Query formats, database selection, organism codes, and filter options for all genomics tools.

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

Genomics inputs and parameters