Phenotero is a simple tool for referencing phenotypes and diseases in written text and allows clinicians and clinical researchers to readily stay within word processing software. This enables a novel workflow for direct in-text annotations of ontology classes, which we call annotate as you write.

Zotero

Phenotero is based on the free, open-source citation software Zotero and thus builds on existing features such as a word-processor plugin, standardised and extendible citation styles, a search functionality, and active community support.

Why Phenotero ?

Phenotero provides a quick and easy solution for referencing ontology-based phenotypes and diseases by direct in-text annotations of classes of ontologies such as the HPO or MONDO. It is an extension of the Zotero citation management open source software, which runs on all common operating systems and is easily integrated into multiple word processors. Users are confronted with a minimal amount of computational complexity and can readily stay within their usual working environment, e.g. Microsoft Word or LibreOffice.

Data & Documentation

Please find links to all data and to the documentation in the upper right corner of this web site.

The Creators

Phenotero has been developed by the Translational Genomics Team and the Phenomics Team in Berlin. Specifically these are Daniela Hombach, Jana Marie Schwarz, Dominik Seelow, Markus Schuelke, Ellen Knierim, and Sebastian Köhler.

Publication

We have uploaded the current manuscript to bioRxiv. Please check it out at https://doi.org/10.1101/324053.

Related projects

If you have a professional informatics infrastructure, you might consider using PhenoTips. For analysing you text retrospectively, you might want to have a look at the NCBO annotator. (Note that for the latter your text is sent through the internet)

Feedback

Contact us at sebastian.koehler@charite.de.