---
title: PubMed quickstart
description: Type a plain-English query, read the matching titles and abstracts off the canvas, then ask the model to pull the genes, compounds and diseases it names.
tags:
  - pubmed
  - quickstart
---

You want to find the published literature on a target, mutation, or drug and mine it for entities; this searches [PubMed](/docs/pubmed), then asks the model to extract entities from the returned abstracts in a few steps.

## PubMed Quickstart

## Step 1: Search

In chat, type a natural-language query:

```
Search PubMed for EGFR C797S resistance mechanisms
```

The platform translates this into an E-utilities query and returns matching publications with titles, abstracts, and PubMed links. PubMed does not provide citation counts; for those, ask Ivy to look the papers up in Semantic Scholar.

## Step 2: Review Results

Results appear on the canvas showing:
- Publication titles and authors
- Journal and publication date
- Abstract previews
- PubMed links

## Step 3: Extract entities

Ask the model to mine the results — it reads the returned abstracts directly, no separate tool call:

```
Now extract the genes, compounds, and diseases mentioned in these abstracts
```

The model extracts:
- **Proteins and genes** mentioned (e.g., EGFR, T790M, C797S)
- **Compounds** referenced (e.g., osimertinib, rociletinib)
- **Diseases** discussed
- **Relationships** between entities

## Step 4: Build a Literature Passport

For a comprehensive analysis:

```
Build a literature passport for EGFR resistance mechanisms
```

This orchestrates PubMed search + entity extraction + trend analysis into a single report.

## Next Steps

- **Investigate a target**: Send extracted protein names to Target Passport
- **Check compound safety**: Send extracted drug names to Safety Passport
- **Find structures**: Chain extracted proteins into ESMFold or PDB Search

## Read next