DOI Reference Extractor: Open-Source Tool for Effortless Literature Reviews

Academic research often involves navigating through a labyrinth of references and citations. While exploring papers, I found myself spending more time copying references than engaging with the actual ideas. This repetitive task was stealing valuable time that could be better spent on critical thinking and analysis.

I built DOI Reference Extractor — an open-source tool that instantly pulls every reference from an academic paper using just its DOI, converts them to over 5000 different citation formats, and enables bulk downloads as individual files or ZIP archives.

Live Demo

Try the reference extractor below or visit references.mireklzicar.com:

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  <iframe
    src="https://references.mireklzicar.com/"
    width="100%"
    height="100%"
    title="DOI Reference Extractor"
    style="border: none;"
  />
</div>

Live DOI Reference Extractor running at references.mireklzicar.com

Features & Capabilities

The tool offers comprehensive reference extraction and formatting capabilities:

Reference Formats

BibTeX - Perfect for LaTeX documents and academic writing
RIS - Compatible with EndNote, Mendeley, Zotero, and other reference managers
EndNote - Direct EndNote format support
RefWorks - RefWorks native format
CSL JSON - Citation Style Language JSON for advanced processing
RDF XML - Resource Description Framework XML
Turtle RDF - Turtle RDF serialization format

Citation Styles

Choose from over 5000 citation styles including:

APA - American Psychological Association
Harvard - Harvard referencing system
Vancouver - Vancouver medical citation style
IEEE - Institute of Electrical and Electronics Engineers
Chicago - Chicago Manual of Style
MLA - Modern Language Association
Nature - Nature journal style
And thousands more from the CSL community

Download Options

Single File - All references combined in one text file
ZIP Archive - Individual files for each reference with descriptive filenames
Copy to Clipboard - Quick copying for immediate use
Share Links - URL sharing with pre-filled DOIs

How It Works

Technical Architecture

The DOI Reference Extractor leverages a sophisticated three-step process using multiple academic APIs:

1. Reference Discovery

// Step 1: Extract all referenced DOIs from a paper
const response = await fetch(`https://opencitations.net/index/api/v2/references/${doi}`);
const references = await response.json();

The application queries the OpenCitations API v2 to retrieve all references cited by the input paper. OpenCitations maintains a comprehensive database of scholarly citations, making it the perfect starting point for reference extraction.

2. Metadata Retrieval

// Step 2: Fetch detailed metadata for each reference
const metadataResponse = await fetch(`https://doi.org/${referenceDoi}`, {
  headers: {
    'Accept': 'application/json' // or other format
  }
});

For each discovered reference DOI, the tool uses DOI Content Negotiation provided by Crossref to fetch comprehensive metadata including:

Paper titles and abstracts
Author names and affiliations
Publication dates and venues
Publisher information
Citation counts and metrics

3. Format Conversion

// Step 3: Convert to desired citation format
const citationResponse = await fetch(`https://doi.org/${referenceDoi}`, {
  headers: {
    'Accept': 'text/x-bibliography; style=apa' // or other CSL style
  }
});

The final step leverages DOI Content Negotiation’s support for Citation Style Language (CSL) to convert each reference into the user’s chosen format or style.

API Integration Details

The application integrates with three key services:

OpenCitations API
- Provides comprehensive citation indexing
- Returns DOIs of all papers referenced by the input DOI
- Offers citation metadata and relationship mapping
DOI Content Negotiation
- Crossref’s API for metadata retrieval and format conversion
- Supports multiple output formats (BibTeX, RIS, CSL JSON, etc.)
- Implements Citation Style Language for text formatting
Citation Style Language (CSL)
- Community-maintained repository of 5000+ citation styles
- Standardized formatting for academic citations
- Support for journal-specific requirements

Tech Stack & Implementation

The application is built with modern web technologies for optimal performance and user experience:

{
  "framework": "React 19 with TypeScript",
  "build_tool": "Vite",
  "styling": "Tailwind CSS + ShadCN UI",
  "api_client": "Axios",
  "file_processing": "JSZip",
  "routing": "React Router",
  "deployment": "Docker + Vercel"
}

Key Technical Features

Responsive Design - Works seamlessly on desktop and mobile devices
Error Handling - Graceful handling of invalid DOIs and API failures
Progress Tracking - Real-time progress indicators for large reference sets
Batch Processing - Efficient handling of papers with hundreds of references
Caching Strategy - Optimized API calls to reduce redundant requests

Docker Deployment

The application includes production-ready Docker configuration:

FROM node:18-alpine as builder
WORKDIR /app
COPY package*.json ./
RUN npm ci --only=production

COPY . .
RUN npm run build

FROM nginx:alpine
COPY --from=builder /app/dist /usr/share/nginx/html
EXPOSE 80
CMD ["nginx", "-g", "daemon off;"]

This enables easy deployment across different environments and cloud providers.

Why I Built This & Open Source Philosophy

During a recent literature review, I realized I was spending more time on the mechanical task of copying citations than on analyzing and connecting ideas. What started as a simple evening project to solve my own problem quickly became a tool others found useful too.

I believe academic tools should be open and accessible to everyone. That’s why DOI Reference Extractor is completely open-source under the Apache 2.0 license. The entire codebase, including documentation and deployment scripts, is available on GitHub.

Benefits for Researchers

The DOI Reference Extractor eliminates this busywork, allowing researchers to:

Save time by instantly capturing all references from any paper
Follow citation trails efficiently across research domains
Standardize references using consistent formatting
Focus on ideas rather than mechanical citation work
Collaborate easily by sharing formatted reference lists
Support reproducibility through consistent citation practices

Open Source Advantages

By making this tool open-source, the research community benefits from:

Transparency - Full visibility into how references are processed
Customization - Ability to modify for specific institutional needs
Community contributions - Improvements and bug fixes from users worldwide
No vendor lock-in - Complete control and self-hosting options
Academic freedom - No restrictions or usage limits

Example Usage & Output Formats

BibTeX Output Example

For DOI: 10.1103/physrevlett.10.84, the tool generates properly formatted BibTeX citations:

@article{Mandel_1961,
  title={Correlation in the Fluctuating Outputs from Two Square-Law Detectors Illuminated by Light of Any State of Coherence and Polarization},
  volume={124},
  ISSN={0031-899X},
  url={http://dx.doi.org/10.1103/physrev.124.1696},
  DOI={10.1103/physrev.124.1696},
  number={6},
  journal={Physical Review},
  publisher={American Physical Society (APS)},
  author={Mandel, L. and Wolf, E.},
  year={1961},
  month=dec,
  pages={1696–1702}
}

@article{BROWN_1956,
  title={Correlation between Photons in two Coherent Beams of Light},
  volume={177},
  ISSN={1476-4687},
  url={http://dx.doi.org/10.1038/177027a0},
  DOI={10.1038/177027a0},
  number={4497},
  journal={Nature},
  publisher={Springer Science and Business Media LLC},
  author={BROWN, R. HANBURY and TWISS, R. Q.},
  year={1956},
  month=jan,
  pages={27–29}
}

RIS Format Example

The same references in RIS format for EndNote/Mendeley:

TY  - JOUR
AU  - Mandel, L.
AU  - Wolf, E.
TI  - Correlation in the Fluctuating Outputs from Two Square-Law Detectors
JO  - Physical Review
VL  - 124
IS  - 6
SP  - 1696
EP  - 1702
PY  - 1961
DO  - 10.1103/physrev.124.1696
ER  -

TY  - JOUR
AU  - Brown, R. Hanbury
AU  - Twiss, R. Q.
TI  - Correlation between Photons in two Coherent Beams of Light
JO  - Nature
VL  - 177
IS  - 4497
SP  - 27
EP  - 29
PY  - 1956
DO  - 10.1038/177027a0
ER  -

APA Citation Style Example

For direct inclusion in manuscripts:

Mandel, L., & Wolf, E. (1961). Correlation in the fluctuating outputs from two square-law detectors illuminated by light of any state of coherence and polarization. Physical Review, 124(6), 1696-1702.

Brown, R. H., & Twiss, R. Q. (1956). Correlation between photons in two coherent beams of light. Nature, 177(4497), 27-29.

Getting Started

Using the Web Application

Visit references.mireklzicar.com
Enter any DOI (e.g., 10.1073/pnas.1118373109)
Click “Get References” and wait for processing
Select your preferred format or citation style
Download as single file or ZIP archive

Self-Hosting with Docker

Clone and deploy your own instance:

# Clone the repository
git clone https://github.com/mireklzicar/doi-reference-extractor.git
cd doi-reference-extractor

# Build and run with Docker
docker build -t doi-reference-extractor .
docker run -p 80:80 doi-reference-extractor

Development Setup

For local development and contributions:

# Install dependencies
npm install
# or
pnpm install

# Start development server
npm run dev
# or
pnpm dev

# Build for production
npm run build
# or
pnpm build

Roadmap

Future enhancements under consideration:

Bulk DOI processing - Upload lists of DOIs for batch processing
Citation network visualization - Interactive graphs of citation relationships
Additional APIs - Integration with PubMed, arXiv, and other databases
Citation analysis - Impact metrics and citation pattern analysis
Custom style editor - Create and modify citation styles

By eliminating the tedious busywork of manually copying and formatting references, we can all spend more time where it matters - engaging with ideas and advancing knowledge. Try it now at references.mireklzicar.com and join the open-source research community!