Quick Reference

One-page guide to CATO essentials

Getting Started

Create Project — Click "New Project" from home
Upload Data — Go to Database, drag and drop or click Upload
Start Chat — Open Chat tab and ask questions
View Results — Figures appear in the Visualizations panel

Supported File Formats

Category	Extensions
Tabular	.csv, .tsv, .xlsx, .parquet, .feather, .json, .sas7bdat, .dta
Genomics	.fasta, .fastq, .vcf, .gff, .gtf, .bed, .gb, .gmt, .nwk
Single-Cell	.h5ad, .h5, .hdf5, .fcs
Molecular	.pdb, .cif, .sdf, .mol, .mol2, .smi
Imaging	.nii, .nii.gz, .dcm
Proteomics	.mzml, .mgf
Other	.pdf, .mat, .npy, .gml, .graphml, .zip, .tar.gz

Max size: 25MB (Free) to Unlimited (Enterprise)

Chat Features

@-Mention Datasets

Type @ to reference datasets with autocomplete

Slash Commands

/profile · /visualize · /clean · /test
/code · /export · /help

Plan Mode

Press Shift+Tab to outline steps before executing

Output Types

Visualizations (PNG, inline + side panel)
Figure editing (pencil icon to edit, Base+ plans)
3D molecular viewer (interactive PDB structures)
File artifacts (CSV, Excel, DOCX, PPTX)
Code blocks (Python & R)
Conversation sharing (public read-only links)

Keyboard Shortcuts

Shortcut	Action
`Enter`	Send message
`Shift` + `Enter`	New line
`Shift` + `Tab`	Toggle Plan mode
`Ctrl/⌘` + `K`	Open search
`Ctrl/⌘` + `/`	Toggle sidebar
`Ctrl/⌘` + `U`	Upload dataset
`Esc`	Close modal / dismiss Plan mode

Example Prompts

"Show me the first 10 rows of @patient_data"
"Create a scatter plot of weight vs height"
"Run a t-test comparing treatment and control"
"Generate a DOCX report of the results"
"Search PubMed for NSCLC immunotherapy studies"
"Look up gene TP53 and its pathways"

Biomedical Tools

200+ integrated biomedical tools:

Gene & Protein Lookup
Pathway Analysis
Drug Interaction Checks
Clinical Trial Search
Literature Search (PubMed, BioRxiv)
Sequence Analysis & Ontology Queries

Literature Intelligence

Dedicated academic search & analysis module:

Query Studio:Natural-language search across 7 sources
Search Modes:Evidence-first, Novelty-first
Study Type Filters:RCT, Meta-analysis, Review, etc.
Evidence Matrix:PICO extraction & bias indicators
Citation Network:Interactive graph with PageRank
Document Gen:Review briefs, landscape & gap reports
Chat Bridge:Send papers with prompt templates

Literature Sources

PubMed (up to 10K results)
BioRxiv (TF-IDF ranking)
arXiv (with retry)
ClinicalTrials.gov (with retry)
Patents (USPTO, with retry)
OpenAlex (citations)
Semantic Scholar

Tips

Use @-mentions to reference datasets precisely
Use Plan mode for complex multi-step analyses
Reference exact column names in queries
Use study type filters for precise literature results
Edit figures with the pencil icon before exporting
Review CATO's assumptions after each analysis
Share conversations via the share button
Check AI budget in Settings → Billing

Support

Documentation: /docs
FAQ: /help/faq
Contact: /help/contact
Release Notes: /help/release-notes

CATO v1.3.0 · March 2026