biom-format
Biological Observation Matrix (BIOM) format
Decision gist · record as of 2026-08-14
Yes, if you work with microbiome or metagenomic data in BIOM format. The package is stable, permissively licensed, and widely compatible across platforms and Python versions. However, maintenance is aging (last release 353 days ago), so verify that it meets your specific pipeline requirements before committing to it for production workflows. No known security vulnerabilities.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires h5py, which depends on HDF5 system libraries; installation may require a C compiler or prebuilt wheels for your platform.
- Medium install friction due to compiled dependencies (numpy, scipy, h5py).
- Wheels available for Python 3.9–3.13 on macOS, Linux, and Windows.
License · maintenance · safety
BSD (permissive) — BSD license is permissive; you may use, modify, and distribute this package freely in commercial and private projects with minimal restrictions.
last release 2025-08-26 (353 days)
0 known vulnerabilities (OSV.dev, 2026-08-14) · 134,204 downloads/mo, #11,483 on PyPI
Alternatives
Verify before relying
pip install biom-format
import biom
table = biom.load_table('data.biom')
print(table.shape)- Whether the package actively maintains compatibility with major microbiome analysis pipelines.
- Performance characteristics for large matrices.
- Availability of comprehensive documentation beyond the homepage.
What it is and what it does
biom-format is a Python library for working with the BIOM (Biological Observation Matrix) file format, a standard in microbiome and metagenomic research for storing abundance data—counts of observations such as OTUs, KO categories, or lipid types across multiple biological samples. It provides read/write access to BIOM files, typically in HDF5 format, and allows you to load, manipulate, and export these matrices for downstream analysis.
The package depends on numpy, scipy, pandas, h5py, and click, making it suitable for integration into data pipelines. It supports Python 3.9 through 3.13 on major platforms. The library is designed to be a general-purpose container for observation counts from various high-throughput biological assays.
Use it for
- Load and parse BIOM files from microbiome pipelines for downstream statistical analysis.
- Convert between BIOM and tabular formats for integration with other analysis tools.
- Manipulate sample metadata and observation taxonomy within a BIOM matrix programmatically.
- Export abundance tables from your own analysis pipeline in the standard BIOM format.
- Batch process multiple BIOM files to extract subsets of samples or observations.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes, if you work with microbiome or metagenomic data in BIOM format.
The package is stable, permissively licensed, and widely compatible across platforms and Python versions. However, maintenance is aging (last release 353 days ago), so verify that it meets your specific pipeline requirements before committing to it for production workflows. No known security vulnerabilities.
Install
biom-format on PyPI
Before you install
Medium install friction due to compiled dependencies (numpy, scipy, h5py). Wheels available for Python 3.9–3.13 on macOS, Linux, and Windows. Last release 353 days ago; maintenance status is aging, so expect slower response to issues.
Requires h5py, which depends on HDF5 system libraries; installation may require a C compiler or prebuilt wheels for your platform.
License in practice
BSD license is permissive; you may use, modify, and distribute this package freely in commercial and private projects with minimal restrictions.
Quickstart
pip install biom-format
import biom
table = biom.load_table('data.biom')
print(table.shape)Verify before relying
- Whether the package actively maintains compatibility with major microbiome analysis pipelines.
- Performance characteristics for large matrices.
- Availability of comprehensive documentation beyond the homepage.
Package facts
| License | BSD permissive |
| Python support | Supports the current Python release >=3.9 |
| Install friction | Medium. Platform-specific wheel |
| Runtime dependencies | 5 packagesclicknumpyscipypandash5py |
| Maintenance | Aging 353 days since the last release |
| First released | |
| Downloads | 134,204 / month, #11,483 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaLicense :: OSI Approved :: BSD LicenseOperating System :: MacOS :: MacOS XOperating System :: Microsoft :: WindowsOperating System :: OS IndependentOperating System :: POSIX :: LinuxProgramming Language :: PythonProgramming Language :: Python :: 3Programming Language :: Python :: 3 :: OnlyProgramming Language :: Python :: 3.10Programming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: 3.9Programming Language :: Python :: Implementation :: CPythonTopic :: Scientific/Engineering :: Bio-InformaticsTopic :: Software Development :: Libraries :: Application FrameworksTopic :: Software Development :: Libraries :: Python Modules |
Evidence: biom_format-2.1.17-cp310-cp310-macosx_10_9_x86_64.whl; biom_format-2.1.17-cp310-cp310-macosx_11_0_arm64.whl; biom_format-2.1.17-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp310-cp310-win_amd64.whl; biom_format-2.1.17-cp311-cp311-macosx_10_9_x86_64.whl; biom_format-2.1.17-cp311-cp311-macosx_11_0_arm64.whl; biom_format-2.1.17-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp311-cp311-win_amd64.whl; biom_format-2.1.17-cp312-cp312-macosx_10_13_x86_64.whl; biom_format-2.1.17-cp312-cp312-macosx_11_0_arm64.whl; biom_format-2.1.17-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp312-cp312-win_amd64.whl; biom_format-2.1.17-cp313-cp313-macosx_10_13_x86_64.whl; biom_format-2.1.17-cp313-cp313-macosx_11_0_arm64.whl; biom_format-2.1.17-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl; biom_format-2.1.17-cp313-cp313-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl; biom_format-2.1.17-cp313-cp313-win_amd64.whl
Tags
Let your AI agent find packages like this
Example. Real query, live index.
You found this page by searching. An agent finds it by wishing: SkillFed indexes 14,416 PyPI packages by what they can do, searchable in plain language.
wish › “biom format reader writer”
- biom-formatReads, writes, and manipulates Biological Observation Matrix (BIOM)…
- libconfReads and writes configuration files in libconfig format, a format…
- linear-tsvParses and writes tabular data in Linear TSV format, a line-oriented…
Give your agent the search over MCP, or paste the wish link into any chat.
More Python Modules packages
Converts domain names between Unicode and ASCII-compatible encoding (Punycode) according to IDNA 2008 and Unicode Technical Standard 46, with security validation and broader script coverage than the standard library.
Install it if you work with internationalized domain names, need to validate domains, or use HTTP clients that depend on it transitively.
Setuptools is a Python build backend and package management tool that handles building, distributing, and installing Python packages, including support for C/C++ extension modules.
PyYAML parses and emits YAML 1.1 data format, enabling serialization and deserialization of configuration files and Python objects to and from human-readable YAML text.
Pydantic validates Python data structures against type hints, coercing and checking input at runtime to ensure it matches a declared schema.
Provides reusable metadata objects for use with PEP-593 `typing.Annotated` to express common constraints like bounds, collection sizes, and predicates on types.
Install it if you use or build libraries that need to express type constraints in a standardized, inspectable way—or if you want to annotate your own types with…
Provides runtime tools to inspect and introspect Python type annotations, enabling programmatic examination of type hints at execution time.
See also scikit-bio · bionty · biotite · deepbiop · biocommons.seqrepo · peppy · bio · python-libsbml · bioversions · mudata