Class: glycan (Glycan)

name: Glycan
id_prefixes:
- KEGG.GLYCAN
- GLYTOUCAN
- glycosciencesdb
description: A molecule consisting of monosaccharide residues joined to one another
  by glycosidic linkages. Glycans may be linear or branched, and may be composed of
  a single kind of residue or of many.
title: glycan
comments:
- Glycans composed of a single type of monosaccharide residue (homopolysaccharide,
  synonym homoglycan) are named by replacing the ending '-ose' of the sugar by '-an',
  e.g. mannans, fructans, xylans, arabinans
- A glycan differs from other polymers modelled here in that it is frequently branched,
  so has_monosaccharide_residues plus has_glycosidic_linkages (a node and edge list)
  is used in preference to the linear sequence representation used for peptides and
  nucleic acids
- This class is placed under Macromolecule to sit alongside Peptide and Protein, but
  note that short oligosaccharides such as the Lewis X trisaccharide are conventionally
  glycans while not being macromolecules. Whether to relax the parent of this class
  is under discussion
- The ChEBI mappings are narrow rather than exact because this class subsumes both
  polysaccharide (CHEBI:18154) and oligosaccharide (CHEBI:50699), and ChEBI has no
  single term covering exactly that union
examples:
- value: https://www.glycoepitope.jp/epitopes/EP0311
  description: GalNAc(b1-4)[Neu5Ac(a2-3)]Gal(b1)
from_schema: https://w3id.org/chemrof
aliases:
- polysaccharides
- oligosaccharide
narrow_mappings:
- CHEBI:18154
- CHEBI:50699
is_a: Macromolecule
slots:
- has_monosaccharide_residues
- has_glycosidic_linkages
- has_reducing_end
- is_branched
- carbohydrate_representation
- wurcs_representation
- glycoct_condensed
- iupac_condensed_representation
- carbbank_representation
- linucs_representation
- glycominds_linearcode_representation
- kegg_chemical_function_representation

name: Glycan
id_prefixes:
- KEGG.GLYCAN
- GLYTOUCAN
- glycosciencesdb
description: A molecule consisting of monosaccharide residues joined to one another
  by glycosidic linkages. Glycans may be linear or branched, and may be composed of
  a single kind of residue or of many.
title: glycan
comments:
- Glycans composed of a single type of monosaccharide residue (homopolysaccharide,
  synonym homoglycan) are named by replacing the ending '-ose' of the sugar by '-an',
  e.g. mannans, fructans, xylans, arabinans
- A glycan differs from other polymers modelled here in that it is frequently branched,
  so has_monosaccharide_residues plus has_glycosidic_linkages (a node and edge list)
  is used in preference to the linear sequence representation used for peptides and
  nucleic acids
- This class is placed under Macromolecule to sit alongside Peptide and Protein, but
  note that short oligosaccharides such as the Lewis X trisaccharide are conventionally
  glycans while not being macromolecules. Whether to relax the parent of this class
  is under discussion
- The ChEBI mappings are narrow rather than exact because this class subsumes both
  polysaccharide (CHEBI:18154) and oligosaccharide (CHEBI:50699), and ChEBI has no
  single term covering exactly that union
examples:
- value: https://www.glycoepitope.jp/epitopes/EP0311
  description: GalNAc(b1-4)[Neu5Ac(a2-3)]Gal(b1)
from_schema: https://w3id.org/chemrof
aliases:
- polysaccharides
- oligosaccharide
narrow_mappings:
- CHEBI:18154
- CHEBI:50699
is_a: Macromolecule
attributes:
  has_monosaccharide_residues:
    name: has_monosaccharide_residues
    description: Relates a glycan to the monosaccharide residues that constitute it.
      Together with has_glycosidic_linkages this forms a graph representation of the
      glycan, in which residues are the nodes and linkages are the edges.
    title: has monosaccharide residues
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    alias: has_monosaccharide_residues
    owner: Glycan
    domain_of:
    - Glycan
    range: MonosaccharideResidue
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_glycosidic_linkages:
    name: has_glycosidic_linkages
    description: Relates a glycan to the glycosidic linkages connecting its monosaccharide
      residues. These are the edges of the graph whose nodes are given by has_monosaccharide_residues.
    title: has glycosidic linkages
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_glycosidic_linkages
    owner: Glycan
    domain_of:
    - Glycan
    range: GlycosidicLinkage
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_reducing_end:
    name: has_reducing_end
    description: The monosaccharide residue of a glycan whose anomeric carbon is not
      involved in a glycosidic linkage, and which therefore retains the free (reducing)
      hemiacetal. By convention this residue is drawn or written at the right-hand
      end of the glycan.
    title: has reducing end
    comments:
    - A cyclic glycan, or one whose reducing end is substituted (for example a glycoconjugate
      attached to a protein or lipid), has no free reducing end.
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://iupac.qmul.ac.uk/2carb/38.html
    rank: 1000
    alias: has_reducing_end
    owner: Glycan
    domain_of:
    - Glycan
    range: MonosaccharideResidue
  is_branched:
    name: is_branched
    title: is branched
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://en.wikipedia.org/wiki/Branching_(polymer_chemistry)
    rank: 1000
    alias: is_branched
    owner: Glycan
    domain_of:
    - Glycan
    - MonomolecularPolymer
    range: boolean
  carbohydrate_representation:
    name: carbohydrate_representation
    description: A line or graph notation that encodes the structure of a carbohydrate
      (glycan), minimally its monosaccharide composition and the glycosidic linkages
      connecting them. Unlike general-purpose notations such as SMILES, these formats
      make the monosaccharide residue and the linkage first-class syntactic elements.
    title: carbohydrate representation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_representation
    abstract: true
    domain: ChemicalEntity
    alias: carbohydrate_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  wurcs_representation:
    name: wurcs_representation
    description: A linear notation that encodes a glycan as a count of unique residues,
      residues and linkages, followed by a list of unique residue skeleton codes,
      the sequence in which they occur, and the linkages between them. Aligned so
      that one structure has one string, which is what allows GlyTouCan to mint a
      stable accession per structure.
    title: wurcs representation
    comments:
    - The segment following WURCS= is the version number of the format, for example
      2.0. An earlier revision of this schema used the pattern ^WURCS=Version/.* which
      read the placeholder in the format specification as a literal, and so matched
      no real WURCS string
    examples:
    - value: WURCS=2.0/3,3,2/[u2122h_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1
      description: Lewis X trisaccharide, GlyTouCan G39995KJ
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://doi.org/10.1093/bioinformatics/btv220
    aliases:
    - WURCS
    - Web3 Unique Representation of Carbohydrate Structures
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: wurcs_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
    pattern: ^WURCS=[0-9]+\.[0-9]+/.*
  glycoct_condensed:
    name: glycoct_condensed
    description: This is a multiline format used by GlycomeDB, among others, and uses
      a graph notation to represent glycans, similar to KCF. Monosaccharides are specified
      more strictly to be able to map the monosaccharides between different representations.
      Substituents, such as N-acetyl, are specified as separate nodes from their basetypes
      and are linked together in the edge section. If newlines are removed, this format
      can be made linear.
    title: glycoct condensed
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: glycoct_condensed
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  iupac_condensed_representation:
    name: iupac_condensed_representation
    description: The condensed form of the IUPAC nomenclature for carbohydrates, in
      which each monosaccharide is written using its three-letter abbreviation and
      each glycosidic linkage is written in parentheses as an anomeric descriptor
      followed by the two carbon positions joined. Branches are written in square
      brackets. This is the notation most commonly used in the glycobiology literature.
    title: IUPAC condensed representation
    examples:
    - value: Gal(b1-4)[Fuc(a1-3)]GlcNAc
      description: Lewis X trisaccharide
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://www.ncbi.nlm.nih.gov/glycans/snfg.html
    aliases:
    - IUPAC condensed
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: iupac_condensed_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  carbbank_representation:
    name: carbbank_representation
    description: 'The carbohydrate structure format used by the Complex Carbohydrate
      Structure Database (CCSD) originally developed at the University of Georgia.
      This is a 2D structure where bars and hyphens are used to indicate linkages,
      and monosaccharides are specified in the following order, separated by hyphens:
      anomer - configuration symbol - monosaccharide abbreviation.'
    title: carbbank representation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: carbbank_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  linucs_representation:
    name: linucs_representation
    description: A unique linear notation proposed and used by GLYCOSCIENCES.de, with
      the reducing end specified on the left. Monosaccharides, written according to
      CarbBank rules, are surrounded by square brackets and anomers, and stereochemistry
      is specified and separated by hyphens. Glycosidic linkages are also surrounded
      by hyphens, and carbon numbers of the linkages are separated by the plus sign.
      Branches are indicated by curly brackets.
    title: linucs representation
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://github.com/biopragmatics/bioregistry/issues/537
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: linucs_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  glycominds_linearcode_representation:
    name: glycominds_linearcode_representation
    description: A linear notation proposed by GlycoMinds, Ltd., where monosaccharides
      are indicated by a one- or two-letter code, linkages are indicated by “a” or
      “b” for anomers and a single number for the carbon number linkage on the reducing
      end, and branches are indicated by parentheses. This format is the most compact
      among existing formats, and several databases use a modified form of this format
      to accommodate additional codes and varying carbohydrate structures (such as
      ambiguous structures).
    title: glycominds linearcode representation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: glycominds_linearcode_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  kegg_chemical_function_representation:
    name: kegg_chemical_function_representation
    description: A multiline format used by the KEGG GLYCAN database and represents
      glycans as graphs. Monosaccharides are represented as nodes, and glycosidic
      linkages are represented as edges. Each node is given a unique number, and x-
      and y- coordinates are specified such that the glycan structure can be drawn
      on a 2D plane. Edge information uses the node numbers to specify anomeric and
      carbon number information. Monosaccharide names are specified as text, and no
      particular rules are specified to represent these names.
    title: kegg chemical function representation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: carbohydrate_representation
    domain: ChemicalEntity
    alias: kegg_chemical_function_representation
    owner: Glycan
    domain_of:
    - Glycan
    range: ChemicalEncoding
  has_atom_occurrences:
    name: has_atom_occurrences
    description: An individuated atom in the context of a chemical structure.
    title: has atom occurrences
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_atom_occurrences
    owner: Glycan
    domain_of:
    - Molecule
    range: AtomOccurrence
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_cardinality: 2
  has_bonds:
    name: has_bonds
    description: The set of all bonds connecting atoms in a molecule
    title: has bonds
    from_schema: https://w3id.org/chemrof
    aliases:
    - adjacency matrix
    rank: 1000
    domain: Molecule
    alias: has_bonds
    owner: Glycan
    domain_of:
    - Molecule
    range: AtomicBond
    multivalued: true
  has_submolecules:
    name: has_submolecules
    description: Relation between a molecule and the molecules it is made from.
    title: has submolecules
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_submolecules
    owner: Glycan
    domain_of:
    - Molecule
    range: Molecule
    multivalued: true
  has_atoms:
    name: has_atoms
    description: 'Relation between a molecule and the atoms it contains. Note that
      this is a shortcut relation: for granular representations go via atom occurrences'
    title: has atoms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_atoms
    owner: Glycan
    domain_of:
    - Molecule
    range: Atom
    multivalued: true
  has_part:
    name: has_part
    description: basic parthood relations
    title: has part
    from_schema: https://w3id.org/chemrof
    mappings:
    - BFO:0000050
    - schema:hasBioChemEntityPart
    exact_mappings:
    - RO:0002131
    rank: 1000
    is_a: chemical_to_chemical_relationship
    slot_uri: BFO:0000051
    alias: has_part
    owner: Glycan
    domain_of:
    - MoleculeGroupingClassDefinedByComponents
    - Molecule
    - Atom
    range: string
    minimum_cardinality: 1
  is_organic:
    name: is_organic
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: An organic molecule is a molecule composed of organic atoms (at least
      carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
    title: is organic
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - SIO:010072
    rank: 1000
    domain: ChemicalEntity
    alias: is_organic
    owner: Glycan
    domain_of:
    - Molecule
    range: boolean
  inchi_atom_connections_sublayer:
    name: inchi_atom_connections_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    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: Glycan
    domain_of:
    - ChemicalEntity
    - PolyatomicEntity
    - StandardInchiObject
    - EntityWithConnectivitySpecificied
    range: string
    required: false
    recommended: true
    pattern: ^c.*
  IUPAC_name:
    name: IUPAC_name
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: IUPAC name
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - MI:2007
    - CHEMINF:000107
    rank: 1000
    is_a: information_property
    alias: IUPAC_name
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: string
  is_radical:
    name: is_radical
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: is radical
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: ChemicalEntity
    alias: is_radical
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: boolean
  has_chemical_role:
    name: has_chemical_role
    title: has chemical role
    from_schema: https://w3id.org/chemrof
    rank: 1000
    slot_uri: RO:0000087
    alias: has_chemical_role
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalRole
  inchi_string:
    name: inchi_string
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    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
    - CHEMINF:000113
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: inchi_string
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_key_string:
    name: inchi_key_string
    annotations:
      hash_of:
        tag: hash_of
        value: inchi_string
    description: A hashed representation of an InChi string
    title: inchi key string
    from_schema: https://w3id.org/chemrof
    aliases:
    - InChiKey
    - inchi key
    rank: 1000
    is_a: hashed_chemical_formula
    domain: ChemicalEntity
    key: false
    alias: inchi_key_string
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    annotations:
      inchi.index:
        tag: inchi.index
        value: 2
      owl:
        tag: owl
        value: AnnotationAssertion
    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
    comments:
    - in the case of hydrates, the dot separates the formula of the compound from
      the water molecules. For example, CuSO₄·5H₂O represents copper(II) sulfate pentahydrate,
      indicating that there are five water molecules associated with each copper(II)
      sulfate unit in the crystal.
    - 'Salt Formulations: Dots can also be used to denote the proportions in which
      different components are combined to form a salt. For instance, "CaCl₂·2AgNO₃"
      would suggest a complex formed from one unit of calcium chloride and two units
      of silver nitrate, though this particular example is more illustrative than
      practical.'
    - 'Coordination Complexes: In coordination chemistry, dots can separate the metal
      complex from its counterions or ligands that are not directly bonded to the
      metal center. For example, "[Co(NH₃)₆]Cl₃" indicates a complex of cobalt with
      six ammonia ligands, and the three chloride ions are counterions. If written
      as "[Co(NH₃)₆]·3Cl", it would similarly denote the presence of three chloride
      ions associated with the complex, though this notation is less common'
    - 'Molecular Assemblies: For certain supramolecular structures or assemblies,
      dots might be used to indicate a non-covalent association of components. This
      usage is less common and more context-dependent'
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_chemical_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithAtomsEnumerated
    range: string
    required: false
    recommended: true
    pattern: ^[A-Za-z0-9\.]+$
  inchi_hydrogen_connections_sublayer:
    name: inchi_hydrogen_connections_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: Describes how many hydrogen atoms are connected to each of the other
      atoms.
    title: inchi hydrogen connections sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_hydrogen_connections_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithConnectivitySpecificied
    range: string
    pattern: ^h.*
  inchi_charge_sublayer:
    name: inchi_charge_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi charge sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_charge_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithChargeSpecified
    range: string
    pattern: ^q.*
  inchi_proton_sublayer:
    name: inchi_proton_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi proton sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_proton_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    range: string
    pattern: ^p[+\-]\d+
  inchi_stereochemical_double_bond_sublayer:
    name: inchi_stereochemical_double_bond_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi stereochemical double bond sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_stereochemical_double_bond_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithStereochemistrySpecified
    range: string
    pattern: ^b.*
  inchi_tetrahedral_stereochemical_sublayer:
    name: inchi_tetrahedral_stereochemical_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi tetrahedral stereochemical sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_tetrahedral_stereochemical_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithStereochemistrySpecified
    range: string
    pattern: ^[tm].*
  inchi_stereochemical_type_sublayer:
    name: inchi_stereochemical_type_sublayer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi stereochemical type sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_stereochemical_type_sublayer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithStereochemistrySpecified
    range: string
    pattern: ^s.*
  inchi_isotopic_layer:
    name: inchi_isotopic_layer
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    title: inchi isotopic layer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer
    alias: inchi_isotopic_layer
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithIsotopeSpecified
    range: string
    pattern: ^[ih].*
  smiles_string:
    name: smiles_string
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    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
    exact_mappings:
    - CHEMINF:000018
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: smiles_string
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  cxsmiles_string:
    name: cxsmiles_string
    description: A ChemAxon Extended SMILES string that appends a feature block to
      a SMILES string to capture annotations such as atom labels, R-groups, S-groups,
      coordinates, radicals, and enhanced stereochemistry.
    title: CXSMILES string
    examples:
    - value: '[H][C@@](COC([*])=O)(COP(O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](OP(O)(O)=O)[C@H]1O)OC([*])=O
        |$;;;;;_R1;;;;;;;;;;;;;;;;;;;;;;;;;_R2$|'
      description: CXSMILES for 1-phosphatidyl-1D-myo-inositol 3-phosphate (R1,R2)
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://docs.chemaxon.com/latest/formats_chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.html
    aliases:
    - CXSMILES
    - ChemAxon extended SMILES
    - extended SMILES
    exact_mappings:
    - wd:P10718
    rank: 1000
    is_a: smiles_string
    domain: ChemicalEntity
    alias: cxsmiles_string
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - ChemicalGroupingClass
    range: ChemicalEncoding
  empirical_formula:
    name: empirical_formula
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: A chemical formula where numbers denote relative proportion of atoms.
      E.g. CH2O for glucose
    title: empirical formula
    comments:
    - Distinct from molecular_formula, which gives the actual atom counts rather than
      their smallest whole-number ratio
    - The mapping to CHEMINF:000042 is close rather than exact because that term denotes
      the molecular formula. CHEMINF has no term for the empirical formula
    examples:
    - value: CH2O
      description: glucose, whose atom counts 6:12:6 reduce to 1:2:1
    - value: O
      description: dioxygen, whose molecular formula is O2
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - CHEMINF:000042
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: empirical_formula
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  molecular_formula:
    name: molecular_formula
    description: A chemical formula where numbers denote atom count. E.g. C6H12O6
      for glucose
    title: molecular formula
    comments:
    - Distinct from empirical_formula, which reduces the same counts to their smallest
      whole-number ratio. The two coincide only where the counts share no common factor,
      so citric acid is C6H8O7 either way while glucose is C6H12O6 molecularly but
      CH2O empirically
    - Not every chemical entity has one. A polymer of indeterminate length has a repeat
      unit and an empirical formula but no single molecular formula
    examples:
    - value: C6H12O6
      description: glucose
    - value: C8H10N4O2
      description: caffeine, whose empirical formula is C4H5N2O
    from_schema: https://w3id.org/chemrof
    aliases:
    - chemical_formula
    - Hill notation
    exact_mappings:
    - CHEMINF:000042
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: molecular_formula
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_major_microspecies_at_pH7_3:
    name: has_major_microspecies_at_pH7_3
    annotations:
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    description: Links different variants of the same chemical in different protonation
      states, where the target of this link is the (predicited) to be most common
      protonation state for this chemical at a pH of 7.3. This link may point to it's
      source. 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: ChemicalEntity
    alias: has_major_microspecies_at_pH7_3
    owner: Glycan
    domain_of:
    - ChemicalEntity
    inverse: major_microspecies_at_pH7_3_of
    range: ChemicalEntity
    multivalued: true
  conjugate_base_of:
    name: conjugate_base_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    description: 'connects the base form of an acid to an acid. Also connects the
      different charge states of the base. Example: the different charge states of
      lactate (CHEBI:24996) conjugate base of lactic acid (CHEBI:28358)'
    title: conjugate base of
    notes:
    - sometimes chebi hops over a state skipping an intermediate
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
    aliases:
    - is conjugate base of (chebi)
    exact_mappings:
    - RO:0018033
    rank: 1000
    is_a: direct_conjugatated_form_of
    mixins:
    - has_lower_charge_from
    domain: ChemicalEntity
    alias: conjugate_base_of
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - GroupingClassForAcidsOrBases
    - PolyatomicIon
    range: DomainEntity
  conjugate_acid_of:
    name: conjugate_acid_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    title: conjugate acid of
    todos:
    - decide on domain/range. in chebi, daidzein monosulfate is conjugate acid of
      daidzein monosulfate(1-), yet it is an acid derivative, not an acid
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
    aliases:
    - is conjugate acid of (chebi)
    exact_mappings:
    - RO:0018034
    rank: 1000
    is_a: direct_conjugatated_form_of
    mixins:
    - has_higher_charge_from
    domain: ChemicalEntity
    alias: conjugate_acid_of
    owner: Glycan
    domain_of:
    - ChemicalEntity
    - GroupingClassForAcidsOrBases
    - PolyatomicIon
    inverse: conjugate_base_of
    range: DomainEntity
  tautomer_of:
    name: tautomer_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf, ObjectSomeValuesFrom
    description: 'structural isomers (constitutional isomers) of chemical compounds
      that readily interconvert. Examples: a neutral amino acid and its zwitterion'
    title: tautomer of
    todos:
    - subtypes such as  keto-enol tautomerism
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - RO:0018036
    rank: 1000
    is_a: structural_isomer_of
    domain: Molecule
    alias: tautomer_of
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: Molecule
    multivalued: true
  molecular_mass:
    name: molecular_mass
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: The sum of the relative atomic masses of the constituent atoms of
      a molecule.
    title: molecular mass
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - NCIT:C28272
    - FIX:0000270
    - chebi.property:mass
    - CHEMINF:000198
    rank: 1000
    is_a: molecular_property
    alias: molecular_mass
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: u
  water_solubility:
    name: water_solubility
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    description: The maximum amount of a substance that can dissolve in water at 25°C,
      expressed in grams per liter (g/L).
    title: water solubility
    comments:
    - Standard temperature is 25°C (298.15 K)
    - This property represents the maximum equilibrium solubility in pure water
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: water_solubility
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: g/L
  pka_ionization_constant:
    name: pka_ionization_constant
    description: The negative logarithm of the acid dissociation constant (Ka) for
      ionizable groups in a molecule. Multiple pKa values may exist for molecules
      with multiple ionizable groups.
    title: pKa ionization constant
    comments:
    - Lower pKa values indicate stronger acids
    - For molecules with multiple ionizable groups, this field can contain multiple
      values
    - 'Standard conditions: aqueous solution at 25°C'
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_ionization_constant
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    multivalued: true
  pka_temperature:
    name: pka_temperature
    description: Temperature in Celsius at which pKa was measured. Default is 25°C
      if not specified.
    title: pKa temperature
    comments:
    - Standard temperature is 25°C (298.15 K)
    - pKa values can shift significantly with temperature following the van't Hoff
      equation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_temperature
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: Cel
  pka_ionic_strength:
    name: pka_ionic_strength
    description: Ionic strength of solution in mol/L at which pKa was measured. Default
      is 0.0 M if not specified.
    title: pKa ionic strength
    comments:
    - Standard ionic strength is 0.0 M (zero ionic strength corresponding to distilled
      water)
    - Salt concentration affects pKa through electrostatic shielding of charges
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_ionic_strength
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: mol/L
  pka_solvent:
    name: pka_solvent
    description: Solvent system for pKa measurement. Default is water (H₂O) if not
      specified.
    title: pKa solvent
    comments:
    - Standard solvent is water (H₂O)
    - pKa values in non-aqueous solvents can be dramatically different due to polarity
      effects
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_solvent
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: string
  pka_pressure:
    name: pka_pressure
    description: Pressure in atmospheres at which pKa was measured. Default is 1 atm
      if not specified.
    title: pKa pressure
    comments:
    - Standard pressure is 1 atm
    - Generally minor effect under standard laboratory conditions
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_pressure
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: atm
  classified_by:
    name: classified_by
    description: A subtype_of relationship holds between I and C if I is a specific
      entity of type C. Here I and C denotes instances of OWL classes, where I is
      a specific class and C is a grouping class
    title: classified by
    examples:
    - description: glucose classified by monosaccharide
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - rdf:type
    rank: 1000
    is_a: chemical_to_chemical_relationship
    mixins:
    - owl_subclass_of
    domain: OwlClass
    slot_uri: rdfs:subClassOf
    alias: classified_by
    owner: Glycan
    domain_of:
    - ChemicalEntity
    range: ChemicalGroupingClass
    multivalued: true
  owl_subclass_of:
    name: owl_subclass_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf
    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: Glycan
    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: Glycan
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  name:
    name: name
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    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: Glycan
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  type:
    name: type
    annotations:
      owl.ignore:
        tag: owl.ignore
        value: 'true'
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: Glycan
    domain_of:
    - DomainEntity
    range: uriorcurie