bridge.builders package

Public Interface

This section documents user-facing interface of the bridge.builders package (as defined in its __init__.py file).

Functions

compose_github_repo(**kwargs)
compose_biotools_metadata(**kwargs)
compose_europe_pmc_metadata([pmid, pmcid, doi])	Fetch and transform Europe PMC entry into a Publication model.
compose_spdx_license_metadata(spdx_id)	Fetch and transform SPDX license entry into a SPDXLicense model.
compose_edam_term_metadata(term_name)	Fetch and transform EDAM term data into an EDAMTerm model.

Builders assemble core models from raw ingested data.

async bridge.builders.compose_biotools_metadata(**kwargs)

async bridge.builders.compose_edam_term_metadata(term_name)

Fetch and transform EDAM term data into an EDAMTerm model.

Parameters:

term_name (str) – The name of the EDAM term to fetch and transform.

Returns:

An EDAMTerm model representing the metadata of the specified EDAM term.

Return type:

EDAMTerm

Raises:

Exception – If there is an error during ingestion or transformation.

async bridge.builders.compose_europe_pmc_metadata(pmid=None, pmcid=None, doi=None)

Fetch and transform Europe PMC entry into a Publication model.

Parameters:

• pmid (str, optional) – PubMed identifier (e.g., “36173614”).

• pmcid (str, optional) – PubMed Central identifier (e.g., “PMC9903320”).

• doi (str, optional) – Digital Object Identifier (e.g., “10.1021/acs.jproteome.2c00457”).

Returns:

A Publication model representing the Europe PMC metadata.

Return type:

Publication

Raises:

Exception – If there is an error during ingestion or transformation.

async bridge.builders.compose_github_repo(**kwargs)

async bridge.builders.compose_spdx_license_metadata(spdx_id)

Fetch and transform SPDX license entry into a SPDXLicense model.

Parameters:

spdx_id (str) – SPDX license identifier (e.g. “MIT”, “GPL-3.0-only”).

Returns:

A SPDXLicense model representing the SPDX license metadata.

Return type:

SPDXLicense

Raises:

Exception – If there is an error during ingestion or transformation.

Subpackages

biotools	Composition utilities for bio.tools: fetch raw tool JSON and transform it into a validated BiotoolsToolModel.
edam	Composition utilities for EMBL-EBI OLS4: fetch raw term JSON and transform it into a validated EDAM term model.
europe_pmc	Composition utilities for Europe PMC: fetch raw publication JSON and transform it into a validated Publication model.
github	Composition utilities for GitHub: fetch repository data and transform it into a GitHubRepoModel.
protocols	Protocol definitions for builder components.
spdx	Composition utilities for SPDX: fetch raw license JSON and transform it into a validated SPDXLicense model.

Dependencies diagram

Each architecture diagram below visualizes the internal dependency structure of the bridge.builders package. It shows how modules and subpackages within the package depend on each other, based on direct Python imports.

• Packages are shown as purple rectangles

• Modules are shown as pink rectangles

• Arrows (A → B) indicate that A directly imports B

Each subpackage’s diagram focuses only on its own internal structure, it does not include imports to or from higher-level packages (those appear in the parent package’s diagram).