Bioregistry

Common errors

• AttributeError: 'NoneType' object has no attribute 'name' (or similar for other attributes)

  cause Attempting to access attributes (e.g., `name`, `homepage`) on a `None` object returned by `bioregistry.get_resource()` or `bioregistry.normalize_prefix()`, indicating that the requested prefix is not recognized or found in the Bioregistry.
  fix Always check if the result of `br.get_resource()` or `br.normalize_prefix()` is `None` before attempting to access its attributes. Example: `entry = br.get_resource('unknown_prefix'); if entry: print(entry.name)`.

• Failed to resolve CURIE 'prefix:invalid_id' / No URI found for 'prefix:invalid_id'

  cause The provided identifier part of the CURIE ('invalid_id') does not conform to the expected regular expression pattern defined for the 'prefix' in the Bioregistry, or there are no configured providers to generate a URI for that prefix.
  fix Verify the identifier's format against the expected pattern, which can sometimes be found in the resource's metadata via `br.get_resource(prefix).pattern`. Ensure the prefix itself is valid and has registered providers for resolution.

Warnings

• breaking Changes in Bioregistry's internal canonicalization for certain non-biological prefixes (e.g., 'rdf') can lead to unexpected case changes (e.g., 'RDF' instead of 'rdf') in merged prefix maps, affecting downstream tools that consume Bioregistry's output and assume lowercase canonicalization for such prefixes.
  Fix: Review and adapt any pipelines that rely on Bioregistry's output for case-sensitive prefix handling, especially for non-biological or common data prefixes. Consider explicit case normalization in consuming applications if strict lowercase is required.
• gotcha The Bioregistry does not fully cover or align with all external registries due to varying quality standards, lack of metadata, or resources being decommissioned. This means some prefixes from external sources may not be present or have complete metadata.
  Fix: Always check for prefix existence and metadata completeness using `br.get_resource()` or `br.normalize_prefix()`. If a prefix is missing, consider contributing it or consulting the original external registry directly.
• gotcha CURIEs can fail to resolve or validate for three main reasons: the prefix is not registered, the identifier does not match the validation pattern, or no providers are available for that prefix. The `resolve()` and `expand_curie()` functions will return `None` or raise an error in these cases.
  Fix: Before resolving, use `br.get_resource(prefix)` to check if a prefix is registered and has associated metadata, including a `pattern` for validation and `providers` for resolution. Validate identifiers using `br.validate_identifier()` if necessary.
• gotcha Some ontology identifiers embed redundant prefixes (e.g., `GO:GO:0006915`). Bioregistry handles these cases, but this can be a source of confusion as different registries might manage these 'banana-style' identifiers differently.
  Fix: Be aware of potential redundant prefixes in identifiers, especially when working with OBO Foundry or Gene Ontology resources. The Bioregistry's `normalize_prefix()` and `parse_curie()` functions are designed to handle these variations consistently.

Install

• pip install bioregistry Install from PyPI

Imports

• bioregistry

  import bioregistry

  Commonly imported directly or aliased as 'br'
• br

  import bioregistry as br

  Standard community alias for convenience

Quickstart

This quickstart demonstrates how to fetch metadata for a given resource, normalize various forms of a prefix to its canonical Bioregistry form, and resolve/expand a Compact URI (CURIE) into a full URI.

import bioregistry as br

# Get metadata for a resource
taxonomy_entry = br.get_resource('taxonomy')
print(f"Taxonomy Name: {taxonomy_entry.name}")
print(f"Taxonomy Homepage: {taxonomy_entry.homepage}")

# Normalize a prefix
normalized_ec = br.normalize_prefix('ec-code')
print(f"'ec-code' normalized to: {normalized_ec}")

normalized_pubchem = br.normalize_prefix('pubchem')
print(f"'pubchem' normalized to: {normalized_pubchem}")

# Resolve a CURIE to a URI
curie = 'chebi:138488'
uri = br.resolve(curie)
print(f"Resolved {curie} to: {uri}")

# Expand a CURIE to a URI
expanded_uri = br.expand_curie(curie)
print(f"Expanded {curie} to: {expanded_uri}")