Charles Tapley Hoyt cthoyt

## BiologicalDatabasesDayOne.ipynb

      
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                cthoyt
                / BiologicalDatabasesDayOne.ipynb
            
            
              Created
              January 12, 2016 20:10
            
              
                Biological Databases Practical 2016 Day 1
              
          
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## compare_bel_compilers.sh
mkdir /tmp/beltest
cd /tmp/beltest

curl http://resources.openbel.org/belframework/1.0/knowledge/small_corpus.bel > small.bel
curl http://resources.openbel.org/belframework/1.0/knowledge/large_corpus.bel > large.bel

# Test Python
python -m pip install pybel
time python -m pybel convert --path small.bel --pickle small.gpickle
time python -m pybel convert --path large.bel --pickle large.gpickle

## use_pip.py
# Pip is actually a python package!
import pip

# It's screwy and not really written to be used this way, but we still can
pip_install_cmd = pip.commands.InstallCommand()

# load up all the args you'd use after pip install and away we go!
args = ['--upgrade', '--user', 'requests']
pip_install_cmd.main(args)

## update_resources.sh
#!/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 ..

## truthycontext.py
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

## southan_challenge.py
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

## hbp_ideogram.html
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <title>Human Brain Pharmacome Knowledge</title>
    <script src="https://unpkg.com/ideogram@1.5.0/dist/js/ideogram.min.js"></script>
</head>
<body>
<script>
    var ideogram = new Ideogram({

## README.md

      
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                cthoyt
                / README.md
            
            
              Last active
              April 17, 2020 13:23
            
              
                Remapping organism names in BioGRID identifiers dump
              
          
    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

  
## constrained-evaluation-on-hetionet.ipynb

      
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                cthoyt
                / constrained-evaluation-on-hetionet.ipynb
            
            
              Created
              August 25, 2020 02:38
            
              
                Constrained Evaluation on Hetionet.ipynb
              
          
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## generate_literals.py
"""
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
	mkdir /tmp/beltest
	cd /tmp/beltest

	curl http://resources.openbel.org/belframework/1.0/knowledge/small_corpus.bel > small.bel
	curl http://resources.openbel.org/belframework/1.0/knowledge/large_corpus.bel > large.bel

	# Test Python
	python -m pip install pybel
	time python -m pybel convert --path small.bel --pickle small.gpickle
	time python -m pybel convert --path large.bel --pickle large.gpickle
	# Pip is actually a python package!
	import pip

	# It's screwy and not really written to be used this way, but we still can
	pip_install_cmd = pip.commands.InstallCommand()

	# load up all the args you'd use after pip install and away we go!
	args = ['--upgrade', '--user', 'requests']
	pip_install_cmd.main(args)
	#!/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 ..
	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
	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
	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>Human Brain Pharmacome Knowledge</title>
	<script src="https://unpkg.com/ideogram@1.5.0/dist/js/ideogram.min.js"></script>
	</head>
	<body>
	<script>
	var ideogram = new Ideogram({
	"""
	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