comments:
- A SampleComponent row of type nucleic_acid for the same sample and strand is the
  inventory entry and the handle a SampleComponentInteraction points at; this association
  is the per-preparation detail. A dataset that records no interactions may carry
  this row alone. Where role or copy_number is set on both, they must agree.
from_schema: http://w3id.org/lambda/
related_mappings:
- IHMCIF:_ihm_struct_assembly_details
- IHMCIF:_ihm_entity_poly_segment
attributes:
  sample_id:
    name: sample_id
    description: Reference to the sample
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleComponent
    - SamplePreparation
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - SampleComponentInteraction
    range: Sample
    required: true
  nucleic_acid_id:
    name: nucleic_acid_id
    description: Reference to the nucleic acid
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleComponent
    - SampleNucleicAcidAssociation
    range: NucleicAcid
    required: true
  role:
    name: role
    description: Part this nucleic acid plays in the sample
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleComponent
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ExperimentInstrumentAssociation
    - StudyPersonAssociation
    - ExperimentPersonAssociation
    - WorkflowPersonAssociation
    - StudyOrganizationAssociation
    - PersonOrganizationAssociation
    range: SampleNucleicAcidRoleEnum
  copy_number:
    name: copy_number
    description: 'Copies of this strand per assembly in the sample: 2 for a self-complementary
      duplex, 1 for each strand of a duplex made of two different strands. Omit when
      unknown rather than assuming 1.'
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_entity.pdbx_number_of_molecules
    domain_of:
    - SampleComponent
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: integer
  residue_range:
    name: residue_range
    description: 'Nucleotides of the reference sequence present in this sample (e.g.,
      ''1-76'', ''30-45''), for fragments of a longer RNA or DNA. Omit when the whole
      sequence is present. Positions or ranges, comma-separated: ''1-76'', ''30-45,60-72''.'
    from_schema: http://w3id.org/lambda/
    related_mappings:
    - IHMCIF:_ihm_entity_poly_segment
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ProteinAnnotation
    pattern: ^[0-9]+(-[0-9]+)?(,[0-9]+(-[0-9]+)?)*$
  sequence_coverage:
    name: sequence_coverage
    description: 'Fraction of the reference sequence present in this sample (range:
      0-1)'
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: float
    minimum_value: 0
    maximum_value: 1
  chain_ids:
    name: chain_ids
    description: Chain identifiers this strand occupies in the deposited structure,
      where the sample is a PDB entity
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_entity_poly.pdbx_strand_id
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    multivalued: true
  structural_form:
    name: structural_form
    description: 'Form the strand takes in this sample: single-stranded, paired in
      a duplex, folded as a hairpin, a quadruplex, and so on. Both strands of a heteroduplex
      say double_stranded.'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleNucleicAcidAssociation
    range: NucleicAcidFormEnum
  source_method:
    name: source_method
    description: 'How this strand was made for this preparation: chemical synthesis,
      in vitro transcription, PCR, ...'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleNucleicAcidAssociation
    range: NucleicAcidSourceEnum
  modifications:
    name: modifications
    description: 'Modifications carried by this strand in this sample: fluorophore
      or biotin labels, 2''-O-methyl groups, phosphorothioate linkages, a 5'' triphosphate
      left on, methylated bases. One modification per entry, its position or extent
      first where it has one, then the chemistry: "5'' 6-FAM", "3'' biotin", "2''-O-methyl
      at 1-3", "phosphorothioate at 1-2,21-22", "m6A at 15", "5'' triphosphate". A
      modification with no position is named alone: "phosphorothioate backbone".'
    from_schema: http://w3id.org/lambda/
    domain_of:
    - MolecularComposition
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    multivalued: true
  observed_molecular_weight:
    name: observed_molecular_weight
    description: Mass as measured for this preparation (mass spectrometry, SEC-MALS,
      SAXS), typically in kDa. The sequence-derived mass lives on NucleicAcid.molecular_weight_theoretical.
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: QuantityValue
    inlined: true

Induced

name: SampleNucleicAcidAssociation
description: 'M:N link between Sample and NucleicAcid. A sample may hold several strands
  - the two strands of a duplex, a guide RNA with its target DNA, a primer with its
  template - and one strand turns up in many samples. What changes from preparation
  to preparation lives here: the role, the copy number, the form the strand takes
  (single, duplex, hairpin, quadruplex), how it was made, the modifications it carries,
  and the mass actually measured.'
comments:
- A SampleComponent row of type nucleic_acid for the same sample and strand is the
  inventory entry and the handle a SampleComponentInteraction points at; this association
  is the per-preparation detail. A dataset that records no interactions may carry
  this row alone. Where role or copy_number is set on both, they must agree.
from_schema: http://w3id.org/lambda/
related_mappings:
- IHMCIF:_ihm_struct_assembly_details
- IHMCIF:_ihm_entity_poly_segment
attributes:
  sample_id:
    name: sample_id
    description: Reference to the sample
    from_schema: http://w3id.org/lambda/
    alias: sample_id
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleComponent
    - SamplePreparation
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - SampleComponentInteraction
    range: Sample
    required: true
  nucleic_acid_id:
    name: nucleic_acid_id
    description: Reference to the nucleic acid
    from_schema: http://w3id.org/lambda/
    alias: nucleic_acid_id
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleComponent
    - SampleNucleicAcidAssociation
    range: NucleicAcid
    required: true
  role:
    name: role
    description: Part this nucleic acid plays in the sample
    from_schema: http://w3id.org/lambda/
    alias: role
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleComponent
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ExperimentInstrumentAssociation
    - StudyPersonAssociation
    - ExperimentPersonAssociation
    - WorkflowPersonAssociation
    - StudyOrganizationAssociation
    - PersonOrganizationAssociation
    range: SampleNucleicAcidRoleEnum
  copy_number:
    name: copy_number
    description: 'Copies of this strand per assembly in the sample: 2 for a self-complementary
      duplex, 1 for each strand of a duplex made of two different strands. Omit when
      unknown rather than assuming 1.'
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_entity.pdbx_number_of_molecules
    alias: copy_number
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleComponent
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: integer
  residue_range:
    name: residue_range
    description: 'Nucleotides of the reference sequence present in this sample (e.g.,
      ''1-76'', ''30-45''), for fragments of a longer RNA or DNA. Omit when the whole
      sequence is present. Positions or ranges, comma-separated: ''1-76'', ''30-45,60-72''.'
    from_schema: http://w3id.org/lambda/
    related_mappings:
    - IHMCIF:_ihm_entity_poly_segment
    alias: residue_range
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ProteinAnnotation
    range: string
    pattern: ^[0-9]+(-[0-9]+)?(,[0-9]+(-[0-9]+)?)*$
  sequence_coverage:
    name: sequence_coverage
    description: 'Fraction of the reference sequence present in this sample (range:
      0-1)'
    from_schema: http://w3id.org/lambda/
    alias: sequence_coverage
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: float
    minimum_value: 0
    maximum_value: 1
  chain_ids:
    name: chain_ids
    description: Chain identifiers this strand occupies in the deposited structure,
      where the sample is a PDB entity
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_entity_poly.pdbx_strand_id
    alias: chain_ids
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: string
    multivalued: true
  structural_form:
    name: structural_form
    description: 'Form the strand takes in this sample: single-stranded, paired in
      a duplex, folded as a hairpin, a quadruplex, and so on. Both strands of a heteroduplex
      say double_stranded.'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: structural_form
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleNucleicAcidAssociation
    range: NucleicAcidFormEnum
  source_method:
    name: source_method
    description: 'How this strand was made for this preparation: chemical synthesis,
      in vitro transcription, PCR, ...'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: source_method
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleNucleicAcidAssociation
    range: NucleicAcidSourceEnum
  modifications:
    name: modifications
    description: 'Modifications carried by this strand in this sample: fluorophore
      or biotin labels, 2''-O-methyl groups, phosphorothioate linkages, a 5'' triphosphate
      left on, methylated bases. One modification per entry, its position or extent
      first where it has one, then the chemistry: "5'' 6-FAM", "3'' biotin", "2''-O-methyl
      at 1-3", "phosphorothioate at 1-2,21-22", "m6A at 15", "5'' triphosphate". A
      modification with no position is named alone: "phosphorothioate backbone".'
    from_schema: http://w3id.org/lambda/
    alias: modifications
    owner: SampleNucleicAcidAssociation
    domain_of:
    - MolecularComposition
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: string
    multivalued: true
  observed_molecular_weight:
    name: observed_molecular_weight
    description: Mass as measured for this preparation (mass spectrometry, SEC-MALS,
      SAXS), typically in kDa. The sequence-derived mass lives on NucleicAcid.molecular_weight_theoretical.
    from_schema: http://w3id.org/lambda/
    alias: observed_molecular_weight
    owner: SampleNucleicAcidAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: QuantityValue
    inlined: true