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TALISMAN

Introduction

TALISMAN is a Python package for summarizing gene set functions using large language models (LLMs).

It uses the OntoGPT package to interface with LLMs.

For more details, please see the full documentation.

Quick Start

TBD

Functionality

The goal of gene summary enrichment is to assemble a textual summary of the functions of a set of genes and their products.

TALISMAN can run in three different ways:

1. Map gene symbols to IDs using the resolver (unless IDs are specified)
2. Fetch gene descriptions using Alliance API
3. Create a prompt using descriptions

Options:

• -r, --resolver TEXT - OAK selector for the gene ID resolver, e.g., sqlite:obo:hgnc for HGNC gene IDs.
• -C, --context TEXT - domain, e.g., anatomy, industry, health-related
• --strict / --no-strict - If set, there must be a unique mappings from labels to IDs. Defaults to True.
• -U, --input-file TEXT - Path to a file with gene IDs to enrich if not passed as arguments.
• --randomize-gene-descriptions-using-file TEXT - For evaluation only. Path to a file containing gene identifiers and descriptions; if this option is used, TALISMAN will swap out gene descriptions with those from this gene set file.
• --ontological-synopsis / --no-ontological-synopsis - If set, use automated rather than manual gene descriptions. Defaults to True.
• --combined-synopsis / --no-combined-synopsis - If set, combine gene descriptions. Defaults to False.
• --end-marker TEXT - Specify a character or string to end prompts with. For testing minor variants of prompts.
• --annotations / --no-annotations - If set, include annotations in the prompt. Defaults to True.
• --prompt-template TEXT - Path to a file containing the prompt.
• --interactive / --no-interactive - Interactive mode - rather than call the API, the function will present a walkthrough process. Defaults to False.

Example:

ontogpt enrichment -r sqlite:obo:hgnc -U tests/input/genesets/EDS.yaml

In this case, the prompt will include gene summaries retrieved from the database.

The response text will include, among other fields, a summary like this:

Summary: The common function among these genes is their involvement in the regulation and organization of the extracellular matrix, particularly collagen fibril organization and biosynthesis.

Citation

The gene summarization approach used in TALISMAN is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: http://arxiv.org/abs/2305.13338

Acknowledgements

This project is part of the Monarch Initiative.