CellBase code is open-source and freely available at https://github.com/opencb/cellbase
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 thecellbase_hsapiens_grch37_v4
database and creating the indexes as indicated in the.js
scripts withincellbase/cellbase-app/app/mongodb-scripts/
, run:
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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