Fundamentals

Introduction

Research Data Management

FAIR Data Principles

Metadata

Data Sharing

Data Publications

Data Management Plan

Version Control & Git

Public Data Repositories

Persistent Identifiers

Implementation within DataPLANT

Annotated Research Context

ARC Commander

Swate - a workflow annotation tool for Excel

DataHUB

Training & Tutorials

QuickStart on ARCs

ARC Commander QuickStart

Swate QuickStart

Best practices for data annotation

SWATE QuickStart

last updated at 2022-08-05

This document is work in progress. If you experience any inconsistencies, have questions or would like to suggest additions, please feel free to contact us or open an issue in our Helpdesk.

We are very happy that you chose our tools and infrastructure to create and share your own ARCs. In this QuickStart we assume that your ARC already contains one or more isa.study.xlsx and isa.assay.xlsx file(s), respectively. Use the isa.study.xlsx to describe the characteristics of your samples, e.g. how you grew your plant, and isa.assay.xlsx to annotate the experimental analyses. In the following we will focus on adding metadata to your studies and assays with our excel tool Swate.

Swate

DataPLANT provides the Excel Add-In Swate to support you in data annotation.

Customize your table by adding building blocks
  1. Choose the type of building block you want to add (A).

  2. If you chose a descriptive building block type (building blocks besides Sample Name, Source Name, and Data File Name), use search field (B) to search for an Ontology Term. Swate accesses the SwateDB with a list of established external ontologies designated suitable for use in plant science. In addition, we feature our own ontology NFDI4PSO to extend the DB with missing, but necessary terms.

  3. If you want to add a building block with a unit, check box (C) and use search field (D) to look for a fitting unit term, e.g. degree Celsius as unit for Parameter [temperature].

  4. If you could not find a fitting term, you can use the Advanced Term Search with the blue links above the Add building block button. If you still could not find a fitting term, use free text input.

  1. For more information on customizing your annotation table click here.
Use templates

Alternatively, you can also use one of DataPLANT’s Swate templates. You can find them under the Protocol Insert tab in Swate.

Annotate your samples and data

Fill the cells beneath each building block with ontology terms to note the respective Characteristics, Parameter, and Factor values of your experiment. Using the ontology term search function, you can fill multiple cells at once.

  1. When Use related term directed search (A) is enabled, Swate will suggest a selection of suitable terms within the ontology for the column header, e.g. TripleTOF 5600 for instrument model.

  2. When term directed search (A) is disabled, Swate will still suggest ontology terms, but without relation to the column header.

  3. If you could not find a fitting term, use free text input.

Note: More information on how to use Swate can be found here.

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 .
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