Integration

Rat Genome Database integration

Rat Genome Database (RGD, Medical College of Wisconsin) REST API: look up rat, human, mouse and other species genes by RGD ID, symbol, alias or keyword, their orthologs, alleles, variants, ontology annotations (disease, GO, phenotype, pathway) and expression values, translate RGD IDs to NCBI Gene, UniProt, Ensembl, HGNC, MGI and GenBank IDs, list genes, QTLs, strains, SSLP markers and synteny blocks in a chromosome region, read ontology terms and their parents, search rat strain models by disease and query PhenoMiner phenotype measurements. Left out: the VCMap viewer and SCGE track routes (duplicates of the gene, variant and synteny routes), the Alliance bulk submission and whole-species gene dumps, the statistics routes (empty for every date tried), the annotation count, is-descendant and standard-unit routes (bare number, boolean or text answers), the enrichment and POST annotation routes (request bodies undocumented), and the disease-category annotation and strain variant routes (server error for every ID tried; use list_object_annotations_by_ontology with DOID for disease annotations). No authentication: the API is public and free; an unknown ID often answers HTTP 500 rather than 404.

Connect Rat Genome Database How integrations work

Ask it in chat

Say what should happen.
The workflow builds itself.

When this happens, do that in Rat Genome Database.Built from the 85 Rat Genome Database tools below, on the connection you add once.

What you can do with Rat Genome Database

Each of these is one operation on one endpoint, available both as a workflow step and as a tool an AI agent can call on its own. Nothing bundles several operations into one action, so what a run did stays readable afterwards.

Most endpoints run on the free plan. A few, mainly the ones that publish on your behalf, need a paid plan.

Annotation, 5 operations

list_genes_annotated_to_termList genes annotated to termGETLists the genes of every species annotated to one ontology term (for example a disease or GO term). Use list_species_genes_annotated_to_term to limit it to one species.
list_object_annotations_for_termList object annotations for termGETLists the annotations linking one RGD object to one ontology term.
list_species_genes_annotated_to_termList species genes annotated to termGETLists the genes of one species annotated to one ontology term.
list_term_annotationsList term annotationsGETLists the annotations of one species to an ontology term, optionally including the annotations to its child terms. Broad terms can return very large lists.
search_genes_annotated_to_termSearch genes annotated to termPOSTRead-only: lists the genes annotated to one ontology term, filtered to the given species and, optionally, evidence codes.

Gene, 4 operations

get_geneGet geneGETGets one gene by its RGD ID: symbol, name, gene type, species, RefSeq status and curated descriptions. An unknown ID answers HTTP 500, not 404.
get_gene_by_symbolGet gene by symbolGETGets one gene by its official symbol in one species, for example A2m in rat (species 3). Use search_genes_by_keyword when the exact symbol is unknown.
list_genes_by_positionList genes by positionGETLists the full gene records located in a region of one assembly (no positions in the answer; use list_mapped_genes for positions).
list_gene_variantsList gene variantsGETLists the variants located in one gene on one assembly.

Mapped, 4 operations

list_mapped_genesList mapped genesGETLists the genes in a region of one assembly with their positions (chromosome, start, stop, strand) and the full gene record under gene.
list_mapped_qtlsList mapped qtlsGETLists the QTLs in a region of one assembly with their positions and the full QTL record under qtl.
list_mapped_sslpsList mapped sslpsGETLists the SSLP markers (simple sequence length polymorphisms) in a region of one assembly with their positions, primer sequences and expected size.
list_mapped_strainsList mapped strainsGETLists the strains in a region of one assembly with their positions and the full strain record under strain.

Search, 3 operations

search_pathwaysSearch pathwaysGETSearches RGD pathway diagrams by free text and returns each pathway (PW term ID, name, description, categories, references and objects). The list may contain null entries.
search_strain_modelsSearch strain modelsGETLists rat strain models for a disease or phenotype term (for example hypertension): strain, strain RGD ID, qualifier, term, evidence and reference.
search_strain_models_by_typeSearch strain models by typeGETSame as search_strain_models, limited to one strain type (congenic, inbred, mutant, transgenic, consomic, outbred).

Block, 2 operations

list_synteny_blocksList synteny blocksGETLists the synteny blocks between a backbone region of one assembly and another assembly: matching chromosome, start, stop, orientation and chain level.
list_synteny_blocks_at_chain_levelList synteny blocks at chain levelGETSame as list_synteny_blocks, limited to one chain level or a range of levels.

Chart, 2 operations

get_phenotype_measurementsGet phenotype measurementsGETGets quantitative phenotype values (PhenoMiner) for a combination of measurement, condition, strain and method terms. Broad terms return megabytes; narrow them with more terms.
get_reference_phenotype_measurementsGet reference phenotype measurementsGETSame as get_phenotype_measurements, limited to the study published in one reference (refRgdId).

Chr, 2 operations

get_assembly_chromosomeGet assembly chromosomeGETGets one chromosome of an assembly: RefSeq and GenBank IDs, sequence length, gap length and count, contig count.
list_assembly_chromosomesList assembly chromosomesGETLists the chromosome names of one assembly, as a list of strings (1, 2, ..., X, Y, MT).

Ensembl gene, 2 operations

map_rgd_ids_to_ensembl_geneMap rgd ids to ensembl genePOSTRead-only: translates several RGD IDs to their Ensembl gene IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_ensembl_geneMap rgd id to ensembl geneGETTranslates one RGD ID to its Ensembl gene ID(s). Returns an object keyed by the RGD ID; an empty object means no Ensembl gene ID is linked.

Ensembl protein, 2 operations

map_rgd_ids_to_ensembl_proteinMap rgd ids to ensembl proteinPOSTRead-only: translates several RGD IDs to their Ensembl protein IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_ensembl_proteinMap rgd id to ensembl proteinGETTranslates one RGD ID to its Ensembl protein ID(s). Returns an object keyed by the RGD ID; an empty object means no Ensembl protein ID is linked.

Ensembl transcript, 2 operations

map_rgd_ids_to_ensembl_transcriptMap rgd ids to ensembl transcriptPOSTRead-only: translates several RGD IDs to their Ensembl transcript IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_ensembl_transcriptMap rgd id to ensembl transcriptGETTranslates one RGD ID to its Ensembl transcript ID(s). Returns an object keyed by the RGD ID; an empty object means no Ensembl transcript ID is linked.

Expression record, 2 operations

get_gene_expression_recordGet gene expression recordGETGets one gene expression record by its ID (id from list_gene_expression_records): experiment, sample, conditions and measurement methods.
list_gene_expression_recordsList gene expression recordsGETLists the gene expression records (experiment, sample, condition IDs) of one gene in one tissue, without the values. Use get_gene_expression_record for one record.

Gap, 2 operations

list_synteny_gapsList synteny gapsGETLists the gaps in synteny between a backbone region of one assembly and another assembly.
list_synteny_gaps_at_chain_levelList synteny gaps at chain levelGETSame as list_synteny_gaps, limited to one chain level or a range of levels.

Gen bank nucleotide, 2 operations

map_rgd_ids_to_genbank_nucleotideMap rgd ids to genbank nucleotidePOSTRead-only: translates several RGD IDs to their GenBank nucleotide IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_genbank_nucleotideMap rgd id to genbank nucleotideGETTranslates one RGD ID to its GenBank nucleotide ID(s). Returns an object keyed by the RGD ID; an empty object means no GenBank nucleotide ID is linked.

Gen bank protein, 2 operations

map_rgd_ids_to_genbank_proteinMap rgd ids to genbank proteinPOSTRead-only: translates several RGD IDs to their GenBank protein IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_genbank_proteinMap rgd id to genbank proteinGETTranslates one RGD ID to its GenBank protein ID(s). Returns an object keyed by the RGD ID; an empty object means no GenBank protein ID is linked.

Gtex, 2 operations

map_rgd_ids_to_gtexMap rgd ids to gtexPOSTRead-only: translates several RGD IDs to their GTEx IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_gtexMap rgd id to gtexGETTranslates one RGD ID to its GTEx ID(s). Returns an object keyed by the RGD ID; an empty object means no GTEx ID is linked.

Hgnc, 2 operations

map_rgd_ids_to_hgncMap rgd ids to hgncPOSTRead-only: translates several RGD IDs to their HGNC IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_hgncMap rgd id to hgncGETTranslates one RGD ID to its HGNC ID(s). Returns an object keyed by the RGD ID; an empty object means no HGNC ID is linked.

Map, 2 operations

list_assembliesList assembliesGETLists the sequence assemblies of one species with their map keys (for rat: GRCr8 380, mRatBN7.2 372), UCSC and RefSeq assembly IDs and which one is the primary reference.
list_species_mapsList species mapsGETLists every map RGD holds for one species, genetic (cM) and radiation hybrid maps included, not only the sequence assemblies (see list_assemblies).

Mgi, 2 operations

map_rgd_ids_to_mgiMap rgd ids to mgiPOSTRead-only: translates several RGD IDs to their MGI IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_mgiMap rgd id to mgiGETTranslates one RGD ID to its MGI ID(s). Returns an object keyed by the RGD ID; an empty object means no MGI ID is linked.

Ncbigene, 2 operations

map_rgd_ids_to_ncbi_geneMap rgd ids to ncbi genePOSTRead-only: translates several RGD IDs to their NCBI Gene IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_ncbi_geneMap rgd id to ncbi geneGETTranslates one RGD ID to its NCBI Gene ID(s). Returns an object keyed by the RGD ID; an empty object means no NCBI Gene ID is linked.

Ont, 2 operations

get_ontology_term_by_nameGet ontology term by nameGETGets one ontology term by its exact name within one ontology, for example diabetes mellitus in DOID.
get_term_parents_and_childrenGet term parents and childrenGETLists the parent and child term IDs of one ontology term, as parentTerms and childTerms lists.

Ortholog, 2 operations

list_gene_orthologsList gene orthologsGETLists the orthologs of one gene in the other species RGD holds, as gene records with their own RGD IDs and species keys.
list_orthologs_for_genesList orthologs for genesPOSTRead-only: lists the orthologs of several genes at once, in the species asked for. Returns an object keyed by each input RGD ID, each holding a list of gene records.

Qtl, 2 operations

get_qtlGet qtlGETGets one QTL (quantitative trait locus) by its RGD ID: symbol, name, LOD, p-value, variance, flanking and peak markers, inheritance type. An unknown ID answers HTTP 500, not 404.
list_qtls_by_positionList qtls by positionGETLists the QTLs located in a region of one assembly, as QTL records without positions (use list_mapped_qtls for positions).

Reference, 2 operations

list_reference_annotationsList reference annotationsGETLists the annotations supported by one reference (publication), identified by the reference RGD ID found in refRgdId of an annotation.
list_study_reference_idsList study reference idsGETLists the RGD IDs of the references (publications) of one study, as a list of numbers.

Rgd id, 2 operations

list_object_annotationsList object annotationsGETLists every ontology annotation of one RGD object (gene, strain, QTL): term, term ID, evidence code, reference and qualifiers.
list_object_annotations_by_ontologyList object annotations by ontologyGETLists the annotations of one RGD object in one ontology, for example only its disease (DOID) or GO annotations.

Strain, 2 operations

get_strainGet strainGETGets one rat strain by its RGD ID: symbol, strain type, origin, genetics, research use and availability status log.
list_strains_by_positionList strains by positionGETLists the active strains positioned in a region of one assembly, as strain records without positions (use list_mapped_strains for positions).

Uni prot, 2 operations

map_rgd_ids_to_uniprotMap rgd ids to uniprotPOSTRead-only: translates several RGD IDs to their UniProt IDs in one call. Returns an object keyed by each RGD ID.
map_rgd_id_to_uniprotMap rgd id to uniprotGETTranslates one RGD ID to its UniProt ID(s). Returns an object keyed by the RGD ID; an empty object means no UniProt ID is linked.

Variant, 2 operations

list_variants_by_positionList variants by positionGETLists the variants in a region of one assembly: reference and variant nucleotides, type, rs ID, ClinVar ID, positions and genic status.
list_variants_by_rs_idList variants by rs idGETLists the variant records for one dbSNP rs ID (for example rs8153963), one per assembly where it is mapped.

Acc id, 1 operation

list_annotated_term_idsList annotated term idsGETLists the ontology term IDs (keyValue) and names (stringValue) annotated to one RGD object, without the annotation detail.

Affy id, 1 operation

list_genes_by_affymetrix_idList genes by affymetrix idGETLists the genes of one species linked to an Affymetrix probe set ID.

Alia, 1 operation

list_genes_by_aliasList genes by aliasGETLists the genes of one species that carry a given alias (an old or alternative symbol).

All, 1 operation

list_strainsList strainsGETLists every active strain in RGD, as full strain records. The answer is large; prefer search_strain_models to find strains for a disease or phenotype.

Allele, 1 operation

list_gene_allelesList gene allelesGETLists the allele records of a gene, as gene records. An empty list means RGD has no allele for that gene.

Assembly, 1 operation

get_assemblyGet assemblyGETGets one assembly by its map key: name, version, unit, species, UCSC, RefSeq and GenBank assembly accessions.

Chr for species, 1 operation

list_species_chromosomesList species chromosomesGETLists the chromosome names of the primary reference assembly of one species, as a list of strings.

Diagrams for category, 1 operation

list_pathways_by_categoryList pathways by categoryGETLists the RGD pathway diagrams in one category, for example disease.

Experiment, 1 operation

get_expression_experimentGet expression experimentGETGets one experiment by its ID (experimentId of an expression record): name, study ID and trait terms.

Expression, 1 operation

list_gene_expression_valuesList gene expression valuesGETLists the expression values of one gene in one tissue, each with its expression record (experiment, sample, conditions). Answers can be large (megabytes for well studied genes).

Gene type, 1 operation

list_gene_typesList gene typesGETLists the gene type values RGD uses (protein-coding, pseudo, ncrna and others), as a list of strings.

Keyword, 1 operation

search_genes_by_keywordSearch genes by keywordGETSearches the genes of one species by a keyword and returns the matching gene records with their RGD IDs.

Last, 1 operation

list_newsList newsGETLists the latest RGD news items (title with date, excerpt, link), at most ten unless limit is set. Items are under resultset.result[0].news.

Meeting, 1 operation

list_meetingsList meetingsGETLists upcoming meetings and conferences relevant to RGD (title with date, excerpt, link). Items are under resultset.result[0].meetings.

Parent term, 1 operation

list_term_ancestorsList term ancestorsGETLists the parent terms of one ontology term up to the root, as an object of term ID to term name.

Record, 1 operation

list_experiment_recordsList experiment recordsGETLists the measurement records of one experiment with their sample, measurement method, clinical measurement and conditions.

Region, 1 operation

list_genes_in_regionList genes in regionGETLists the genes in a region of one assembly in a compact form: RGD ID, symbol, chromosome, start, stop and strand.

Rgd id list, 1 operation

list_annotations_for_objectsList annotations for objectsGETLists the annotations of several RGD objects in one ontology. Pass the RGD IDs comma-separated.

Species type key, 1 operation

list_species_type_keysList species type keysGETLists the species RGD holds and their species type keys, as an object of species name to key (for example Rat 3). Call it first to get speciesTypeKey values.

Study, 1 operation

get_studyGet studyGETGets one study by its ID (studyId of an experiment): name, source, data type, GEO series accession and the RGD IDs of its references.

Term, 1 operation

get_ontology_termGet ontology termGETGets one ontology term by its accession ID: term name, ontology, definition, comment, cross-references and obsolete flag.

Term and parent term with synonym, 1 operation

list_term_ancestors_with_synonymsList term ancestors with synonymsGETLists, as one flat list of strings, the IDs and names of a term and its parent terms followed by their synonyms and cross-reference IDs. Useful for text search.

Video, 1 operation

list_videosList videosGETLists RGD tutorial videos (title with date, excerpt, link). Items are under resultset.result[0].videos.

Use Rat Genome Database from Claude Code, Cursor or Codex

Connect Rat Genome Database in LiveContext, create an API key in Settings, then add the LiveContext MCP server to your client. Its Rat Genome Database operations become tools the client can call, next to every other integration you connected.

Claude Code

claude mcp add --transport http livecontext https://livecontext.ai/mcp --header "X-API-Key: YOUR_API_KEY"

Codex (~/.codex/config.toml)

[mcp_servers.livecontext]
url = "https://livecontext.ai/mcp"

[mcp_servers.livecontext.http_headers]
"X-API-Key" = "YOUR_API_KEY"

Cursor, Claude Desktop and other JSON configs

{
  "mcpServers": {
    "livecontext": {
      "type": "http",
      "url": "https://livecontext.ai/mcp",
      "headers": {
        "X-API-Key": "YOUR_API_KEY"
      }
    }
  }
}

Set up the MCP server step by step

How to connect Rat Genome Database

Create your workspace
Sign up free. Nothing to install.
Connect Rat Genome Database once
Rat Genome Database needs no credential, so its tools work immediately.
Describe the job in chat
The workflow builds itself in front of you and picks the endpoints it needs. Drag the steps yourself on the canvas whenever you would rather be explicit.