Initial draft of FDA-approvals in va-spec~ish (in progress) format

README.md

@@ -11,6 +11,37 @@ If you wish to suggest an assertion for cataloging in this database, you can do
 - Suggesting an entry through our [web browser's form](https://moalmanac.org/add)
 - Suggesting an entry through our [Google Chrome extension](https://chrome.google.com/webstore/detail/molecular-oncology-almana/jliaipolchffpaccagodphgjpfdpcbcm)
 
+## Installation
+### Download
+This repository can be downloaded through GitHub by either using the website or terminal. To download on the website, navigate to the top of this page, click the green `Clone or download` button, and select `Download ZIP` to download this repository in a compressed format. To install using GitHub on terminal, type:
+
+```bash
+git clone https://github.com/vanallenlab/moalmanac-db.git
+cd moalmanac-db
+```
+
+### Python dependencies
+This repository uses Python 3.12. We recommend using a [virtual environment](https://docs.python.org/3/tutorial/venv.html) and running Python with either [Anaconda](https://www.anaconda.com/download/) or [Miniconda](https://conda.io/miniconda.html). 
+
+Run the following from this repository's directory to create a virtual environment and install dependencies with Anaconda or Miniconda:
+```bash
+conda create -y -n moalmanac-db python=3.12
+conda activate moalmanac-db
+pip install -r requirements.txt
+```
+
+Or, if using base Python: 
+```bash
+virtualenv venv
+source activate venv/bin/activate
+pip install -r requirements.txt
+```
+
+To make the virtual environment available to jupyter notebooks, execute the following code while the virtual environment is activated:
+```bash
+ipython kernel install --user --name=moalmanac-db
+```
+
 ## Citation
 If you find this tool or any code herein useful, please cite:  
 > [Reardon, B., Moore, N.D., Moore, N.S., *et al*. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. *Nat Cancer* (2021). https://doi.org/10.1038/s43018-021-00243-3](https://www.nature.com/articles/s43018-021-00243-3)

docs/assets/README.md

@@ -0,0 +1,18 @@
+# Documentation assets
+The following assets are used by documentation within the `docs/` folder of this repository.
+
+# Table of contents
+- [Database schema diagram](#database-schema-diagram)
+
+# Assets
+## Database schema diagram
+[moalmanac-db-schema-diagram.svg](moalmanac-db-schema-diagram.svg) is a diagram of the database schema. Here, we aim to highlight: 
+1. Connections between the [different references between files that make up the database](../../references/)
+2. What parts of our schema is represented within [GA4GH's va-spec](https://github.com/ga4gh/va-spec)
+3. What parts of our schema are compliant with va-spec
+
+This diagram was created with [Google Draw](https://docs.google.com/drawings/d/1fLOOwtc87YVEJfy4oTiP04cUFgKVGalv8vv4k0L__2c/edit?usp=sharing).
+
+![moalmanac-db-schema-diagram.svg](moalmanac-db-schema-diagram.svg)
+
+[Back to table of contents](#table-of-contents)

referenced/about.json

@@ -0,0 +1,8 @@
+{
+    "github": "https://github.com/vanallenlab/moalmanac-db",
+    "label": "Molecular Oncology Almanac",
+    "license": "GPL-2.0",
+    "release": "pre draft",
+    "url": "https://moalmanac.org",
+    "last_updated": "2025-01-10"
+}

referenced/agents.json

@@ -0,0 +1,9 @@
+[
+  {
+    "id": 0,
+    "type": "Agent",
+    "subtype": "organization",
+    "label": "Van Allen lab",
+    "description": "Van Allen lab, Dana-Farber Cancer Institute"
+  }
+]