rhea-linkml schema
Experimental alpha version of a rendering of Rhea as LinkML
For additional context, see linkml-rhea docs
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
Classes
- Class - compounds and reactions are represented as classes in Rhea
- AbstractReaction - Grouping class for all three reaction forms
- BidirectionalReaction - A chemical reaction which can happen in one direction or the other, depending on the physiological conditions.
- DirectionalReaction - A chemical reaction, with the direction specified by substrates and products.
- Reaction - A chemical reaction, with unspecified direction.
- Compound - A chemical compound
- GenericCompound - A chemical compound whose complete chemical structure is not described. Have one or or more reactive part(s) with chemical structure(s).
- GenericPolynucleotide - A generic compound that is a polynucleotide. Have one or or more reactive part(s) with chemical structure(s).
- GenericPolypeptide - A generic compound that is a polypeptide. Have one or or more reactive part(s) with chemical structure(s).
- Polymer - A chemical compound that is a polymer. Described by a polymerization index, and an underlying polymer from ChEBI.
- SmallMolecule - A chemical compound that is a small molecule. A subclass of a given ChEBI chemical entity.
- GenericCompound - A chemical compound whose complete chemical structure is not described. Have one or or more reactive part(s) with chemical structure(s).
- ReactionParticipant - A reaction participant. Contained in a reaction side.
- ReactivePart - A reactive part in a generic compound, with a defined chemical structure. A subclass of a given ChEBI chemical entity.
- AbstractReaction - Grouping class for all three reaction forms
- ReactionSide - A reaction side in a chemical reaction. Contains one or more reaction participants.
Mixins
Slots
- accession
- charge
- chebi
- citation
- comment
- compound
- contains
- contains1
- contains10
- contains11
- contains12
- contains13
- contains14
- contains16
- contains17
- contains18
- contains19
- contains2
- contains20
- contains21
- contains22
- contains24
- contains26
- contains27
- contains28
- contains2n
- contains3
- contains32
- contains4
- contains40
- contains5
- contains6
- contains7
- contains8
- contains9
- containsN
- containsNminus1
- containsNplus1
- curatedOrder
- ec
- AbstractReaction➞ec - EC is always specified for unspecified direction
- equation
- formula
- hasBidirectionalReaction
- hasDirectionalReaction
- htmlEquation
- htmlName
- id
- isChemicallyBalanced
- isTransport
- label
- location
- name
- polymerizationIndex
- position
- products
- reactivePart
- seeAlso
- side
- status
- subClassOf
- substrates
- substratesOrProducts
- transformableTo
- type
- underlyingChebi
Enums
Subsets
Types
Built in
- Bool
- Decimal
- ElementIdentifier
- NCName
- NodeIdentifier
- URI
- URIorCURIE
- XSDDate
- XSDDateTime
- XSDTime
- float
- int
- str
Defined
- CHEBIIdentifier (DatabaseIdentifier)
- DatabaseIdentifier (Uriorcurie)
- Boolean (Bool) - A binary (true or false) value
- Date (XSDDate) - a date (year, month and day) in an idealized calendar
- Datetime (XSDDateTime) - The combination of a date and time
- Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
- Double (float) - A real number that conforms to the xsd:double specification
- Float (float) - A real number that conforms to the xsd:float specification
- Integer (int) - An integer
- Ncname (NCName) - Prefix part of CURIE
- Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
- Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
- String (str) - A character string
- Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
- Uri (URI) - a complete URI
- Uriorcurie (URIorCURIE) - a URI or a CURIE