recipe bionym

Resolve bioinformatics identifiers into confidence-scored knowledge graphs

Homepage:

d-callan/bionym

Documentation:

d-callan/bionym

License:

MIT / MIT

Recipe:

/bionym/meta.yaml

BioNym gathers evidence for a gene identifier from public APIs — NCBI, VEuPathDB, OMA, UniProt, KEGG — and asks a typed-question judge (JEV / any POST /v1/systemone-compatible backend) an ordered workflow of questions to produce a confidence-scored knowledge graph with evidence provenance on every edge. Ships a CLI, a Python library, and a self-contained HTML report (`bionym resolve --report`). A FastAPI service and static D3 UI live in the source repo only — they are not part of the installed package.

package bionym#

(downloads) docker_bionym

Versions:

0.1.0-0

Depends:

  • on diskcache >=5.6

  • on httpx >=0.27

  • on pydantic >=2.6

  • on python >=3.10

  • on python-dotenv >=1.0

  • on typer >=0.12

Additional platforms:

Installation#

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi#

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bionym

to add into an existing workspace instead, run:

pixi add bionym

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda#

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bionym

Alternatively, to install into a new environment, run:

conda create -n envname bionym

with envname being the name of the desired environment.

Container#

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bionym:<tag>

(see bionym/tags for valid values for <tag>).

Integrated deployment#

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page#

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bionym/README.html)