Supporting data for "Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects"

Organizing and annotating biological sample data is critical in data-intensive bioinformatics. Unfortunately, metadata formats from a data provider are often incompatible with requirements of a processing tool. There is no broadly accepted standard to organize metadata across biological projects and bioinformatics tools, restricting the portability and reusability of both annotated datasets and analysis software.<br>To address this, we present Portable Encapsulated Projects (PEP), a formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. In addition to standardization, the PEP specification provides descriptors and modifiers for project-level and sample-level metadata, which improve portability across both computing environments and data processing tools. PEP includes a schema validator framework, allowing formal definition of required metadata attributes for data analysis broadly. We have implemented packages for reading PEPs in both Python and R to provide a language-agnostic interface for organizing project metadata. PEP therefore presents an important step toward unifying data annotation and processing tools in data-intensive biological research projects. The formal PEP specification and links to associated tools and documentation are available at pep.databio.org.