> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/correlation-engine/querying-and-interpreting-results/literature.md).

# Literature

**Literature** shows PubMed publications relevant to your query term, with innovative biomedical tag-cloud filtering that helps you rapidly narrow results to the most relevant papers.

{% hint style="info" %}
Literature results come from **text-based searches**, not from genomic data correlations. A gene appearing prominently in Literature does not necessarily mean it has a significant data correlation — use Disease Atlas, Body Atlas, or other apps for data-driven associations.
{% endhint %}

## What Can You Query?

Literature accepts any query term or keyword — genes, concepts (diseases, tissues, compounds), biogroup names, or free text.

## How to Query Literature

1. Enter your term in the query field.
2. Click the **Literature icon** in the app menu.

## Understanding Literature Results

Results are listed in order of relevance by default. To sort by publication date, select **Date** from the sort drop-down above the results.

### How CE Ranks Literature Results

CE indexes over 19 million abstracts from PubMed and over 130,000 full-text articles from PubMed Central. Ranking uses:

* An extensive ontology with term relationships, synonyms, and hierarchies
* A customised domain-specific stop word list and analyser that emphasises biomedical ontology terms
* The overall authority of the journal in which the paper was published
* Date of publication

### Tag Cloud Filtering

Below the search bar, a **tag cloud** displays key biomedical terms extracted from the abstracts of the current result set. Tags are listed alphabetically; larger typeface indicates stronger association with your query term.

**To filter using a tag:** Click any tag in the cloud to restrict results to papers mentioning that term.

**To filter by tag type:** Click the filter category buttons (e.g., **Phenotype**, **Tissue**, **Compound**) to control which types of tags appear in the cloud.

**To filter by keyword:** Enter a term in the filter box below the tag cloud and click **Filter**.

**To reset filters:** Click **Clear all** to return to the original, unfiltered results.

{% hint style="info" %}
By default, the tag cloud is constructed from the top 50 results. Select 200 or 1000 from the drop-down on the far right of the filter bar to include more results in the tag cloud construction — this produces a more informative cloud but increases compute time.
{% endhint %}

## Exporting Results

Use the standard **Export** functionality to download the current list of literature results.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/correlation-engine/querying-and-interpreting-results/literature.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.