aipband/gliobase

Glioblastoma multiforme (GBM) biomarker knowledge base

gliobase

Glioblastoma multiforme (GBM) biomarker knowledge base

Quickstart

1. Clone the repo.
2. Make sure you have MongoDB installed locally or a cloud instance.
3. npm install in the root directory.
4. Copy and rename sample.env file to .env and edit the "DB_CONNECTION" string to point to your MongoDB instance.
5. npm start in the root directory.

gliobase's Issues

Cleanup ETL script

Prototype landing page

Intro, summary stats, navigation

Prototype Evidence information page

Used terminologies definition page

Here we will list the definitions of all the terminologies used in the schema. For ex.: we need to define terms like category, biomarker name, etc.

Create category label Component and color code

DNA
RNA
Protein
Others

Choose frontend component library

https://hackernoon.com/23-best-react-ui-component-libraries-and-frameworks-250a81b2ac42

Add total number of samples field in the Evidence page

Make components of repeated code in UI

Display the main abbreviation in the Entities table

Add createdDate, updatedDate, deletedDate to all schemas

Rename Biomarker to "Biological entity" and BiomarkerSet to "Biomarker" in the backend and API

Check latin species name capitalization

Harmonize visual aspects of the UI

Prototype biomarker set information page

Information about the biomarker set, followed by a list of experiments and their outcome.

Make gender count a Component

Prototype login page

Initiate a simple login page: username, password
Depends on #9

Reproducibility

Ensure application state is encoded in path. A user should be able to share a link to a colleague who will obtain the same application state by following the link. This should be kept in mind when developing any part of the application.

Testing discussion

What to use for tests and how?

Prototype Header

A Header to show current user and a small menu for profile, settings and logout.

Make species label Component and coloring

Homo Sapiens
Mus Musculus
Macaca mulatta

Add abbreviation and category for each Entity in the Biomarker page

Double click Biomarker or Evidences in the Data Summary will jump to Entities information

Prototype exploration page

Show statistics of biomarkers, biomarker sets and evidences.
A place for users to explore the data

Add Skeleton component for loading queries

Prototype biomarker and biomarker set search page

Make age count Component

Add abbreviation column to the Biomarker table component and popover for the full entity name on the abreviation

Add column for Biomarker, PubmedID in the Evidence table component

Prototype biomarker information page

Page for a single biomarker

Write production ETL script

Authentication API

Either from scratch with with Passport.js or with auth0.com

Add description field to Biomarker in the backend and Biomarker page

Change list of entities IDs to list of Entities IDs with name, abbreviation and category (make reusable component for use in the Biomarker page)

Prototype user profile page

Make Source label Component with coloring

Tissue
Blood
CSF
Serum
Cell Line
Cells

Rename Biomarker to "Biological entity" and BiomarkerSet to "Biomarker" in the user interface

Automatically add . for Methods, Results and Conclusions if not already present

Make stage label a component and add coloring

Add routing to frontend

BiomarkerSet schema

Move Validated field below classification field in the Evidence field

Adjust Entity page style to be consistent with the others

Hosting and CD discussion

Where to host and continuous deployment.

Ensure missing field do not cause errors

Data model discussion

Make stage classification a component with coloring that links to corresponding NCBI paper

Development database seed

Populate the database in development mode.

Entities should have a single abbreviation and a list of alternative abbreviations

Currently it is a list of abbreviations.

Evidence schema

Biomarker schema