valuesets 0.3.1__py3-none-any.whl

valuesets/schema/chemistry/chemical_entities.yaml

@@ -0,0 +1,639 @@
+name: chemical_entities
+title: Chemical Entities Value Sets
+description: 'Value sets for chemical entities including subatomic particles, chemical elements, bond types, and chemical
+  classifications. Based on the ChemROF ontological framework.
+
+  '
+id: https://w3id.org/valuesets/chemistry/chemical_entities
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  RXNO: http://purl.obolibrary.org/obo/RXNO_
+  MOP: http://purl.obolibrary.org/obo/MOP_
+  goldbook: https://goldbook.iupac.org/terms/view/
+  gc: http://purl.org/gc/
+  damlpt: http://www.daml.org/2003/01/periodictable/PeriodicTable#
+  pdg: https://pdgapi.lbl.gov/summaries/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  subatomic_particle:
+    description: Fundamental and composite subatomic particles
+    range: SubatomicParticleEnum
+  bond_type:
+    description: Types of chemical bonds
+    range: BondTypeEnum
+  periodic_table_block:
+    description: Blocks of the periodic table
+    range: PeriodicTableBlockEnum
+  element_family:
+    description: Chemical element families/groups
+    range: ElementFamilyEnum
+  element_metallic_classification:
+    description: Metallic character classification
+    range: ElementMetallicClassificationEnum
+  hard_or_soft:
+    description: HSAB (Hard Soft Acid Base) classification
+    range: HardOrSoftEnum
+  bronsted_acid_base_role:
+    description: Brønsted-Lowry acid-base roles
+    range: BronstedAcidBaseRoleEnum
+  lewis_acid_base_role:
+    description: Lewis acid-base roles
+    range: LewisAcidBaseRoleEnum
+  oxidation_state:
+    description: Common oxidation states
+    range: OxidationStateEnum
+  chirality:
+    description: Chirality/stereochemistry descriptors
+    range: ChiralityEnum
+  nanostructure_morphology:
+    description: Types of nanostructure morphologies
+    range: NanostructureMorphologyEnum
+enums:
+  SubatomicParticleEnum:
+    description: Fundamental and composite subatomic particles
+    permissible_values:
+      ELECTRON:
+        description: Elementary particle with -1 charge, spin 1/2
+        meaning: CHEBI:10545
+        annotations:
+          mass: 0.51099895 MeV/c²
+          charge: '-1'
+          spin: 1/2
+          type: lepton
+      POSITRON:
+        description: Antiparticle of electron with +1 charge
+        meaning: CHEBI:30225
+        annotations:
+          mass: 0.51099895 MeV/c²
+          charge: '+1'
+          spin: 1/2
+          type: lepton
+      MUON:
+        description: Heavy lepton with -1 charge
+        meaning: CHEBI:36356
+        annotations:
+          mass: 105.658 MeV/c²
+          charge: '-1'
+          spin: 1/2
+          type: lepton
+      TAU_LEPTON:
+        description: Heaviest lepton with -1 charge
+        meaning: CHEBI:36355
+        annotations:
+          mass: 1777.05 MeV/c²
+          charge: '-1'
+          spin: 1/2
+          type: lepton
+      ELECTRON_NEUTRINO:
+        description: Electron neutrino, nearly massless
+        meaning: CHEBI:30223
+        annotations:
+          mass: <2.2 eV/c²
+          charge: '0'
+          spin: 1/2
+          type: lepton
+      MUON_NEUTRINO:
+        description: Muon neutrino
+        meaning: CHEBI:36353
+        annotations:
+          mass: <0.17 MeV/c²
+          charge: '0'
+          spin: 1/2
+          type: lepton
+      TAU_NEUTRINO:
+        description: Tau neutrino
+        meaning: CHEBI:36354
+        annotations:
+          mass: <15.5 MeV/c²
+          charge: '0'
+          spin: 1/2
+          type: lepton
+      UP_QUARK:
+        title: up quark
+        description: First generation quark with +2/3 charge
+        meaning: CHEBI:36366
+        annotations:
+          mass: 2.16 MeV/c²
+          charge: +2/3
+          spin: 1/2
+          type: quark
+          generation: '1'
+      DOWN_QUARK:
+        description: First generation quark with -1/3 charge
+        meaning: CHEBI:36367
+        annotations:
+          mass: 4.67 MeV/c²
+          charge: -1/3
+          spin: 1/2
+          type: quark
+          generation: '1'
+      CHARM_QUARK:
+        title: charm quark
+        description: Second generation quark with +2/3 charge
+        meaning: CHEBI:36369
+        annotations:
+          mass: 1.27 GeV/c²
+          charge: +2/3
+          spin: 1/2
+          type: quark
+          generation: '2'
+      STRANGE_QUARK:
+        title: strange quark
+        description: Second generation quark with -1/3 charge
+        meaning: CHEBI:36368
+        annotations:
+          mass: 93.4 MeV/c²
+          charge: -1/3
+          spin: 1/2
+          type: quark
+          generation: '2'
+      TOP_QUARK:
+        description: Third generation quark with +2/3 charge
+        meaning: CHEBI:36371
+        annotations:
+          mass: 172.76 GeV/c²
+          charge: +2/3
+          spin: 1/2
+          type: quark
+          generation: '3'
+      BOTTOM_QUARK:
+        title: bottom quark
+        description: Third generation quark with -1/3 charge
+        meaning: CHEBI:36370
+        annotations:
+          mass: 4.18 GeV/c²
+          charge: -1/3
+          spin: 1/2
+          type: quark
+          generation: '3'
+      PHOTON:
+        description: Force carrier for electromagnetic interaction
+        meaning: CHEBI:30212
+        annotations:
+          mass: '0'
+          charge: '0'
+          spin: '1'
+          type: gauge boson
+      W_BOSON:
+        title: composite particle
+        description: Force carrier for weak interaction
+        meaning: CHEBI:36343
+        annotations:
+          mass: 80.379 GeV/c²
+          charge: ±1
+          spin: '1'
+          type: gauge boson
+      Z_BOSON:
+        title: hadron
+        description: Force carrier for weak interaction
+        meaning: CHEBI:36344
+        annotations:
+          mass: 91.1876 GeV/c²
+          charge: '0'
+          spin: '1'
+          type: gauge boson
+      GLUON:
+        description: Force carrier for strong interaction
+        annotations:
+          mass: '0'
+          charge: '0'
+          spin: '1'
+          type: gauge boson
+          color_charge: 'yes'
+      HIGGS_BOSON:
+        description: Scalar boson responsible for mass
+        meaning: CHEBI:146278
+        annotations:
+          mass: 125.25 GeV/c²
+          charge: '0'
+          spin: '0'
+          type: scalar boson
+      PROTON:
+        description: Positively charged nucleon
+        meaning: CHEBI:24636
+        annotations:
+          mass: 938.272 MeV/c²
+          charge: '+1'
+          spin: 1/2
+          type: baryon
+          composition: uud
+      NEUTRON:
+        description: Neutral nucleon
+        meaning: CHEBI:30222
+        annotations:
+          mass: 939.565 MeV/c²
+          charge: '0'
+          spin: 1/2
+          type: baryon
+          composition: udd
+      ALPHA_PARTICLE:
+        description: Helium-4 nucleus
+        meaning: CHEBI:30216
+        annotations:
+          mass: 3727.379 MeV/c²
+          charge: '+2'
+          composition: 2 protons, 2 neutrons
+      DEUTERON:
+        description: Hydrogen-2 nucleus
+        meaning: CHEBI:29233
+        annotations:
+          mass: 1875.613 MeV/c²
+          charge: '+1'
+          composition: 1 proton, 1 neutron
+      TRITON:
+        description: Hydrogen-3 nucleus
+        meaning: CHEBI:29234
+        annotations:
+          mass: 2808.921 MeV/c²
+          charge: '+1'
+          composition: 1 proton, 2 neutrons
+  BondTypeEnum:
+    description: Types of chemical bonds
+    permissible_values:
+      SINGLE:
+        description: Single covalent bond
+        meaning: gc:Single
+        annotations:
+          bond_order: '1'
+          electrons_shared: '2'
+      DOUBLE:
+        description: Double covalent bond
+        meaning: gc:Double
+        annotations:
+          bond_order: '2'
+          electrons_shared: '4'
+      TRIPLE:
+        description: Triple covalent bond
+        meaning: gc:Triple
+        annotations:
+          bond_order: '3'
+          electrons_shared: '6'
+      QUADRUPLE:
+        description: Quadruple bond (rare, in transition metals)
+        meaning: gc:Quadruple
+        annotations:
+          bond_order: '4'
+          electrons_shared: '8'
+      AROMATIC:
+        description: Aromatic bond
+        meaning: gc:AromaticBond
+        annotations:
+          bond_order: '1.5'
+          delocalized: 'true'
+      IONIC:
+        title: organic molecular entity
+        description: Ionic bond
+        meaning: CHEBI:50860
+        annotations:
+          type: electrostatic
+      HYDROGEN:
+        description: Hydrogen bond
+        annotations:
+          type: weak interaction
+          energy: 5-30 kJ/mol
+      METALLIC:
+        description: Metallic bond
+        annotations:
+          type: delocalized electrons
+      VAN_DER_WAALS:
+        description: Van der Waals interaction
+        annotations:
+          type: weak interaction
+          energy: 0.4-4 kJ/mol
+      COORDINATE:
+        title: coordination entity
+        description: Coordinate/dative covalent bond
+        meaning: CHEBI:33240
+        annotations:
+          electrons_from: one atom
+      PI:
+        description: Pi bond
+        annotations:
+          orbital_overlap: side-to-side
+      SIGMA:
+        description: Sigma bond
+        annotations:
+          orbital_overlap: head-to-head
+  PeriodicTableBlockEnum:
+    description: Blocks of the periodic table
+    permissible_values:
+      S_BLOCK:
+        title: s-block molecular entity
+        description: s-block elements (groups 1 and 2)
+        meaning: CHEBI:33674
+        annotations:
+          valence_orbital: s
+          groups: 1,2
+      P_BLOCK:
+        title: p-block molecular entity
+        description: p-block elements (groups 13-18)
+        meaning: CHEBI:33675
+        annotations:
+          valence_orbital: p
+          groups: 13,14,15,16,17,18
+      D_BLOCK:
+        title: d-block element atom
+        description: d-block elements (transition metals)
+        meaning: CHEBI:33561
+        annotations:
+          valence_orbital: d
+          groups: 3-12
+      F_BLOCK:
+        title: f-block element atom
+        description: f-block elements (lanthanides and actinides)
+        meaning: CHEBI:33562
+        annotations:
+          valence_orbital: f
+          series: lanthanides, actinides
+  ElementFamilyEnum:
+    description: Chemical element families/groups
+    permissible_values:
+      ALKALI_METALS:
+        title: alkali metal atom
+        description: Group 1 elements (except hydrogen)
+        meaning: CHEBI:22314
+        annotations:
+          group: '1'
+          elements: Li, Na, K, Rb, Cs, Fr
+      ALKALINE_EARTH_METALS:
+        title: alkaloid
+        description: Group 2 elements
+        meaning: CHEBI:22315
+        annotations:
+          group: '2'
+          elements: Be, Mg, Ca, Sr, Ba, Ra
+      TRANSITION_METALS:
+        title: transition element atom
+        description: d-block elements
+        meaning: CHEBI:27081
+        annotations:
+          groups: 3-12
+      LANTHANIDES:
+        title: titanium group molecular entity
+        description: Lanthanide series
+        meaning: CHEBI:33768
+        annotations:
+          atomic_numbers: 57-71
+      ACTINIDES:
+        title: fuconates
+        description: Actinide series
+        meaning: CHEBI:33769
+        annotations:
+          atomic_numbers: 89-103
+      CHALCOGENS:
+        title: chalcogen
+        description: Group 16 elements
+        meaning: CHEBI:33303
+        annotations:
+          group: '16'
+          elements: O, S, Se, Te, Po
+      HALOGENS:
+        title: idopyranuronic acid
+        description: Group 17 elements
+        meaning: CHEBI:47902
+        annotations:
+          group: '17'
+          elements: F, Cl, Br, I, At
+      NOBLE_GASES:
+        title: neon atom
+        description: Group 18 elements
+        meaning: CHEBI:33310
+        annotations:
+          group: '18'
+          elements: He, Ne, Ar, Kr, Xe, Rn
+      METALLOIDS:
+        title: s-block element atom
+        description: Elements with intermediate properties
+        meaning: CHEBI:33559
+        annotations:
+          elements: B, Si, Ge, As, Sb, Te, Po
+      POST_TRANSITION_METALS:
+        description: Metals after the transition series
+        annotations:
+          elements: Al, Ga, In, Tl, Sn, Pb, Bi
+      NONMETALS:
+        title: nonmetal atom
+        description: Non-metallic elements
+        meaning: CHEBI:25585
+        annotations:
+          elements: H, C, N, O, F, P, S, Cl, Se, Br, I
+  ElementMetallicClassificationEnum:
+    description: Metallic character classification
+    permissible_values:
+      METALLIC:
+        description: Metallic elements
+        meaning: damlpt:Metallic
+        annotations:
+          properties: conductive, malleable, ductile
+      NON_METALLIC:
+        description: Non-metallic elements
+        meaning: damlpt:Non-Metallic
+        annotations:
+          properties: poor conductors, brittle
+      SEMI_METALLIC:
+        description: Semi-metallic/metalloid elements
+        meaning: damlpt:Semi-Metallic
+        annotations:
+          properties: intermediate properties
+  HardOrSoftEnum:
+    description: HSAB (Hard Soft Acid Base) classification
+    permissible_values:
+      HARD:
+        description: Hard acids/bases (small, high charge density)
+        annotations:
+          examples: H+, Li+, Mg2+, Al3+, F-, OH-
+          polarizability: low
+      SOFT:
+        description: Soft acids/bases (large, low charge density)
+        annotations:
+          examples: Cu+, Ag+, Au+, I-, S2-
+          polarizability: high
+      BORDERLINE:
+        description: Borderline acids/bases
+        annotations:
+          examples: Fe2+, Co2+, Ni2+, Cu2+, Zn2+
+          polarizability: intermediate
+  BronstedAcidBaseRoleEnum:
+    description: Brønsted-Lowry acid-base roles
+    permissible_values:
+      ACID:
+        title: Bronsted acid
+        description: Proton donor
+        meaning: CHEBI:39141
+        annotations:
+          definition: species that donates H+
+      BASE:
+        title: Bronsted base
+        description: Proton acceptor
+        meaning: CHEBI:39142
+        annotations:
+          definition: species that accepts H+
+      AMPHOTERIC:
+        description: Can act as both acid and base
+        annotations:
+          definition: species that can donate or accept H+
+          examples: H2O, HSO4-, H2PO4-
+  LewisAcidBaseRoleEnum:
+    description: Lewis acid-base roles
+    permissible_values:
+      LEWIS_ACID:
+        description: Electron pair acceptor
+        annotations:
+          definition: species that accepts electron pair
+          examples: BF3, AlCl3, H+
+      LEWIS_BASE:
+        description: Electron pair donor
+        annotations:
+          definition: species that donates electron pair
+          examples: NH3, OH-, H2O
+  OxidationStateEnum:
+    description: Common oxidation states
+    permissible_values:
+      MINUS_4:
+        description: Oxidation state -4
+        annotations:
+          value: '-4'
+          example: C in CH4
+      MINUS_3:
+        description: Oxidation state -3
+        annotations:
+          value: '-3'
+          example: N in NH3
+      MINUS_2:
+        description: Oxidation state -2
+        annotations:
+          value: '-2'
+          example: O in H2O
+      MINUS_1:
+        description: Oxidation state -1
+        annotations:
+          value: '-1'
+          example: Cl in NaCl
+      ZERO:
+        description: Oxidation state 0
+        annotations:
+          value: '0'
+          example: elemental forms
+      PLUS_1:
+        description: Oxidation state +1
+        annotations:
+          value: '+1'
+          example: Na in NaCl
+      PLUS_2:
+        description: Oxidation state +2
+        annotations:
+          value: '+2'
+          example: Ca in CaCl2
+      PLUS_3:
+        description: Oxidation state +3
+        annotations:
+          value: '+3'
+          example: Al in Al2O3
+      PLUS_4:
+        description: Oxidation state +4
+        annotations:
+          value: '+4'
+          example: C in CO2
+      PLUS_5:
+        description: Oxidation state +5
+        annotations:
+          value: '+5'
+          example: P in PO4³⁻
+      PLUS_6:
+        description: Oxidation state +6
+        annotations:
+          value: '+6'
+          example: S in SO4²⁻
+      PLUS_7:
+        description: Oxidation state +7
+        annotations:
+          value: '+7'
+          example: Mn in MnO4⁻
+      PLUS_8:
+        description: Oxidation state +8
+        annotations:
+          value: '+8'
+          example: Os in OsO4
+  ChiralityEnum:
+    description: Chirality/stereochemistry descriptors
+    permissible_values:
+      R:
+        description: Rectus (right) configuration
+        annotations:
+          cahn_ingold_prelog: 'true'
+      S:
+        description: Sinister (left) configuration
+        annotations:
+          cahn_ingold_prelog: 'true'
+      D:
+        description: Dextrorotatory
+        annotations:
+          fischer_projection: 'true'
+          optical_rotation: positive
+      L:
+        description: Levorotatory
+        annotations:
+          fischer_projection: 'true'
+          optical_rotation: negative
+      RACEMIC:
+        description: Racemic mixture (50:50 of enantiomers)
+        annotations:
+          optical_rotation: zero
+      MESO:
+        description: Meso compound (achiral despite stereocenters)
+        annotations:
+          internal_symmetry: 'true'
+      E:
+        description: Entgegen (opposite) configuration
+        annotations:
+          geometric_isomer: 'true'
+      Z:
+        description: Zusammen (together) configuration
+        annotations:
+          geometric_isomer: 'true'
+  NanostructureMorphologyEnum:
+    description: Types of nanostructure morphologies
+    permissible_values:
+      NANOTUBE:
+        description: Cylindrical nanostructure
+        meaning: CHEBI:50796
+        annotations:
+          dimensions: 1D
+          examples: carbon nanotubes
+      NANOPARTICLE:
+        description: Particle with nanoscale dimensions
+        meaning: CHEBI:50803
+        annotations:
+          dimensions: 0D
+          size_range: 1-100 nm
+      NANOROD:
+        description: Rod-shaped nanostructure
+        meaning: CHEBI:50805
+        annotations:
+          dimensions: 1D
+          aspect_ratio: 3-20
+      QUANTUM_DOT:
+        description: Semiconductor nanocrystal
+        meaning: CHEBI:50853
+        annotations:
+          dimensions: 0D
+          property: quantum confinement
+      NANOWIRE:
+        description: Wire with nanoscale diameter
+        annotations:
+          dimensions: 1D
+          diameter: <100 nm
+      NANOSHEET:
+        description: Two-dimensional nanostructure
+        annotations:
+          dimensions: 2D
+          thickness: <100 nm
+      NANOFIBER:
+        description: Fiber with nanoscale diameter
+        annotations:
+          dimensions: 1D
+          diameter: <1000 nm

valuesets/schema/chemistry/reaction_directionality.yaml

@@ -0,0 +1,60 @@
+name: reaction_directionality
+title: Reaction Directionality
+description: Directionality of chemical reactions and processes
+id: https://w3id.org/common-value-sets/chemistry/reaction_directionality
+imports:
+- linkml:types
+- ../core
+prefixes:
+  linkml: https://w3id.org/linkml/
+  SBO: http://biomodels.net/SBO/
+  cvs: https://w3id.org/common-value-sets/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  reaction_directionality:
+    description: The directionality of a chemical reaction or process
+    range: ReactionDirectionality
+enums:
+  ReactionDirectionality:
+    title: Reaction Directionality
+    description: The directionality of a chemical reaction or process
+    permissible_values:
+      LEFT_TO_RIGHT:
+        description: Reaction proceeds from left to right (forward direction)
+        aliases:
+        - LR
+        - forward
+        - -->
+      RIGHT_TO_LEFT:
+        description: Reaction proceeds from right to left (reverse direction)
+        aliases:
+        - RL
+        - reverse
+        - backward
+        - <--
+      BIDIRECTIONAL:
+        description: Reaction can proceed in both directions
+        aliases:
+        - BIDI
+        - reversible
+        - <-->
+        exact_mappings:
+        - SBO:0000650
+      AGNOSTIC:
+        description: Direction is unknown or not specified
+        aliases:
+        - unknown
+        - unspecified
+      IRREVERSIBLE_LEFT_TO_RIGHT:
+        description: Reaction proceeds only from left to right and cannot be reversed
+        aliases:
+        - irreversible forward
+        - ->>
+        exact_mappings:
+        - SBO:0000651
+      IRREVERSIBLE_RIGHT_TO_LEFT:
+        description: Reaction proceeds only from right to left and cannot be reversed
+        aliases:
+        - irreversible reverse
+        - <<-