This n8n workflow automates the process of retrieving, organizing, and analyzing genomic data from the Rat Genome Database (RGD) through a series of structured API calls and data processing steps. Designed for bioinformatics researchers, the workflow streamlines data collection related to genes, phenotypes, pathways, ontologies, and various statistical metrics, enabling efficient integration and analysis.

The workflow begins with a REST API trigger named ‘Rat Genome Database REST MCP Server,’ which acts as the entry point for external events or scheduled runs. Several sticky notes (‘Advanced Warning,’ ‘Setup Instructions,’ and ‘Workflow Overview’) provide guidance and documentation for users.

Data is fetched through a sequence of HTTP request nodes that query specific endpoints of the RGD API, such as extracting detailed information on AGR annotations, gene data, annotations, pathways, ontologies, and statistical measures. Each request is followed by a ‘Get’ node that captures the API response.

In addition to data retrieval, the workflow includes nodes for creating annotations, enrichments, and lookups, which prepare data for further analysis or integration into other systems. Special nodes named ‘Create Enrichment,’ ‘Create Gene,’ and ‘Create Lookup’ interact with the API to submit new data or update existing records.

Multiple set of nodes, often organized with descriptive sticky notes, collectively support complex multi-step processes such as gathering gene information, mapping pathways, retrieving phenotypes, ontology details, and statistical metrics. The ‘Map’ nodes assist in geographical or categorical data mapping, while ‘Description’ nodes document each section’s purpose.

Overall, this workflow provides a comprehensive automation pipeline for bioinformatics data collection, enabling researchers to significantly reduce manual data extraction tasks, ensure data consistency, and facilitate downstream analysis or visualization in research projects or web applications.