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Class: SampleProteinAssociation

M:N link between Sample and Protein. A sample may hold several proteins - the subunits of a complex, a target with its chaperone, a fusion partner - and one protein turns up in many samples. What changes from preparation to preparation lives here: the role, the copy number, the residue range actually present, the modifications carried, the mass actually measured, and the construct it was made from.

URI: lambda:SampleProteinAssociation

classDiagram class SampleProteinAssociation click SampleProteinAssociation href "../SampleProteinAssociation/" SampleProteinAssociation : chain_ids SampleProteinAssociation : construct_id SampleProteinAssociation --> "0..1" ProteinConstruct : construct_id click ProteinConstruct href "../ProteinConstruct/" SampleProteinAssociation : copy_number SampleProteinAssociation : modifications SampleProteinAssociation : observed_molecular_weight SampleProteinAssociation --> "0..1" QuantityValue : observed_molecular_weight click QuantityValue href "../QuantityValue/" SampleProteinAssociation : protein_id SampleProteinAssociation --> "1" Protein : protein_id click Protein href "../Protein/" SampleProteinAssociation : residue_range SampleProteinAssociation : role SampleProteinAssociation --> "0..1" SampleProteinRoleEnum : role click SampleProteinRoleEnum href "../SampleProteinRoleEnum/" SampleProteinAssociation : sample_id SampleProteinAssociation --> "1" Sample : sample_id click Sample href "../Sample/" SampleProteinAssociation : sequence_coverage

Slots

Name Cardinality and Range Description Inheritance
sample_id 1
Sample		 Reference to the sample direct
protein_id 1
Protein		 Reference to the protein direct
role 0..1
SampleProteinRoleEnum		 Part this protein plays in the sample direct
construct_id 0..1
ProteinConstruct		 The construct that produced this protein in this sample, where cloning detail... direct
copy_number 0..1
Integer		 Copies of this protein per assembly in the sample (e direct
residue_range 0..1
String		 Residues of the canonical sequence present in this sample (e direct
sequence_coverage 0..1
Float		 Fraction of the canonical sequence present in this sample (range: 0-1) direct
chain_ids *
String		 Chain identifiers this protein occupies in the deposited structure, where the... direct
modifications *
String		 Modifications carried by this protein in this sample: tags left on, mutations... 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_protein_associations range SampleProteinAssociation

Comments

  • A SampleComponent row of type protein for the same sample and protein 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:SampleProteinAssociation
native lambda:SampleProteinAssociation
related IHMCIF:_ihm_struct_assembly_details, IHMCIF:_ihm_entity_poly_segment

LinkML Source

Direct

name: SampleProteinAssociation
description: 'M:N link between Sample and Protein. A sample may hold several proteins
  - the subunits of a complex, a target with its chaperone, a fusion partner - and
  one protein turns up in many samples. What changes from preparation to preparation
  lives here: the role, the copy number, the residue range actually present, the modifications
  carried, the mass actually measured, and the construct it was made from.'
comments:
- A SampleComponent row of type protein for the same sample and protein 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
  protein_id:
    name: protein_id
    description: Reference to the protein
    from_schema: http://w3id.org/lambda/
    domain_of:
    - ProteinConstruct
    - SampleComponent
    - SampleProteinAssociation
    - ProteinAnnotation
    - ConformationalEnsemble
    range: Protein
    required: true
  role:
    name: role
    description: Part this protein plays in the sample
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleComponent
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ExperimentInstrumentAssociation
    - StudyPersonAssociation
    - ExperimentPersonAssociation
    - WorkflowPersonAssociation
    - StudyOrganizationAssociation
    - PersonOrganizationAssociation
    range: SampleProteinRoleEnum
  construct_id:
    name: construct_id
    description: The construct that produced this protein in this sample, where cloning
      detail is recorded
    from_schema: http://w3id.org/lambda/
    domain_of:
    - ProteinConstruct
    - SampleProteinAssociation
    range: ProteinConstruct
  copy_number:
    name: copy_number
    description: Copies of this protein per assembly in the sample (e.g., 4 for a
      homotetramer, 2 for each chain of an alpha2-beta2 heterotetramer). 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: 'Residues of the canonical sequence present in this sample (e.g.,
      ''1-141'', ''25-300''), for fragments and truncations. Omit when the full-length
      protein is present. Residues or ranges, comma-separated: ''1-141'', ''25,27,30-35''.'
    from_schema: http://w3id.org/lambda/
    related_mappings:
    - IHMCIF:_ihm_entity_poly_segment
    rank: 1000
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ProteinAnnotation
    pattern: ^[0-9]+(-[0-9]+)?(,[0-9]+(-[0-9]+)?)*$
  sequence_coverage:
    name: sequence_coverage
    description: 'Fraction of the canonical sequence present in this sample (range:
      0-1)'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: float
    minimum_value: 0
    maximum_value: 1
  chain_ids:
    name: chain_ids
    description: Chain identifiers this protein 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
    rank: 1000
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    multivalued: true
  modifications:
    name: modifications
    description: 'Modifications carried by this protein in this sample: tags left
      on, mutations, labels, post-translational modifications'
    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 Protein.molecular_weight_theoretical.
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: QuantityValue
    inlined: true

Induced

name: SampleProteinAssociation
description: 'M:N link between Sample and Protein. A sample may hold several proteins
  - the subunits of a complex, a target with its chaperone, a fusion partner - and
  one protein turns up in many samples. What changes from preparation to preparation
  lives here: the role, the copy number, the residue range actually present, the modifications
  carried, the mass actually measured, and the construct it was made from.'
comments:
- A SampleComponent row of type protein for the same sample and protein 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: SampleProteinAssociation
    domain_of:
    - SampleComponent
    - SamplePreparation
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - SampleComponentInteraction
    range: Sample
    required: true
  protein_id:
    name: protein_id
    description: Reference to the protein
    from_schema: http://w3id.org/lambda/
    alias: protein_id
    owner: SampleProteinAssociation
    domain_of:
    - ProteinConstruct
    - SampleComponent
    - SampleProteinAssociation
    - ProteinAnnotation
    - ConformationalEnsemble
    range: Protein
    required: true
  role:
    name: role
    description: Part this protein plays in the sample
    from_schema: http://w3id.org/lambda/
    alias: role
    owner: SampleProteinAssociation
    domain_of:
    - SampleComponent
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - ExperimentInstrumentAssociation
    - StudyPersonAssociation
    - ExperimentPersonAssociation
    - WorkflowPersonAssociation
    - StudyOrganizationAssociation
    - PersonOrganizationAssociation
    range: SampleProteinRoleEnum
  construct_id:
    name: construct_id
    description: The construct that produced this protein in this sample, where cloning
      detail is recorded
    from_schema: http://w3id.org/lambda/
    alias: construct_id
    owner: SampleProteinAssociation
    domain_of:
    - ProteinConstruct
    - SampleProteinAssociation
    range: ProteinConstruct
  copy_number:
    name: copy_number
    description: Copies of this protein per assembly in the sample (e.g., 4 for a
      homotetramer, 2 for each chain of an alpha2-beta2 heterotetramer). 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: SampleProteinAssociation
    domain_of:
    - SampleComponent
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: integer
  residue_range:
    name: residue_range
    description: 'Residues of the canonical sequence present in this sample (e.g.,
      ''1-141'', ''25-300''), for fragments and truncations. Omit when the full-length
      protein is present. Residues or ranges, comma-separated: ''1-141'', ''25,27,30-35''.'
    from_schema: http://w3id.org/lambda/
    related_mappings:
    - IHMCIF:_ihm_entity_poly_segment
    rank: 1000
    alias: residue_range
    owner: SampleProteinAssociation
    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 canonical sequence present in this sample (range:
      0-1)'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: sequence_coverage
    owner: SampleProteinAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: float
    minimum_value: 0
    maximum_value: 1
  chain_ids:
    name: chain_ids
    description: Chain identifiers this protein 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
    rank: 1000
    alias: chain_ids
    owner: SampleProteinAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: string
    multivalued: true
  modifications:
    name: modifications
    description: 'Modifications carried by this protein in this sample: tags left
      on, mutations, labels, post-translational modifications'
    from_schema: http://w3id.org/lambda/
    alias: modifications
    owner: SampleProteinAssociation
    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 Protein.molecular_weight_theoretical.
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: observed_molecular_weight
    owner: SampleProteinAssociation
    domain_of:
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    range: QuantityValue
    inlined: true