The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
| Autor: | Susan M. Huse, Rob Knight, Jose C. Clemente, Jesse Stombaugh, Justin Kuczynski, John Hufnagle, Folker Meyer, J. Gregory Caporaso, Daniel McDonald, Doug Wendel, Jai Ram Rideout, Andreas Wilke |
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| Rok vydání: | 2012 |
| Předmět: |
Computer science
Interoperability Health Informatics lcsh:Computer applications to medicine. Medical informatics Bottleneck Microbial ecology Software VAMPS Technical Note Implementation BIOM computer.programming_language MG-RAST business.industry Comparative genomics QIIME Python (programming language) File format JSON Data science Computer Science Applications Metadata lcsh:R858-859.7 Metagenomics business computer |
| Zdroj: | GigaScience GigaScience, vol 1, iss 1 McDonald, D; Clemente, JC; Kuczynski, J; Rideout, JR; Stombaugh, J; Wendel, D; et al.(2012). The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. GigaScience, 464(1). doi: 10.1186/2047-217X-1-7. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/565380jb GigaScience, Vol 1, Iss 1, p 7 (2012) |
| ISSN: | 2047-217X |
| Popis: | Background: We present the Biological Observation Matrix (BIOM, pronounced " biome" ) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the " ome-ome" ) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses.Findings: The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages.Conclusions: The BIOM file format and the biom-format project are steps toward reducing the " bioinformatics bottleneck" that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium. © 2012 2012 McDonald et al.; licensee BioMed Central Ltd. |
| Databáze: | OpenAIRE |
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