Welcome to the
bycon project documentation¶
Bycon - a Python-based environment for the Beacon v2 genomics API¶
bycon project - at least at its current stage - is a mix of Progenetix (i.e. GA4GH object model derived, MongoDB implemented) - data management, and the implementation of middleware & server for the Beacon API.
bycon code is maintained in the
progenetix/bycon repository. Utility scripts & functions reside in the
byconaut and (this one is really "scripty")
byconeer repositories but are so far not (well) documented & may contain deprecated or "internal use" code.
More information about the original use Progenetix case can be found on the project's documentation site.
bycon Directory Structure¶
- web applications for data access
- Python modules for Beacon query and response functions in
- top-level, general configurations
services... specific configuration files for the individual endpoints
- these specify e.g. which configurations are loaded or response content
- YAML ...
- documentation, in Markdown, as source for documentation builded with
- Python libraries
- various resources beyond configuration data
- mapping input table(s)
- external schema dumps
bycon | |- bycon | | | |- beaconServer | | | | | |- beacon.py | | |- datasets.py | | |- configuration.py | | |- entryTypes.py | | |- filteringTerms.py | | `- ... .py | | | |- config | | | | | |- beacon_mappings.yaml | | |- config.yaml | | |- dataset_definitions.yaml | | |- filter_definitions.yaml | | `- ..._definitions.yaml | | | |- lib | | | | | |- cgi_parsing.py | | |- read_specs.py | | |- filter_parsing.py | | |- query_generation.py | | |- query_execution.py | | `- ... | | | |- rsrc | | `- ... | | | `- schemas | `- ... | |- docs | `- ... documentation website source files ... | |- local | | | |- beacon_defaults.yaml | |- dataset_definitions.yaml | `- local_paths.yaml | |- install.py |- install.yaml `- `requirements.txt` and other Python packaging files ...
The bycon environment - together with the Progenetix
resource - provide a growing numer of data services in (cancer) genomics and
disease ontologies. Since
bycon 1.0.55 (2023-06-22)
/services resides in the