Note for Docker users

The export commands will need to run inside the container, perhaps with the dcanto shell function.

Exporting to JSON

The curation data can be exported in JSON format with the canto_export.pl script from the script directory. This JSON file can then be loaded into a Chado database (see below).

To export data only from sessions that have been "approved" by administrators using the admin interface, use the --dump-approved flag. Note that metadata and publication details will still be included for all sessions, but only approved sessions will include data on annotations and biological features (genes, genotypes, and so on).

Example:

script/canto_export.pl canto-json --dump-approved > canto_approved.json

(From the canto top level directory).

If you use the flag --export-approved instead of --dump-approved, the exported sessions with be marked as "EXPORTED" in the Canto database. These sessions won't be exported next time. This option is provided so that annotation will be exported only once from Canto.

Add the flag --all to include details of all publications and people in the JSON output.

Reading Canto data into Chado

The code for loading Canto JSON format files into a Chado database is available from the pombase-chado code repository. Follow the installation instructions then use this command:

./script/pombase-import.pl load-config-example.yaml canto --organism-taxonid=4896 \
   --db-prefix=PomBase $HOST DB_NAME $USER $PASSWORD < canto_approved.json

where HOST, DB_NAME, USER and PASSWORD are the details of your local Chado database.

The pombase-import.pl command will never delete or alter existing data it only adds annotation.

To test loading without modifying the Chado database, add the -d or --dry-run option to the command line.