Further infrastructure to make YAML masterfile

SuLab / DrugMechDB

A database of paths that represent the mechanism of action from a drug to a disease in an indication.

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Further infrastructure to make YAML masterfile #2

Open mmayers12 opened 4 years ago

mmayers12 commented 4 years ago

Currently, .json and .yaml implementations of DrugMechDB are built from the excel spreadsheet available on Zenodo.

However, to more easily incorporate new drug mechanisms, the YAML file will be used as the primary source for DrugMechDB, with new paths added via pull requests. With this setup, we need a simple way to build excel spreadsheet from the YAML file and submit periodic updates to Zenodo.

andrewsu commented 4 years ago

There's nothing to say that we have to deposit an excel file at zenodo. what would we lose if we deposited the YAML there on a periodic release schedule?

mmayers12 commented 4 years ago

Excel is inherently easier for people to interact with, especially those without a background in coding... However, it's occurring to me that someone like that may have little utility with this resource in the first place...

cmungall commented 4 years ago

It seems you have no end of ways to make this accessible for people - e.g. translate the yaml to markdown, hyperlnk the entities, show the markdown using github pages

Would it be possible to add provenance to the yaml?

Note sure if it is of interest but I made a ticket on representation of paths in a KG: https://github.com/biolink/biolink-model/issues/348