Our work. In collaboration with the H3Africa Phenotype Harmonisation Working Group, we are working to establish common phenotype-specific data collection toolkits that can be implemented across the African continent (and beyond). These toolkits incorporate both existing and newly developed phenotype standards, to promote harmonised collection of phenotype data for genomic research. The benefits of using these toolkits are multi-fold; (1) The toolkits are all aligned with existing, global data collection standards, (2) the toolkits are specifically adapted for biomedical phenotype data collection in Africa, and (3) the toolkits are highly interoperable, with variables mapped to existing and maintained ontologies.
The toolkits illustrated in Figure 1 below (.xlsx data dictionaries; .xml redcap project templates; .pdf case report forms (CRFs) and .pdf toolkit guidelines) can be found under the corresponding folders.
Figure 1. Toolkits developed by the H3ABioNet Phenotype Standards Project.
The developed sample CRFs can be used on the ground for paper-based data collection from participants, alongside the associated guidelines, whilst the XML templates imported directly into REDCap will set up a new project with the toolkit compiled and ready for use as a database for direct data capture or use in conjunction with the paper CRFs. The data dictionaries provide the necessary metadata for all the data elements/variables and can be imported into REDCap or replicated in your desired electronic data management platform. All the components of a given toolkit are illustrated in Figure 2 below.
Figure 2. Toolkit components and use.
Documentation
Read up on the history and methodology of our project in our full documentation page, here.
Want to work with us? How to get involved. We encourage participation from the community! If you have a bug, suggestion or idea, browse the open issues before opening a new one. Please use the GitHub issue tracker to submit any comments or suggestions. We value the continued maintenance and improvement of the developed packages, and appreciate your feedback.
How to connect with us. Want to ask a question regarding this work? We'd love to hear from you. Please visit our Helpdesk, and log a ticket or query under the Phenotype Standards queue.
Ways to acknowledge use of H3ABioNet toolkits.
- In methods section of publications:
"The data collection toolkits (DOI) used were developed by H3ABioNet/H3Africa and were compiled using a variety of resources described in "standards github link ".
- In acknowledgements section:
"We acknowledge the use of data collection toolkits (DOI) from H3ABioNet/H3Africa which can be found, including associated references, at https://github.com/h3abionet, funded by the H3Africa NIH grant U24HG006941."
Contributors
Big thanks to all our contributors! A full list of contributors can be found in our documentation.