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Bioinformatics Tools: Text Mining

This guide contains a curated set of resources and tools that will help you with your research data analysis. It also includes those medical library workshops available at Yale University on many of these bioinformatics tools.


Welcome to the Bioinformatics Tools Subject Guide. In this guide you'll find:

  • resources for gene prediction and annotation
  • resources for gene regulation
  • resources for plants
  • resources for variation
  • resources for animals
  • links to key journals


Visualization and Statistics Tools for Mining the Biomedical Literature

PubNet (Publication Network Graph Utility) is a web-based tool that extracts several types of relationships returned by PubMed queries and maps them on to networks, allowing for graphical visualization, textual navigation, and topological analysis.

Semantic Medline is a web application that uses natural language processing to exract semantic predications from a PubMed search. Resutls are presented as an interrelated network of concepts.

 Quertle retrieves information within the biomedical literature by using its own semantic database of 300 million relationships.

NextBio (Literature) Uses a tag cloud approach to help discovering the most important concepts resulting from a query.

Coremine presents search results as a graphic network that describes relationships discovered through text-mining. Relationship networks provide an overview of a topic by clustering important terms. The network is also a navigational tool that can help searchers explore concepts related to their search term.

Chilibot searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords presenting the results as networked relationships.

Purchase Request

To submit a collections purchase request to the library click here: Purchase Request. A library selector will be in touch with you.

Biomedical Sciences Research Support Librarian

Director for Research Support & Outreach Programs

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Jeremy Garritano
Marx Science and Social Science Library
Office C33
219 Prospect Street
Concourse Level
Kline Biology Tower
Subjects: Global Affairs