bhklab / pharmacodb-js

Search across publicly available datasets to find instances where a drug or cell line of interest has been profiled.

PharmacoDB-JS Web Application

Setup Instructions

• Clone the repo

git clone https://github.com/bhklab/PharmacoDB-JS.git
cd PharmacoDB-JS

• In the project directory, install all server dependencies npm i
• Create .env using .env.example as a reference to access the database
• Start the server by running npm start or npm run devstart(development mode) command
• Start the client (development mode) by running npm start
• Open http://localhost:3000 to view it in the browser.

Dependencies

• React
• React-Router
• Express
• Knex
• Body-parser

Dev Dependenices

• Nodemon
• Eslint

Servers

• Production Server: https://pharmacodb.ca/
• Beta Server: beta.pharmacodb.ca

pharmacodb-js's Issues

Debug: Tissue Summary Table

Debug and fix the issue with the tissue summary table; multiple tissues are displayed in the table.

Add new gene_compound API.

Add new APIs related to gene-compound tables with analytic data.

• gene_compound_tissue_dataset API.
• gene_compound_dataset API.

Link to DTC using SQL dump

The goal is to link drug names in PharmacoDB to a link to the Drug name in DTC. Probably no need to store their SQL dump, just need to have the correct links, maybe from their API?

Update: GraphQL Queries

Update the graphql queries to use fragments for the code reusability.

Update drug table to include the unique ids.

Forest Plot and API for the plot

Create a forest plot for the biomarker page.

• Add forest plot
• Add APIs for plots/biomarker page

Molecular Features table for compound Individual page

Revamping Individual page design.

To redesign the individual pages for a better user experience.

Enhanced data analysis

Add biomarker and tissue specific analysis

Front Page

Updates to the front page.

• Clickable text on the front page.

Fix the UI according to the newly updated database.

The UI has to be updated as the APIs have been updated according to the new database schema design.

Add new gene_compound_tissue API

Add a new gene compound tissue table API that will be consumed by the front end.

• gene_compound_tissue APIs.

Datasets intersection - Venn Diagram

Update: GraphQL Queries

Update the graphql queries to use fragments for the code reusability.

Tissue autocomplete in search repeating entries

When I try to search for Breast, the autocomplete is suggesting Breast 5 times in the autocomplete list.

Cell line individual page missing AAC/IC50 plot

Cell Line vs. Drug Page

Update all the APIs except for gene-drug (gene-compound) related APIs.

Update all the APIs except for gene-drug (gene-compound) related APIs. This includes APIs like compound, gene, dataset, tissue etc.

Capture gene description for a specific gene on the gene individual page.

Add gene description to the gene individual page using the http://useast.ensembl.org/index.html website.
Example: http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32315086-32400268.

Upset Plot for dataset summary page.

To add an upset plot to the dataset summary page.

• Update cell API schema and resolver function to include dataset detail for all the cells.
• Update tissue API schema and resolver function to include dataset detail for all the tissues.
• Update compound API schema and resolver function to include dataset detail for all the compounds.
• Add parser function to parse and prepare data for the upset plot.
• Create upset plot.

Tissue Individual page: Annotation table

https://test.pharmacodb.ca/tissues/1

If we go to the tissue individual page, there is duplication of the data in the annotation table.

Make github link in About section open in new tab

As this is an external link, it might be better to not leave PharmacoDB page

Tissue Individual Page

Fix the plots and tables of tissueInvid pages which load too slow. (e.g. id=13)

• Tables query is too slow
• Make the table cell values clickable

Update new datasets (NCI60, PRISM, GDSC_2) indiv page info

Updated descriptions of GDSC_2, NCI60, and PRISM on datasets.js file
(client/src/Components/IndividualComponents/IndivDatasets/datasets.js)

Fix: Summary piechart

https://test.pharmacodb.ca/cell_lines

Update the piechart to add the other (the cell lines that don't belong to any of the tissue types).

Fix Tissue API

Fix: issue with repetitive data as a single tissue can belong to multiple datasets.

Fix: UI based on the changes to the gene compound APIs

Gene Individual Page.

This will keep track of the updates required for the gene individual pages.

• gene_compound_dataset API
• Plots (data: target annotations)
• Drug Summary
• Top Drug Summary (Data: gene_drug_dataset, Petr: get every result for that gene, and ascending sort by p value)

Introduction, addition of new datasets, connectivity to new databases

Dataset Individual Page.

This will keep track of the updates required for the dataset individual pages.

• Plots (may need a new query to collect data)
• Summary Cell Line table.
• Summary Drugs table.
• Re-struct data - merge the table and merge cells with same data type
• Make the table cells clickable

Cell Line Summary Page

Updates required to cell line summary page.

• Update tissue column in the table to have the text in the title case and update them to make them links to the corresponding page

Compound Individual Page

This will keep track of the updates required for the compound individual pages (except Molecular feature table).

• Cell Line Summary table.
• Tissue Summary table.
• Modify synonyms table
• Make table cells clickable
• add svg/csv buttons to plots/tables
• Molecular Features table

Cell line Individual Page.

This will keep track of the updates required for the cell individual pages.

• Molecular Profiling table once data is located (mol_cell)
• Make the cells and bars clickable
• Add svg/csv buttons for plots and tables

New tests for the new APIs (gene compound).

Add new tests related to newly created API endpoints for the gene compound table.

Update cell line table to include the unique ids.

Implementation of reproducible pipelines

Add details of Orcestra and PharmacoDI to the section in the manuscript

IC50 Plots should display y axis in log scale

I think this applies to drug and cell line individual pages.

Make identifiers clickable https://test.pharmacodb.ca/compounds/102

Update the individual compounds page to make the identifiers clickable.

Update drug annotations in Compounds table.

Some of the current annotations are outdated. Have to run AnnotationGx functions to obtain new data for drugs that are common with nci60 other psets (~2490)

Fix: Issue with the tests related to gene compound table(s).

Fix the issue with existing tests for the gene compound table.

Error component

Add an error component to manage the errors encountered in the UI.

Download SVG/ CSV for plots/tables

Should truncate IC50s to realistic values (maximum possible ic50 possibly?) in the ingestion pipeline

Tissue vs. Drug Page

• After implementation of this page, correct the link in the Experiments column of Drugs Summary table, on Individual cell line page

Update the stats on the landing page.

Right now the stats are hard coded and old; update and make them dynamic using an API I suppose.

Gene Summary Page

Tracking the updates required to the gene summary page.

• Fix compound_target API
• Bar plot (num compounds vs num targets)

Gene summary page takes time to render and freezes while rendering.

Gene summary page takes time to render and freezes while rendering.

Text Responsiveness

Fix the responsiveness of the text throughout the web application (ie increase or decrease the size based on the screen size).

Search Bar

Discuss the design and implementation of the UI search bar.

For now, we will keep the search implementation similar to the earlier version of the pharmacodb, later on, we will implement something similar to xevadb for the search.