Resolve query failures, empty results, identifier mismatches, and cross-database linking issues.

This page helps you diagnose the failures you hit when querying genomics databases — empty results, gene and variant identifiers that won't resolve, cross-database links that come back empty, malformed record fetches, and rate-limit or timeout errors.

Genomics troubleshooting

Gene not found in Ensembl

Symptom: "Unknown error" or empty result when looking up a gene.

Fixes:

Check the gene symbol spelling. Use official HGNC symbols (e.g., TP53 not p53)
If using an Ensembl ID, ensure it starts with the correct prefix (ENSG for human, ENSMUSG for mouse)
Make sure the species matches your gene. Human is the default; name another species in your prompt
Some non-coding genes and pseudogenes may not have Ensembl entries. Ask Ivy to search NCBI Gene instead

No KEGG pathway results

Symptom: Zero results returned from KEGG pathway search.

Fixes:

Try broader search terms. KEGG pathway names may differ from common names (e.g., "p53 signaling" instead of "TP53 pathway")
Check the organism. The default is human (hsa); name mouse (mmu), rat (rno) or another organism in your prompt
Ask Ivy to search KEGG genes rather than pathways when you are searching by gene symbol
Some recently discovered pathways may not yet be in KEGG. Try Reactome as an alternative

ClinVar returns no variants

Symptom: Zero variants found for a gene query.

Fixes:

Ensure correct gene symbol spelling (case-sensitive)
For rsID queries, include the rs prefix (e.g., rs334 not 334)
HGVS expressions must match exactly (check transcript version)
Ask without a significance filter to see all variants, then narrow down
Some genes have very few clinically reported variants. This is expected for non-disease-associated genes

OpenTargets query fails

Symptom: Error or empty results from OpenTargets associations.

Fixes:

Gene symbols are resolved to Ensembl IDs automatically. If resolution fails, provide the Ensembl ID directly (e.g., ENSG00000146648 for EGFR)
For disease queries, try using the EFO ID (e.g., EFO_0000685) instead of a disease name
The default minimum score (0.1) may exclude weak associations. Ask for a lower cutoff, such as 0.01, for comprehensive results
OpenTargets covers primarily human diseases. Non-human queries will not return results

Entrez Link returns zero linked records

Symptom: No linked records found between databases.

Fixes:

Verify that the source IDs are valid for the source database (ask Ivy to search that database to confirm)
Not all link paths exist. For example, taxonomy_structure is not a standard link. Check the common link paths table
Some records may not have cross-references. A gene may not have any associated PDB structures
Leave the link path unspecified so Ivy auto-detects the available links

Entrez Fetch returns wrong format

Symptom: Content appears garbled or in an unexpected format.

Fixes:

Not all formats work with all databases. FASTA only works for sequence databases (protein, nucleotide)
For gene records, ask for XML instead of FASTA
For PubMed records, ask for the abstract for readable text
Large records (>50,000 characters) are truncated. Check the truncated field in the output

MeSH term not resolved

Symptom: "MeSH term not found" even for common medical concepts.

Fixes:

MeSH uses specific controlled vocabulary. Ask Ivy to suggest matching MeSH headings
Check spelling carefully. MeSH terms use American English ("tumor" not "tumour")
Some concepts are entry terms (synonyms) rather than main headings. The suggestion mode will show the official heading
Very recent concepts may not yet have MeSH descriptors. Check the MeSH Browser directly

Reactome returns no pathways

Symptom: Zero pathways found for a search term.

Fixes:

Reactome pathway names may differ from other databases. Try broader terms
Check the species (the default is Homo sapiens). Reactome has limited coverage for non-model organisms
If you have a Reactome ID (e.g., R-HSA-109582), search by ID for a direct lookup
For gene-based searches, the gene symbol must match Reactome's naming convention

Rate limiting or timeout errors

Symptom: "Request failed" or timeout errors.

Explanation: NCBI E-utilities enforce rate limits (3 requests/second without API key, 10/second with key). All genomics tools respect these limits automatically.

Fixes:

Wait a few seconds and retry. The rate limiter queues requests automatically
If querying multiple genes, Ivy will space requests appropriately
Large result sets (>50 records) may take longer. Ask for fewer results if speed is important
Ensembl, KEGG, OpenTargets, and Reactome have independent rate limits and are rarely throttled

Getting help

If issues persist:

Check the tool error message for specific suggestions
Verify your identifier format matches the expected input
Try the same query on the database's web interface to confirm data availability
Describe the issue to Ivy

Genomics troubleshooting