rhea.yaml

id: https://w3id.org/rhea
name: rhea-linkml
description: |-
  Experimental alpha version of a rendering of Rhea as LinkML

  For additional context, see [linkml-rhea docs](https://chemkg.github.io/linkml-rhea/home)

  This schema should largely correspond one-to-one with classes and properties in Rhea.
  Modifications:
    
  * Added a AbstractReaction grouping
  * prefixed properties directional/bidirectionalReaction with 'has'
      - mkdocs requires case-insensitive names, so this avoids name clash with classes
      - we retain the true rdf property as slot_uri
  
imports:
- linkml:types
prefixes:
  rhea: http://rdf.rhea-db.org/
  linkml: https://w3id.org/linkml/
  chemrof: https://w3id.org/chemrof/  
default_curi_maps:
  - semweb_context
default_prefix: rhea
types:
  Database identifier:
    typeof: uriorcurie
  CHEBI identifier:
    typeof: Database identifier
    pattern: "^CHEBI:\\d+$"
classes:

  ## generic/root
  Class:
    description: compounds and reactions are represented as classes in Rhea
    slots:
    - id
    - comment
    - type
    - label
    slot_usage: {}
    class_uri: http://www.w3.org/2000/01/rdf-schema#Class
    
  ## Reactions
  
  AbstractReaction:
    abstract: true
    is_a: Class
    description: Grouping class for all three reaction forms
    slots:
    - status
    - accession
    - seeAlso
    - isTransport
    - isChemicallyBalanced
    - citation
    - htmlEquation
    - equation
    - subClassOf
    slot_usage:
      ec:
        description: EC is always specified for unspecified direction
      subClassOf:
        range: AbstractReaction
  Reaction:
    is_a: AbstractReaction
    aliases:
      - direction neutral reaction
    description: A chemical reaction, with unspecified direction.
    slots:
    - hasDirectionalReaction
    - hasBidirectionalReaction
    - side
    - ec
    slot_usage:
      subClassOf:
        range: Reaction
    class_uri: http://rdf.rhea-db.org/Reaction
    exact_mappings:
      - chemrof:Reaction
  DirectionalReaction:
    is_a: AbstractReaction
    description: A chemical reaction, with the direction specified by substrates and products.
    slots:
    - substrates
    - products
    slot_usage:
      subClassOf:
        range: DirectionalReaction
    class_uri: http://rdf.rhea-db.org/DirectionalReaction
  BidirectionalReaction:
    is_a: AbstractReaction
    description: A chemical reaction which can happen in one direction or the other, depending on the physiological conditions.
    slots:
    - substratesOrProducts
    slot_usage:
      subClassOf:
        range: BidirectionalReaction
    class_uri: http://rdf.rhea-db.org/BidirectionalReaction
    
  ReactionParticipant:
    is_a: Class
    description: A reaction participant. Contained in a reaction side.
    slots:
    - compound
    - location
    slot_usage:
      subClassOf:
        range: Compound
    class_uri: http://rdf.rhea-db.org/ReactionParticipant
    exact_mappings:
      - chemrof:ReactionParticipant
    
  ReactionSide:
    description: A reaction side in a chemical reaction. Contains one or more reaction participants.
    slots:
    - id
    - contains
    - transformableTo
    - type
    - curatedOrder
    - contains1
    - contains2
    - contains4
    - contains3
    - contains6
    - contains5
    - contains8
    - containsN
    - contains7
    - contains16
    - contains9
    - contains20
    - contains11
    - contains12
    - containsNminus1
    - contains2n
    - contains10
    - contains22
    - contains24
    - containsNplus1
    - contains27
    - contains18
    - contains28
    - contains32
    - contains17
    - contains13
    - contains14
    - contains40
    - contains26
    - contains21
    - contains19
    slot_usage: {}
    class_uri: http://rdf.rhea-db.org/ReactionSide
    
  ReactivePart:
    is_a: Class
    description: A reactive part in a generic compound, with a defined chemical structure. A subclass of a given ChEBI chemical entity.
    slots:
    - name
    - charge
    - chebi
    - formula
    - htmlName
    - position
    slot_usage:
      subClassOf:
        range: Compound
    class_uri: http://rdf.rhea-db.org/ReactivePart
    

  ## compounds
  Compound:
    is_a: Class
    description: A chemical compound
    slots:
      - name
      - accession
      - htmlName
      - formula
    slot_usage:
      subClassOf:
        range: Compound
    class_uri: http://rdf.rhea-db.org/Compound
  SmallMolecule:
    is_a: Compound
    description: A chemical compound that is a small molecule. A subclass of a given ChEBI chemical entity.
    slots:
      - chebi
      - htmlName
      - charge
      - name
    slot_usage:
      subClassOf:
        range: SmallMolecule
    class_uri: http://rdf.rhea-db.org/SmallMolecule
  GenericCompound:
    is_a: Compound
    description: A chemical compound whose complete chemical structure is not described. Have one or or more reactive part(s) with chemical structure(s).
    slots:
      - reactivePart      
    class_uri: http://rdf.rhea-db.org/GenericCompound
  GenericPolynucleotide:
    is_a: GenericCompound
    description: A generic compound that is a polynucleotide. Have one or or more reactive part(s) with chemical structure(s).
    class_uri: http://rdf.rhea-db.org/GenericPolynucleotide
  GenericPolypeptide:
    is_a: GenericCompound
    description: A generic compound that is a polypeptide. Have one or or more reactive part(s) with chemical structure(s).
    class_uri: http://rdf.rhea-db.org/GenericPolypeptide
  Polymer:
    is_a: Compound
    description: A chemical compound that is a polymer. Described by a polymerization index, and an underlying polymer from ChEBI.
    slots:
      - charge
      - underlyingChebi
      - polymerizationIndex
    slot_usage: {}
    class_uri: http://rdf.rhea-db.org/Polymer

    
slots:

  ## generic/metadata
  
  id:
    identifier: true
    range: uriorcurie
    examples:
    - value: http://rdf.rhea-db.org/Compound_12075
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/id

  name:
    range: string
    examples:
    - value: beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-[alpha-L-fucosyl-(1->3)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide
    slot_uri: http://rdf.rhea-db.org/name
    exact_mappings:
      - rdfs:label

  accession:
    range: Database identifier
    examples:
    - value: CHEBI:90358
    slot_uri: http://rdf.rhea-db.org/accession

  chebi:
    range: string
    examples:
    - value: CHEBI_90358
    slot_uri: http://rdf.rhea-db.org/chebi
  htmlName:
    range: string
    examples:
    - value: 700;)-ceramide
    slot_uri: http://rdf.rhea-db.org/htmlName

  status:
    range: status_enum
    examples:
    - value: Approved
    slot_uri: http://rdf.rhea-db.org/status
  label:
    range: string
    examples:
    - value: 3-(4-hydroxyphenyl)pyruvate + L-glutamate => 2-oxoglutarate + L-tyrosine
    slot_uri: http://www.w3.org/2000/01/rdf-schema#label
  seeAlso:
    range: string
    examples:
    - value: R-HSA-517444.2
    multivalued: true
    slot_uri: http://www.w3.org/2000/01/rdf-schema#seeAlso
  comment:
    range: string
    examples:
    - value: RHEA:51568 part of RHEA:51564.
    slot_uri: http://www.w3.org/2000/01/rdf-schema#comment
  citation:
    range: integer
    examples:
    - value: '10074065'
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/citation



  ## relationships

  type:
    range: uriorcurie
    slot_uri: http://www.w3.org/1999/02/22-rdf-syntax-ns#type

  subClassOf:
    range: Class
    examples:
    - value: CHEBI_90358
    slot_uri: http://www.w3.org/2000/01/rdf-schema#subClassOf


  ## chemical

  formula:
    range: string
    examples:
    - value: C50H83N3O37R2
    slot_uri: http://rdf.rhea-db.org/formula
  charge:
    range: integer
    examples:
    - value: '0'
    slot_uri: http://rdf.rhea-db.org/charge

  
  ## reaction

  equation:
    range: string
    examples:
    - value: 3-(4-hydroxyphenyl)pyruvate + L-glutamate => 2-oxoglutarate + L-tyrosine
    slot_uri: http://rdf.rhea-db.org/equation

  htmlEquation:
    range: string
    examples:
    - value: small>-tyrosine
    slot_uri: http://rdf.rhea-db.org/htmlEquation

  ec:
    range: string
    examples:
    - value: 4.2.3.87
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/ec

  compound:
    range: Compound
    examples:
    - value: Compound_1264
    slot_uri: http://rdf.rhea-db.org/compound

  location:
    range: location_enum
    examples:
    - value: In
    slot_uri: http://rdf.rhea-db.org/location
  isTransport:
    range: boolean
    slot_uri: http://rdf.rhea-db.org/isTransport
  isChemicallyBalanced:
    range: boolean
    slot_uri: http://rdf.rhea-db.org/isChemicallyBalanced

  substratesOrProducts:
    range: ReactionSide
    examples:
    - value: 49544_R|49544_L
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/substratesOrProducts
  substrates:
    range: ReactionSide
    examples:
    - value: 15093_R
    slot_uri: http://rdf.rhea-db.org/substrates
  products:
    range: ReactionSide
    examples:
    - value: 15093_L
    slot_uri: http://rdf.rhea-db.org/products
  side:
    range: ReactionSide
    examples:
    - value: 28843_L|28843_R
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/side

  hasBidirectionalReaction:
    range: BidirectionalReaction
    examples:
    - value: '28846'
    slot_uri: http://rdf.rhea-db.org/bidirectionalReaction
  hasDirectionalReaction:
    range: DirectionalReaction
    examples:
    - value: 28844|28845
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/directionalReaction

  transformableTo:
    range: ReactionSide
    examples:
    - value: 38219_L
    slot_uri: http://rdf.rhea-db.org/transformableTo
  curatedOrder:
    range: integer
    examples:
    - value: '2'
    slot_uri: http://rdf.rhea-db.org/curatedOrder

  position:
    range: integer
    examples:
    - value: '2457'
    slot_uri: http://rdf.rhea-db.org/position
  reactivePart:
    range: string
    examples:
    - value: Compound_10195_rp1
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/reactivePart
  underlyingChebi:
    range: CHEBI identifier
    examples:
    - value: CHEBI_131728
    slot_uri: http://rdf.rhea-db.org/underlyingChebi
  polymerizationIndex:
    range: polymerizationIndex_enum
    examples:
    - value: n
    slot_uri: http://rdf.rhea-db.org/polymerizationIndex


  contains:
    range: ReactionParticipant
    examples:
    - value: Participant_38219_compound_7375|Participant_38219_compound_1264
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains

  contains1:
    is_a: contains
    range: string
    examples:
    - value: Participant_38219_compound_7375|Participant_38219_compound_1264
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains1
  contains2:
    is_a: contains
    range: string
    examples:
    - value: Participant_33599_compound_10439
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains2
  contains4:
    is_a: contains
    range: string
    examples:
    - value: Participant_56272_compound_12863
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains4
  contains3:
    is_a: contains
    range: string
    examples:
    - value: Participant_58440_compound_6127
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains3
  contains6:
    is_a: contains
    range: string
    examples:
    - value: Participant_40963_compound_1283
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains6
  contains5:
    is_a: contains
    range: string
    examples:
    - value: Participant_56864_compound_5188
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains5
  contains8:
    is_a: contains
    range: string
    examples:
    - value: Participant_58904_compound_2780
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains8
  containsN:
    is_a: contains
    range: string
    examples:
    - value: Participant_58948_compound_2790
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/containsN
  contains7:
    is_a: contains
    range: string
    examples:
    - value: Participant_35179_compound_5125
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains7
  contains16:
    is_a: contains
    range: string
    examples:
    - value: Participant_58904_compound_3438
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains16
  contains9:
    is_a: contains
    range: string
    examples:
    - value: Participant_50352_compound_3249
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains9
  contains20:
    is_a: contains
    range: string
    examples:
    - value: Participant_66812_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains20
  contains11:
    is_a: contains
    range: string
    examples:
    - value: Participant_18565_compound_3438
    slot_uri: http://rdf.rhea-db.org/contains11
  contains12:
    is_a: contains
    range: string
    examples:
    - value: Participant_58944_compound_3249
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains12
  containsNminus1:
    is_a: contains
    range: string
    examples:
    - value: Participant_23392_compound_1283
    slot_uri: http://rdf.rhea-db.org/containsNminus1
  contains2n:
    is_a: contains
    range: string
    examples:
    - value: Participant_20157_compound_3249|Participant_20157_compound_10350
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains2n
  contains10:
    is_a: contains
    range: string
    examples:
    - value: Participant_27614_compound_2106
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains10
  contains22:
    is_a: contains
    range: string
    examples:
    - value: Participant_58028_compound_3438
    slot_uri: http://rdf.rhea-db.org/contains22
  contains24:
    is_a: contains
    range: string
    examples:
    - value: Participant_58904_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains24
  containsNplus1:
    is_a: contains
    range: string
    examples:
    - value: Participant_22452_compound_5518
    slot_uri: http://rdf.rhea-db.org/containsNplus1
  contains27:
    is_a: contains
    range: string
    examples:
    - value: Participant_50468_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains27
  contains18:
    is_a: contains
    range: string
    examples:
    - value: Participant_15645_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains18
  contains28:
    is_a: contains
    range: string
    examples:
    - value: Participant_34391_compound_3249|Participant_34391_compound_2692
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains28
  contains32:
    is_a: contains
    range: string
    examples:
    - value: Participant_58028_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains32
  contains17:
    is_a: contains
    range: string
    examples:
    - value: Participant_66808_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains17
  contains13:
    is_a: contains
    range: string
    examples:
    - value: Participant_66812_compound_5188
    slot_uri: http://rdf.rhea-db.org/contains13
  contains14:
    is_a: contains
    range: string
    examples:
    - value: Participant_58908_compound_3438
    slot_uri: http://rdf.rhea-db.org/contains14
  contains40:
    is_a: contains
    range: string
    examples:
    - value: Participant_55540_compound_5518|Participant_55540_compound_2710
    multivalued: true
    slot_uri: http://rdf.rhea-db.org/contains40
  contains26:
    is_a: contains
    range: string
    examples:
    - value: Participant_55540_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains26
  contains21:
    is_a: contains
    range: string
    examples:
    - value: Participant_58908_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains21
  contains19:
    is_a: contains
    range: string
    examples:
    - value: Participant_18565_compound_3249
    slot_uri: http://rdf.rhea-db.org/contains19

enums:
  location_enum:
    permissible_values:
      Out:
        description: Out
        meaning: http://rdf.rhea-db.org/Out
      In:
        description: In
        meaning: http://rdf.rhea-db.org/In
  status_enum:
    permissible_values:
      Approved:
        description: Approved
        meaning: http://rdf.rhea-db.org/Approved
      Obsolete:
        description: Obsolete
        meaning: http://rdf.rhea-db.org/Obsolete
      Preliminary:
        description: Preliminary
        meaning: http://rdf.rhea-db.org/Preliminary
  polymerizationIndex_enum:
    permissible_values:
      n-2:
        description: n-2
      n+1:
        description: n+1
      n-3:
        description: n-3
      n-1:
        description: n-1
      n:
        description: n
      n-5:
        description: n-5
      n-4:
        description: n-4
      n+2:
        description: n+2