L1000CDS use MongoDB schema to store all the information.

Installation

1. Install MongoDB. Please select release 2.4.14 for download. The 
MongoDB files on this page are not compatible with newer versions 
of MongoDB

2. Download the LINCS_L1000_CD.tar.gz file and unzip.

3. Place all the LINCS_L1000_CD.x files in the unzipped folder 
into the MongoDB database folder.

4. Start mongod.

5. Open a mongo shell and switch to LINCS_L1000_CD db. The LINCScloud 
collection in the db stores all the processed LINCS L1000 data 
download from LINCS cloud. The GSE70138 collection contains all 
the processed LINCS L1000 data downlaoded from GEO. 
The two collections do not overlap.

6. Optionally it is suggested to download and install Robomongo 
which provides a nice GUI to browse the data.

6. Refer to the MongoDB documentation for query specifications 
and drivers for different languages.

Import and export between MongoDB and .json files

mongoimport
mongoexport
will help to dump json file in and out from a mongodb

For Jacqui, temporarily stored here

epigquickstart_508

I have mongodb installed on my Windows10 desktop and Linux CentOS7. To installed L1000CDS on my linux and windows desktop:

Download two files from the download page
On linux: copy two files to /tmp/mongo/

cpcd-gse70138.metadata.json

and

cpcd-gse70138.bson

mongorestore -d databasename /tmp/mongo/ mongorestore -d databasename -c collectionname /path/to/both_json_and_bson_files In my case, I tested both ways and they all worked:

mongorestore -d LINCS_L1000_CD -c cpc2014 /path/to/cpcd-gse70138.bson

mongorestore -d LINCS_L1000_CD /home/li11/LINCS-L1000/

Although both ways work, however, the second method (without collection name)

produced a collection called “cpcd-gse70138”. This makes query very cumbersome as

I have to deal withlittle dash. Therefore, it is with more control to do

mongorestore -d LINCS_L1000_CD -c cpc2014 /home/li11/LINCS-L1000/cpcd-gse70138.bson