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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		 NamedThing
description 0..1
String		 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
    rank: 1000
    domain_of:
    - 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
    rank: 1000
    domain_of:
    - 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
    rank: 1000
    alias: protein_name
    owner: AggregatedProteinView
    domain_of:
    - 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
    rank: 1000
    alias: mutations
    owner: AggregatedProteinView
    domain_of:
    - 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
    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
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: AggregatedProteinView
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string