Towards self-describing and FAIR bulk formats for biomedical data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36913405.
- Also identified by DOI 10.1371/journal.pcbi.1010944 and PMC identifier 10035862.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
We introduce a self-describing serialized format for bulk biomedical data called the Portable Format for Biomedical (PFB) data. The Portable Format for Biomedical data is based upon Avro and encapsulates a data model, a data dictionary, the data itself, and pointers to third party controlled vocabularies. In general, each data element in the data dictionary is associated with a third party controlled vocabulary to make it easier for applications to harmonize two or more PFB files. We also introduce an open source software development kit (SDK) called PyPFB for creating, exploring and modifying PFB files. We describe experimental studies showing the performance improvements when importing and exporting bulk biomedical data in the PFB format versus using JSON and SQL formats.
Medical subject headings
- Software
- Vocabulary, Controlled