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Related Experiment Video

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Writing and Low-Temperature Characterization of Oxide Nanostructures

Writing and Low-Temperature Characterization of Oxide Nanostructures

Published on: July 18, 2014

Phenotero: Annotate as you write.

Daniela Hombach^1,2, Jana M Schwarz¹, Ellen Knierim¹

¹NeuroCure Clinical Research Center, Charité Universitätsmedizin, Berlin, Germany.

Clinical Genetics

|November 13, 2018

Summary

Phenotero simplifies annotating patient phenotypes and diseases using ontologies during clinical report writing. This tool integrates with word processing, reducing workload and improving data quality for genetic research.

Keywords:

clinical text controlled vocabularies deep phenotyping human phenotype ontology ontology

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Area of Science:

Clinical Genetics
Bioinformatics
Medical Informatics

Background:

Ontologies like the Human Phenotype Ontology are crucial for deep phenotyping and clinical diagnosis coding.
Current methods for assigning ontology classes to patient data are often separate from clinical documentation, increasing workload.
This disconnect discourages ontology use among clinicians and researchers.

Purpose of the Study:

To introduce Phenotero, a novel, freely available tool designed to annotate patient phenotypes and diseases within clinical reports and manuscripts.
To streamline the process of associating patient descriptions with ontology classes at the point of writing.
To reduce the additional workload associated with ontology annotation and enhance data quality.

Main Methods:

Phenotero leverages Zotero, a citation management software, as its foundation.
The tool enables users to reference ontology classes directly within their text while writing.
It integrates ontology annotation seamlessly into the word processing workflow.

Main Results:

Phenotero minimizes the extra effort required for ontology annotation.
It ensures high-quality associations between patient descriptions and ontology classes.
The tool facilitates standardized collection of phenotypic information, improving clinic workflow and data entry.

Conclusions:

Phenotero significantly eases the adoption and use of ontologies and controlled vocabularies in clinical genetics.
By integrating annotation into the writing process, it promotes efficient data collection for clinical and molecular diagnosis.
This approach ultimately aids in a better understanding of genetic diseases.