Sebastian Lobentanzer

BioCypher `pipeline`

3

Implement a high-level interface to coordinate multiple adapters and their contents for application purposes. Workflow: - `pipeline.start()` - `pipeline.add_adapter()` - `pipeline.find_identifiers()`: identify the identifier systems (namespaces, Bioregistry) that are represented...

Move from tuples to BioCypher classes in the adapter input fields

4

Providing an input class with ID, type, properties fields is more transparent than using tuples that are not self-explanatory. This class would be used in the adapter to pass data...

E.g. https://github.com/biocypher/collectri

Including its own repository in the biocypher org

Uses: #117 #262

Adapter for the REST endpoint of clinicaltrials.gov

A pipeline for the genetics workflow in the Hautaniemi lab to facilitate molecular tumour board drug recommendations. Integrates data from point mutations, CNVs, signatures, etc. Uses: #117 #244 #245