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Load Data

Please, note that before

After you have generated the JSON data files (see Building the CellBase database), you can now load them in your Mongo database.

Configure Database Credentials

Before loading the data into the database

CellBase configuration.json

, your settings.xml file must have been appropriately configured indicating the database host names, ports, user and password.

CellBase code is open-source and freely available at https://github.com/opencb/cellbaseHere are the expected parameters:

namedefault
CELLBASE.DB.MONGODB.HOST
localhost:27017
CELLBASE.DB.USER
<empty>
CELLBASE.DB.PASSWORD
<empty>
CELLBASE.SERVER.REST.PORT
9090


Load JSON files into MongoDB

Use the CellBase CLI to load the data models:. For

example,

to

load

all

human

(GRCh37)

data

models

from

the

/tmp/data/cellbase/v4/homo_sapiens_grch37/mongodb/

created

in

section

"Build

Data

Models",

into

the

cellbase_hsapiens_grch37_v4

database

and creating the indexes as indicated in the .js scripts within cellbase/cellbase-app/app/mongodb-scripts/, run:

:

Code Block
cellbase/build/bin$ ./cellbase.sh load -d variation --database cellbase_hsapiens_grch37_v4 -i /mnt/data/downloads/cellbase/v4/homo_sapiens_grch37/mongodb/ -L debug -Dmongodb-index-folder=/home/cafetero/appl/dev/cellbase/cellbase-app/app/mongodb-scripts/

Please, note that the whole loading and indexing process may need ~24h to complete, depending on the available hardware.

After successful load of all data, the corresponding database shall look like:

$ mongo mongodb-dev/cellbase_hsapiens_grch37_v4
MongoDB shell version: 3.0.9
connecting to: mongodb-dev/cellbase_hsapiens_grch37_v4clinical_variants
> show collections;
clinical_variants
conservation
gene
genome_info
genome_sequence
metadata
protein
protein_functional_prediction
protein_protein_interaction
regulatory_region
repeats
variation
variation_functional_score

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