Gmod-dbsf
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dbsf
Contents
Overview
The GMOD Drupal Bioinformatic Server Framework (GMOD-DBSF) is an
Application Programming Interface module for the
Drupal CMS which simplifies programming bioinformatic
Drupal modules. This Drupal API is not a visualization module, like
Tripal. It is aimed for developers and seeks to
make the co-existence of Chado and Drupal seamless to the end-user and
reduces the learning curve for the bioinformatic community. It was
developed with the non-model species community in mind and is especially
interested in enhancing support for non-genome data types. It is an
open-source package and the community is invited to contribute to its
development.
It is freely available from
http://drupal.org/project/gmod_dbsf and
http://gmod-dbsf.googlecode.com with the latter being
a more complete repository.
Dependencies
GMOD-DBSF depends on Drupal 6.
Features
GMOD-DBSF offers:
- imports a subset of the Chado tables to Drupal
- creates new tables in Drupal using Chado-conventions in order to
better support sequence-less features.
- provides functions to communicate with Chado and Drupal database
schemas
- provides other, generic, functions useful for bioinformatic module
development.
- makes use of other GMOD tools such as BioPerl
Examples
Websites using it
The InsectaCentral database is coded using the GMOD-DBSF
engine and the custom genes4all module for visualization
Drupal modules using it
Examples of capabilities
- Chado manipulation:
- The function gmod_dbsf_add_cv() allows for one to add a new
Controlled Vocabulary (CV) by providing the name of the CV and an
array with the CV terms they wish to add.
- This and other functions can connect to a Chado database via the
gmod_dbsf_db_execute() function or operate on the local Drupal
database (or make use of the gmod_dbsf_is_chado(), an auto-detect
function).
- Similar functions operate to add, delete and populate the feature,
db, pub and other Chado tables: ancillary Chado tables, such as the
featureprop, feature_cvterm tables, often require complicated SQL
commands with multiple joins and a number of gmod_dbsf functions
cater to simplify manipulating these tables by simply passing the
desired variables. Thus a featureprop table can be populated with a
single line of code which passes the feature ID or feature name, the
CV term and properties one wishes to associate.
- Secure approaches for often-used tasks:
- The gmod_dbsf_create_uid() function creates a unique MD5 identifier,
based on a user’s session ID, time and optionally a text string,
which can be used for file uploads.
- The gmod_dbsf_batch_upload_fasta() function allows web-users to
upload a FASTA file to the server even if it is many megabytes large
or takes a considerable amount of time
- A few functions have been created to make use of BioPerl functions,
for example:
- Creating and parsing GFF3 files
- The gmod_dbsf_get_taxonomy_from_ncbi() function uses
Bio::DB::Taxon to query NCBI (via Entrez or via a local NCBI
Taxonomy database flatfile) for the taxonomy of a species.
- and an evergrowing list of many others…
Demos and Screenshots
License
This software is GPLv2+ licensed as part of the Drupal package. It is
currently supported by Alexie
Papanicolaou while at CSIRO, the
Australian Commonwealth Scientific and Research Organization
(http://www.csiro.au).
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