The bulk loader is a tool that Tripal provides for loading of data contained
in tab
delimited files. Tripal supports loading of files in standard formats (e.g.
FASTA, GFF, OBO),
but Chado can support a variety of different biological data types and there
are often no
community standard file formats for loading these data. For example, there
is no file
format for importing genotype and phenotype data. Those data can be stored
in the feature,
stock and natural diversity tables of Chado. The Bulk Loader was introduced
in Tripal v1.1
and provides a web interface for building custom data loader. In short, the
site developer
creates the bulk loader "template". This template can then be used and
re-used for any tab
delimited file that follows the format described by the template.
Additionally, bulk loading
templates can be exported allowing Tripal sites to share loaders with one
another. Loading
templates that have been shared are available on the Tripal website here:
.
General Usage
- Plan how to store your data.
This is the most important and often the most difficult step. This
is because it requires familiarity with the Chado database schema and
due to the
flexibility of the schema, you may be able to store your data multiple
ways. It is
considered best practice to consult the GMOD website and the Chado
community (via the
) when deciding how to store data.
- Create a new Bulk Loading Template to map the columns from your
data file to chado.
Creating a new template can be done by clicking on the "Templates"
tab above
and then the "Add Template" link. Note that the template is designed
with a single line
from your file in mind. Furthermore, the term "record" refers to a
single entry in chado
and the term "field" refers to a column in a specific chado table.
- Create a Bulk Loader Job with file-specific details that uses
your template to load a
specific file.
Create a Bulk Loading Job by clicking on the "Jobs" tab above and
then "Add Bulk
Loading Job". Remember to select the template you just created and to
ensure that you
provide the absolute path to the file. Note: The file must already be
uploaded to the
same server as your Drupal installation and must be readable by the
command-line
user who executes the tripal job.
For the full tutorial, see
the
.