Fundamentals
Research Data Management
FAIR Data Principles
Metadata
Ontologies
Data Sharing
Data Publications
Data Management Plan
Version Control & Git
Public Data Repositories
Persistent Identifiers
Implementation within DataPLANT
Annotated Research Context
User Journey
ARC Commander
QuickStart
QuickStart (experts)
Swate
QuickStart
Walk-through
Best Practices For Data Annotation
DataHUB
DataPLAN
ARC Commander Manual
Setup
Installing Dependencies
Configure Git
Installing the ARC Commander
Windows
MacOS
Linux
DataHUB Access
Before we start
Central Functions
Initialize
Clone
Connect
Synchronize
Configure
Branch
ISA Metadata Functions
ISA Metadata
Investigation
Study
Assay
Update
Export
Swate Manual
Setup
Installing Swate
Browser
Desktop, via installer (beta-stage)
Desktop, manually (recommended)
MacOS
Organization-wide
Core Features
Annotation tables
Building blocks
Building Block Types
Adding a Building Block
Using Units with Building Blocks
Filling cells with ontology terms
Advanced Term Search
Templates
Contribute Templates
File Picker
Expert Features
ISA-JSON
Frequently Asked Questions
Teaching Materials
DataPLANT Overview
Big Picture
ARC structure
ARC Demo
last updated at 2023-05-11
General
Is it necessary to fill in the empty fields in the investigation-file manually?
No. Although it is possible to fill in the workbook manually, we recommend using ARC Commander to add this metadata.
Annotated Research Context
Should the metadata annotation be made in the same document in which the dataset resides?
No. The metadata describing the data is annotated in a separate xlsx-file that resides in the parent folder of the data sets.
Is it necessary to fill in the empty fields in the investigation-file manually?
No. Although it is possible to fill out the workbook manually, we recommend using ARC Commander to add this metadata.
ARC Commander
Are there any recommendations for titles or identifiers?
Avoid using spaces in the identifier. Use underscores and capital letters instead. There are no specific restrictions regarding the title. Although it is possible to fill in the workbook manually, we recommend using ARC Commander to add this metadata.
How to retrieve a valid access token?
Please follow the short instructions below.
Alternatively, please visit #157 in the ARC Commander repository's discussion section for detailed instructions.
Note: This also works for "arc get"
TLDR:
- Have a GitLab account (here: DataPLANT DataHUB)
- Generate a GitLab access token (Preferences → Access Tokens) (with API and read/write repository)
- Copy token string
- Clone a GitLab repo with adjusted address (one for which you have the respective access rights):
git clone https://oauth2:TOKENSTRING@git.nfdi4plants.org/abc/xyz
Swate
Is it possible to use common Excel functionalities?
Yes. In fact, this is one of the reasons why we decided to embed Swate within Excel, as it allows users to continue using the Excel functionality they are accustomed to.
Do I have to fill in all columns when using a template?
No. However, if you want to submit your data to a public data repository, these will require specific metadata. For this purpose we provide the corresponding templates helping you to annotate your data accordingly.
ISA
Which format must be used to enter a date?
String formatted as ISO8601 date: YYYY-MM-DD
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DataPLANT Support
Besides these technical solutions, DataPLANT supports you with community-engaged data stewardship. For further assistance, feel free to reach out via our
helpdesk
or by contacting us
directly
.