Linking Big Biomedical Datasets to Modular Analysis with Portable Encapsulated Projects

Overview

Journal Gigascience

Publisher Oxford University Press

Specialties Biology
Genetics

Date 2021 Dec 10

PMID 34890448

Citations 14

Authors

Nathan C Sheffield

Michal Stolarczyk

Vincent P Reuter

Andre F Rendeiro

Affiliations

Soon will be listed here.

Abstract

Background: 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.

Results: To 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.

Conclusions: The 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/.

Citing Articles

FAIRSCAPE: An Evolving AI-readiness Framework for Biomedical Research.

Al Manir S, Levinson M, Niestroy J, Churas C, Parker J, Clark T bioRxiv. 2025; .

PMID: 39763764 PMC: 11703166. DOI: 10.1101/2024.12.23.629818.

Expanding the genome information on Bacillales for biosynthetic gene cluster discovery.

Song L, Nielsen L, Xu X, Mohite O, Nuhamunada M, Xu Z Sci Data. 2024; 11(1):1267.

PMID: 39572589 PMC: 11582795. DOI: 10.1038/s41597-024-04118-x.

Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights.

Kananen K, Veseli I, Quiles Perez C, Miller S, Eren A, Bradley P bioRxiv. 2024; .

PMID: 39005339 PMC: 11245035. DOI: 10.1101/2024.07.03.601779.

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.

LeRoy N, Khoroshevskyi O, OBrien A, Stepien R, Arslan A, Sheffield N Gigascience. 2024; 13.

PMID: 38991851 PMC: 11238423. DOI: 10.1093/gigascience/giae033.

BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.

Nuhamunada M, Mohite O, Phaneuf P, Palsson B, Weber T Nucleic Acids Res. 2024; 52(10):5478-5495.

PMID: 38686794 PMC: 11162802. DOI: 10.1093/nar/gkae314.

References

Volchenboum S, Cox S, Heath A, Resnick A, Cohn S, Grossman R . Data Commons to Support Pediatric Cancer Research. Am Soc Clin Oncol Educ Book. 2017; 37:746-752. DOI: 10.1200/EDBK_175029. View

Smith J, Dutta A, Sathyan K, Guertin M, Sheffield N . PEPPRO: quality control and processing of nascent RNA profiling data. Genome Biol. 2021; 22(1):155. PMC: 8126160. DOI: 10.1186/s13059-021-02349-4. View

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L . The EBI RDF platform: linked open data for the life sciences. Bioinformatics. 2014; 30(9):1338-9. PMC: 3998127. DOI: 10.1093/bioinformatics/btt765. View

Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, cech M . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016; 44(W1):W3-W10. PMC: 4987906. DOI: 10.1093/nar/gkw343. View

Kurtzer G, Sochat V, Bauer M . Singularity: Scientific containers for mobility of compute. PLoS One. 2017; 12(5):e0177459. PMC: 5426675. DOI: 10.1371/journal.pone.0177459. View

Stolarczyk M, Reuter V, Smith J, Magee N, Sheffield N . Refgenie: a reference genome resource manager. Gigascience. 2020; 9(2). PMC: 6988606. DOI: 10.1093/gigascience/giz149. View

Leinonen R, Sugawara H, Shumway M . The sequence read archive. Nucleic Acids Res. 2010; 39(Database issue):D19-21. PMC: 3013647. DOI: 10.1093/nar/gkq1019. View

Hoehndorf R, Slater L, Schofield P, Gkoutos G . Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics. 2015; 16:26. PMC: 4384359. DOI: 10.1186/s12859-015-0456-9. View

Gu A, Cho H, Sheffield N . Bedshift: perturbation of genomic interval sets. Genome Biol. 2021; 22(1):238. PMC: 8379854. DOI: 10.1186/s13059-021-02440-w. View

10.

Corces M, Granja J, Shams S, Louie B, Seoane J, Zhou W . The chromatin accessibility landscape of primary human cancers. Science. 2018; 362(6413). PMC: 6408149. DOI: 10.1126/science.aav1898. View

11.

Smith J, Corces M, Xu J, Reuter V, Chang H, Sheffield N . PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments. NAR Genom Bioinform. 2021; 3(4):lqab101. PMC: 8632735. DOI: 10.1093/nargab/lqab101. View

12.

Fenstermacher D, Street C, McSherry T, Nayak V, Overby C, Feldman M . The Cancer Biomedical Informatics Grid (caBIG). Conf Proc IEEE Eng Med Biol Soc. 2007; 2006:743-6. DOI: 10.1109/IEMBS.2005.1616521. View

13.

Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K . ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010; 26(18):2354-6. PMC: 2935443. DOI: 10.1093/bioinformatics/btq415. View

14.

Sheffield N, Stolarczyk M, Reuter V, Rendeiro A . Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. Gigascience. 2021; 10(12). PMC: 8673555. DOI: 10.1093/gigascience/giab077. View

15.

Datlinger P, Rendeiro A, Schmidl C, Krausgruber T, Traxler P, Klughammer J . Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 2017; 14(3):297-301. PMC: 5334791. DOI: 10.1038/nmeth.4177. View

16.

Zhou Y, Sun Y, Huang D, Li M . epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. Front Genet. 2020; 11:53. PMC: 7029718. DOI: 10.3389/fgene.2020.00053. View

17.

Krumholz H, Waldstreicher J . The Yale Open Data Access (YODA) Project--A Mechanism for Data Sharing. N Engl J Med. 2016; 375(5):403-5. DOI: 10.1056/NEJMp1607342. View

18.

Sheffield N, Pierron G, Klughammer J, Datlinger P, Schonegger A, Schuster M . DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma. Nat Med. 2017; 23(3):386-395. PMC: 5951283. DOI: 10.1038/nm.4273. View

19.

Stolarczyk M, Xue B, Sheffield N . Identity and compatibility of reference genome resources. NAR Genom Bioinform. 2021; 3(2):lqab036. PMC: 8121092. DOI: 10.1093/nargab/lqab036. View

20.

Wilkinson M, Dumontier M, Aalbersberg I, Appleton G, Axton M, Baak A . The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016; 3:160018. PMC: 4792175. DOI: 10.1038/sdata.2016.18. View