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Class: AggregatedProteinView

Aggregated view of all structural and functional data for a protein

URI: lambdaber:AggregatedProteinView

classDiagram class AggregatedProteinView click AggregatedProteinView href "../AggregatedProteinView/" NamedThing <|-- AggregatedProteinView click NamedThing href "../NamedThing/" AggregatedProteinView : biophysical_properties AggregatedProteinView --> "*" BiophysicalProperty : biophysical_properties click BiophysicalProperty href "../BiophysicalProperty/" AggregatedProteinView : conformational_ensemble AggregatedProteinView --> "0..1" ConformationalEnsemble : conformational_ensemble click ConformationalEnsemble href "../ConformationalEnsemble/" AggregatedProteinView : cross_references AggregatedProteinView --> "*" DatabaseCrossReference : cross_references click DatabaseCrossReference href "../DatabaseCrossReference/" AggregatedProteinView : description AggregatedProteinView : evolutionary_conservation AggregatedProteinView --> "0..1" EvolutionaryConservation : evolutionary_conservation click EvolutionaryConservation href "../EvolutionaryConservation/" AggregatedProteinView : functional_sites AggregatedProteinView --> "*" FunctionalSite : functional_sites click FunctionalSite href "../FunctionalSite/" AggregatedProteinView : id AggregatedProteinView : ligand_interactions AggregatedProteinView --> "*" LigandInteraction : ligand_interactions click LigandInteraction href "../LigandInteraction/" AggregatedProteinView : mutations AggregatedProteinView --> "*" MutationEffect : mutations click MutationEffect href "../MutationEffect/" AggregatedProteinView : organism AggregatedProteinView : organism_id AggregatedProteinView : pdb_entries AggregatedProteinView : protein_interactions AggregatedProteinView --> "*" ProteinProteinInteraction : protein_interactions click ProteinProteinInteraction href "../ProteinProteinInteraction/" AggregatedProteinView : protein_name AggregatedProteinView : ptms AggregatedProteinView --> "*" PostTranslationalModification : ptms click PostTranslationalModification href "../PostTranslationalModification/" AggregatedProteinView : structural_features AggregatedProteinView --> "*" StructuralFeature : structural_features click StructuralFeature href "../StructuralFeature/" AggregatedProteinView : title AggregatedProteinView : uniprot_id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
uniprot_id 1
String		 UniProt accession direct
protein_name 1
String		 Protein name direct
organism 0..1
String		 Source organism direct
organism_id 0..1
Integer		 NCBI taxonomy ID direct
pdb_entries *
String		 All PDB entries for this protein direct
functional_sites *
FunctionalSite		 All functional site annotations direct
structural_features *
StructuralFeature		 All structural feature annotations direct
protein_interactions *
ProteinProteinInteraction		 All protein-protein interactions direct
ligand_interactions *
LigandInteraction		 All ligand interactions direct
mutations *
MutationEffect		 All mutation annotations direct
ptms *
PostTranslationalModification		 All post-translational modifications direct
biophysical_properties *
BiophysicalProperty		 All biophysical properties direct
conformational_ensemble 0..1
ConformationalEnsemble		 Conformational ensemble data direct
evolutionary_conservation 0..1
EvolutionaryConservation		 Conservation analysis direct
cross_references *
DatabaseCrossReference		 Database cross-references direct
id 1
Uriorcurie		 Globally unique identifier as an IRI or CURIE for machine processing and exte... NamedThing
title 0..1
String		 A human-readable name or title for this entity NamedThing
description 0..1
String		 A detailed textual description of this entity NamedThing

Usages

used by used in type used
Study aggregated_protein_views range AggregatedProteinView

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:AggregatedProteinView
native lambdaber:AggregatedProteinView

LinkML Source

Direct

name: AggregatedProteinView
description: Aggregated view of all structural and functional data for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  uniprot_id:
    name: uniprot_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - ProteinConstruct
    - AggregatedProteinView
    required: true
  protein_name:
    name: protein_name
    description: Protein name
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    required: true
  organism:
    name: organism
    description: Source organism
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
  organism_id:
    name: organism_id
    description: NCBI taxonomy ID
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - AggregatedProteinView
    range: integer
  pdb_entries:
    name: pdb_entries
    description: All PDB entries for this protein
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - ConformationalState
    - AggregatedProteinView
    multivalued: true
  functional_sites:
    name: functional_sites
    description: All functional site annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: FunctionalSite
    multivalued: true
    inlined: true
    inlined_as_list: true
  structural_features:
    name: structural_features
    description: All structural feature annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: StructuralFeature
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_interactions:
    name: protein_interactions
    description: All protein-protein interactions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ProteinProteinInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  ligand_interactions:
    name: ligand_interactions
    description: All ligand interactions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  mutations:
    name: mutations
    description: All mutation annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: MutationEffect
    multivalued: true
    inlined: true
    inlined_as_list: true
  ptms:
    name: ptms
    description: All post-translational modifications
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - AggregatedProteinView
    range: PostTranslationalModification
    multivalued: true
    inlined: true
    inlined_as_list: true
  biophysical_properties:
    name: biophysical_properties
    description: All biophysical properties
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: BiophysicalProperty
    multivalued: true
    inlined: true
    inlined_as_list: true
  conformational_ensemble:
    name: conformational_ensemble
    description: Conformational ensemble data
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ConformationalEnsemble
    inlined: true
  evolutionary_conservation:
    name: evolutionary_conservation
    description: Conservation analysis
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - Sample
    - AggregatedProteinView
    range: EvolutionaryConservation
    inlined: true
  cross_references:
    name: cross_references
    description: Database cross-references
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - AggregatedProteinView
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: AggregatedProteinView
description: Aggregated view of all structural and functional data for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  uniprot_id:
    name: uniprot_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: uniprot_id
    owner: AggregatedProteinView
    domain_of:
    - ProteinConstruct
    - AggregatedProteinView
    range: string
    required: true
  protein_name:
    name: protein_name
    description: Protein name
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: protein_name
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: string
    required: true
  organism:
    name: organism
    description: Source organism
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: organism
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: string
  organism_id:
    name: organism_id
    description: NCBI taxonomy ID
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: organism_id
    owner: AggregatedProteinView
    domain_of:
    - AggregatedProteinView
    range: integer
  pdb_entries:
    name: pdb_entries
    description: All PDB entries for this protein
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: pdb_entries
    owner: AggregatedProteinView
    domain_of:
    - ConformationalState
    - AggregatedProteinView
    range: string
    multivalued: true
  functional_sites:
    name: functional_sites
    description: All functional site annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: functional_sites
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: FunctionalSite
    multivalued: true
    inlined: true
    inlined_as_list: true
  structural_features:
    name: structural_features
    description: All structural feature annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: structural_features
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: StructuralFeature
    multivalued: true
    inlined: true
    inlined_as_list: true
  protein_interactions:
    name: protein_interactions
    description: All protein-protein interactions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: protein_interactions
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ProteinProteinInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  ligand_interactions:
    name: ligand_interactions
    description: All ligand interactions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: ligand_interactions
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - FunctionalSite
    - AggregatedProteinView
    range: LigandInteraction
    multivalued: true
    inlined: true
    inlined_as_list: true
  mutations:
    name: mutations
    description: All mutation annotations
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: mutations
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: MutationEffect
    multivalued: true
    inlined: true
    inlined_as_list: true
  ptms:
    name: ptms
    description: All post-translational modifications
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: ptms
    owner: AggregatedProteinView
    domain_of:
    - AggregatedProteinView
    range: PostTranslationalModification
    multivalued: true
    inlined: true
    inlined_as_list: true
  biophysical_properties:
    name: biophysical_properties
    description: All biophysical properties
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: biophysical_properties
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: BiophysicalProperty
    multivalued: true
    inlined: true
    inlined_as_list: true
  conformational_ensemble:
    name: conformational_ensemble
    description: Conformational ensemble data
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: conformational_ensemble
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: ConformationalEnsemble
    inlined: true
  evolutionary_conservation:
    name: evolutionary_conservation
    description: Conservation analysis
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: evolutionary_conservation
    owner: AggregatedProteinView
    domain_of:
    - Sample
    - AggregatedProteinView
    range: EvolutionaryConservation
    inlined: true
  cross_references:
    name: cross_references
    description: Database cross-references
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: cross_references
    owner: AggregatedProteinView
    domain_of:
    - AggregatedProteinView
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: AggregatedProteinView
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    description: A human-readable name or title for this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: AggregatedProteinView
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A detailed textual description of this entity
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: AggregatedProteinView
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string