Genomics quickstart
Step-by-step workflows for gene lookup, pathway search, variant interpretation, and cross-database linking.
You want to answer a gene, pathway, variant, or target-validation question without visiting each database by hand; this walks you through five common workflows — gene lookup, pathway search, variant interpretation, drug-target evaluation, and cross-database linking — each a single prompt to Ivy.
Genomics quickstart
This guide covers five common workflows: looking up a gene, searching pathways, interpreting variants, evaluating drug targets, and linking records across databases.
Workflow 1: Look up a gene
Search by gene symbol
Ask Ivy in chat:
Ivy runs an Ensembl gene lookup to return genomic coordinates, or an Entrez Gene search for broader NCBI Gene information.
Review the results
| Field | Example Value |
|---|---|
| Ensembl ID | ENSG00000141510 |
| Chromosome | 17 |
| Start | 7668402 |
| End | 7687550 |
| Strand | -1 |
| Biotype | protein_coding |
| Assembly | GRCh38 |
Include transcripts (optional)
Asking for isoforms returns all known transcript variants with their lengths and canonical status.
Workflow 2: Search pathways
Search KEGG
Ivy searches KEGG pathways for the gene, in human by default. Name another organism in the prompt (for example "in mouse") to change it.
Review pathway results
Each result includes a KEGG pathway ID, description, and diagram URL:
Explore in Reactome (optional)
For curated pathway diagrams with disease annotations:
Reactome returns pathway IDs, summaries, disease flags, and interactive diagram URLs.
Workflow 3: Interpret clinical variants
Search ClinVar
You can narrow by clinical significance (for example "pathogenic and likely pathogenic only") and ask for a number of results (for example "the top 20").
Review variant classifications
| Variant | Significance | Review Status | Condition |
|---|---|---|---|
| NM_000492.4:c.1521_1523del | Pathogenic | Reviewed by expert panel | Cystic fibrosis |
| NM_000492.4:c.1624G>T | Pathogenic | Criteria provided, multiple submitters | Cystic fibrosis |
Understand the classification
| Significance | Meaning |
|---|---|
| Pathogenic | Disease-causing, high confidence |
| Likely pathogenic | Probably disease-causing, strong evidence |
| Uncertain significance (VUS) | Not enough evidence to classify |
| Likely benign | Probably not disease-causing |
| Benign | Not disease-causing |
| Conflicting | Labs disagree on classification |
Workflow 4: Evaluate a drug target
Query OpenTargets
You can ask from either side (a target's diseases, or a disease's targets), set a minimum association score (for example "score above 0.1"), and ask for a number of results.
Review association scores
| Disease | Overall | Genetic | Somatic | Known Drug | Literature |
|---|---|---|---|---|---|
| Non-small cell lung carcinoma | 0.89 | 0.45 | 0.82 | 0.91 | 0.67 |
| Glioblastoma | 0.72 | 0.38 | 0.65 | 0.78 | 0.51 |
| Colorectal cancer | 0.68 | 0.22 | 0.41 | 0.85 | 0.44 |
Interpret the evidence
| Score Range | Interpretation |
|---|---|
| 0.7 - 1.0 | Strong association, well-validated target |
| 0.4 - 0.7 | Moderate association, emerging evidence |
| 0.1 - 0.4 | Weak association, limited evidence |
| < 0.1 | Minimal association |
Workflow 5: Link records across databases
Review linked records
The result includes UIDs, titles, accessions, and organisms for all linked protein records.
Retrieve a full record
Ivy runs an Entrez fetch in FASTA format to download the complete amino acid sequence.
Next steps
- See inputs for query formats, database options, and organism codes
- See outputs for result field descriptions and score interpretation
- Use BLAST for sequence homology searches
- Use UniProt for protein annotation and functional information
Read next
Was this page helpful?