sirensolutions/chembl

Name: chembl

Owner: Siren

Description: NEW: now "Big Life Science demo" not only Cheml but also Clinical Trials and PUBMED

Created: 2017-03-31 10:14:02.0

Updated: 2018-02-08 12:40:23.0

Pushed: 2018-04-06 16:58:36.0

Homepage:

Size: 407

Language: Python

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README

KIBI ChEMBL DEMO II

The code in this repo can reproduce the second Kibi ChEMBL demo. This are the steps to reproduce the demo.

1) Start up a kibi instance. E.g. using docker:

```docker run  -d -p 5606:5606 -p 9201:9220 --net=chembl --name chembl-kibi sirensolutions/kibi-community-standard:4.6.4```

2) `pip install -r requirements.txt`

3) run `python import.py -es http://localhost:9201` using the port your elasticsearch instance is exposed to and wait for it to complete this will:

• Download and extract the chembl dumps in SQLite format
• Query the database and generate the input json file in the import directory
• Load the json in elasticsearch with the proper mapping
• Create the necessary index-pattern in kibi

4) explore the data at your kibi instance: http://localhost:5606

5) To persist the state of kibi you can run dump_kibi.sh. This requires elasticdump to be installed. To save the data and the kibi configuartion in a compressed file you can run dump_all.sh.