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Class: ProteinConstruct

Detailed information about a protein construct including cloning and sequence design

URI: lambdaber:ProteinConstruct

classDiagram class ProteinConstruct click ProteinConstruct href "../ProteinConstruct/" NamedThing <|-- ProteinConstruct click NamedThing href "../NamedThing/" ProteinConstruct : cleavage_site ProteinConstruct : cloning_method ProteinConstruct : codon_optimization_organism ProteinConstruct : construct_description ProteinConstruct : construct_id ProteinConstruct : description ProteinConstruct : gene_name ProteinConstruct : gene_synthesis_provider ProteinConstruct : id ProteinConstruct : insert_boundaries ProteinConstruct : ncbi_taxid ProteinConstruct : promoter ProteinConstruct : selectable_marker ProteinConstruct : sequence_file_path ProteinConstruct : sequence_length_aa ProteinConstruct : sequence_verified_by ProteinConstruct : signal_peptide ProteinConstruct : tag_cterm ProteinConstruct : tag_nterm ProteinConstruct : title ProteinConstruct : uniprot_id ProteinConstruct : vector_backbone ProteinConstruct : vector_name ProteinConstruct : verification_notes

Inheritance

Slots

Name Cardinality and Range Description Inheritance
construct_id 1
String		 Unique identifier for this construct direct
uniprot_id 0..1
String		 UniProt accession for the target protein direct
gene_name 0..1
String		 Gene name direct
ncbi_taxid 0..1
String		 NCBI Taxonomy ID for source organism direct
sequence_length_aa 0..1
Integer		 Length of the protein sequence in amino acids direct
construct_description 0..1
String		 Human-readable description of the construct direct
gene_synthesis_provider 0..1
String		 Company or facility that synthesized the gene direct
codon_optimization_organism 0..1
String		 Organism for which codons were optimized direct
vector_backbone 0..1
String		 Base plasmid backbone used direct
vector_name 0..1
String		 Complete vector name direct
promoter 0..1
String		 Promoter used for expression direct
tag_nterm 0..1
String		 N-terminal tag (e direct
tag_cterm 0..1
String		 C-terminal tag direct
cleavage_site 0..1
String		 Protease cleavage site sequence direct
signal_peptide 0..1
String		 Signal peptide sequence if present direct
selectable_marker 0..1
String		 Antibiotic resistance or other selectable marker direct
cloning_method 0..1
String		 Method used for cloning (e direct
insert_boundaries 0..1
String		 Start and end positions of insert in vector direct
sequence_file_path 0..1
String		 Path to sequence file direct
sequence_verified_by 0..1
String		 Method or person who verified the sequence direct
verification_notes 0..1
String		 Notes from sequence verification 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 protein_constructs range ProteinConstruct

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: ProteinConstruct
description: Detailed information about a protein construct including cloning and
  sequence design
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  construct_id:
    name: construct_id
    description: Unique identifier for this construct
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
    required: true
  uniprot_id:
    name: uniprot_id
    description: UniProt accession for the target protein
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
    - AggregatedProteinView
  gene_name:
    name: gene_name
    description: Gene name
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI Taxonomy ID for source organism
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  sequence_length_aa:
    name: sequence_length_aa
    description: Length of the protein sequence in amino acids
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
    range: integer
  construct_description:
    name: construct_description
    description: Human-readable description of the construct
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  gene_synthesis_provider:
    name: gene_synthesis_provider
    description: Company or facility that synthesized the gene
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  codon_optimization_organism:
    name: codon_optimization_organism
    description: Organism for which codons were optimized
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  vector_backbone:
    name: vector_backbone
    description: Base plasmid backbone used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  vector_name:
    name: vector_name
    description: Complete vector name
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  promoter:
    name: promoter
    description: Promoter used for expression
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  tag_nterm:
    name: tag_nterm
    description: N-terminal tag (e.g., His6, MBP, GST)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  tag_cterm:
    name: tag_cterm
    description: C-terminal tag
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  cleavage_site:
    name: cleavage_site
    description: Protease cleavage site sequence
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  signal_peptide:
    name: signal_peptide
    description: Signal peptide sequence if present
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  selectable_marker:
    name: selectable_marker
    description: Antibiotic resistance or other selectable marker
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  cloning_method:
    name: cloning_method
    description: Method used for cloning (e.g., restriction digest, Gibson, InFusion)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  insert_boundaries:
    name: insert_boundaries
    description: Start and end positions of insert in vector
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  sequence_file_path:
    name: sequence_file_path
    description: Path to sequence file
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  sequence_verified_by:
    name: sequence_verified_by
    description: Method or person who verified the sequence
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct
  verification_notes:
    name: verification_notes
    description: Notes from sequence verification
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ProteinConstruct

Induced

name: ProteinConstruct
description: Detailed information about a protein construct including cloning and
  sequence design
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  construct_id:
    name: construct_id
    description: Unique identifier for this construct
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: construct_id
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
    required: true
  uniprot_id:
    name: uniprot_id
    description: UniProt accession for the target protein
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: uniprot_id
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    - AggregatedProteinView
    range: string
  gene_name:
    name: gene_name
    description: Gene name
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: gene_name
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  ncbi_taxid:
    name: ncbi_taxid
    description: NCBI Taxonomy ID for source organism
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ncbi_taxid
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  sequence_length_aa:
    name: sequence_length_aa
    description: Length of the protein sequence in amino acids
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sequence_length_aa
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: integer
  construct_description:
    name: construct_description
    description: Human-readable description of the construct
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: construct_description
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  gene_synthesis_provider:
    name: gene_synthesis_provider
    description: Company or facility that synthesized the gene
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: gene_synthesis_provider
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  codon_optimization_organism:
    name: codon_optimization_organism
    description: Organism for which codons were optimized
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: codon_optimization_organism
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  vector_backbone:
    name: vector_backbone
    description: Base plasmid backbone used
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: vector_backbone
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  vector_name:
    name: vector_name
    description: Complete vector name
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: vector_name
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  promoter:
    name: promoter
    description: Promoter used for expression
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: promoter
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  tag_nterm:
    name: tag_nterm
    description: N-terminal tag (e.g., His6, MBP, GST)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: tag_nterm
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  tag_cterm:
    name: tag_cterm
    description: C-terminal tag
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: tag_cterm
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  cleavage_site:
    name: cleavage_site
    description: Protease cleavage site sequence
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cleavage_site
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  signal_peptide:
    name: signal_peptide
    description: Signal peptide sequence if present
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: signal_peptide
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  selectable_marker:
    name: selectable_marker
    description: Antibiotic resistance or other selectable marker
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: selectable_marker
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  cloning_method:
    name: cloning_method
    description: Method used for cloning (e.g., restriction digest, Gibson, InFusion)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: cloning_method
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  insert_boundaries:
    name: insert_boundaries
    description: Start and end positions of insert in vector
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: insert_boundaries
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  sequence_file_path:
    name: sequence_file_path
    description: Path to sequence file
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sequence_file_path
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  sequence_verified_by:
    name: sequence_verified_by
    description: Method or person who verified the sequence
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: sequence_verified_by
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  verification_notes:
    name: verification_notes
    description: Notes from sequence verification
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: verification_notes
    owner: ProteinConstruct
    domain_of:
    - ProteinConstruct
    range: string
  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: ProteinConstruct
    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: ProteinConstruct
    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: ProteinConstruct
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string