Note for Docker users
The export commands will need to run inside the container, perhaps
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
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
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
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
PASSWORD are the details of your local
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
--dry-run option to the command line.