Charles Tapley Hoyt cthoyt

BioGRID Identifiers Problem, Solved

The file I included here has a set of organisms in the BioGRID identifiers download (version 3.5.184), latest as of time of writing on 2020-04-17) whose ORGANISM_OFFICIAL_NAME is not correct. I went and mapped these all with a mixture of synonym search on NCBITaxon and manual intervention. Each has the taxonomy identifier, so it can be used to get the most up-to-date information.

I would highly suggest including a taxonomy ID in this dump as well as the name, so it can be programatically mapped for anyone trying to integrate this

Charlie's PhD, The Drinking Game

How to play:

Read Charlie's PhD thesis... or just skim through it looking for fun
Drink based on the following rules:

1 Sip

Charlie uses too many references

	import json
	import sys

	import click

	import bioregistry


	@click.command()
	@click.option('--output', default=sys.stdout)

	Experiment1.m5_node_label,Experiment1.m5_fold_change,Experiment1.m5_tstats
	COX1,0.0442820351919402,1.27430203477638
	ATP6,0.0829436812093022,2.86171297191134
	SCGB1A1,-0.0829577087977886,-2.31945514137341
	BPIFB1,0.303399473563391,7.82213833931689
	RPL41,-0.0316199085257711,-1.3019865836353
	ND2,0.0609064988662182,1.5913565091562
	HBB,-0.60815873574393,-2.82215934759009
	SCGB3A1,-0.114966188117398,-1.12153734714022
	EEF1A1,-0.0856593570605189,-2.61018187225134

	"""
	Author: Charles Tapley Hoyt (@cthoyt)
	License: MIT
	See related blog post at https://cthoyt.com/2020/12/07/generating-literal-datasets.html
	"""

	from typing import Any, List, TextIO, Tuple, Type, Union

	import click
	import torch

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>Human Brain Pharmacome Knowledge</title>
	<script src="https://unpkg.com/[email protected]/dist/js/ideogram.min.js"></script>
	</head>
	<body>
	<script>
	var ideogram = new Ideogram({

	import pubchempy as pcp

	keys = '''MXDPZUIOZWKRAA-UZOALHFESA-K
	MJUVRTYWUMPBTR-MRXNPFEDSA-N
	HJBWBFZLDZWPHF-UHFFFAOYSA-N
	HZIYEEMJNBKMJH-UHFFFAOYSA-N
	CPZBLNMUGSZIPR-NVXWUHKLSA-N
	GKDRMWXFWHEQQT-UHFFFAOYSA-N
	KSMAGQUYOIHWFS—UHFFFAOYSA-N
	OFZJKCQENFPZBH-UHFFFAOYSA-N

	import unittest

	from contextlib import contextmanager

	# see https://stackoverflow.com/questions/12594148/skipping-execution-of-with-block

	@contextmanager
	def when_truthy(argument):
	"""
	The point of this function is to make it so you never have to write

	#!/usr/bin bash

	mkdir output

	# Download and install pybel-tools
	git clone https://github.com/pybel/pybel-tools
	cd pybel-tools
	python3 -m pip install --user .

	cd ..