bridge.services.edam package

bridge.services.edam package#

Public Interface#

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

Classes#

EDAMTermByNameIngestor(name, *[, exact, ...])

Resolve an EDAM ontology concept by human-readable name.

EDAM integrations: async metadata ingestor from EMBL-EBI OLS4.

class bridge.services.edam.EDAMTermByNameIngestor(name, *, exact=True, include_obsolete=False)[source]#

Bases: Ingestor

Resolve an EDAM ontology concept by human-readable name.

Parameters:

  • name (str) – Preferred label or synonym, for example "proteomics".

  • exact (bool, default=True) – Ask OLS4 to restrict results to exact text matches.

  • include_obsolete (bool, default=False) – Whether obsolete EDAM concepts may be returned.

async fetch()[source]#

Resolve one unambiguous EDAM concept.

Returns:

Compact OLS4 search result. Common fields include iri, label, short_form, ontology_name, description, and synonym.

Return type:

dict

Raises:

  • EDAMTermNotFoundError – If no usable EDAM concept matches the requested name.

  • httpx.RequestError, httpx.HTTPStatusError – For network or HTTP failures.

ontology = 'edam'#

Submodules#

edam_auth

Helper for constructing EMBL-EBI OLS4 API request headers.

edam_ingestor

Async client for resolving EDAM ontology terms by name through EMBL-EBI OLS4.

Dependencies diagram#

Each architecture diagram below visualizes the internal dependency structure of the bridge.services.edam 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).

bridge package dependencies
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