biogrid / ims3

BioGRID 4.3

This repository contains the entire codebase for the BioGRID 4.3 web application.

STATUS

• IN PROGRESS
• ALPHA 0.0.5

Requirements

• GIT 2.23+ (https://git-scm.com/download)
• Node.js 12.13.2+ (https://nodejs.org/en/)

.env file variables

• VUE_APP_AUTH_URL (url to authentication API)
• VUE_APP_ACE_WEBSOCKET (url to websocket API)
• VUE_APP_ACE_URL (url to curation API)
• VUE_APP_ANNOTATION_URL (url to annotation API)
• VUE_APP_SEARCH_URL (url to search API)

Project Setup for Development

1. Manually install all of the requirements listed above
2. Create a directory for development
3. Clone this repository git clone [email protected]:BioGRID/BioGRID.git
4. Create a .env.development.local and .env.production.local file to match your setup using the descriptions above in the .env file variables section
5. Run npm install to install all dependencies
6. Run npm run dev to launch the application with hotloading
7. Run npm run build to compile the application for your platform

Build Setup

# install dependencies
$ npm install

# serve with hot reload at localhost:3000
$ npm run dev

# build for production and launch server
$ npm run build
$ npm run start

# generate static project
$ npm run generate

For detailed explanation on how things work, check out Nuxt.js docs.

ims3's Issues

pubmed ids in project_pubmeds and not in publications

There is some 1508 pubmed ids in the IMS2.project_pubmeds table but not in the publications table. Going to skip these for now.

project_pubmeds->project_publications where publication_query_id=0

Storing items where IMS2.project_pubmeds.publication_query_id=0 as NULLS in IMS3.project_publications.publication_query_id

IMS2.project_users has dup entries in it

mysql> select * from (select distinct project_id,user_id,count(*)as count from project_users group by project_id,user_id)as a where count > 1;
+------------+---------+-------+
| project_id | user_id | count |
+------------+---------+-------+
|          1 |       3 |     2 |
|          1 |      18 |     2 |
|          1 |      19 |     2 |
|          2 |       2 |     3 |
|          2 |       3 |     2 |
|         24 |       2 |     2 |
|         24 |       9 |     2 |
+------------+---------+-------+
7 rows in set (0.00 sec)

mysql> 

pmid errors in the publication table

publication_id=761 skipped since PubmedID is 0
publication_id=2693 skipped since PubmedID is 1.52209E+15
publication_id=3163 skipped since PubmedID is 8.90562E+14
publication_id=4203 skipped since PubmedID is 1.47347E+14
publication_id=4451 skipped since PubmedID is 7.79748E+13
publication_id=5371 skipped since PubmedID is 1.0632E+23
publication_id=5705 skipped since PubmedID is 1.1314E+14
publication_id=5706 skipped since PubmedID is Others
publication_id=5852 skipped since PubmedID is Mouse-Mouse
publication_id=7632 skipped since PubmedID is 8.84535E+14
publication_id=10285 skipped since PubmedID is Human
publication_id=10286 skipped since PubmedID is -
publication_id=10771 skipped since PubmedID is 1.56019E+15
publication_id=11846 skipped since PubmedID is 1.1945E+15
publication_id=11868 skipped since PubmedID is 1.46992E+15
publication_id=11921 skipped since PubmedID is 1.29725E+15
publication_id=12289 skipped since PubmedID is 1.51256E+15
publication_id=12801 skipped since PubmedID is 1.27594E+15
publication_id=12959 skipped since PubmedID is Human-Human
Skipping dup entry where publication_pubmed_id=7695910
Skipping dup entry where publication_pubmed_id=9685400
Skipping dup entry where publication_pubmed_id=9271372
Skipping dup entry where publication_pubmed_id=17923092

dup entries need to be fixed before IMS3 dump.

WHERE ims2.ptms.gene_id=37031

gene_id=37031 is in ims2.ptm table, but not an interaction in the interactions table.