nfdi4plants/nfdi4plants_ontology

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F#
License
MIT License
Created almost 4 years ago
Updated 4 months ago

nfdi4plants/nfdi4plants_ontology

nfdi4plants

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An intermediate ontology for plants used by DataPLANT to fill the ontology gap

Swate

Excel Add-In for annotation of experimental data and computational workflows.

ARC-specification

ARCtrl

Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtime-agnostic contract systems.

ARCCommander

Tool to manage your ARCs

ARC

ARC - Annotated Research Context

ARCitect

Cross-platform app to create and manage ARCs.

Swobup

Swate DB update tool

isa-ro-crate-profile

nfdi4plants.github.io

DataPLANT static website using Fornax

web-components

DataPLANT branded web-components for diverse elements. Used in knowledgebase and main pages.

cwl-examples

various example cwl workflows

Common Workflow Language

Branding

logos, colorschemes, etc. of DataPLANT and associated applications

Swate-templates

A collection of templates for Swate (https://github.com/nfdi4plants/Swate).

CWLGenerator

Hackathon_SampleRun

Common Workflow Language

arc-validate

Home of all the tools and libraries to create and run validation of ARCs

Hackathon_ARCexample_rnaseq

ARCtrl.NET

This library contains reader functions to interact with the different formats present in an ARC

ARCTokenization

Definition of controlled vocabulary tokens and library to tokenize ARC metadata into these tokens

raw_data_parser

raw data pasers (fastq, mzml) and their work

Jupyter Notebook

arcCommander-docs

ARCWebAPI

Project for supplying a Common API for ARC related tasks

ARC-Symposium

nfdi4plants.knowledgebase

This is the source repo for the nfdi4plants knowledge base webpage.

Nfdi4Plants.Fornax

Fornax library and template for nfdi4plants/web-components used as docs framework.

user-stories

user stories for tools in the DataPLANT stack via github issues

ARC_ontology

Repository containing the ARC ontology (currently only ISA-JSON model; cwl is wip (runs & workflows))

BOAT-Builder-for-Ontology-ARC-Templates

This tool/website is for a user friendly creating of an ARC template (essay or study) out of your free text protocols with self-annotated ontology labeled terms. These templates can be used in your ARC afterwards.

converters

Converters for different endpoint repositories

WebHub

DataPLANT science gateway

arc-to-invenio

Automatic building of a Docker container for converting ARCs to Invenio Metadata

dmpg

a light version of Data Management Plan Generator

Spawn

Word Add-In to create workflow annotations from protocols.

dataplant-keycloak-theme

The official DataPLANT keycloak theme

teaching-materials-concept

Working repo for NFDI Cordi Abstract

arc-validate-package-registry

A repository of validation packages for ARCs

AnnotationPrinciples

Draft of best practices for data and workflow annotation

actions-workflows

reusable github actions tailored for our needs

arc-playground

CommunicationPlatform

arc-rdm.org

The official ARC website!

DataHUB

This repository may be used to collect issues, bugs or similar regarding the DataPLANT DataHUB.

ARCfs

helpdesk

DataPLANT helpdesk as SPA website with server for creating MS Teams issues.

arc-to-rocrate

dataplan

DataPLAN is the Data Management Plan (DMP) generator developed in DataPLANT