Bugphyzz Integration: Data Import Pipeline

Develop pages for microbial physiologies and for taxa. Physiologies are a property, defined by ontology, associated with a taxon. They could be viewed by users either as:
1. a list of physiologies belonging to a taxon, or
2. a list of taxa having the given physiology

They should be exportable in bulk. Currently, we are handling these as spreadsheets that are imported by the Bioconductor bugphyzz package (https://www.bioconductor.org/packages/bugphyzz/).

Develop a workflow to ingest bugphyzz phenotype-taxon associations and create corresponding BugSigDB signature pages.

Requirements:

• each taxon:physiology link in bugphyzz has evidence codes (ASR, experimental, inferred from genome, etc.), confidence levels for sources, and frequencies (always, usually, sometimes, etc) that should be maintained.
• bugphyzz data editable manually or in bulk
• bulk exports for bugphyzz data, probably an addition to current Studies/Experiments/Signatures exports

Questions:

• Does this actually belong in bugsigdb? In some ways it would be nice because these pages could enrich Taxon pages and add Physiology pages, but if it's not a natural fit for SMW, we can continue to handle them elsewhere.

Start by reviewing the bugphyzz phenotype-taxon associations and the existing Studies/Experiments/Signatures export workflow. Clarify whether BugSigDB should own Taxon and Physiology pages, then define how evidence codes, source confidence, frequencies, manual or bulk editing, and bulk export will be represented; done means the workflow and ownership questions are resolved before implementation.