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Getting Started

1. Go to https://chat.openai.com/ and sign in (make an account if you do not have one)
2. Copy and paste the following text into the text bar at the bottom of the page (after accepting the various terms and disclosures):

Imagine you are helping me interact with several dataset of cancer genomics data. At any given point of time, you have the following abilities. You are also required to output code for some of the requests.

Question: Ask me a clarification question 
Reason: Explain why you did something the way you did it. 

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PARTICIPANT_A	INTERACTION_TYPE	PARTICIPANT_B	INTERACTION_DATA_SOURCE	INTERACTION_PUBMED_ID	PATHWAY_NAMES	MEDIATOR_IDS
ACTA2	in-complex-with	CALD1	Reactome	NA	Smooth Muscle Contraction	http://pathwaycommons.org/pc12/Complex_0518f6295b1ef06468655bd97bab06cd;http://pathwaycommons.org/pc12/Complex_31d66cd5a279d9da536a7808146a93e4;http://pathwaycommons.org/pc12/Complex_c0fb59281e2cbea8227d357ffd78f564;http://pathwaycommons.org/pc12/Complex_73a822be281ea321fb7bbc8d3b2e5b10
ACTA2	in-complex-with	ITGA1	Reactome	NA	Smooth Muscle Contraction	http://pathwaycommons.org/pc12/Complex_0518f6295b1ef06468655bd97bab06cd;http://pathwaycommons.org/pc12/Complex_31d66cd5a279d9da536a7808146a93e4;http://pathwaycommons.org/pc12/Complex_c0fb59281e2cbea8227d357ffd78f564;http://pathwaycommons.org/pc12/Complex_73a822be281ea321fb7bbc8d3b2e5b10
ACTA2	in-complex-with	ITGB5	Reactome	NA	Smooth Muscle Contraction	http://pathwaycommons.org/pc12/Complex_0518f6295b1ef06468655bd97bab06cd;http://pathwaycommons.org/pc12/Complex_31d66cd5a279d9da536a7

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KaiOS Data

Key Mapping

• arrows: 37 L, 38 T, 39 R, 40 B
• OK or sides: 0
• OK hold is 13
• 1: 49
• 2: 50
• 3: 51
• 0: 48

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/* Classless.css v1.0

Table of Contents:
 1. Theme Settings
 2. Reset
 3. Base Style
 4. Extras  (remove unwanted)
 5. Classes  (remove unwanted)
*/

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{"layoutOptions": {
    "name": "fcose",
    "randomize": true,
    "padding": 30
    },
    "imageOptions": {
        "format": "png",
        "background": "transparent",
        "width": 1280, 
        "height": 1280, 

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# REMAPPING START ----

# Load data
load("20220809_module_mapping.RData")

# Focus on genes present in both sets of results or the Rand Index cannot be calculated
lec_df_no_all <- merge(nb2010_noweights$moduleMembership, pc_noweights$moduleMembership, by = "geneSymbol")

sort(table(nb2010_noweights$moduleMembership$membership))
sort(table(pc_noweights$moduleMembership$membership))

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library(xml2)
library(magrittr)

# NOTE: Example Uses Vemurafenib, PubChem CID: 42611257

url <- "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/42611257/XML"
#download.file(url, "pubchem_42611257.xml")

# READ FILE ----
doc <- read_xml('pubchem_42611257.xml')

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Map Clinical Trial Data (clinicaltrials.gov) to DrugBank Identifiers

1. Run get_ctrdata.R to get drug names associated with a set of drug trials
2. Run map_clinical_trials_to_drugbank.R to map names to DrugBank IDs

Results are exported to a CSV file

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