ArticleGigaScience2021
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Mevalonate pathway activation in Ewing sarcoma reveals a 3D-specific synergy between statins and BCL-xL inhibition.Molecular therapy. Oncology · 2026Article
- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.bioRxiv : the preprint server for biology · 2026Article
- The FAIRSCAPE AI-readiness Framework for Biomedical Research.bioRxiv : the preprint server for biology · 2026Article
- Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.Bioinformatics advances · 2025Article
- Expanding the genome information on Bacillales for biosynthetic gene cluster discovery.Scientific data · 2024Article
- BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.Nucleic acids research · 2024Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.bioRxiv : the preprint server for biology · 2024Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.GigaScience · 2024Article
- Buffering of transcription rate by mRNA half-life is a conserved feature of Rett syndrome models.Nature communications · 2023Article
- Transcriptional buffering and 3'UTR lengthening are shaped during human neurodevelopment by shifts in mRNA stability and microRNA load.bioRxiv : the preprint server for biology · 2023Article
- GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA.Bioinformatics (Oxford, England) · 2023Article
- Challenges to sharing sample metadata in computational genomics.Frontiers in genetics · 2023Article
- SODAR: managing multiomics study data and metadata.GigaScience · 2022Article
- Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.GigaScience · 2021Article
- PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.NAR genomics and bioinformatics · 2021Article
- Bedshift: perturbation of genomic interval sets.Genome biology · 2021Article
- PEPPRO: quality control and processing of nascent RNA profiling data.Genome biology · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundOrganizing 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.
resultsTo address this, we present the Portable Encapsulated Project (PEP) specification, 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. PEPs include 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.
conclusionsThe PEP specification is an important step toward unifying data annotation and processing tools in data-intensive biological research projects. Links to tools and documentation are available at http://pep.databio.org/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.