Tripal

Tripal integrates the GMOD Chado database schema with Drupal to store, manage, load, and visualize genomic, genetic, and related biological data.

Key Features:

• Integration with GMOD Chado: Tripal utilizes the Chado database schema for structured storage of genomic, genetic, and related biological data.
• Drupal integration: Tripal maps Chado data into Drupal and exposes Chado tables via Drupal Views for display and search page construction.
• Data import and visualization tools: Includes loaders and tools supporting organisms, genomic libraries, biological stocks, stock collections, genomic features, alignments, and annotations with support for FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files, and InterProScan XML formats.
• API and templates: Provides default templates for biological data display and an Application Programming Interface (API) for customization and extension.
• Release v1.1 enhancements: Adds a bulk loader for custom tab-delimited formats, full support for every Chado table within Drupal Views, and modules Feature Map, Genetic, Publication, Project, Contact, and Natural Diversity.
• GMOD tool integration: Integrates with GBrowse and provides extensions for loading and visualizing analyses from NCBI BLAST, InterPro, KEGG, and Gene Ontology.

Scientific Applications:

• Organism-specific genomic databases: Construction and hosting of species-focused genomic and genetic datasets using Chado-backed storage.
• Genetics and natural diversity data management: Storage and organization of biological stocks, stock collections, and natural diversity data.
• Annotation and alignment visualization: Loading, storing, and visualizing genomic features, annotations, and alignments from standard analysis outputs.
• Search and display page construction: Creation of custom display and search pages by exposing Chado tables through Drupal Views.

Methodology:

Maps the GMOD Chado schema into Drupal; uses loaders for FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files, and InterProScan XML; provides a bulk loader for custom tab-delimited formats; supports every Chado table within Drupal Views; includes modules Feature Map, Genetic, Publication, Project, Contact, and Natural Diversity; integrates with GBrowse and extensions for loading/visualizing NCBI BLAST, InterPro, KEGG, and Gene Ontology analyses; provides default templates and an API for customization.