Merge pull request #12 from Crispae/documentation

Documentation

.github/workflows/ci.yml

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+name: ci 
+on:
+  push:
+    branches:
+      - documentation 
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install mkdocs-material
+      - run: pip install pillow cairosvg
+      - run: mkdocs gh-deploy --force

docs/index.md

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+# AOPWIKI Explorer
+
+AOPWiki Explorer is a Labeld property graph (LPG) adaptation of AOPwiki. LPG schema is adapted using neo4j graph database providing cypher and natural language based query engine to explore AOPs. Explorer provides intutive network visualization of AOPs component.AOPwiki Explorer is developed under project [**Partnership for the Assessment of Risks from Chemicals (PARC)**](https://www.eu-parc.eu)
+
+
+## Requirements 🐳
+- Docker  
+- Docker-compose  
+
+Follow the documentation [documentation](https://docs.docker.com/engine/install/), to install docker and docker compose
+
+## Quick Installation
+
+The recommended method to use AOPWIKI explorer is through Docker container.
+
+## Step 1: Clone the Repository
+Open the command prompt and write the following command
+  ```shell
+git clone https://github.com/Crispae/AOPWiki_Explorer.git
+cd AOPWiki_Explorer
+```  
+## Step 2: Build Docker Container
+
+In the [`docker-compose.yaml`](https://github.com/Crispae/AOPWiki_Explorer/blob/main/docker-compose.yaml) file, it's essential to update the `OPENAI_API_KEY` to enable the query translation service.
+
+### Instructions:
+
+1. **Obtain Your OpenAI API Key:**
+   - Get your OpenAI API key from the [OpenAI API page](https://openai.com/blog/openai-api).
+
+2. **Update the `OPENAI_API_KEY`:**
+   - Locate the `docker-compose.yaml` file in the cloned repository.
+   - Replace the placeholder for `OPENAI_API_KEY` with your obtained API key.
+
+3. **Build the Docker Container:**
+   - After updating the OpenAI key, initiate the container build using the following command:
+   ```shell
+   docker compose up
+
+## Step 3: Populate the Graph Database with AOP Information
+
+To update the graph database with the latest AOP information, follow these steps. This process is a one-time setup.
+
+### Instructions:
+
+1. **Open the Jupyter Notebook:**
+   - Access the Jupyter Lab by clicking on the provided URL captured from the console while running the Docker instance. The URL will resemble: `http://127.0.0.1:8888/lab?token=your_token`
+
+2. **Run the `GraphEnricher.ipynb` Notebook:**
+   - After accessing the Jupyter Lab, locate and run the `GraphEnricher.ipynb` notebook within the interface.
+
+3. **Updating the Database:**
+   - If it's the first installation on your system:
+     - Run the entire Jupyter Notebook. This process will update the database with the latest AOP information.
+
+   - If it's an update to the existing installation:
+     - Uncomment the relevant cells in the notebook to delete the information in the graph database before running the notebook. This step ensures that the database gets updated with the most recent information.
+
+These steps are essential for maintaining an updated graph database containing the latest AOP information. Make sure to follow these instructions to keep the database current.
+
+
+## Step 4. Acess the interface  
+Open following link on your web browser to access the AOPwiki-Explorer  ```http://127.0.0.1:3000/```
+
+## Examples
+
+Will be available soon
+
+1. Direct cypher query
+2. Natural language query
+3. Step wise query

mkdocs.yml

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+site_name: AOPwiki Explorer
+theme:
+  name: material
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - toc.integrate
+    - navigation.top
+    - search.suggest
+    - search.highlight
+    - content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+  language: en
+  palette:
+    - scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline 
+        name: Switch to dark mode
+      primary: teal
+      accent: purple 
+    - scheme: slate 
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode    
+      primary: teal
+      accent: lime
+
+plugins:
+  - social
+
+extra:
+  social:
+    - icon: fontawesome/brands/github-alt
+      link: https://github.com/Crispae
+    - icon: fontawesome/brands/twitter
+      link: https://twitter.com/sauravk76534078
+    - icon: fontawesome/brands/linkedin
+      link: https://www.linkedin.com/in/saurav-kumar-51593a1b9/
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.mark
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:materialx.emoji.twemoji
+      emoji_generator: !!python/name:materialx.emoji.to_svg