Phenotero: Annotate as you write. Hombach, D., Schwarz, J. M., Knierim, E., Schuelke, M., Seelow, D., & Köhler, S. Clinical Genetics, 95(2):287–292, 2019. tex.ids: 2018_hombach![Phenotero: Annotate as you write [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex In clinical genetics, the Human Phenotype Ontology as well as disease ontologies are often used for deep phenotyping of patients and coding of clinical diagnoses. However, assigning ontology classes to patient descriptions is often disconnected from writing patient reports or manuscripts in word processing software. This additional workload and the requirement to install dedicated software may discourage usage of ontologies for parts of the target audience. Here we present 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 citation management software to create a tool which allows to reference classes from ontologies within text at the time of writing. We expect this approach to decrease the additional workload to a minimum while ensuring high quality associations with ontology classes. Standardized collection of phenotypic information at the time of describing the patient allows for streamlining the clinic workflow and efficient data entry. It will subsequently promote clinical and molecular diagnosis with the ultimate goal of better understanding genetic diseases. Thus, we believe that Phenotero eases the usage of ontologies and controlled vocabularies in the field of clinical genetics.
@article{hombach_phenotero_2019,
title = {Phenotero: {Annotate} as you write},
volume = {95},
copyright = {© 2018 The Authors. Clinical Genetics published by John Wiley \& Sons A/S. Published by John Wiley \& Sons Ltd.},
issn = {1399-0004},
shorttitle = {Phenotero},
url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/cge.13471},
doi = {10.1111/cge.13471},
abstract = {In clinical genetics, the Human Phenotype Ontology as well as disease ontologies are often used for deep phenotyping of patients and coding of clinical diagnoses. However, assigning ontology classes to patient descriptions is often disconnected from writing patient reports or manuscripts in word processing software. This additional workload and the requirement to install dedicated software may discourage usage of ontologies for parts of the target audience. Here we present 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 citation management software to create a tool which allows to reference classes from ontologies within text at the time of writing. We expect this approach to decrease the additional workload to a minimum while ensuring high quality associations with ontology classes. Standardized collection of phenotypic information at the time of describing the patient allows for streamlining the clinic workflow and efficient data entry. It will subsequently promote clinical and molecular diagnosis with the ultimate goal of better understanding genetic diseases. Thus, we believe that Phenotero eases the usage of ontologies and controlled vocabularies in the field of clinical genetics.},
language = {en},
number = {2},
urldate = {2020-01-28},
journal = {Clinical Genetics},
author = {Hombach, Daniela and Schwarz, Jana M. and Knierim, Ellen and Schuelke, Markus and Seelow, Dominik and Köhler, Sebastian},
year = {2019},
doi = {10.1101/324053},
note = {tex.ids: 2018\_hombach},
keywords = {zfrancophone\_bulletin\_veille},
pages = {287--292},
}
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