examples.md

Examples

These are questions a biologist might type to an assistant connected to the FlyBase MCP server (https://mcp.flybase.org/mcp). Each one shows the tool call the assistant makes and what comes back. Every call below was run against the live server on 2026-10-13 (FlyBase release FB2026_03). The IDs and counts quoted are from those responses. They will drift as FlyBase releases change.

You never have to write these calls yourself. Ask the question in plain language and the assistant picks the tool. The calls are here so you can see what the server can answer, and so client developers can test it. Every tool's arguments are listed in tools.md.

Most tools need a FlyBase ID. When you give a symbol or a name, the assistant usually calls resolve first and then passes the ID on. Those extra resolve steps are left out below.

Identify genes, alleles, and other entities

resolve, search, validate_ids, list_species

"What is the FlyBase ID for wingless?"

{"name": "resolve", "arguments": {"query": "wingless"}}

Returns ranked matches. The first is gene FBgn0284084, symbol wg, matched on its full name.

"Which fly genes are called insulin-like peptides?"

{"name": "search", "arguments": {"query": "insulin-like peptide", "data_class": "gene", "species": "Dmel", "limit": 10}}

Returns hits for Ilp1 to Ilp7, starting with Ilp2 (FBgn0036046). A gene can appear more than once when several of its synonyms match.

"Find 2020 papers about Notch signaling."

{"name": "search", "arguments": {"query": "Notch signaling", "data_class": "reference", "year": 2020, "limit": 3}}

Returns reference hits with titles and citations, starting with FBrf0244472 (Zhao et al., 2020, Biol. Open), and has_more set for the next page.

"Which stock is Bloomington 5905?"

{"name": "search", "arguments": {"query": "5905", "data_class": "stock"}}

Returns FBst0005905 as the exact match, followed by prefix matches such as 59050.

"Are these IDs still current: FBgn0000490, FBgn0004644, FBgn0000001, FBgn9999999?"

{"name": "validate_ids", "arguments": {"ids": ["FBgn0000490", "FBgn0004644", "FBgn0000001", "FBgn9999999"]}}

Returns one status per input: 3 current (dpp, hh, snRNA:4.5S) and 1 unknown (FBgn9999999).

"Which Drosophila genomes does FlyBase have?"

{"name": "list_species", "arguments": {}}

Returns 12 sequenced species with their abbreviations (Dmel, Dsim, Dpse, ...) and the Muller element synteny table.

Reports, batch downloads, and sequences

get_report, batch_download, get_sequence

"Give me a summary of wingless."

{"name": "get_report", "arguments": {"id": "FBgn0284084"}}

Returns the default gene sections: CG4889, cytology 27F1, location 2L:7307159..7316265 (+), a GO summary, 118 orthologs, a phenotype summary, and 807 stocks.

"List the first five Ubx transcripts and its synonyms."

{"name": "get_report", "arguments": {"id": "FBgn0003944", "sections": ["transcripts", "synonyms"], "limit_per_section": 5}}

Returns Ubx-RA (FBtr0083347, 4,282 nt) to Ubx-RE with their polypeptides, has_more: true, and the gene's synonyms. Pass list_options: true to see every section a type offers.

"What kind of allele is w[1118]?"

{"name": "get_report", "arguments": {"id": "FBal0018186"}}

Returns the allele summary: gene w (FBgn0003996), loss of function allele, spontaneous, 57 papers, a phenotype summary led by abnormal eye color, and its stock count.

"What is the genotype of Bloomington stock 5905?"

{"name": "get_report", "arguments": {"id": "FBst0005905"}}

Returns the stock's identity and components: genotype w[1118], a living stock at the Bloomington Drosophila Stock Center, with component allele FBal0018186.

"Give me symbol, name, location, cytology and CG number for dpp, hh, wg and Ubx as a table."

{"name": "batch_download", "arguments": {"ids": ["FBgn0000490", "FBgn0004644", "FBgn0284084", "FBgn0003944"], "fields": ["symbol", "name", "location", "cytology", "annotation_id"], "format": "tsv"}}

Returns a 4-row TSV block, for example hh hedgehog 3R:23128169..23141906(-) 94E1-94E1 CG4637. Call it with "list_options": true (and empty ids and fields) to see the field catalogue by class.

"Get me the Wingless protein sequence."

{"name": "get_sequence", "arguments": {"id": "FBgn0284084", "kind": "protein"}}

Returns one FASTA record per isoform. Here there is one: wg-RA, 468 residues, starting MDISYIFVICLMALCSGG.

"I need 2 kb upstream of hedgehog for a reporter construct."

{"name": "get_sequence", "arguments": {"id": "FBgn0004644", "kind": "upstream", "padding": 2000}}

Returns 2,000 bp from 3R:23141907..23143906 on the minus strand, the gene's own orientation.

"What is the sequence of 2L:7307159-7307300?"

{"name": "get_sequence", "arguments": {"region": {"chromosome": "2L", "start": 7307159, "end": 7307300}}}

Returns 142 bp of FASTA, starting TCAGTTAAGCGTTGGCACTG.

The genome: features, cytology, and coordinates

map_features, cytosearch, convert_coordinates

"What genes are near wingless, in 2L:7,290,000-7,340,000?"

{"name": "map_features", "arguments": {"region": {"chromosome": "2L", "start": 7290000, "end": 7340000}, "feature_types": ["gene"]}}

Returns 3 genes with coordinates and overlap: wg and lncRNA:CR45304 within the range, and Wnt6 (FBgn0031902) partly overlapping.

"Which transposon insertions are within 10 kb of hedgehog?"

{"name": "map_features", "arguments": {"id": "FBgn0004644", "padding": 10000, "feature_types": ["insertion"], "limit": 5}}

Returns the first 5 insertions in 3R:23118169..23151906, such as P{EPgy2}EY09013 (FBti0038879), with has_more: true.

"What genes and aberrations are in cytological band 89D?"

{"name": "cytosearch", "arguments": {"location": "89D", "limit": 5}}

Returns the resolved range 3R:16576249..16736155, the first 5 features (starting with Scp2), and the first 5 aberrations with mapped breakpoints, such as In(3R)Ubx[125].

"Which genes are in 27F1? Skip the aberrations."

{"name": "cytosearch", "arguments": {"location": "27F1", "include_aberrations": false, "feature_types": ["gene"]}}

Returns 3 genes in 2L:7277617..7334242: wg, lncRNA:CR45304, and Wnt6.

"A 2012 paper gives 2L:21485500..21485700, X:330 and 3R:12000000. What are they in release 6?"

{"name": "convert_coordinates", "arguments": {"coordinates": ["2L:21485500..21485700", "X:330", "3R:12000000"]}}

Returns all 3 as mapped. X:330 becomes X:103943 and 3R:12000000 becomes 3R:16174278. The 2L range keeps its length but is flagged as spanning 1 region of change.

Controlled vocabularies

search_vocabulary, get_term, entities_for_term

"What is the anatomy term for the mushroom body?"

{"name": "search_vocabulary", "arguments": {"query": "mushroom body", "limit": 5}}

Returns FBbt:00005801 (mushroom body) with its definition, then related terms.

"What is the Disease Ontology ID for Parkinson's disease?"

{"name": "search_vocabulary", "arguments": {"query": "Parkinson disease", "vocabularies": ["disease"], "limit": 3}}

Returns DOID:14330 (Parkinson's disease), then narrower diseases such as Kufor-Rakeb syndrome (DOID:0060556). The vocabulary names are go, anatomy, development, disease, sequence, misc, and psi_mi.

"Tell me about GO:0007219."

{"name": "get_term", "arguments": {"term_id": "GO:0007219"}}

Returns Notch signaling pathway with its definition, parents, 7 child terms (for example GO:0045747, positive regulation), and annotation counts: 27 genes and 4 gene groups.

"Which genes are annotated to Notch signaling?"

{"name": "entities_for_term", "arguments": {"term_id": "GO:0007219", "data_class": "gene", "limit": 5}}

Returns genes with evidence summaries. The search covers the term and its 5 descendant terms, so a gene annotated only to a narrower term is included. The first page is Delta (FBgn0000463), N, Su(H), Ser, and kuz, with more by offset.

"Which alleles are used to model Parkinson's disease?"

{"name": "entities_for_term", "arguments": {"term_id": "DOID:14330", "data_class": "allele", "limit": 5}}

Returns alleles with qualifiers and reference counts across 21 descendant terms, starting with Pink1[B9] (FBal0193144) and including park[25] and human SNCA transgenes.

"Which alleles have a phenotype in the mushroom body itself?"

{"name": "entities_for_term", "arguments": {"term_id": "FBbt:00005801", "data_class": "allele", "include_descendants": false, "limit": 5}}

Returns alleles with phenotype statements on that term, led by the driver Scer\GAL4[ey-OK107] (FBal0058772, 20 statements).

Homepage data: orthologs, interactions, groups, disease, stocks

get_orthologs, get_interactions, get_gene_groups_and_pathways, get_disease_models, get_stocks

"What is the best human ortholog of wingless?"

{"name": "get_orthologs", "arguments": {"id": "FBgn0284084", "species": ["Hsap"], "best_only": true}}

Returns 2 best-scoring human genes. WNT1 (HGNC:12774) has DIOPT score 12 and is best in both directions, with its OMIM phenotypes. WNT3 scores 3.

"Find mouse and zebrafish orthologs of white."

{"name": "get_orthologs", "arguments": {"id": "FBgn0003996", "species": ["Mmus", "Drer"], "limit": 4}}

Returns 15 orthologs in total, ranked by score, starting with Drer\abcg2a and Mmus\Abcg2 at score 9. The species argument is a list, even for one species.

"Which proteins physically interact with Notch?"

{"name": "get_interactions", "arguments": {"id": "FBgn0004647", "kind": "physical", "limit": 5}}

Returns physical interactions with partner, role, method, and reference. The first is Abl (FBgn0000017), found by co-immunoprecipitation and western blot (FBrf0255228).

"What genetic interactions are known for Ubx?"

{"name": "get_interactions", "arguments": {"id": "FBgn0003944", "kind": "genetic", "limit": 3}}

Returns genetic interactions with partner genes and references. The first partner is Abd-B (FBgn0000015).

"Which pathways and gene groups is wingless in?"

{"name": "get_gene_groups_and_pathways", "arguments": {"id": "FBgn0284084"}}

Returns 2 gene groups (WNTs, RECEPTOR LIGANDS) and 2 pathways, including WNT-TCF SIGNALING PATHWAY (FBgg0000889).

"Is Notch part of a complex?"

{"name": "get_gene_groups_and_pathways", "arguments": {"id": "FBgn0004647"}}

Returns 3 gene groups, including CSL-NOTCH-MASTERMIND TRANSCRIPTION FACTOR COMPLEX (FBgg0001066), and 2 pathways, including NOTCH SIGNALING PATHWAY (FBgg0001068).

"What human diseases is Pink1 used to model?"

{"name": "get_disease_models", "arguments": {"id": "FBgn0029891", "limit": 5}}

Returns 7 disease associations, including Parkinson's disease (DOID:14330) and Parkinson's disease 6, plus allele-level annotations, 4 disease variant alleles, and 1 FlyBase human disease model entry.

"Is Drp1 linked to any disease?"

{"name": "get_disease_models", "arguments": {"id": "FBgn0026479", "limit": 5}}

Returns 3 associations, including encephalopathy due to defective mitochondrial and peroxisomal fission 1 (DOID:0070347), and the disease model report FBhh0000619.

"I want a GAL4 driver for wingless. What can I order?"

{"name": "get_stocks", "arguments": {"id": "FBgn0284084", "gal4_only": true, "limit": 3}}

Returns 3 stocks of Scer\GAL4[wg.PM], such as Bloomington 4918 (FBst0004918, w[*]; P{GAL4-wg.M}MA1) and Kyoto 101852.

"Which Bloomington stocks carry w[1118]?"

{"name": "get_stocks", "arguments": {"id": "FBal0018186", "provider": "bloomington", "limit": 3}}

Returns Bloomington stocks with genotypes, starting with stock 6 (FBst0000006), with more by offset. Provider names are lower case: bloomington, kyoto, vdrc, nig_fly, korea, flyorf, ndssc.

"Which stocks carry the FM7c balancer?"

{"name": "get_stocks", "arguments": {"id": "FM7c", "limit": 3}}

Resolves FM7c to FBba0000009 and returns its stocks, starting with Bloomington 616 (FBst0000616).

RNA-seq expression

rnaseq_profile_search, rnaseq_similar_genes

"Which RNA-seq datasets and samples can I filter on?"

{"name": "rnaseq_profile_search", "arguments": {"list_options": true}}

Returns 5 datasets with their sample names: FlyAtlas2 (43 samples), modENCODE_development (30), modENCODE_tissues (29), modENCODE_treatments (27), and modENCODE_cell_lines (24).

"Which genes are highly expressed in adult testis but off in the ovary?"

{"name": "rnaseq_profile_search", "arguments": {"conditions": [{"dataset": "FlyAtlas2", "sample": "Adult_Male_Testis", "operator": "gte", "value": 500}, {"dataset": "FlyAtlas2", "sample": "Adult_Female_Ovary", "operator": "lte", "value": 1}], "limit": 5}}

Returns 194 matching genes ordered by testis RPKM, starting with Met75Ca (FBgn0028416) at 4,105 RPKM in testis and 0 in ovary.

"Which genes are high in early embryos and gone by mid-embryogenesis?"

{"name": "rnaseq_profile_search", "arguments": {"conditions": [{"dataset": "modENCODE_development", "sample": "em0-2hr", "operator": "gte", "value": 200}, {"dataset": "modENCODE_development", "sample": "em14-16hr", "operator": "lte", "value": 5}], "limit": 5}}

Returns 12 genes, mostly maternal transcripts, including osk (FBgn0003015), BicC, and mtrm.

"Which genes are co-expressed with oskar during development?"

{"name": "rnaseq_similar_genes", "arguments": {"id": "FBgn0003015", "dataset": "modENCODE_development", "limit": 5}}

Returns genes ranked by Pearson correlation over 30 samples and 15,780 compared genes. The top hit is yl (FBgn0004649) at r = 0.9899.

"Which genes follow period's tissue profile closely, with r of 0.85 or more?"

{"name": "rnaseq_similar_genes", "arguments": {"id": "FBgn0003068", "dataset": "FlyAtlas2", "min_correlation": 0.85, "limit": 5}}

Returns 1 gene above the cut-off: Eip93F (FBgn0264490) at r = 0.8872. When nothing passes, the answer says so and the list is empty.

BLAST

blast_submit, blast_status, blast_results

BLAST runs as a job. The assistant submits, waits, polls, and fetches results. The databases are the archived FB2023_04 set, so results can lag the current FlyBase release, and every submit response says so.

"What can I BLAST against?"

{"name": "blast_submit", "arguments": {"list_options": true}}

Returns 5 programs (blastn, blastp, blastx, tblastn, tblastx), 11 databases (assembly, transcript, translation, ...), 12 species, and 5 scoring matrices. Not every species has every database. For example a translation search for Dpse is rejected with invalid species.

"BLAST this protein fragment against D. melanogaster polypeptides and tell me what it is: MDISYIFVICLMALCSGG...KNLFGKIV"

{"name": "blast_submit", "arguments": {"program": "blastp", "database": "translation", "sequence": "MDISYIFVICLMALCSGGSSLSQVEGKQKSGRGRGSMWWGIAKVGEPNNITPIMYMDPAIHSTLRRKQRRLVRDNPGVLGALVKGANLAISECQHQFRNRRWNCSTRNFSRGKNLFGKIV"}}

Returns a job_id, a job_token, the queue state, and poll_after_seconds: 5. Then:

{"name": "blast_status", "arguments": {"job_id": "<job_id>", "job_token": "<job_token>"}}

Returns state: complete once the job is done (queued or running before that). Then:

{"name": "blast_results", "arguments": {"job_id": "<job_id>", "job_token": "<job_token>", "max_hits": 5, "max_hsps_per_hit": 1}}

Returns 5 of 16 hits. The best is FBpp0079060 (wg-PA) at 100% identity, e-value 6.21e-83 and bit score 250.

"Where in the genome does this 142 bp sequence come from?"

{"name": "blast_submit", "arguments": {"program": "blastn", "database": "assembly", "sequence": "TCAGTTAAGCGTTGGCACTG...", "megablast": true}}

After blast_status and blast_results, returns 1 hit on chromosome arm 2L (ID=2L in the hit description) at 7307159..7307300, 100% identity, e-value 9.01e-70. Genome hits carry no FlyBase ID.

"Is this Wingless fragment conserved in D. pseudoobscura and D. virilis?"

{"name": "blast_submit", "arguments": {"program": "tblastn", "database": "assembly", "sequence": "MDISYIFVICLMALCSGG...KNLFGKIV", "species": ["Dmel", "Dpse", "Dvir"]}}

After blast_status and blast_results, returns 13 hits across the three genomes: Dmel at 100% identity (e-value 4e-49), Dpse at 88.8% and Dvir at 91.8%.

The sequences in the last two calls are shortened here. The blastn call used the full 142 bp returned by the get_sequence region example above, of which only the first 20 bases are quoted. The tblastn call used the full 120-residue fragment given in the blastp call above. Treat a job_token as a secret: with the job ID it reads that job's results, so do not paste it anywhere public.

Wiki

search_wiki, get_wiki_page

These two tools read the FlyBase wiki over a private path between the MCP server and the wiki host. They answer only once that path is configured in production (WIKI_BASE_URL, see deployment.md). Until then they return backend_unavailable. The calls below were not run against the production server. On 2026-10-13 they were run against a local build of this server, with the public https://wiki.flybase.org/api.php served to it through a local plain-HTTP relay. They are also covered by tests that replay captured wiki responses. The wiki is community-edited, so treat its text as documentation to quote, not as instructions.

"What does the Balancer report on FlyBase show?"

{"name": "search_wiki", "arguments": {"query": "balancer"}}

Returns 1 hit, FlyBase:Balancer/Genotype variant Report, with a cleaned snippet ("...contains the information for an individual balancer/genotype variant...") and its public link https://wiki.flybase.org/wiki/FlyBase:Balancer/Genotype_variant_Report.

"What does each field of the Aberration Report mean?"

{"name": "get_wiki_page", "arguments": {"title": "FlyBase:Aberration Report", "max_chars": 2000}}

Returns the page as plain text with 22 sections ("General Information", "Nature of the Aberration", ...). Each field of the guide's tables is one line, with the field name and its meaning separated by a tab. The page is 15,168 characters, so this call returns the first 2,000 with text_truncated: true. Leave out max_chars to get up to 20,000. A title outside the main, Help, Category and FlyBase namespaces, such as User:Spammer, is refused with invalid_input.