Class: sequence interval (SequenceInterval)

a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence.

• NOTE: this is an abstract class and should not be instantiated directly

URI: chemrof:SequenceInterval

 classDiagram
    class SequenceInterval
    click SequenceInterval href "../SequenceInterval"
      MolecularComponent <|-- SequenceInterval
        click MolecularComponent href "../MolecularComponent"


      SequenceInterval <|-- AminoAcidSequenceInterval
        click AminoAcidSequenceInterval href "../AminoAcidSequenceInterval"
      SequenceInterval <|-- NucleotideSequenceInterval
        click NucleotideSequenceInterval href "../NucleotideSequenceInterval"


      SequenceInterval : empirical_formula

      SequenceInterval : has_chemical_role




    SequenceInterval --> "0..1" ChemicalRole : has_chemical_role
    click ChemicalRole href "../ChemicalRole"


      SequenceInterval : has_physiologically_stable_form




    SequenceInterval --> "*" MoleculeByChargeState : has_physiologically_stable_form
    click MoleculeByChargeState href "../MoleculeByChargeState"


      SequenceInterval : has_sequence_representation

      SequenceInterval : id

      SequenceInterval : inchi_atom_connections_sublayer

      SequenceInterval : inchi_chemical_sublayer

      SequenceInterval : inchi_string

      SequenceInterval : is_radical

      SequenceInterval : IUPAC_name

      SequenceInterval : name

      SequenceInterval : owl_subclass_of




    SequenceInterval --> "0..1" OwlClass : owl_subclass_of
    click OwlClass href "../OwlClass"


      SequenceInterval : smiles_string

      SequenceInterval : type

Inheritance

• DomainEntity
  • PhysicochemicalEntity
    • ChemicalEntity [ OwlClass]
      • PolyatomicEntity
        • MolecularComponent
          • SequenceInterval
            • AminoAcidSequenceInterval
            • NucleotideSequenceInterval

Slots

Name	Cardinality and Range	Description	Inheritance
has_sequence_representation	0..1 SequenceString		direct
inchi_atom_connections_sublayer	0..1 recommended String	The atoms in the chemical formula (except for hydrogens) are numbered in sequ...	PolyatomicEntity
IUPAC_name	0..1 String		ChemicalEntity
is_radical	0..1 Boolean		ChemicalEntity
has_chemical_role	0..1 ChemicalRole		ChemicalEntity
inchi_string	0..1 ChemicalEncoding		ChemicalEntity
inchi_chemical_sublayer	0..1 recommended String	The part of an InChI string that represents the chemical formula, occurring a...	ChemicalEntity
smiles_string	* ChemicalEncoding	A string encoding of a molecular graph, no chiral or isotopic information	ChemicalEntity
empirical_formula	0..1 ChemicalEncoding	A chemical formula where numbers denote relative proportion of atoms	ChemicalEntity
has_physiologically_stable_form	* MoleculeByChargeState	connects an acid to the form that is stable at physiological pH (7	ChemicalEntity
owl_subclass_of	0..1 OwlClass	Holds between C and P if C owl:subClassOf P	OwlClass
id	1 String		DomainEntity
name	0..1 String	name of chemical entity	DomainEntity
type	0..1 Uriorcurie		DomainEntity

Comments

• • includes an interval corresponding to the whole molecule as an edge case

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/chemrof

Mappings

Mapping Type	Mapped Value
self	chemrof:SequenceInterval
native	chemrof:SequenceInterval

LinkML Source

Direct

name: SequenceInterval
description: a chain of connected monomers in a linear polymer - for example, a sub-region
  of an amino acid or nucleotide sequence.
title: sequence interval
comments:
- '- includes an interval corresponding to the whole molecule as an edge case'
from_schema: https://w3id.org/chemrof
is_a: MolecularComponent
abstract: true
slots:
- has_sequence_representation

Induced

name: SequenceInterval
description: a chain of connected monomers in a linear polymer - for example, a sub-region
  of an amino acid or nucleotide sequence.
title: sequence interval
comments:
- '- includes an interval corresponding to the whole molecule as an edge case'
from_schema: https://w3id.org/chemrof
is_a: MolecularComponent
abstract: true
attributes:
  has_sequence_representation:
    name: has_sequence_representation
    title: has sequence representation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_representation
    domain: ChemicalEntity
    alias: has_sequence_representation
    owner: SequenceInterval
    domain_of:
    - SequenceInterval
    range: SequenceString
  inchi_atom_connections_sublayer:
    name: inchi_atom_connections_sublayer
    description: The atoms in the chemical formula (except for hydrogens) are numbered
      in sequence; this sublayer describes which atoms are connected by bonds to which
      other ones.
    title: inchi atom connections sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_atom_connections_sublayer
    owner: SequenceInterval
    domain_of:
    - PolyatomicEntity
    - StandardInchiObject
    - EntityWithConnectivitySpecificied
    range: string
    required: false
    recommended: true
    pattern: ^c.*
  IUPAC_name:
    name: IUPAC_name
    title: IUPAC name
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - MI:2007
    rank: 1000
    is_a: information_property
    slot_uri: CHEMINF:000107
    alias: IUPAC_name
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: string
  is_radical:
    name: is_radical
    title: is radical
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: ChemicalEntity
    alias: is_radical
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: boolean
  has_chemical_role:
    name: has_chemical_role
    title: has chemical role
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_chemical_role
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: ChemicalRole
  inchi_string:
    name: inchi_string
    title: InChi
    todos:
    - declare this as a key once compound_key is introduced to linkml
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://chemistry.stackexchange.com/questions/151072/can-cis-trans-isomers-have-same-inchi
    aliases:
    - InChi
    exact_mappings:
    - OntoRXN:hasInChi
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: inchi_string
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    description: The part of an InChI string that represents the chemical formula,
      occurring after the version string. E.g. C6H12O6 for glucose
    title: inchi chemical sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_chemical_sublayer
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithAtomsEnumerated
    range: string
    required: false
    recommended: true
    pattern: ^[A-Z0-9\.]+$
  smiles_string:
    name: smiles_string
    description: A string encoding of a molecular graph, no chiral or isotopic information.
      There are usually a large number of valid SMILES which represent a given structure.
      For example, CCO, OCC and C(O)C all specify the structure of ethanol.
    title: smiles string
    comments:
    - a problematic set of structures to describe using SMILES notation is those which
      cannot be easily described using molecular graphs (see “Limitations of molecular
      graph representations” section), such as organometallic compounds and ionic
      salts.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: smiles_string
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
    multivalued: true
  empirical_formula:
    name: empirical_formula
    description: A chemical formula where numbers denote relative proportion of atoms.
      E.g. CH2O for glucose
    title: empirical formula
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: empirical_formula
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an acid to the form that is stable at physiological pH (7.3).
      E.g. citric acid has physiological base citrate(3-)
    title: has physiologically stable form
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv
    aliases:
    - protonation neutral form of
    - has Ph 7.3 mapping
    rank: 1000
    is_a: acid_form_of
    domain: MoleculeByChargeState
    alias: has_physiologically_stable_form
    owner: SequenceInterval
    domain_of:
    - ChemicalEntity
    range: MoleculeByChargeState
    multivalued: true
  owl_subclass_of:
    name: owl_subclass_of
    description: 'Holds between C and P if C owl:subClassOf P. Note that in this model,
      most classes are metaclasses (see ''owl class''), where these metaclasses may
      represent *groupings* or specific countable elements or species. We provide
      two different sub-properties of subclass of for two cases: (1) subtype_of, which
      connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a
      amino-acid), (2) classified_by, which connects a specific element to a grouping
      class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)'
    title: owl subclass of
    from_schema: https://w3id.org/chemrof
    aliases:
    - is a
    exact_mappings:
    - rdfs:subClassOf
    narrow_mappings:
    - bo:family
    rank: 1000
    is_a: classification_relationship
    mixin: true
    domain: OwlClass
    alias: owl_subclass_of
    owner: SequenceInterval
    domain_of:
    - OwlClass
    range: OwlClass
  id:
    name: id
    title: id
    from_schema: https://w3id.org/chemrof
    mappings:
    - schema:identifier
    rank: 1000
    is_a: information_property
    identifier: true
    alias: id
    owner: SequenceInterval
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  name:
    name: name
    description: name of chemical entity. E.g. nickel, carbon-16
    title: name
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - bo:symbol
    rank: 1000
    is_a: information_property
    slot_uri: rdfs:label
    alias: name
    owner: SequenceInterval
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  type:
    name: type
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: SequenceInterval
    domain_of:
    - DomainEntity
    range: uriorcurie