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Access Rat Genome Database with 100+ Operations via REST API MCP Server

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Created by: David Ashby || cfomodz

David Ashby

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Last update 5 days ago

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⚠️ ADVANCED USE ONLY - Rat Genome Database REST MCP Server (100 operations)

🚨 This workflow is for advanced users only!

This MCP server contains 100 operations which is significantly more than the recommended maximum of tools for most AI clients.

🔍 Recommended Alternative for basic use cases

Seek a simplified MCP server that utilizes the official n8n tool implementation for Rat Genome Database REST if available, or an MCP server with only common operations as it will be more efficient and easier to manage.

🛠️ Advanced Usage Requirements

BEFORE adding this MCP server to your client:

Disable or delete unused nodes - Review sections and disable/delete those you don't need

AFTER adding the MCP server to your client:
1.Selective tool enabling - Instead of enabling all tools (default), manually select only the specific tools you need for that Workflow's MCP client.
2. Monitor performance - Too many tools can slow down AI responses

💡 Pro Tips

Keep maximum 40 enabled tools - Most AI clients perform better with fewer tools

  • Group related operations and only enable one group at a time

  • Use the overview note to understand what each operation group does

  • Ping me on discord if your business needs this implemented professionally

⚡ Quick Setup

  1. Import this workflow into your n8n instance
  2. Credentials Add Rat Genome Database REST API credentials
  3. Activate the workflow to start your MCP server
  4. Copy the webhook URL from the MCP trigger node
  5. Connect AI agents using the MCP URL

🔧 How it Works

This workflow converts the Rat Genome Database REST API into an MCP-compatible interface for AI agents.

• MCP Trigger: Serves as your server endpoint for AI agent requests
• HTTP Request Nodes: Handle API calls to //rest.rgd.mcw.edu/rgdws
• AI Expressions: Automatically populate parameters via $fromAI() placeholders
• Native Integration: Returns responses directly to the AI agent

📋 Available Operations (100 total)

🔧 Agr (6 endpoints)

• GET /agr/affectedGenomicModels/{taxonId}: Get affected genomic models (rat strains with gene alleles) submitted by RGD ...
• GET /agr/alleles/{taxonId}: Get gene allele records submitted by RGD to AGR by taxonId
• GET /agr/expression/{taxonId}: Get expression annotations submitted by RGD to AGR by taxonId
• GET /agr/phenotypes/{taxonId}: Get phenotype annotations submitted by RGD to AGR by taxonId
• GET /agr/variants/{taxonId}: Get basic variant records submitted by RGD to AGR by taxonId
• GET /agr/{taxonId}: Get gene records submitted by RGD to AGR by taxonId

🔧 Annotations (10 endpoints)

• POST /annotations/: Get Annotation 17
• GET /annotations/accId/{rgdId}: Returns a list ontology term accession IDs annotated to an rgd object
• GET /annotations/count/{accId}/{includeChildren}: Returns annotation count for ontology accession ID
• GET /annotations/count/{accId}/{speciesTypeKey}/{includeChildren}: Returns annotation count for ontology accession ID and speicies
• GET /annotations/count/{accId}/{speciesTypeKey}/{includeChildren}/{objectType}: Returns annotation count for ontology accession ID and object type
• GET /annotations/reference/{refRgdId}: Returns a list of annotations for a reference
• GET /annotations/rgdId/{rgdId}: Returns a list of annotations by RGD ID
• GET /annotations/rgdId/{rgdId}/{ontologyPrefix}: Returns a list of annotations by RGD ID and ontology prefix
• GET /annotations/{accId}/{rgdId}: Returns a list of annotations by RGD ID and ontology term accession ID
• GET /annotations/{accId}/{speciesTypeKey}/{includeChildren}: Returns a list annotations for an ontology term or a term and it's children

🔧 Enrichment (2 endpoints)

• POST /enrichment/annotatedGenes: Create Enrichment 2
• POST /enrichment/data: Create Enrichment 3

🔧 Genes (16 endpoints)

• GET /genes/affyId/{affyId}/{speciesTypeKey}: Return a list of genes for an affymetrix ID
• GET /genes/alias/{aliasSymbol}/{speciesTypeKey}: Return a list of genes for an alias and species
• GET /genes/allele/{rgdId}: Return a list of gene alleles
• POST /genes/annotation: Get Gene 18
• GET /genes/annotation/{accId}: Return a list of genes annotated to an ontology term
• GET /genes/annotation/{accId}/{speciesTypeKey}: Return a list of genes annotated to an ontology term
• GET /genes/keyword/{keyword}/{speciesTypeKey}: Return a list of genes by keyword and species type key
• GET /genes/map/{mapKey}: Return a list of all genes with position information for an assembly
• GET /genes/mapped/{chr}/{start}/{stop}/{mapKey}: Return a list of genes position and map key
• POST /genes/orthologs: Get Gene 22
• GET /genes/orthologs/{rgdId}: Return a list of gene orthologs
• GET /genes/region/{chr}/{start}/{stop}/{mapKey}: Return a list of genes in region
• GET /genes/species/{speciesTypeKey}: Return a list of all genes for a species in RGD
• GET /genes/{chr}/{start}/{stop}/{mapKey}: Return a list of genes position and map key
• GET /genes/{rgdId}: Get a gene record by RGD ID
• GET /genes/{symbol}/{speciesTypeKey}: Get a gene record by symbol and species type key

🔧 Lookup (24 endpoints)

• GET /lookup/geneTypes: Get Lookup 14
• POST /lookup/id/map/EnsemblGene: Get Lookup 15
• GET /lookup/id/map/EnsemblGene/{rgdId}: Translate an RGD ID to an Ensembl Gene ID
• POST /lookup/id/map/EnsemblProtein: Get Lookup 16
• GET /lookup/id/map/EnsemblProtein/{rgdId}: Translate an RGD ID to an Ensembl Protein ID
• POST /lookup/id/map/EnsemblTranscript: Get Lookup 17
• GET /lookup/id/map/EnsemblTranscript/{rgdId}: Translate an RGD ID to an Ensembl Transcript ID
• POST /lookup/id/map/GTEx: Get Lookup 18
• GET /lookup/id/map/GTEx/{rgdId}: Translate an RGD ID to an GTEx ID
• POST /lookup/id/map/GenBankNucleotide: Get Lookup 19
• GET /lookup/id/map/GenBankNucleotide/{rgdId}: Translate an RGD ID to a GenBank Nucleotide ID
• POST /lookup/id/map/GenBankProtein: Get Lookup 20
• GET /lookup/id/map/GenBankProtein/{rgdId}: Translate an RGD ID to a GenBank Protein ID
• POST /lookup/id/map/HGNC: Get Lookup 21
• GET /lookup/id/map/HGNC/{rgdId}: Translate an RGD ID to an HGNC ID
• POST /lookup/id/map/MGI: Get Lookup 22
• GET /lookup/id/map/MGI/{rgdId}: Translate an RGD ID to an MGI ID
• POST /lookup/id/map/NCBIGene: Get Lookup 23
• GET /lookup/id/map/NCBIGene/{rgdId}: Translate an RGD ID to an NCBI Gene ID
• POST /lookup/id/map/UniProt: Get Lookup 24
• GET /lookup/id/map/UniProt/{rgdId}: Translate an RGD ID to a UniProt ID
• GET /lookup/maps/{speciesTypeKey}: Return a list assembly maps for a species
• GET /lookup/speciesTypeKeys: Get Lookup 26
• GET /lookup/standardUnit/{accId}: Return a standardUnit for an ontology if it exists

🔧 Maps (3 endpoints)

• GET /maps/chr/{chromosome}/{mapKey}: Return a list of chromosomes
• GET /maps/chr/{mapKey}: Return a list of chromosomes
• GET /maps/{speciesTypeKey}: Return a list of assemblies

🔧 Ontology (3 endpoints)

• GET /ontology/ont/{accId}: Returns child and parent terms for Accession ID
• GET /ontology/term/{accId1}/{accId2}: Returns true or false for terms
• GET /ontology/term/{accId}: Returns term for Accession ID

🔧 Pathways (2 endpoints)

• GET /pathways/diagrams/search/{searchString}: Return a list of pathways based on search term
• GET /pathways/diagramsForCategory/{category}: Return a list of pathways based on category provided

🔧 Phenotype (2 endpoints)

• GET /phenotype/phenominer/chart/{speciesTypeKey}/{refRgdId}/{termString}: Get {Termstring}
• GET /phenotype/phenominer/chart/{speciesTypeKey}/{termString}: Get {Termstring}

🔧 Qtls (3 endpoints)

• GET /qtls/mapped/{chr}/{start}/{stop}/{mapKey}: Returns a list QTL for given position and assembly map
• GET /qtls/{chr}/{start}/{stop}/{mapKey}: Returns a list QTL for given position and assembly map
• GET /qtls/{rgdId}: Return a QTL for provided RGD ID

🔧 Sslps (1 endpoints)

• GET /sslps/mapped/{chr}/{start}/{stop}/{mapKey}: Returns a list SSLP for given position and assembly map

🔧 Stats (25 endpoints)

• GET /stats/count/activeObject/{speciesTypeKey}/{dateYYYYMMDD}: Count of active objects by type, for specified species and date
• GET /stats/count/geneType/{speciesTypeKey}/{dateYYYYMMDD}: Count of gene types, for specified species and date
• GET /stats/count/objectStatus/{speciesTypeKey}/{dateYYYYMMDD}: Count of objects with given status, for specified species and date
• GET /stats/count/objectWithRefSeq/{speciesTypeKey}/{dateYYYYMMDD}: Count of objects with reference sequence(s), by object type, for specified sp...
• GET /stats/count/objectWithReference/{speciesTypeKey}/{dateYYYYMMDD}: Count of objects with reference, by object type, for specified species and date
• GET /stats/count/objectWithXdb/{speciesTypeKey}/{objectKey}/{dateYYYYMMDD}: Get {Dateyyyymmdd}
• GET /stats/count/proteinInteraction/{speciesTypeKey}/{dateYYYYMMDD}: Count of protein interactions, for specified species and date
• GET /stats/count/qtlInheritanceType/{speciesTypeKey}/{dateYYYYMMDD}: Count of strains, by qtl inheritance type, for specified species and date
• GET /stats/count/retiredObject/{speciesTypeKey}/{dateYYYYMMDD}: Count of retired objects by type, for specified species and date
• GET /stats/count/strainType/{speciesTypeKey}/{dateYYYYMMDD}: Count of strain types, for specified species and date
• GET /stats/count/withdrawnObject/{speciesTypeKey}/{dateYYYYMMDD}: Count of withdrawn objects by type, for specified species and date
• GET /stats/count/xdb/{speciesTypeKey}/{dateYYYYMMDD}: Count of external database ids, for specied species and date
• GET /stats/diff/activeObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of active objects, by type, for specified species and date r...
• GET /stats/diff/geneType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of gene types, for specified species and date range
• GET /stats/diff/objectStatus/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of objects with given status, for specified species and date...
• GET /stats/diff/objectWithRefSeq/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Get {Datetoyyyymmdd}
• GET /stats/diff/objectWithReference/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of objects with reference, by object type, for specified spe...
• GET /stats/diff/objectWithXdb/{speciesTypeKey}/{objectKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Get {Datetoyyyymmdd}
• GET /stats/diff/proteinInteraction/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of protein interactions, for specified species and date range
• GET /stats/diff/qtlInheritanceType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of strains, by qtl inheritance type, for specified species a...
• GET /stats/diff/retiredObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of retired objects, by type, for specified species and date ...
• GET /stats/diff/strainType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of strain types, for specified species and date range
• GET /stats/diff/withdrawnObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of withdrawn objects, by type, for specified species and dat...
• GET /stats/diff/xdb/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD}: Count difference of external database ids, for specified species and date range
• GET /stats/term/{accId}/{filterAccId}: getTermStats

🔧 Strains (3 endpoints)

• GET /strains/all: Get Strains 1
• GET /strains/{chr}/{start}/{stop}/{mapKey}: Return all active strains by position
• GET /strains/{rgdId}: Return a strain by RGD ID

🤖 AI Integration

Parameter Handling: AI agents automatically provide values for:
• Path parameters and identifiers
• Query parameters and filters
• Request body data
• Headers and authentication

Response Format: Native Rat Genome Database REST API responses with full data structure

Error Handling: Built-in n8n HTTP request error management

💡 Usage Examples

Connect this MCP server to any AI agent or workflow:

• Claude Desktop: Add MCP server URL to configuration
• Cursor: Add MCP server SSE URL to configuration
• Custom AI Apps: Use MCP URL as tool endpoint
• API Integration: Direct HTTP calls to MCP endpoints

✨ Benefits

• Zero Setup: No parameter mapping or configuration needed
• AI-Ready: Built-in $fromAI() expressions for all parameters
• Production Ready: Native n8n HTTP request handling and logging
• Extensible: Easily modify or add custom logic

🆓 Free for community use! Ready to deploy in under 2 minutes.