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Class: SampleComponentInteraction

A relationship between two components of one sample: this ligand binds that protein, this metal is coordinated by that enzyme, this guide RNA pairs with that DNA strand, this membrane protein sits in that nanodisc. One row per ordered pair and relationship, read subject to object as interaction_type is worded. Rows can say what the sample was made to test as well as what the data showed: interaction_status separates the design from the result, so a ligand soaked in and not seen in the density is recorded rather than silently dropped.

URI: lambda:SampleComponentInteraction

classDiagram class SampleComponentInteraction click SampleComponentInteraction href "../SampleComponentInteraction/" SampleComponentInteraction : affinity SampleComponentInteraction --> "0..1" QuantityValue : affinity click QuantityValue href "../QuantityValue/" SampleComponentInteraction : affinity_type SampleComponentInteraction --> "0..1" BindingAffinityTypeEnum : affinity_type click BindingAffinityTypeEnum href "../BindingAffinityTypeEnum/" SampleComponentInteraction : description SampleComponentInteraction : evidence SampleComponentInteraction --> "*" InteractionEvidenceEnum : evidence click InteractionEvidenceEnum href "../InteractionEvidenceEnum/" SampleComponentInteraction : interaction_status SampleComponentInteraction --> "0..1" InteractionStatusEnum : interaction_status click InteractionStatusEnum href "../InteractionStatusEnum/" SampleComponentInteraction : interaction_type SampleComponentInteraction --> "1" ComponentInteractionTypeEnum : interaction_type click ComponentInteractionTypeEnum href "../ComponentInteractionTypeEnum/" SampleComponentInteraction : object_id SampleComponentInteraction --> "1" SampleComponent : object_id click SampleComponent href "../SampleComponent/" SampleComponentInteraction : object_site SampleComponentInteraction : sample_id SampleComponentInteraction --> "1" Sample : sample_id click Sample href "../Sample/" SampleComponentInteraction : stoichiometry SampleComponentInteraction : subject_id SampleComponentInteraction --> "1" SampleComponent : subject_id click SampleComponent href "../SampleComponent/" SampleComponentInteraction : subject_site

Slots

Name Cardinality and Range Description Inheritance
sample_id 1
Sample		 The sample both components belong to direct
subject_id 1
SampleComponent		 The component that acts on, binds to or sits in the object direct
object_id 1
SampleComponent		 The component acted on, bound or hosting direct
interaction_type 1
ComponentInteractionTypeEnum		 What the subject does to the object direct
interaction_status 0..1
InteractionStatusEnum		 Whether the interaction is the design of the sample, expected from prior work... direct
stoichiometry 0..1
String		 Copies of subject to copies of object per assembly, written 'subject:object':... direct
subject_site 0..1
String		 Where on the subject the interaction takes place: residues or positions as 'D... direct
object_site 0..1
String		 Where on the object the interaction takes place, in the same form as subject_... direct
affinity 0..1
QuantityValue		 Binding affinity as a quantity with its unit (e direct
affinity_type 0..1
BindingAffinityTypeEnum		 Which constant affinity reports: Kd, Ki, IC50, direct
evidence *
InteractionEvidenceEnum		 Kind of evidence for the interaction direct
description 0..1
String		 Free-text detail: the binding mode, the reference the expectation comes from,... direct

Usages

used by used in type used
Dataset sample_component_interactions range SampleComponentInteraction

Comments

  • Subject and object are components of the same sample, and sample_id names that sample. Add the component rows first; the entities they point at are what the interaction is between, and the components are what it is between in this preparation.
  • Affinity and site may be known from prior work rather than measured here. Say which in evidence.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type Mapped Value
self lambda:SampleComponentInteraction
native lambda:SampleComponentInteraction
related mmCIF:_struct_conn, mmCIF:_struct_site, mmCIF:_pdbx_entity_nonpoly

LinkML Source

Direct

name: SampleComponentInteraction
description: 'A relationship between two components of one sample: this ligand binds
  that protein, this metal is coordinated by that enzyme, this guide RNA pairs with
  that DNA strand, this membrane protein sits in that nanodisc. One row per ordered
  pair and relationship, read subject to object as interaction_type is worded. Rows
  can say what the sample was made to test as well as what the data showed: interaction_status
  separates the design from the result, so a ligand soaked in and not seen in the
  density is recorded rather than silently dropped.'
comments:
- Subject and object are components of the same sample, and sample_id names that sample.
  Add the component rows first; the entities they point at are what the interaction
  is between, and the components are what it is between in this preparation.
- Affinity and site may be known from prior work rather than measured here. Say which
  in evidence.
from_schema: http://w3id.org/lambda/
related_mappings:
- mmCIF:_struct_conn
- mmCIF:_struct_site
- mmCIF:_pdbx_entity_nonpoly
attributes:
  sample_id:
    name: sample_id
    description: The sample both components belong to
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SampleComponent
    - SamplePreparation
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - SampleComponentInteraction
    range: Sample
    required: true
  subject_id:
    name: subject_id
    description: The component that acts on, binds to or sits in the object
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    range: SampleComponent
    required: true
  object_id:
    name: object_id
    description: The component acted on, bound or hosting
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    range: SampleComponent
    required: true
  interaction_type:
    name: interaction_type
    description: What the subject does to the object
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    - LigandInteraction
    range: ComponentInteractionTypeEnum
    required: true
  interaction_status:
    name: interaction_status
    description: Whether the interaction is the design of the sample, expected from
      prior work, observed in this dataset's data, or expected and not observed
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    range: InteractionStatusEnum
  stoichiometry:
    name: stoichiometry
    description: 'Copies of subject to copies of object per assembly, written ''subject:object'':
      ''1:1'', ''2:1'', ''3:1'' for three zinc ions per finger domain. A fractional
      count is allowed for partial occupancy (''0.5:1''), and ''n'' for a count that
      is many or unknown, as for the subunits of a filament (''n:1''). What n is,
      where known, goes in description.'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    pattern: ^([0-9]+(\.[0-9]+)?|n):([0-9]+(\.[0-9]+)?|n)$
  subject_site:
    name: subject_site
    description: 'Where on the subject the interaction takes place: residues or positions
      as ''D184,D186'' or ''45-60'', or a named site such as ''active site'' or ''ATP-binding
      pocket'''
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
  object_site:
    name: object_site
    description: Where on the object the interaction takes place, in the same form
      as subject_site
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
  affinity:
    name: affinity
    description: Binding affinity as a quantity with its unit (e.g., 12 nanomolar);
      affinity_type says which constant it is
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    range: QuantityValue
    inlined: true
  affinity_type:
    name: affinity_type
    description: 'Which constant affinity reports: Kd, Ki, IC50, ...'
    from_schema: http://w3id.org/lambda/
    domain_of:
    - SamplePreparation
    - SampleComponentInteraction
    range: BindingAffinityTypeEnum
  evidence:
    name: evidence
    description: Kind of evidence for the interaction
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SampleComponentInteraction
    range: InteractionEvidenceEnum
    multivalued: true
  description:
    name: description
    description: 'Free-text detail: the binding mode, the reference the expectation
      comes from, why an expected interaction was not seen'
    from_schema: http://w3id.org/lambda/
    domain_of:
    - NamedThing
    - AttributeGroup
    - SampleComponentInteraction
    range: string

Induced

name: SampleComponentInteraction
description: 'A relationship between two components of one sample: this ligand binds
  that protein, this metal is coordinated by that enzyme, this guide RNA pairs with
  that DNA strand, this membrane protein sits in that nanodisc. One row per ordered
  pair and relationship, read subject to object as interaction_type is worded. Rows
  can say what the sample was made to test as well as what the data showed: interaction_status
  separates the design from the result, so a ligand soaked in and not seen in the
  density is recorded rather than silently dropped.'
comments:
- Subject and object are components of the same sample, and sample_id names that sample.
  Add the component rows first; the entities they point at are what the interaction
  is between, and the components are what it is between in this preparation.
- Affinity and site may be known from prior work rather than measured here. Say which
  in evidence.
from_schema: http://w3id.org/lambda/
related_mappings:
- mmCIF:_struct_conn
- mmCIF:_struct_site
- mmCIF:_pdbx_entity_nonpoly
attributes:
  sample_id:
    name: sample_id
    description: The sample both components belong to
    from_schema: http://w3id.org/lambda/
    alias: sample_id
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponent
    - SamplePreparation
    - StudySampleAssociation
    - ExperimentSampleAssociation
    - SampleProteinAssociation
    - SampleNucleicAcidAssociation
    - SampleComponentInteraction
    range: Sample
    required: true
  subject_id:
    name: subject_id
    description: The component that acts on, binds to or sits in the object
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: subject_id
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: SampleComponent
    required: true
  object_id:
    name: object_id
    description: The component acted on, bound or hosting
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: object_id
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: SampleComponent
    required: true
  interaction_type:
    name: interaction_type
    description: What the subject does to the object
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: interaction_type
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    - LigandInteraction
    range: ComponentInteractionTypeEnum
    required: true
  interaction_status:
    name: interaction_status
    description: Whether the interaction is the design of the sample, expected from
      prior work, observed in this dataset's data, or expected and not observed
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: interaction_status
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: InteractionStatusEnum
  stoichiometry:
    name: stoichiometry
    description: 'Copies of subject to copies of object per assembly, written ''subject:object'':
      ''1:1'', ''2:1'', ''3:1'' for three zinc ions per finger domain. A fractional
      count is allowed for partial occupancy (''0.5:1''), and ''n'' for a count that
      is many or unknown, as for the subunits of a filament (''n:1''). What n is,
      where known, goes in description.'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: stoichiometry
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: string
    pattern: ^([0-9]+(\.[0-9]+)?|n):([0-9]+(\.[0-9]+)?|n)$
  subject_site:
    name: subject_site
    description: 'Where on the subject the interaction takes place: residues or positions
      as ''D184,D186'' or ''45-60'', or a named site such as ''active site'' or ''ATP-binding
      pocket'''
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: subject_site
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: string
  object_site:
    name: object_site
    description: Where on the object the interaction takes place, in the same form
      as subject_site
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: object_site
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: string
  affinity:
    name: affinity
    description: Binding affinity as a quantity with its unit (e.g., 12 nanomolar);
      affinity_type says which constant it is
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: affinity
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: QuantityValue
    inlined: true
  affinity_type:
    name: affinity_type
    description: 'Which constant affinity reports: Kd, Ki, IC50, ...'
    from_schema: http://w3id.org/lambda/
    alias: affinity_type
    owner: SampleComponentInteraction
    domain_of:
    - SamplePreparation
    - SampleComponentInteraction
    range: BindingAffinityTypeEnum
  evidence:
    name: evidence
    description: Kind of evidence for the interaction
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: evidence
    owner: SampleComponentInteraction
    domain_of:
    - SampleComponentInteraction
    range: InteractionEvidenceEnum
    multivalued: true
  description:
    name: description
    description: 'Free-text detail: the binding mode, the reference the expectation
      comes from, why an expected interaction was not seen'
    from_schema: http://w3id.org/lambda/
    alias: description
    owner: SampleComponentInteraction
    domain_of:
    - NamedThing
    - AttributeGroup
    - SampleComponentInteraction
    range: string