brapi2arc
This API allows researchers to submit phenotyping observations to a dataset stored as an Annotated Research Context (ARC). The ARC provides a standardized structure for capturing and sharing research data, enabling reproducibility and transparency in scientific investigations.
Science Score: 44.0%
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Low similarity (8.3%) to scientific vocabulary
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This API allows researchers to submit phenotyping observations to a dataset stored as an Annotated Research Context (ARC). The ARC provides a standardized structure for capturing and sharing research data, enabling reproducibility and transparency in scientific investigations.
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- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 1
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Metadata Files
README.md
BrAPI2ARC
Description
This API allows researchers to submit phenotyping observations to a dataset stored as an Annotated Research Context (ARC). The ARC provides a standardized structure for capturing and sharing research data, enabling reproducibility and transparency in scientific investigations.
Installation
The brapi2arc tool is offered as a docker container. To install it start a new container with the environment variables ARC_URI, DATAHUB_URL and DATAHUB_TOKEN set.
sh
docker run -e ARC_URI=<ARC_URI_VALUE> -e DATAHUB_URL=<DATAHUB_URL_VALUE> -e DATAHUB_TOKEN=<DATAHUB_TOKEN_VALUE> -p 8000:8000 ghcr.io/ipk-bit/brapi2arc
Or using docker compose.
yml
services:
brapi2arc:
image: ghcr.io/ipk-bit/brapi2arc
ports:
- 8000:8000
environment:
- ARC_URI='<YOUR ARC URI>'
- DATAHUB_URL='<YOUR DATAHUB URL>'
- DATAHUB_TOKEN='<YOUR PERSONAL ACCESS TOKEN>'
Usage
There is a tutorial on how to use brapi2arc in the documentation. The basic idea is that this tool acts as a converter that takes phenotypic observations through the BrAPI interface and writes them to an ARC. This allows the automation of the data import into ARCs from every observation scoring application that is BrAPI enabled.
Owner
- Name: IPK Gatersleben - Bioinformatics and Information Technology
- Login: IPK-BIT
- Kind: organization
- Location: Germany
- Website: https://www.ipk-gatersleben.de/en/breeding-research/bioinformatics-and-information-technology/
- Repositories: 3
- Profile: https://github.com/IPK-BIT
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: BrAPI2ARC
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Manuel
family-names: Feser
orcid: 'https://orcid.org/0000-0001-6546-1818'
email: feser@ipk-gatersleben.de
name-particle: Manuel
affiliation: IPK Gatersleben
repository-code: 'https://github.com/IPK-BIT/brapi2arc'
url: 'https://brapi2arc.rtfd.io/en/latest'
abstract: >-
This API allows researchers to submit phenotyping
observations to a dataset stored as an Annotated Research
Context (ARC). The ARC provides a standardized structure
for capturing and sharing research data, enabling
reproducibility and transparency in scientific
investigations.
keywords:
- BrAPI
- BrAPI Phenotyping
- BrAPI Server
- RO-Crate
license: MIT
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Dependencies
- actions/checkout v2 composite
- peter-evans/autopep8 v2 composite
- python 3.12-slim build
- mkdocs-material *
- mkdocstrings *
- GitPython ==3.1.43
- arctrl ==2.0.0a2
- fsspreadsheet ==6.1.1
- icecream ==2.1.3
- litestar ==2.8.3
- pandas ==2.2.2
- pydantic ==2.6.4
- python-dotenv ==1.0.1
- requests ==2.28.1
- uvicorn ==0.29.0