Purpose

Open Pharmacopoeia provides a harmonized ontology for representing pharmacopoeia monographs from multiple publishers. The project enables cross-publisher comparison of quality standards by normalizing test methods and specifications.

This project integrates with https://github.com/lutaml/data-herbapedia for botanical and medicine system data, while open-pharmacopoeia focuses on quality standards and test specifications.

Architecture

Open-Pharmacopoeia Architecture Layers

data-herbapedia:  Plant → Part → Preparation → Medicine System Profiles
                                              ↓
open-pharmacopoeia:                      PharmacopoeiaMonograph
                                              ├── TestSpecification
                                              ├── Assay
                                              └── SafetyInformation

Integration with data-herbapedia

Layer	Responsibility
data-herbapedia	Botanical data (PlantSpecies, PlantPart), HerbalPreparation, Medicine System Profiles (TCM, Ayurveda, Western)
open-pharmacopoeia	Quality standards (TestSpecification, Assay), Test methods (HarmonizedMethod), Publisher-specific data

The key integration point is op:referencesPreparation, which links a PharmacopoeiaMonograph to a HerbalPreparation in data-herbapedia.

Features

• Harmonized Ontology - Common vocabulary for representing pharmacopoeia monographs from any publisher

• Cross-Publisher Comparison - Harmonized test methods enable comparison across publishers

• Crude Drug Support - Extended model for herbal medicines with macroscopic/microscopic descriptions

• data-herbapedia Integration - Links to botanical and medicine system data

• Multilingual Support - Full internationalization with language-tagged strings

• SHACL Validation - Shapes for validating monograph data

Installation

Add this line to your application’s Gemfile:

gem 'open-pharmacopoeia', git: 'https://github.com/lutaml/open-pharmacopoeia'

And then execute:

bundle install

Usage

Loading a Monograph

require 'open_pharmacopoeia'

# Load from JSON-LD
monograph = OpenPharmacopoeia::CrudeDrugMonograph.from_json(File.read('data/jp/radix-ginseng.jsonld'))

# Access monograph properties
monograph.label("en")  #=> "Ginseng Radix"
monograph.publisher.name  #=> "Japan Pharmacopoeia"
monograph.assays.each do |assay|
  puts "#{assay.assay_target}: #{assay.limit}"
end

Creating a New Monograph

require 'open_pharmacopoeia'

monograph = OpenPharmacopoeia::CrudeDrugMonograph.new(
  monograph_id: "JP18-001",
  publisher: OpenPharmacopoeia::Publisher.find("JP"),
  pref_label: { "en" => "Ginseng Radix", "ja" => "人参" },
  references_preparation: "https://www.herbapedia.org/entity/preparation/dried-ginseng-root"
)

# Add test specification
monograph.test_specifications << OpenPharmacopoeia::PhysicalSpecification.new(
  test_name: "Total Ash",
  test_type: OpenPharmacopoeia::TestType.find("Physical"),
  harmonized_method: OpenPharmacopoeia::HarmonizedMethod.find("TotalAsh"),
  limit: OpenPharmacopoeia::Limit.new(
    limit_type: OpenPharmacopoeia::LimitType.find("NotMoreThan"),
    limit_value: 4.2,
    limit_unit: OpenPharmacopoeia::Unit.find("percent")
  )
)

Ontology Structure

Core Classes

Class	Description
op:PharmacopoeiaMonograph	Central class representing a pharmacopoeia monograph
op:CrudeDrugMonograph	Extended monograph for herbal medicines
op:TestSpecification	Generic test specification (value object)
op:AssaySpecification	Quantitative analysis specification
op:PuritySpecification	Impurity limit specification
op:HarmonizedMethod	Harmonized test method for cross-publisher comparison
op:Publisher	Pharmacopoeia publisher enumeration

External References

Monographs reference external entities in data-herbapedia:

op:Ginseng-Monograph
    op:referencesPreparation <https://www.herbapedia.org/entity/preparation/dried-ginseng-root> ;
    op:referencesTCMProfile <https://www.herbapedia.org/system/tcm/profile/ren-shen> .

Test Method Harmonization

# Harmonized method with publisher equivalents
method:HPLC a op:HarmonizedMethod ;
    rdfs:label "HPLC"@en ;
    op:jpReference "as directed under Liquid Chromatography <2.01>" ;
    op:equivalentMethod api:Appendix-2.2.29 ;
    op:equivalentMethod hkcmms:Appendix-IV-B .

File Structure

open-pharmacopoeia/
├── ontology/
│   ├── core/
│   │   ├── pharmacopoeia.ttl     # Core classes and properties
│   │   └── unit.ttl              # Measurement units
│   ├── quality/
│   │   └── test-method.ttl       # Harmonized test methods
│   └── context/
│       └── pharmacopoeia.jsonld  # JSON-LD context
├── data/
│   ├── jp/                       # Japan Pharmacopoeia monographs
│   ├── hkcmms/                   # Hong Kong CMMS monographs
│   └── api/                      # Ayurvedic Pharmacopoeia of India
├── shapes/
│   └── monograph-shapes.ttl      # SHACL validation shapes
├── tools/
│   └── lib/
│       └── open_pharmacopoeia/   # Ruby models
└── reference-docs/               # Reference pharmacopoeia documents

Supported Publishers

Code	Name	Country
AHP	American Herbal Pharmacopoeia	US
API	Ayurvedic Pharmacopoeia of India	IN
JP	Japan Pharmacopoeia	JP
HKCMMS	Hong Kong Chinese Materia Medica Standards	HK
THP	Thai Herbal Pharmacopoeia	TH
CMHerbarium	CM Herbarium	CN
WHO	WHO Monographs on Selected Medicinal Plants	INT
UPB	Unani Pharmacopoeia of Bangladesh	BD
UPI	Unani Pharmacopoeia of India	IN
APB	Ayurvedic Pharmacopoeia of Bangladesh	BD
APS	Ayurvedic Pharmacopoeia of Sri Lanka	LK

IRI Namespaces

Prefix	Namespace
op:	https://www.openphar.org/ontology/core/
method:	https://www.openphar.org/ontology/method/
unit:	https://www.openphar.org/ontology/core/unit/
herbapedia:	https://www.herbapedia.org/entity/

Development

After checking out the repo, run:

bundle install
bundle exec rake spec    # Run tests
bundle exec rubocop      # Run linter

License

This project is available as open source under the terms of the MIT License.