Disease-Gene pipeline: Identify phenotypes caused by various genes

[joeflack4]

Overview

There are some phenotypes in that are caused by various genes, and we generally (always?) do not want to include these in the pipeline; they should not be marked as having causal germline mutation w/ associated gene in morbidmap.txt. The problem is that this information about whether or not they are caused by various genes is not contained in morbidmap.txt or the other data files. It is found in the first paragraph in the "Text" subsection in omim.org/entry pages.

Possible solution

a. Web scrape, and include that paragraph of text in the spreadsheet
b. Web scrape, and maybe look for specific phrases like “various genes”, and toggle a boolean column when such phrases are found.
c. Do nothing, and import these anyway even though we ideally should/would not.

Background

• GitHub comments
• Slack thread