---
title: Genomics quickstart
description: >-
  Step-by-step workflows for gene lookup, pathway search, variant
  interpretation, and cross-database linking.
tags:
  - genomics
  - quickstart
---

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

### Step 1: Search by gene symbol

Ask Ivy in chat:

```
Look up the gene TP53
```

Ivy runs an Ensembl gene lookup to return genomic coordinates, or an Entrez Gene search for broader NCBI Gene information.

### Step 2: Review the results

| Field | Example Value |
|-------|---------------|
| Ensembl ID | ENSG00000141510 |
| Chromosome | 17 |
| Start | 7668402 |
| End | 7687550 |
| Strand | -1 |
| Biotype | protein_coding |
| Assembly | GRCh38 |

### Step 3: Include transcripts (optional)

```
Look up TP53 with transcript isoforms
```

Asking for isoforms returns all known transcript variants with their lengths and canonical status.

## Workflow 2: Search pathways

### Step 1: Search KEGG

```
What pathways is BRCA1 involved in?
```

Ivy searches KEGG pathways for the gene, in human by default. Name another organism in the prompt (for example "in mouse") to change it.

### Step 2: Review pathway results

Each result includes a KEGG pathway ID, description, and diagram URL:

| ID | Name | Diagram |
|----|------|---------|
| path:hsa03440 | Homologous recombination | [View](https://www.kegg.jp/pathway/hsa03440) |
| path:hsa04120 | Ubiquitin mediated proteolysis | [View](https://www.kegg.jp/pathway/hsa04120) |

### Step 3: Explore in Reactome (optional)

For curated pathway diagrams with disease annotations:

```
Show me Reactome pathways for DNA repair
```

Reactome returns pathway IDs, summaries, disease flags, and interactive diagram URLs.

## Workflow 3: Interpret clinical variants

### Step 1: Search ClinVar

```
Search ClinVar for pathogenic variants in CFTR
```

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").

### Step 2: 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 |

### Step 3: 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

### Step 1: Query OpenTargets

```
What diseases are associated with EGFR according to 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.

### Step 2: 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 |

### Step 3: 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

### Step 1: Start with a gene

```
Find the protein records for NCBI Gene ID 7157 (TP53)
```

Ivy runs an Entrez link from the Gene record to the Protein database.

### Step 2: Review linked records

The result includes UIDs, titles, accessions, and organisms for all linked protein records.

### Step 3: Retrieve a full record

```
Get the FASTA sequence for protein accession NP_000537.3
```

Ivy runs an Entrez fetch in FASTA format to download the complete amino acid sequence.

## Next steps

- See [inputs](/docs/genomics/inputs) for query formats, database options, and organism codes
- See [outputs](/docs/genomics/outputs) for result field descriptions and score interpretation
- Use [BLAST](/docs/blast) for sequence homology searches
- Use [UniProt](/docs/uniprot) for protein annotation and functional information

## Read next