Class: PartsSequence

Data representing the nucleic acid composition of a Modification

classDiagram class PartsSequence PartsSequence : associated_part PartsSequence : date_added PartsSequence : go_term_ids PartsSequence : go_term_labels PartsSequence : id PartsSequence : match_ec_numbers PartsSequence : match_gene_symbols_etc PartsSequence : match_names PartsSequence : nt_sequence PartsSequence : other_accessions PartsSequence : scientific_names PartsSequence : seq_name PartsSequence : seq_type PartsSequence : taxon_ids PartsSequence : uniprot_accessions

Slots

Name	Cardinality and Range	Description	Inheritance
id	1..1 xsd:string	None	direct
associated_part	0..1 Modification	found in this Modification	direct
date_added	0..1 xsd:string	date when this record was added to the Database	direct
go_term_ids	0..* xsd:anyURI	may be described by these annotations, as determined by a sequence similarity search	direct
go_term_labels	0..* xsd:string	may be described by these annotations, as determined by a sequence similarity search	direct
match_ec_numbers	0..* xsd:string	corresponds to this enzyme, as determined by a sequence similarity search	direct
match_gene_symbols_etc	0..* xsd:string	corresponds to this genes, as determined by a sequence similarity search	direct
match_names	0..* xsd:string	similar to this sequence, as determined by a sequence similarity search	direct
nt_sequence	0..1 xsd:string	the nucleotide sequence of this entity	direct
other_accessions	0..* xsd:string	Especially fpbase identifiers. Some Uniprot/Swissprot accessions may leak in if an entry could not be retrieved from the Uniprot API.	direct
scientific_names	0..* xsd:string	may originate in this organism, as determined by a sequence similarity search	direct
seq_name	0..1 xsd:string	a name assigned to this entity by a person involved in teh modification process	direct
seq_type	0..1 SeqTypeEnum	None	direct
taxon_ids	0..* xsd:string	may originate in this organism, as determined by a sequence similarity search	direct
uniprot_accessions	0..* xsd:string	similar to this sequence, as determined by a sequence similarity search	direct

Usages

used by	used in	type	used
Database	sequence_set	range	PartsSequence

TODOs

clarify which slots represent a lookup, like the current match... slots

Identifier and Mapping Information

Schema Source

from schema: https://example.com/synbio

Mappings

Mapping Type	Mapped Value
self	['synbio:PartsSequence']
native	['synbio:PartsSequence']

LinkML Source

Direct

name: PartsSequence
description: Data representing the nucleic acid composition of a Modification
todos:
- clarify which slots represent a lookup, like the current match... slots
from_schema: https://example.com/synbio
rank: 1000
slots:
- id
- associated_part
- date_added
- go_term_ids
- go_term_labels
- match_ec_numbers
- match_gene_symbols_etc
- match_names
- nt_sequence
- other_accessions
- scientific_names
- seq_name
- seq_type
- taxon_ids
- uniprot_accessions
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: ^sequence:\d+$
  associated_part:
    name: associated_part
    domain_of:
    - PartsSequence
    - PartsSequence
    pattern: ^IF:\d+$

Induced

name: PartsSequence
description: Data representing the nucleic acid composition of a Modification
todos:
- clarify which slots represent a lookup, like the current match... slots
from_schema: https://example.com/synbio
rank: 1000
slot_usage:
  id:
    name: id
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    pattern: ^sequence:\d+$
  associated_part:
    name: associated_part
    domain_of:
    - PartsSequence
    - PartsSequence
    pattern: ^IF:\d+$
attributes:
  id:
    name: id
    from_schema: https://example.com/synbio
    rank: 1000
    identifier: true
    alias: id
    owner: PartsSequence
    domain_of:
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    - PartsSequence
    - Strain
    - Modification
    - Organism
    - Person
    range: string
    pattern: ^sequence:\d+$
  associated_part:
    name: associated_part
    description: found in this Modification
    from_schema: https://example.com/synbio
    rank: 1000
    alias: associated_part
    owner: PartsSequence
    domain_of:
    - PartsSequence
    - PartsSequence
    range: Modification
    pattern: ^IF:\d+$
  date_added:
    name: date_added
    description: date when this record was added to the Database
    from_schema: https://example.com/synbio
    rank: 1000
    alias: date_added
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  go_term_ids:
    name: go_term_ids
    description: may be described by these annotations, as determined by a sequence
      similarity search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: go_term_ids
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: uriorcurie
  go_term_labels:
    name: go_term_labels
    description: may be described by these annotations, as determined by a sequence
      similarity search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: go_term_labels
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  match_ec_numbers:
    name: match_ec_numbers
    description: corresponds to this enzyme, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: match_ec_numbers
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  match_gene_symbols_etc:
    name: match_gene_symbols_etc
    description: corresponds to this genes, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: match_gene_symbols_etc
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  match_names:
    name: match_names
    description: similar to this sequence, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: match_names
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  nt_sequence:
    name: nt_sequence
    description: the nucleotide sequence of this entity
    from_schema: https://example.com/synbio
    rank: 1000
    alias: nt_sequence
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  other_accessions:
    name: other_accessions
    description: Especially fpbase identifiers.  Some Uniprot/Swissprot accessions
      may leak in  if an entry could not be retrieved from the Uniprot API.
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: other_accessions
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  scientific_names:
    name: scientific_names
    description: may originate in this organism, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: scientific_names
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  seq_name:
    name: seq_name
    description: a name assigned to this entity by a person involved in teh modification
      process
    from_schema: https://example.com/synbio
    rank: 1000
    alias: seq_name
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  seq_type:
    name: seq_type
    from_schema: https://example.com/synbio
    rank: 1000
    alias: seq_type
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: SeqTypeEnum
  taxon_ids:
    name: taxon_ids
    description: may originate in this organism, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: taxon_ids
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string
  uniprot_accessions:
    name: uniprot_accessions
    description: similar to this sequence, as determined by a sequence similarity
      search
    from_schema: https://example.com/synbio
    rank: 1000
    multivalued: true
    alias: uniprot_accessions
    owner: PartsSequence
    domain_of:
    - PartsSequence
    range: string