BIOM

Biom most commonly refers to the BIOM (Biological Observation Matrix) data format used in microbiome research. BIOM is an open standard for representing biological observation data—such as counts of microbial taxa—across samples, together with associated metadata. The format is designed to enable efficient data exchange and interoperability between analysis tools and workflows.

Origin and use of BIOM dates to the early 2010s, when the microbiome community sought a common container for observation tables. It has been adopted by major microbiome analysis ecosystems and software libraries, and is widely used by pipelines and databases that handle large–scale sequencing data. Tools for reading and writing BIOM files are maintained in common bioinformatics ecosystems, facilitating data sharing between researchers and projects.

Structure and contents: A BIOM file encodes a matrix of observations (for example, taxa or genes) by samples, accompanied by observation metadata (such as taxonomic names or feature identifiers) and sample metadata (such as experimental condition, body site, or treatment). The matrix can be stored in a binary, compact form such as HDF5 for performance, with JSON-based representations also available for readability. The format supports metadata schemas and extensions to accommodate diverse study designs, enabling researchers to preserve rich contextual information alongside counts.

Impact and context: By providing a standardized container for abundance data, feature metadata, and sample metadata, BIOM facilitates data sharing, reproducibility, and interoperability across microbiome analysis pipelines, databases, and projects. It is one of the foundational formats in modern microbiome data management and analysis.

See also: Biome, Microbiome, QIIME, BIOM format.