🧬 EnzymeML Go

A comprehensive Go implementation of the EnzymeML data exchange format for enzymatic data

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📋 Table of Contents

• 🧬 EnzymeML Go
  • 📋 Table of Contents
  • 🌟 Overview
    • Why EnzymeML Go?
  • ✨ Features
  • 🚀 Installation
    • Requirements
  • 📖 Usage
    • Quick Start
    • 🌐 Start v2 REST API
    • 🗄️ Database Example
  • 🤝 Contributing
  • 📄 License

🌟 Overview

Welcome to EnzymeML Go - a robust Go interface for working with EnzymeML documents. EnzymeML is a comprehensive data exchange format specifically designed for enzymatic data, enabling researchers to document, share, and analyze enzymatic experiments in a standardized way.

Why EnzymeML Go?

🎯 Perfect for Database & Web Infrastructure - The key strength of EnzymeML Go lies in powering databases and web applications with enzymatic data while maintaining full compliance with the EnzymeML specification.

✨ Features

EnzymeML Go implements the complete EnzymeML v2 specification, providing you with:

• 📊 Experimental Documentation: Standardized format for enzymatic experiments
• ⚗️ Reaction Conditions: Capture detailed reaction conditions and measurements
• 📈 Kinetic Models: Define and work with kinetic models and parameters
• 🔄 Data Exchange: Seamless data exchange between platforms and modeling tools
• 🌐 FAIR Compliance: Ensures Findable, Accessible, Interoperable, Reusable data principles
• 🗄️ Database Ready: Optimized for database storage and web applications

🚀 Installation

Get started with EnzymeML Go in seconds:

go get github.com/EnzymeML/enzymeml-go

Requirements

• Go 1.25+ - Ensure you have a recent version of Go installed
• Modern Go modules - This package uses Go modules for dependency management

📖 Usage

Quick Start

package main

import (
    "fmt"
    enzymeml_v2 "github.com/EnzymeML/enzymeml-go/src"
)

func main() {
    doc := enzymeml_v2.EnzymeMLDocument{Name: "Example"}
    fmt.Println(doc.Name)
}

🌐 Start v2 REST API

Create a main.go:

package main

import (
 "log"
 "net/http"

 apiv2 "github.com/EnzymeML/enzymeml-go/src/api/v2"
 enzymeml_v2 "github.com/EnzymeML/enzymeml-go/src"
 database "github.com/EnzymeML/enzymeml-go/src/database/v2"
)

func main() {
 models := []interface{}{
  &enzymeml_v2.EnzymeMLDocument{},
  &enzymeml_v2.Creator{},
  &enzymeml_v2.Vessel{},
  &enzymeml_v2.Protein{},
  &enzymeml_v2.Complex{},
  &enzymeml_v2.SmallMolecule{},
  &enzymeml_v2.Reaction{},
  &enzymeml_v2.ReactionElement{},
  &enzymeml_v2.ModifierElement{},
  &enzymeml_v2.Equation{},
  &enzymeml_v2.Variable{},
  &enzymeml_v2.Parameter{},
  &enzymeml_v2.Measurement{},
  &enzymeml_v2.MeasurementData{},
  &enzymeml_v2.UnitDefinition{},
  &enzymeml_v2.BaseUnit{},
 }

 dbManager, err := database.NewDBManager("enzymeml.db", models)
 if err != nil {
  log.Fatalf("failed to init DB: %v", err)
 }
 defer dbManager.Close()

 handler, err := apiv2.NewHandler(dbManager)
 if err != nil {
  log.Fatalf("failed to build API handler: %v", err)
 }

 log.Println("v2 API listening on :8080")
 log.Fatal(http.ListenAndServe(":8080", handler))
}

Run:

go run .

Example CRUD for documents:

curl -X POST http://localhost:8080/v2/documents \
  -H "Content-Type: application/json" \
  -d '{"name":"my-doc","version":"2.0.0"}'

curl http://localhost:8080/v2/documents
curl http://localhost:8080/v2/documents/1

curl -X PUT http://localhost:8080/v2/documents/1 \
  -H "Content-Type: application/json" \
  -d '{"name":"my-doc-updated","version":"2.0.1"}'

curl -X DELETE http://localhost:8080/v2/documents/1

The API exposes CRUD for all v2 resources under /v2: documents, creators, vessels, proteins, complexes, small-molecules, reactions, reaction-elements, modifier-elements, equations, variables, parameters, measurements, measurement-data, unit-definitions, base-units.

With Huma, docs/spec are available automatically:

• http://localhost:8080/v2/docs
• http://localhost:8080/v2/openapi.json
• http://localhost:8080/v2/openapi.yaml

🗄️ Database Example

For a comprehensive example of how to use EnzymeML Go to create an enzymatic data database and power web applications, check out our detailed example:

👉 Database Example

This example demonstrates:

• Setting up an EnzymeML-compliant database
• Storing and retrieving enzymatic data
• Web application integration
• Best practices for data management

🤝 Contributing

We welcome contributions from the community! Please feel free to submit a pull request.

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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Made with ❤️ by the EnzymeML Team