chem-dcat-ap/src/chem_dcat_ap/schema/chemical_entities_ap.yaml at main · nfdi-de/chem-dcat-ap · GitHub

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---
id: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry/entity/
name: chemical-entities-ap
title: Chemical Entities Application Profile
description: |-
  This is an application profile for chemical entities to be used for extending the DCAT-AP-PLUS.
license: CC-BY 4.0
prefixes:
  chemical_entities_ap: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry/entity/
  chemdcatap: https://w3id.org/nfdi-de/dcat-ap-plus/chemistry/
  linkml: https://w3id.org/linkml/
  biolink: https://w3id.org/biolink/vocab/
  schema: http://schema.org/
  dcterms: http://purl.org/dc/terms/
  sosa: http://www.w3.org/ns/sosa/
  rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  owl: http://www.w3.org/2002/07/owl#
  skos: http://www.w3.org/2004/02/skos/core#
  RO: http://purl.obolibrary.org/obo/RO_
  PATO: http://purl.obolibrary.org/obo/PATO_
  OBI: http://purl.obolibrary.org/obo/OBI_
  IAO: http://purl.obolibrary.org/obo/IAO_
  BFO: http://purl.obolibrary.org/obo/BFO_
  ex: http://example.org/
  SIO: http://semanticscience.org/resource/SIO_
  doi: https://doi.org/
  AFE: http://purl.allotrope.org/ontologies/equipment#AFE_
  AFRL: http://purl.allotrope.org/ontologies/role#AFRL_
  AFP: http://purl.allotrope.org/ontologies/process#AFP_
  AFX: http://purl.allotrope.org/ontologies/property#AFX_
  AFR: http://purl.allotrope.org/ontologies/result#AFR_
  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
  VOC4CAT: https://w3id.org/nfdi4cat/voc4cat_
  EDAM: http://edamontology.org/data_
default_prefix: chemical_entities_ap
default_range: string
imports:
  - linkml:types
  - material_entities_ap

classes:

#####################
# EvaluatedEntities #
#####################
  SubstanceSample:
    class_uri: SIO:001378
    is_a: MaterialSample
    aliases:
      - analyte
    description: A MaterialSample derived from a chemical substance that is of interest in an analytical procedure.
    mixins:
      - ChemicalSubstanceMixin

  PolymerSample:
    is_a: SubstanceSample
    class_uri: SIO:001378
    description: A SubstanceSample derived from a Polymer.
    mixins:
      - PolymerMixin
    todos:
      - "Find a better mapping, as it is currently mapped to same ontology class as its parent."

############
# Entities #
############
  ChemicalEntity:
    is_a: Entity
    class_uri: CHEBI:23367
    aliases:
      - molecular entity
    description: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
    slots:
      - inchi
      - inchikey
      - smiles
      - molecular_formula
      - iupac_name
      - has_molar_mass
    slot_usage:
      has_part:
        slot_uri: BFO:0000051
        description: The slot to provide the parts of a ChemicalEntity that are themself chemical entities.
        range: ChemicalEntity
        multivalued: true
        inlined_as_list: true
  Atom:
    class_uri: CHEBI:33250
    is_a: Entity
    description: An Entity constituting the smallest component of a chemical element having the chemical properties of the element.
    slot_usage:
      rdf_type:
        description: The slot to provide the Atom as a ChEBI ID from the atom (CHEBI:33250) branch.
        required: true

#########################
# QuantitativeAttributes #
#########################
  MolarMass:
    class_uri: AFR:0002409
    is_a: Mass
    description: A Mass (physical quality) that quantifies the mass of a homogeneous ChemicalSubstance containing 6.02 x 10^23 atoms or molecules.
    close_mappings:
      - PATO:0001681
  Concentration:
    is_a: QuantitativeAttribute
    class_uri: CHMO:0002820
    description: A QuantitativeAttribute of a ChemicalSubstance that represents the amount of a constituent divided by the volume of the mixture.
    exact_mappings:
      - EDAM:2140
      - NCIT:C41185
      - VOC4CAT:0007244
      - AFR:0002036
    narrow_mappings:
      - CHMO:0002822
    close_mappings:
      - PATO:0000033
    #slot_usage:
      #has_quantity_type:
      # ifabsent: http://qudt.org/vocab/quantitykind/Concentration
      # ifabsent: http://qudt.org/vocab/quantitykind/AmountOfSubstanceConcentration
      # ifabsent: http://qudt.org/vocab/quantitykind/MassConcentration
  AmountOfSubstance:
    class_uri: qudt:Quantity
    is_a: QuantitativeAttribute
    aliases:
      - SubstanceAmount
    description: The total amount of substance used in a ChemicalReaction.
    close_mappings:
      - PATO:0000070
    #slot_usage:
      #has_quantity_type:
      # ifabsent: http://qudt.org/vocab/quantitykind/AmountOfSubstance
  PHValue:
    is_a: QuantitativeAttribute
    class_uri: SIO:001089
    exact_mappings:
      - NCIT:C45997
      - AFR:0001142
    close_mappings:
      - PATO:0001842
      #slot_usage:
      #has_quantity_type:
      #ifabsent: http://qudt.org/vocab/quantitykind/Acidity

########################
# QualitativeAttribute #
########################
  InChIKey:
    class_uri: CHEMINF:000059
    is_a: QualitativeAttribute
  InChi:
    class_uri: CHEMINF:000113
    is_a: QualitativeAttribute
    description: A structure descriptor which conforms to the InChI format specification.
  MolecularFormula:
    class_uri: CHEMINF:000042
    is_a: QualitativeAttribute
    description: A structure descriptor which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecule of that compound.
  IUPACName:
    class_uri: CHEMINF:000107
    is_a: QualitativeAttribute
    description: A systematic name which is formulated according to the rules and recommendations for chemical nomenclature set out by the International Union of Pure and Applied Chemistry (IUPAC).
  SMILES:
    class_uri: CHEMINF:000018
    is_a: QualitativeAttribute
    description: A structure descriptor that denotes a molecular structure as a graph and conforms to the SMILES format specification.


##########
# Mixins #
##########
  ChemicalSubstanceMixin:
    abstract: true
    mixin: true
    is_a: MaterialisticMixin
    description: A LinkML mixin used to pass down properties common to all material entities that are described in a chemical context via being composed of chemical entities (e.g. atom, molecule, ion, ion pair, radical, complex, conformer etc., ) of the same type or of different types.
    slots:
      - has_concentration
      - has_ph_value
      - composed_of
      - has_amount
  PolymerMixin:
    abstract: true
    is_a: ChemicalSubstanceMixin
    mixin: true
    description: A LinkML mixin used to pass down properties common to all chemical substances that are composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..
    # attributes: # Needed attributes will be defined here

slots:

  composed_of:
    slot_uri: BFO:0000051
    is_a: has_part
    description: The slot to provide the chemical entities of which a ChemicalSubstance is composed of.
    range: ChemicalEntity
    multivalued: true
    inlined_as_list: true
    recommended: true
    close_mappings:
      - AFX:0000940
  has_concentration:
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    range: Concentration
    description: The slot to provide the Concentration of a ChemicalSubstance.
  has_amount:
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    range: AmountOfSubstance
    description: The slot to provide the AmountConcentration of a ChemicalSubstance.
  has_ph_value:
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    range: PHValue
    description: The slot to provide the PHValue of a ChemicalSubstance.

  inchi:
    slot_uri: SIO:000008 # using SIO here instead of dcterms:relation of DCAT-AP-PLUS
    range: InChi
    is_a: has_qualitative_attribute
    description: The slot to provide the InChi descriptor of a ChemicalEntity.
    recommended: true
  inchikey:
    slot_uri: SIO:000008
    range: InChIKey
    is_a: has_qualitative_attribute
    description: The slot to provide the InChiKey of a ChemicalEntity.
    recommended: true
  smiles:
    slot_uri: SIO:000008
    range: SMILES
    is_a: has_qualitative_attribute
    description: The slot to provide the canonical SMILES descriptor of a ChemicalEntity.
    recommended: true
  molecular_formula:
    slot_uri: SIO:000008
    range: MolecularFormula
    is_a: has_qualitative_attribute
    description: The slot to provide the IUPAC formula of a ChemicalEntity.
    recommended: true
  iupac_name:
    slot_uri: SIO:000008
    is_a: has_qualitative_attribute
    range: IUPACName
    description: The slot to provide the IUPAC name of a ChemicalEntity.
    recommended: true
  has_molar_mass:
    slot_uri: SIO:000008
    is_a: has_mass
    range: MolarMass
    description: The slot to provide the MolarMass of a ChemicalEntity.
    recommended: true