--- 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