---
title: Genomics inputs and parameters
description: >-
  Query formats, database selection, organism codes, and filter options for all
  genomics tools.
tags:
  - genomics
  - inputs
---

You give Ivy an identifier in your message — a gene symbol, Ensembl or Entrez ID, rsID, HGVS expression, or pathway/disease name — and, where it matters, the database or organism you mean. These lookups run inside a chat turn; there is no form to fill in. Naming the right identifier type and target database in your prompt is what most affects whether Ivy returns the record you meant.

## Genomics inputs and parameters

## Common query formats

Most genomics lookups accept one of these identifier types:

| Identifier | Format | Example | Accepted By |
|------------|--------|---------|-------------|
| Gene symbol | Standard HGNC symbol | `BRCA1`, `TP53`, `EGFR` | All tools |
| Ensembl ID | `ENSG` prefix + digits | `ENSG00000141510` | Ensembl, OpenTargets |
| Entrez Gene ID | Numeric | `7157` | Entrez Search/Link/Fetch |
| rsID | `rs` prefix + digits | `rs334` | ClinVar |
| HGVS | Transcript:change | `NM_000492.4:c.1521_1523del` | ClinVar |
| KEGG ID | Database prefix + code | `hsa:7157`, `path:hsa03440` | KEGG |
| Reactome ID | `R-HSA-` prefix | `R-HSA-109582` | Reactome |
| EFO ID | `EFO_` prefix | `EFO_0000685` | OpenTargets (disease) |

## Entrez Search: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| The search terms | Required | Entrez field tags like `[GENE]` and `[ORGN]` are honoured |
| Which NCBI database to search | Required (Ivy infers it from the question) | One of the databases below |
| How many results | 20 | Up to 100 |
| Sort order | Relevance | Relevance, date, or name |
| A date range | None | Start and/or end date |

### Supported databases

| Database | Content | Example Query |
|----------|---------|---------------|
| `gene` | Gene records | `BRCA1[GENE] AND human[ORGN]` |
| `protein` | Protein sequences | `insulin AND homo sapiens[ORGN]` |
| `nucleotide` | Nucleotide sequences | `TP53 mRNA human` |
| `structure` | 3D structures (MMDB) | `hemoglobin` |
| `taxonomy` | Organism taxonomy | `Escherichia coli` |
| `biosample` | Biological samples | `cancer cell line` |
| `sra` | Sequencing reads | `RNA-seq human brain` |
| `mesh` | MeSH descriptors | `Alzheimer Disease` |
| `pmc` | PubMed Central articles | `CRISPR review` |
| `pubmed` | PubMed citations | `BRCA1 breast cancer` |

## Entrez Link: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| The record IDs to link from | Required | 1-50 IDs from one database |
| The source and target databases | Required | For example gene to protein |
| A specific link path | Auto-detected | For example `gene_protein`; see the table below |
| How many linked records | 20 | Up to 100 |

### Common link paths

| Link Name | Source DB | Target DB | Use Case |
|-----------|----------|-----------|----------|
| `gene_protein` | gene | protein | Proteins encoded by a gene |
| `gene_nuccore` | gene | nucleotide | Nucleotide sequences for a gene |
| `protein_structure` | protein | structure | PDB structures for a protein |
| `gene_pubmed` | gene | pubmed | Literature about a gene |

## Entrez Fetch: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| The record IDs or accessions | Required | 1-20 per fetch |
| The database to fetch from | Required | See the formats table below |
| The record format | FASTA | For example FASTA, GenBank, GenPept, XML, abstract |
| Text, XML, or JSON output | Text | |

### Format options by database

| Database | Formats | Best For |
|----------|---------|----------|
| protein | `fasta`, `gp` (GenPept), `xml` | Sequence analysis, full annotation |
| nucleotide | `fasta`, `gb` (GenBank), `xml` | Sequence analysis, full annotation |
| gene | `xml`, `docsum` | Gene information |
| pubmed | `xml`, `abstract` | Citation data |

## MeSH Lookup: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| The term or concept | Required | 2-200 characters |
| Suggestions for a partial or unofficial term | Off | Ask Ivy to suggest the matching MeSH heading |

## KEGG Pathway Search: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A pathway name, gene symbol, KEGG ID, or compound name | Required | 2-200 characters |
| What to search | Pathways | Pathways, genes, compounds, or reactions |
| The organism | Human (`hsa`) | Name the organism; codes below |
| How many results | 10 | Up to 50 |

### KEGG organism codes

| Code | Organism |
|------|----------|
| `hsa` | Human (*Homo sapiens*) |
| `mmu` | Mouse (*Mus musculus*) |
| `rno` | Rat (*Rattus norvegicus*) |
| `sce` | Yeast (*Saccharomyces cerevisiae*) |
| `eco` | *E. coli* K-12 |
| `dme` | Fruit fly (*Drosophila melanogaster*) |
| `cel` | *C. elegans* |

### KEGG search types

| Search type | Searches | Returns |
|-----------|----------|---------|
| `pathway` | Pathway database | Pathway IDs, names, diagram URLs |
| `gene` | Organism gene database | Gene/ortholog entries |
| `compound` | Compound database | Metabolite entries |
| `reaction` | Reaction database | Enzyme reaction entries |

## Ensembl Gene Lookup: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A gene symbol or Ensembl ID | Required | 2-50 characters |
| The species | Human | See the species below |
| Transcript isoforms | Not included | Ask for isoforms to include them |

### Supported species

| Species Name | Common Name |
|-------------|-------------|
| `homo_sapiens` | Human |
| `mus_musculus` | Mouse |
| `rattus_norvegicus` | Rat |
| `danio_rerio` | Zebrafish |
| `drosophila_melanogaster` | Fruit fly |
| `caenorhabditis_elegans` | Roundworm |

## ClinVar Search: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A gene symbol, rsID, or HGVS expression | Required | 2-200 characters |
| Which clinical significance classes to keep | All | Any of the classes below |
| How many results | 20 | Up to 50 |

### Significance classes Ivy can filter on

| Class | Filters For |
|-------|-------------|
| Pathogenic | Pathogenic variants |
| Likely pathogenic | Likely pathogenic variants |
| Uncertain | Variants of uncertain significance (VUS) |
| Likely benign | Likely benign variants |
| Benign | Benign variants |
| Conflicting | Conflicting interpretations |

## OpenTargets Associations: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A gene symbol, Ensembl ID, disease name, or EFO ID | Required | 2-50 characters |
| Whether you are asking about a target or a disease | Target | |
| A minimum association score | 0.1 | 0-1 |
| How many associations | 20 | Up to 50 |

## Reactome Pathway: what you can ask for

| You can specify | Default | Limits and notes |
|-----------------|---------|------------------|
| A gene symbol, pathway name, or Reactome ID | Required | 2-200 characters |
| The species | *Homo sapiens* | |
| Pathway diagram and image links | Included | |
| How many pathways | 10 | Up to 50 |

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