Easy-to-use and secure deep phenotyping
Today we would like to inform you about Phenotero.
The rationale behind Phenotero is that in precision medicine, especially in clinical genetics, the Human Phenotype Ontology (HPO) as well as disease ontologies like the Orphanet Rare Disease Ontology (ORDO) or Medical Subject Headings (MeSH) are often used for ‘deep phenotyping’ of patients and coding of clinical diagnoses. This is especially important because it allows for streamlining of clinic workflow and efficient data entry, and will subsequently promote clinical and molecular diagnosis, remove ambiguousness from manuscripts, and enable sharing of anonymised patient phenotype data with ultimate goal of a better understanding of diseases.
However, the process of assigning ontology classes to patient descriptions is often disconnected from the process of writing patient reports or manuscripts in word processing software such as Microsoft Word or LibreOffice. This additional workload and the requirement to install dedicated software (e.g. PhenoTips) may discourage usage of ontologies for parts of the target audience. Retrospectively applied text-mining suffers from inaccuracies, noise, and privacy constraints.
To improve this situation, we developed Phenotero, a freely available and simple solution to annotate patient phenotypes and diseases at the time of writing clinical reports or manuscripts. We adopt Zotero, a well-established, actively developed citation management software to generate a tool which allows to reference classes from ontologies within clinical reports or manuscripts at the time of writing. In case you are interested in learning more about Phenoteros key features, you can find our manuscript as a preprint at https://doi.org/10.1101/324053 or more information on the website phenotero.github.io .
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