Home Fundamentals Research Data Management FAIR Data Principles Metadata Ontologies Data Sharing Data Publications Data Management Plan Version Control & Git Public Data Repositories Persistent Identifiers Electronic Lab Notebooks (ELN) DataPLANT Implementations Annotated Research Context User Journey ARC specification ARC Commander QuickStart QuickStart (Experts) Swate QuickStart Walk-through Best Practices For Data Annotation DataHUB DataPLAN Ontology Service Landscape ARC Commander Manual Setup Git Installation ARC Commander Installation Windows MacOS Linux ARC Commander DataHUB Access Before we start Central Functions Initialize Clone Connect Synchronize Configure Branch ISA Metadata Functions ISA Metadata Investigation Study Assay Update Export ARCitect Manual Installation - Windows Installation - macOS Installation - Linux QuickStart QuickStart - Videos ARCmanager Manual What is the ARCmanager? How to use the ARCmanager Swate Manual Annotation tables Building blocks Building Block Types Adding a Building Block Filling cells with ontology terms Advanced Term Search File Picker Templates Contribute Templates ISA-JSON DataHUB Manual Overview User Settings Generate a Personal Access Token (PAT) Projects Panel ARC Panel Forks Working with files ARC Settings ARC Wiki Groups Panel Create a new user group Data publications Passing Continuous Quality Control Submitting ARCs with ARChigator Track publication status Use your DOIs Guides ARC User Journey Create your ARC ARC Commander QuickStart ARC Commander QuickStart (Experts) ARCitect QuickStart Annotate Data in your ARC Annotation Principles ISA File Types Best Practices For Data Annotation Swate QuickStart Swate Walk-through Share your ARC Register at the DataHUB DataPLANT account Invite collaborators to your ARC Sharing ARCs via the DataHUB Work with your ARC Using ARCs with Galaxy Computational Workflows CWL Introduction CWL runner installation CWL Examples CWL Metadata Recommended ARC practices Syncing recommendation Keep files from syncing to the DataHUB Working with large data files Adding external data to the ARC ARCs in Enabling Platforms Publication to ARC Troubleshooting Git Troubleshooting Contribute Swate Templates Knowledge Base Teaching Materials Events 2023 Nov: CEPLAS PhD Module Oct: CSCS CEPLAS Start Your ARC Sept: MibiNet CEPLAS Start Your ARC July: RPTU Summer School on RDM July: Data Steward Circle May: CEPLAS Start Your ARC Series Start Your ARC Series - Videos Events 2024 CEPLAS ARC Trainings – Spring 2024 MibiNet CEPLAS DataPLANT Tool-Workshops Frequently Asked Questions

Annotation Principles

last updated at 2023-06-22 About this guide

Annotation of data and workflows within the ARC builds on the ISA model. In this guide we introduce the different building blocks available to annotate your workflows in isa.study.xlsx and isa.assay.xlsx workbooks.

UserNewbie ModeRead

Source Name

Every annotation table must start with the Source Name column, which defines the input of your table. This input value must be a unique identifier for an organism or a sample.
The number of Source Name columns per table is limited to one.


Characteristic columns describe inherent properties of the source material, e.g., a certain strain or ecotype, but also the temperature an organism was exposed to.
You can use any number of Characteristic columns.


Use Factor columns to describe independent variables that determine the specific output of your experiment when process and analysis were identical.
Most of the time, Factors are the most important building blocks for downstream computational analysis.


Parameter columns describe steps in your experimental workflow, e.g., the temperature or extraction buffer used for your assay. Multiple Parameter columns form a protocol.
You can use any number of Parameter columns.


Use these columns to list anything physical of a protocol that can be consumed, e.g. instrument names, software names, or reagents names.
You can use any number of Component columns.

Protocol Columns

Use Protocol REF columns to reference the protocol used in this table, i.e., the name of the protocol. Protocol Type columns define the type according to your preferred public repository, e.g., a growth protocol.
The number of columns for each subtype is limited to one per table.

Output Columns

Per table only one output column is allowed, which can either be a Sample Name, a Raw Data File or a Derived Data File. Data files can be sources for computational workflows.
The value of this column must be a unique identifier.

Contribution Guide 📖
✏️ Edit this page