PDF reader - NER

This project implements a Named Entity Recognition (NER) API that extracts biological entities from PDFs. It uses Vertex AI for processing the text and identifying biological entities. The API accepts PDF files as input, extracts the text from them, and then sends the text to Vertex AI's Gemini model to perform NER.

Requirements

• Python 3.8+
• Vertex AI account and credentials

Setup

1. Clone the repository:

   git clone https://github.com/amyford/pdf-reader.git
   cd pdf-reader
   

2. Install dependencies:

   python3 -m venv venv
   source venv/bin/activate
   pip install -r requirements.txt
   

3. Set up your Google Cloud project for Vertex AI and authenticate

   gcloud auth application-default login
   export GOOGLE_CLOUD_PROJECT=your-project-id
   

For more details, please See the GCloud website. Configure your API to access Vertex AI API.

Running locally

python3 main.py

Running in the Cloud

Deploy your service to Cloud Run

gcloud run deploy --source .

Then use the url provided.

Usage

Example:

curl -X POST -F "file=@path/to/file.pdf" http://127.0.0.1:5000/api/v1/extract

Example Response:

{
  "entities": [
    {
      "entity": "COVID-19",
      "context": "... was observed in patients with COVID-19",
      "start": 30,
      "end": 45
    },
    {
      "entity": "ERK1",
      "context": "... elevated levels of ERK1 were seen",
      "start": 10,
      "end": 15
    }
  ]
}

Testing

python -m unittest test_main.py