openphar 0.1.0

data/lib/openphar/models/crude_drug_monograph.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a crude drug monograph (herbal medicine)
+    #
+    # Crude drugs are raw plant or animal materials used in medicine.
+    # They have botanical sources and morphological descriptions.
+    class CrudeDrugMonograph < Monograph
+      attribute :botanical_source, :hash, default: {}
+      attribute :macroscopic_description, :hash, default: {}
+      attribute :microscopic_description, :hash, default: {}
+
+      json do
+        map 'botanicalSource', to: :botanical_source
+        map 'macroscopicDescription', to: :macroscopic_description
+        map 'microscopicDescription', to: :microscopic_description
+      end
+
+      class << self
+        def neo4j_labels
+          %w[Monograph CrudeDrug]
+        end
+
+        def jsonld_type
+          'CrudeDrugMonograph'
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/edition.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a pharmacopoeia edition (e.g., JP18, Ph.Int.13)
+    #
+    # An edition is a specific version of a pharmacopoeia publication
+    # with an official publication and effective date.
+    class Edition < Lutaml::Model::Serializable
+      attribute :id, :string
+      attribute :edition_number, :string
+      attribute :pref_label, :hash, default: {}
+      attribute :publication_date, :date
+      attribute :effective_date, :date
+      attribute :monograph_count, :integer
+      attribute :edition_url, :string
+      attribute :official_languages, :string, collection: true, default: []
+      attribute :supplements, :hash, collection: true, default: []
+
+      json do
+        map 'id', to: :id
+        map 'editionNumber', to: :edition_number
+        map 'prefLabel', to: :pref_label
+        map 'publicationDate', to: :publication_date
+        map 'effectiveDate', to: :effective_date
+        map 'monographCount', to: :monograph_count
+        map 'editionUrl', to: :edition_url
+        map 'officialLanguage', to: :official_languages
+        map 'hasSupplement', to: :supplements
+      end
+
+      def iri
+        "#{Openphar.base_iri}/data/edition/#{id}"
+      end
+
+      def label(lang = 'en')
+        pref_label[lang] || pref_label.values.first
+      end
+    end
+  end
+end

data/lib/openphar/models/formulation_monograph.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a formulation monograph
+    #
+    # Formulations are finished pharmaceutical products containing
+    # one or more active ingredients.
+    class FormulationMonograph < Monograph
+      attribute :dosage_form, :string
+      attribute :strength, :string
+      attribute :active_ingredients, :hash, collection: true, default: []
+
+      json do
+        map 'dosageForm', to: :dosage_form
+        map 'strength', to: :strength
+        map 'activeIngredient', to: :active_ingredients
+      end
+
+      class << self
+        def neo4j_labels
+          %w[Monograph Formulation]
+        end
+
+        def jsonld_type
+          'FormulationMonograph'
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/hkcmms.rb

@@ -0,0 +1,26 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Hong Kong Chinese Medicine (HKCMMS) specific models.
+    #
+    # Contains models unique to the Hong Kong Chinese Materia Medica Standards:
+    # - Traditional Chinese Medicine monographs
+    # - Bilingual (Chinese/English) content
+    # - TCM-specific properties (nature, flavor, meridian)
+    #
+    # @example
+    #   # Access HKCMMS models
+    #   Openphar::Models::HKCMMS::TcmMonograph
+    #
+    # @see https://www.cmchk.org.hk/
+    module HKCMMS
+      # Placeholder for HKCMMS-specific models
+      # Will include:
+      # - TcmMonograph (Traditional Chinese Medicine)
+      # - TcmNature (thermal nature: hot/warm/neutral/cool/cold)
+      # - TcmFlavor (five flavors)
+      # - TcmMeridian (meridian tropism)
+    end
+  end
+end

data/lib/openphar/models/identification_specification.rb

@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents an identification specification
+    #
+    # Used for identity tests (TLC, spectroscopy, chemical reactions)
+    # to confirm the identity of a substance.
+    class IdentificationSpecification < TestSpecification
+      attribute :test_method, :string
+      attribute :reference_standard, :string
+
+      json do
+        map 'testMethod', to: :test_method
+        map 'referenceStandard', to: :reference_standard
+      end
+    end
+  end
+end

data/lib/openphar/models/jp/kampo_formula.rb

@@ -0,0 +1,94 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module JP
+      # Represents a Kampo formula monograph from the Japan Pharmacopoeia.
+      #
+      # Kampo is the Japanese study and adaptation of traditional Chinese medicine.
+      # Kampo formulas are standardized herbal preparations with specific
+      # ingredient ratios and preparation methods defined in the JP.
+      #
+      # @example
+      #   formula = JP::KampoFormula.new(
+      #     id: "https://www.openphar.org/data/jp/kampo/sho-saiko-to",
+      #     pref_label: { "en" => "Sho-Saiko-To", "ja" => "小柴胡湯" },
+      #     formula_code: "K001",
+      #     crude_drug_ingredients: [...]
+      #   )
+      #
+      # @see https://www.mhlw.go.jp/topics/bukyoku/iyaku/yakkyoku/
+      class KampoFormula < FormulationMonograph
+        # JP-specific formula code (e.g., "K001")
+        attribute :formula_code, :string
+
+        # Japanese name in kanji
+        attribute :japanese_name, :string
+
+        # Crude drug ingredients with their ratios
+        # Each entry contains:
+        # - crude_drug_id: IRI reference to CrudeDrugMonograph
+        # - ratio: decimal ratio (e.g., 3.0 for 3 parts)
+        # - unit: typically "g" or "parts"
+        attribute :crude_drug_ingredients, :hash, collection: true, default: []
+
+        # Preparation method instructions
+        attribute :preparation_method, :hash, default: {}
+
+        # Daily dosage range
+        attribute :daily_dosage, :hash, default: {}
+
+        # Indications in Japanese traditional medicine terms
+        # References TCM patterns (sho)
+        attribute :indications, :hash, default: {}
+
+        # Contraindications and warnings
+        attribute :contraindications, :hash, default: {}
+
+        # Reference to TCM formula origin (if applicable)
+        attribute :tcm_formula_origin, :string
+
+        json do
+          map 'formulaCode', to: :formula_code
+          map 'japaneseName', to: :japanese_name
+          map 'crudeDrugIngredient', to: :crude_drug_ingredients
+          map 'preparationMethod', to: :preparation_method
+          map 'dailyDosage', to: :daily_dosage
+          map 'indication', to: :indications
+          map 'contraindication', to: :contraindications
+          map 'tcmFormulaOrigin', to: :tcm_formula_origin
+        end
+
+        class << self
+          # Neo4j node labels for graph database export
+          #
+          # @return [Array<String>]
+          def neo4j_labels
+            %w[Monograph Formulation KampoFormula]
+          end
+
+          # JSON-LD @type value
+          #
+          # @return [String]
+          def jsonld_type
+            'KampoFormula'
+          end
+        end
+
+        # Returns the total number of crude drug ingredients
+        #
+        # @return [Integer]
+        def ingredient_count
+          crude_drug_ingredients.size
+        end
+
+        # Returns the total ratio sum (total parts)
+        #
+        # @return [Float]
+        def total_parts
+          crude_drug_ingredients.sum { |i| i[:ratio].to_f }
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/jp.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Japan Pharmacopoeia (JP) specific models.
+    #
+    # Contains models unique to the Japanese Pharmacopoeia:
+    # - Kampo formulas (Japanese traditional medicine formulations)
+    # - JP-specific monograph extensions
+    #
+    # @example
+    #   # Access JP models
+    #   Openphar::Models::JP::KampoFormula
+    #
+    # @see https://www.mhlw.go.jp/topics/bukyoku/iyaku/yakkyoku/
+    module JP
+      # Kampo formulas (Japanese traditional medicine)
+      autoload :KampoFormula, 'openphar/models/jp/kampo_formula'
+    end
+  end
+end

data/lib/openphar/models/limit.rb

@@ -0,0 +1,54 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a quantitative limit for a test specification
+    class Limit < Lutaml::Model::Serializable
+      attribute :id, :string
+      attribute :limit_type, :string
+      attribute :limit_value, :decimal
+      attribute :lower_limit, :decimal
+      attribute :upper_limit, :decimal
+      attribute :limit_unit, :string
+
+      json do
+        map '@id', to: :id
+        map 'limitType', to: :limit_type
+        map 'limitValue', to: :limit_value
+        map 'lowerLimit', to: :lower_limit
+        map 'upperLimit', to: :upper_limit
+        map 'limitUnit', to: :limit_unit
+      end
+
+      # Returns true if this is a range limit
+      def range?
+        !lower_limit.nil? && !upper_limit.nil?
+      end
+
+      # Returns true if this is a minimum limit
+      def minimum?
+        limit_type == 'LimitType-Minimum' ||
+          limit_type == 'LimitType-NotLessThan'
+      end
+
+      # Returns true if this is a maximum limit
+      def maximum?
+        limit_type == 'LimitType-Maximum' ||
+          limit_type == 'LimitType-NotMoreThan'
+      end
+
+      # Returns a human-readable representation
+      def to_s
+        if range?
+          "#{lower_limit} - #{upper_limit} #{limit_unit}"
+        elsif minimum?
+          "Not less than #{limit_value} #{limit_unit}"
+        elsif maximum?
+          "Not more than #{limit_value} #{limit_unit}"
+        else
+          "#{limit_value} #{limit_unit}"
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/mineral_substance_monograph.rb

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a mineral substance monograph
+    #
+    # Mineral substances are inorganic compounds used in medicine.
+    class MineralSubstanceMonograph < ChemicalDrugMonograph
+      attribute :mineral_type, :string
+      attribute :origin, :string
+
+      json do
+        map 'mineralType', to: :mineral_type
+        map 'origin', to: :origin
+      end
+
+      class << self
+        def neo4j_labels
+          %w[Monograph ChemicalDrug Mineral]
+        end
+
+        def jsonld_type
+          'MineralSubstanceMonograph'
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/monograph.rb

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    # Represents a pharmacopoeia monograph
+    #
+    # This is the base class for all monograph types. Each monograph knows
+    # how to serialize itself to Neo4j and JSON-LD formats.
+    class Monograph < BaseEntity
+      attribute :monograph_id, :string
+      attribute :pref_label, :hash, default: {}
+      attribute :definition, :hash, default: {}
+      attribute :publisher, :string
+      attribute :status, :string
+      attribute :belongs_to_edition, :string
+      attribute :test_specifications, TestSpecification, collection: true, default: []
+      attribute :references_preparation, :string
+      attribute :references_tcm_profile, :string
+      attribute :references_ayurveda_profile, :string
+      attribute :same_substance_as, :string, collection: true, default: []
+      attribute :has_equivalent_in, :string, collection: true, default: []
+
+      json do
+        map '@id', to: :id
+        map 'monographId', to: :monograph_id
+        map 'prefLabel', to: :pref_label
+        map 'definition', to: :definition
+        map 'publisher', to: :publisher
+        map 'status', to: :status
+        map 'belongsToEdition', to: :belongs_to_edition
+        map 'testSpecification', to: :test_specifications
+        map 'referencesPreparation', to: :references_preparation
+        map 'referencesTCMProfile', to: :references_tcm_profile
+        map 'referencesAyurvedaProfile', to: :references_ayurveda_profile
+        map 'sameSubstanceAs', to: :same_substance_as
+        map 'hasEquivalentIn', to: :has_equivalent_in
+      end
+
+      class << self
+        def neo4j_labels
+          ['Monograph']
+        end
+
+        def jsonld_type
+          'Monograph'
+        end
+      end
+
+      def iri
+        "#{Openphar.base_iri}/data/monograph/#{id}"
+      end
+
+      def label(lang = 'en')
+        pref_label[lang] || pref_label.values.first
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/buffer_solution.rb

@@ -0,0 +1,38 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Buffer Solution
+      #
+      # A solution that resists changes in pH when small amounts
+      # of acid or base are added.
+      #
+      # @example
+      #   buffer = PhInt::BufferSolution.new(
+      #     id: 'phint-buffer-ph7',
+      #     ph_range: '6.8 - 7.2',
+      #     composition: { 'components' => ['KH2PO4', 'Na2HPO4'] }
+      #   )
+      class BufferSolution < Reagent
+        attribute :ph_range, :string
+        attribute :composition, :hash, default: {}
+
+        json do
+          map 'phRange', to: :ph_range
+          map 'composition', to: :composition
+        end
+
+        class << self
+          def neo4j_labels
+            %w[Reagent BufferSolution]
+          end
+
+          def jsonld_type
+            'BufferSolution'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/dosage_form_monograph.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Dosage Form Monograph
+      #
+      # Represents dosage form monographs (capsules, tablets, injections)
+      # in the International Pharmacopoeia.
+      #
+      # Dosage form monographs define quality standards for specific
+      # pharmaceutical formulations.
+      #
+      # @example
+      #   monograph = PhInt::DosageFormMonograph.new(
+      #     id: 'phint-tablets',
+      #     dosage_form_type: 'Tablet',
+      #     dissolution_specification: { 'time' => '30 min', 'limit' => '80%' }
+      #   )
+      class DosageFormMonograph < Monograph
+        attribute :dosage_form_type, :string
+        attribute :dissolution_specification, :hash, default: {}
+        attribute :uniformity_specification, :hash, default: {}
+
+        json do
+          map 'dosageFormType', to: :dosage_form_type
+          map 'dissolutionSpecification', to: :dissolution_specification
+          map 'uniformitySpecification', to: :uniformity_specification
+        end
+
+        class << self
+          def neo4j_labels
+            %w[Monograph DosageForm]
+          end
+
+          def jsonld_type
+            'DosageFormMonograph'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/radiopharmaceutical_monograph.rb

@@ -0,0 +1,52 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Radiopharmaceutical Monograph
+      #
+      # Represents radiopharmaceutical substances in the International Pharmacopoeia
+      # with radionuclide data (half-life, emission type, etc.)
+      #
+      # Radiopharmaceuticals are unique to Ph.Int. as they contain radioactive
+      # isotopes used in nuclear medicine for diagnosis and therapy.
+      #
+      # @example
+      #   monograph = PhInt::RadiopharmaceuticalMonograph.new(
+      #     id: 'phint-sodium-iodide-i131',
+      #     radionuclide: 'I-131',
+      #     half_life: '8.02 days',
+      #     emission_type: 'beta, gamma'
+      #   )
+      class RadiopharmaceuticalMonograph < ChemicalDrugMonograph
+        attribute :radionuclide, :string
+        attribute :half_life, :string
+        attribute :emission_type, :string
+        attribute :radiochemical_purity, :string
+        attribute :radionuclidic_purity, :string
+        attribute :photon_fraction, :string
+        attribute :precursor, :string
+
+        json do
+          map 'radionuclide', to: :radionuclide
+          map 'halfLife', to: :half_life
+          map 'emissionType', to: :emission_type
+          map 'radiochemicalPurity', to: :radiochemical_purity
+          map 'radionuclidicPurity', to: :radionuclidic_purity
+          map 'photonFraction', to: :photon_fraction
+          map 'precursor', to: :precursor
+        end
+
+        class << self
+          def neo4j_labels
+            %w[Monograph ChemicalDrug Radiopharmaceutical]
+          end
+
+          def jsonld_type
+            'RadiopharmaceuticalMonograph'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/reagent.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Reagent (Base Class)
+      #
+      # Base class for all Ph.Int. reagents including test solutions,
+      # volumetric solutions, and buffer solutions.
+      #
+      # Reagents are chemical solutions used in pharmacopoeial testing.
+      #
+      # @example
+      #   reagent = PhInt::Reagent.new(
+      #     id: 'phint-reagent-sodium-hydroxide',
+      #     reagent_id: 'TS-123',
+      #     reagent_type: 'TestSolution',
+      #     preparation: { 'en' => 'Dissolve 10g in 100ml water...' }
+      #   )
+      class Reagent < BaseEntity
+        attribute :reagent_id, :string
+        attribute :pref_label, :hash, default: {}
+        attribute :reagent_type, :string
+        attribute :preparation, :hash, default: {}
+        attribute :publisher, :string
+        attribute :belongs_to_edition, :string
+
+        json do
+          map '@id', to: :id
+          map 'reagentId', to: :reagent_id
+          map 'prefLabel', to: :pref_label
+          map 'reagentType', to: :reagent_type
+          map 'preparation', to: :preparation
+          map 'publisher', to: :publisher
+          map 'belongsToEdition', to: :belongs_to_edition
+        end
+
+        class << self
+          def neo4j_labels
+            ['Reagent']
+          end
+
+          def jsonld_type
+            'Reagent'
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openphar/models/ph_int/reference_substance.rb

@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+module Openphar
+  module Models
+    module PhInt
+      # Reference Substance
+      #
+      # A chemical substance of known purity used as a reference
+      # standard in analytical testing.
+      #
+      # @example
+      #   substance = PhInt::ReferenceSubstance.new(
+      #     id: 'phint-rs-aspirin',
+      #     reference_id: 'RS-123',
+      #     cas_number: '50-78-2',
+      #     assigned_content: '99.5%'
+      #   )
+      class ReferenceSubstance < BaseEntity
+        attribute :reference_id, :string
+        attribute :pref_label, :hash, default: {}
+        attribute :cas_number, :string
+        attribute :assigned_content, :string
+        attribute :storage_conditions, :hash, default: {}
+        attribute :publisher, :string
+        attribute :belongs_to_edition, :string
+
+        json do
+          map '@id', to: :id
+          map 'referenceId', to: :reference_id
+          map 'prefLabel', to: :pref_label
+          map 'casNumber', to: :cas_number
+          map 'assignedContent', to: :assigned_content
+          map 'storageConditions', to: :storage_conditions
+          map 'publisher', to: :publisher
+          map 'belongsToEdition', to: :belongs_to_edition
+        end
+
+        class << self
+          def neo4j_labels
+            ['ReferenceSubstance']
+          end
+
+          def jsonld_type
+            'ReferenceSubstance'
+          end
+        end
+      end
+    end
+  end
+end