Dataset downloader
===

This folder contains scripts and instructions to download the original datasets that can be used to create the pathway database.

There are two pieces you need:

## [Pathway data](pathway_data.py)
Includes pathway names, gene mappings, pathway relationships. Data is downloaded from reactome.org.

To get this data, use the [download script](pathway_data.py). It requires Python3 and the requests library `pip3 install requests`.

Output is -

* `pathway_genes.tsv` - Contains data with gene-pathway mappings
* `pathways.tsv` - Pathways, their names and ids
* `pathway_relationships.tsv` - Gene relationships


## [Gene data](gene_data.py)
Includes gene names. Unfortunately, nanostring did not tell us how to get this data, so we have to acquire them through a 3rd party service.

To download them manually, see the [instructions](gene_data.MD).

While it might break at any moment, you may use [gene_data.py](gene_data.py) to download this data automatically. It requires Python3 and the request library `pip3 install requests`.

Output is -
* `genes.tsv` - file containing gene names and NCBI ids for use with our database creation script