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