David Ochoa d0choa

👨‍💻

Open Targets Platform Coordinator

d0choa / metadata_SEO

Last active November 25, 2021 13:49

Some possible relevant fields for SEO

	import pyspark.sql.functions as F
	from pyspark import SparkConf
	from pyspark.sql import SparkSession

	sparkConf = SparkConf()
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.mode', 'AUTO')
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.project.id',
	'open-targets-eu-dev')

	# establish spark connection

d0choa / metrics_comparison.R

Created October 6, 2021 14:28

Compare AUCs and OR for 2 pipeline runs

	library(tidyverse)
	library(cowplot)
	library(ggrepel)

	df <- bind_rows(
	read_csv("~/Projects/ot-release-metrics/data/21.06.5.csv"),
	read_csv("~/Projects/ot-release-metrics/data/21.09.2.csv")
	)

	df %>%

d0choa / literatureFailedAndMatches.py

Last active August 27, 2021 19:45

Missing terms in the ontology (failed grounded entities) and the most frequently occurring terms on the same publications

	import pyspark.sql.functions as F
	from pyspark import SparkConf
	from pyspark.sql import SparkSession
	from pyspark.sql.window import Window

	sparkConf = SparkConf()
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.mode', 'AUTO')
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.project.id',
	'open-targets-eu-dev')

d0choa / otAnalytics.r

Last active September 29, 2021 15:37

Open Targets web accesses retrieved from Google Analytics API

	library("tidyverse")
	library("googleAnalyticsR")
	library("zoo")
	library("lubridate")

	date_range <- c("2019-01-01", as.character(Sys.Date() - 1))

	# Authorisation
	ga_auth()

d0choa / nod2AF.py

Last active August 11, 2021 10:41

Overlay variants in NOD2 alphafold model

	from pymol import cmd

	cmd.load("/Users/ochoa/Downloads/AF-Q9HC29-F1-model_v1.cif")

	cmd.bg_color("grey95")

	cmd.set_color("veryHigh", [0, 83, 214])
	cmd.set_color("confident", [101, 203, 243])
	cmd.set_color("low", [255, 219, 19])
	cmd.set_color("veryLow", [255, 125, 69])

d0choa / targetMissenseVariants.py

Last active September 15, 2021 17:24

Target specific (NOD2) coding variants (GWAS + ClinVar pathogenic)

	import pyspark.sql.functions as F
	from pyspark import SparkConf
	from pyspark.sql import SparkSession


	sparkConf = SparkConf()

	spark = (
	SparkSession.builder
	.config(conf=sparkConf)

d0choa / NOD2_variants.py

Last active August 27, 2021 15:32

Pathogenic or L2G significant variants in L2G

	import pyspark.sql.functions as F
	from pyspark import SparkConf
	from pyspark.sql import SparkSession

	sparkConf = SparkConf()
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.mode', 'AUTO')
	sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.project.id', 'open-targets-eu-dev')

	spark = (
	SparkSession.builder

d0choa / newFingenSignals.py

Last active June 21, 2021 15:48

Interesting (validated by drug development) L2G signals found in Finngen but not available in previous sources. DISCLAIMER: No ontology expansion

	import pyspark.sql.functions as F
	from pyspark import SparkConf
	from pyspark.sql import SparkSession

	sparkConf = SparkConf()

	spark = (
	SparkSession.builder
	.config(conf=sparkConf)
	.master('local[*]')

d0choa / nonObviousTermSimilaritiesBasedOnW2V.py

Last active August 5, 2021 11:24

Find W2V similarities between terms in different EFO branches (e.g. disease. vs phenotype)

	from pyspark.sql import SparkSession
	from pyspark.context import SparkContext
	from pyspark.sql import functions as F
	from pyspark.ml.feature import Word2VecModel
	from pyspark.sql.types import DoubleType
	from pyspark.ml.feature import Normalizer

	# establish spark connection
	spark = (
	SparkSession.builder

d0choa / knownDrugsForTargetGQL.py

Last active June 4, 2021 16:09

Querying the known drugs for a given target from Open Targets Platform GraphQL API

	#!/usr/bin/env python3

	# Import relevant libraries for HTTP request and JSON formatting
	import requests
	import json

	# Set gene_id variable
	gene_id = "ENSG00000244734"

	# Build query string