---
title: Genomics on the platform
description: >-
  Multi-database genomics query tools for gene information, pathway analysis,
  variant interpretation, and cross-database linking.
tags:
  - genomics
---

Genomics turns a disease question into a validated, druggable target — querying nine gene, pathway, variant, and target-association databases through one interface so you can go from a gene symbol to evidence a target is worth pursuing. Reach for it at the start of a program, when you need to know which target to drug at all rather than how to drug a known one. It is the entry point of the expression → differential → causal → druggable-target pipeline it forms with [causal genomics](/docs/causal-genomics), which takes over once you have GWAS signal to resolve to causal mechanism. See [what you can achieve](/docs/capabilities#genomics-and-omics) for the full set.

## Genomics overview

The Genomics toolkit provides a unified interface to nine complementary databases for gene information, pathway analysis, clinical variant interpretation, and drug target validation. All tools use direct API calls with no GPU compute, returning results in 2-8 seconds.

## Architecture

 I[Intent detection]
    I -->|Gene lookup| G[Entrez Search or Ensembl Gene Lookup]
    I -->|Pathway search| P[KEGG Pathway Search or Reactome Pathway]
    I -->|Variant query| V[ClinVar Search]
    I -->|Target validation| T[OpenTargets Associations]
    I -->|Cross-reference| X[Entrez Link]
    I -->|Record retrieval| R[Entrez Fetch]
    I -->|MeSH resolution| M[MeSH Lookup]
    G & P & V & T & X & R & M --> A["Direct API call (2-8 s)"]
    A --> Res[Structured results with database URLs]`}
  caption="A genomics query is routed by intent to the right reference database, then returned as structured results."
/>

## Tool inventory

### NCBI Entrez tools

| Lookup | Description | Databases |
|--------|-------------|-----------|
| Entrez Search | Multi-database keyword search with document summaries | gene, protein, nucleotide, structure, taxonomy, biosample, sra, mesh, pmc, pubmed |
| Entrez Link | Cross-database record linking (e.g., gene to protein to structure) | gene, protein, nucleotide, structure, pubmed, taxonomy, pmc |
| Entrez Fetch | Full record retrieval in FASTA, GenBank, XML, or other formats | gene, protein, nucleotide, pubmed, structure, taxonomy |
| MeSH Lookup | Medical Subject Headings term resolution with tree numbers and synonyms | mesh |

### Genomics database tools

| Lookup | Description | Data Source |
|--------|-------------|-------------|
| KEGG Pathway Search | Pathway, gene, compound, and reaction search | KEGG REST API |
| Ensembl Gene Lookup | Gene coordinates, biotype, and transcript isoforms | Ensembl REST API |
| ClinVar Search | Clinical variant classifications (pathogenic, VUS, benign) | NCBI E-utilities |
| OpenTargets Associations | Target-disease association scores with evidence breakdown | OpenTargets GraphQL API |
| Reactome Pathway | Curated pathway diagrams and disease annotations | Reactome Content Service |

These lookups run inside a chat turn: you reach them by asking Ivy in plain language, and Ivy picks the database. There is no form or job to submit for them.

## Capabilities

### Gene information retrieval

Search for genes by symbol, Entrez ID, or Ensembl ID. Results include genomic coordinates, chromosome location, biotype, and cross-references. Use Ensembl Gene Lookup for detailed coordinates and transcript isoforms, or Entrez Search for broader NCBI database coverage.

### Pathway analysis

KEGG provides pathway, gene, compound, and reaction search with diagram URLs. Reactome provides manually curated, peer-reviewed pathway data with detailed diagrams and disease annotations. Both support keyword and ID-based queries.

### Variant interpretation

ClinVar Search returns clinical significance classifications (pathogenic, likely pathogenic, uncertain significance, likely benign, benign) with review status, gene associations, and condition information. Filter results by significance level.

### Target-disease associations

OpenTargets Associations scores target-disease relationships using four evidence categories: genetic association (GWAS, rare disease), somatic mutation (cancer drivers), known drugs (approved/clinical), and literature (text mining). Query by gene symbol or disease name.

### Cross-database linking

Entrez Link connects records across NCBI databases. Common link paths:

| Source | Target | Link Name | Use Case |
|--------|--------|-----------|----------|
| gene | protein | gene_protein | Find proteins encoded by a gene |
| gene | nucleotide | gene_nuccore | Find nucleotide sequences for a gene |
| protein | structure | protein_structure | Find PDB structures for a protein |
| gene | pubmed | gene_pubmed | Find literature about a gene |

### Full record retrieval

Entrez Fetch downloads complete records in the requested format:

| Database | Format | Content |
|----------|--------|---------|
| protein | FASTA | Amino acid sequence |
| protein | gp (GenPept) | Full annotated protein record |
| nucleotide | FASTA | Nucleotide sequence |
| nucleotide | gb (GenBank) | Full annotated nucleotide record |
| gene | xml | Complete gene record |
| pubmed | abstract | Article abstract text |

### MeSH term resolution

MeSH Lookup resolves biomedical concepts to official Medical Subject Headings, returning scope notes, tree numbers (hierarchical classification), and entry terms (synonyms). Use this to build precise PubMed queries with controlled vocabulary.

## What to ask for

| I want to... | Ivy answers it with |
|--------------|---------------------|
| Look up a gene by symbol | An Entrez Gene search or an Ensembl gene lookup |
| Get genomic coordinates | An Ensembl gene lookup |
| Find pathways for a gene | A KEGG or Reactome pathway search |
| Check if a variant is pathogenic | A ClinVar search |
| Evaluate a drug target | OpenTargets associations |
| Get a FASTA sequence | An Entrez fetch in FASTA format |
| Link gene to protein to structure | An Entrez link |
| Resolve a MeSH term | A MeSH lookup |
| Find a pathway diagram | A Reactome pathway search, asking for the diagram |

## When to use other tools instead

| I want to... | Use this instead |
|--------------|------------------|
| Search PubMed for papers | [PubMed](/docs/pubmed) search |
| Download a PDB structure file | An [RCSB PDB](/docs/pdb) download |
| Look up protein info from UniProt | A [UniProt](/docs/uniprot) search or entry fetch |
| Find protein-protein interactions | A STRING interaction lookup |
| Search for chemical compounds | [PubChem](/docs/pubchem) or [ChEMBL](/docs/chembl) |
| Run a BLAST sequence search | [BLAST](/docs/blast) |
| Get or predict a protein structure | An [AlphaFold DB](/docs/alphafold) fetch, or a prediction with [ESMFold](/docs/esmfold) |

## Licensing

All genomics APIs used by the toolkit are commercially permissive:

| Database | License |
|----------|---------|
| NCBI Entrez | Public domain (US Government) |
| Ensembl | Unrestricted (data); Apache 2.0 (Ensembl software) |
| KEGG | Free for academic use, commercial license available |
| ClinVar | Public domain |
| OpenTargets | CC0 1.0 (public domain) |
| Reactome | CC0 (pathway data); CC BY 4.0 (pathway diagrams) |

## Citations

> Sayers EW, et al. Database resources of the National Center for Biotechnology Information. *Nucleic Acids Res*. 2022;50(D1):D20-D26. doi: [10.1093/nar/gkab1112](https://doi.org/10.1093/nar/gkab1112)

> Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. *Nucleic Acids Res*. 2000;28(1):27-30. doi: [10.1093/nar/28.1.27](https://doi.org/10.1093/nar/28.1.27)

> Ochoa D, et al. The next-generation Open Targets Platform: reimagined, redesigned, rebuilt. *Nucleic Acids Res*. 2023;51(D1):D1353-D1359. doi: [10.1093/nar/gkac1046](https://doi.org/10.1093/nar/gkac1046)

## Chat Usage

### Example Prompts

- "What pathways is EGFR involved in?"
- "Look up the genomic coordinates for TP53 and include transcript isoforms"
- "Find pathogenic variants in BRCA2 from ClinVar"
- "What diseases are associated with JAK2 according to OpenTargets?"
- "Get the FASTA sequence for human hemoglobin beta"
- "Link NCBI Gene ID 7157 to its protein records"

### Workflow Chaining

- **Feeds into**: Target Passport (druggability assessment), BLAST (sequence homology), STRING (protein interactions), AlphaFold (structure prediction), Literature search (PubMed via gene_pubmed link)
- **Accepts from**: Literature search (gene mentions), Compound Passport (target genes), UniProt (protein cross-references), BLAST results (gene identification)

## FAQ

### Which databases does the Genomics toolkit query?

  The toolkit queries NCBI Entrez (Gene, Protein, Nucleotide, Structure), Ensembl, KEGG, ClinVar, OpenTargets, and Reactome. Each database is accessed through its own dedicated tool.

### Do I need API keys for any of the genomics databases?

  No. All genomics tools use public APIs that do not require authentication. NCBI E-utilities are rate-limited to 3 requests/second without an API key and 10 requests/second with one (configured server-side).

### Can I search across multiple databases at once?

  The Entrez Search tool supports 10 NCBI databases (gene, protein, nucleotide, structure, taxonomy, biosample, sra, mesh, pmc, pubmed). For cross-database linking, use Entrez Link to connect records between databases.

### What organisms are supported?

  KEGG supports organism codes (hsa=human, mmu=mouse, rno=rat, sce=yeast, and many more). Ensembl supports species names (homo_sapiens, mus_musculus, rattus_norvegicus). Most tools default to human.

## Read next