Dos and Donts

How to Provide a Dataset Before Submission to Avoid Unnecessary Rejections?

Section titled How to Provide a Dataset Before Submission to Avoid Unnecessary Rejections?

Purpose of This Guide

Many dataset rejections are not caused by bad science, but by missing ISA structure , Incomplete metadata, Broken ontology references, Formatting inconsistencies and Incorrect linkage between the ISA (Investigation-Study -Assay files)

1. Recommended Workflow (Before Submission)

Section titled 1. Recommended Workflow (Before Submission)

Follow this checklist in order.

Step 1 — Create Proper ISA Structure

Section titled Step 1 — Create Proper ISA Structure

Your dataset must follow the ISA model:

Investigation
 ├── Study
 ├── Assay
 ├── workflows (if applicable)
 └── runs (if applicable)

Minimum required: investigation.xlsx , isa.study.xlsx and isa.assay.xlsx. Common reason for rejection is uploading only the excel files without ISA structure.

Step 2 — Define Study Naming Convention

Section titled Step 2 — Define Study Naming Convention

Study names must follow a defined convention. For example:

genebankpartner_yearstart-yearend_sitename

Correct:

NPPC_1971-1974_Piestany
CREA_2006_SAL

Incorrect:

trial1
experiment_final
data_new_version

If the site name is missing, use coordinates temporarily:

IPGR_1985_lon-24.93388-lat-42.12002

Step 3 — Ensure All Identifiers Are Stable

Section titled Step 3 — Ensure All Identifiers Are Stable

Identifiers are the backbone of the dataset. Every sample must have sample name(mandatory in study file) , Accession ID and replicate IDs if replicated.

Sample Name	Accession	Replicate
plant_1	ACC1234	1
plant_2	ACC1234	2

Step 4 — Complete the Investigation File

Section titled Step 4 — Complete the Investigation File

Most common rejection problems happen here. Ensure that Study referenced, Assay referenced, Ontologies listed, Contacts are complete, Description filled and All protocols described

2. Structure of the Dataset (What Must Exist)

Section titled 2. Structure of the Dataset (What Must Exist)

A. Investigation File

Section titled A. Investigation File

Must Include

1. Investigation Metadata

Section titled 1. Investigation Metadata

• Title
• Description
• Submission date
• Project name

2. Investigation Contacts (CRITICAL)

Section titled 2. Investigation Contacts (CRITICAL)

• First Name

• Last Name

• Email

• ORCID

• Affiliation (complete, not abbreviated)

  First Name	Last Name	ORCID	Email	Affiliation
  Jagadeeshwar	Etukala	0000-0002-XXXX	jay@ipk.de	Leibniz Institute of Plant Genetics and Crop Plant Research, Germany

Wrong:

Missing ORCID
Only "IPK" as affiliation

3. Ontologies Used (VERY IMPORTANT)

Section titled 3. Ontologies Used (VERY IMPORTANT)

Elena´s comment: Not all ontologies used in study and assays are listed in investigation.

You must list ALL ontologies used.

Term Source Name	Term Source File	Term Source Version
CO	https://cropontology.org	2024
UO	http://purl.obolibrary.org/obo/uo.owl	2023
PO	http://purl.obolibrary.org/obo/po.owl	2023

B. Study File (isa.study.xlsx)

Section titled B. Study File (isa.study.xlsx)

Minimum Required Columns:

• Source Name
• Sample Name
• Organism
• Characteristics
• Geographic co-ordinate (latitude)
• Geographic co-ordinate (longitude)

Proper Coordinate Format

Section titled Proper Coordinate Format

Correct format:

Latitude: 52.210000
Longitude: 20.640000

Incorrect format

52°12’N
20.64E
Germany (approx.)

Basic Passport Data (Domain Specific)

Section titled Basic Passport Data (Domain Specific)

Must include Accession number, Material source information and country or origin and source coordinates. Without passport data the data set is incomplete and not reusable.

C. Assay File (isa.assay.xlsx)

Section titled C. Assay File (isa.assay.xlsx)

Contains:

1. Sample Name (must match Study file exactly)
2. Trait
3. Value
4. Unit
5. Protocol reference

3.Common Formatting Issues (With Examples)

Section titled 3.Common Formatting Issues (With Examples)

1.Term Accession Number & Term Source REF Missing

Section titled 1.Term Accession Number & Term Source REF Missing

Elena´s comment: Usually Term Accession number and term source REF are left empty.

Trait	Term Source REF	Term Accession Number
Days to heading	CO	CO_321:0000025

2. Confusing Trait Ontology vs Unit Ontology

Section titled 2. Confusing Trait Ontology vs Unit Ontology

Common mistake:

Trait = Plant height
Unit = cm

Trait ontology → Crop Ontology (CO)
Unit ontology → Units Ontology (UO)

Correct example:

Trait	Term Source REF	Term Accession Number
Plant height	CO	CO_321:0000012

Unit	Term Source REF	Term Accession Number
centimeter	UO	UO:0000015

3. Duplicated columns

Section titled 3. Duplicated columns

Wrong:

Plant Height	Plant Height
120
130

One column empty-> delete it

4. Missing Link Between Files

Section titled 4. Missing Link Between Files

Common problem:

1. Study not referenced in Investigation
2. Assay not linked to Study
3. Misspelled file names

5. Sample Name Missing

Section titled 5. Sample Name Missing

Sample Name is mandatory because:

Study → defines samples
Assay → links measurements to Sample Name

Without it → ISA structure breaks.

4. Domain-Specific Issues

Section titled 4. Domain-Specific Issues

1. Site Location Must Be Geo Coordinates

Section titled 1. Site Location Must Be Geo Coordinates

Not just:

Versailles
Gatersleben

Must include Latitude and Longitude

2.Traits Must Have Full Names linked to Ontologies

Section titled 2.Traits Must Have Full Names linked to Ontologies

Not acceptable:

PH
TKW
DTH

Must be expanded:

Plant height
Thousand kernel weight
Days to heading

3.Basic Passport Data Required

Section titled 3.Basic Passport Data Required

Missing passport data causes:

1. Broken linkage to EURISCO
2. Incomplete material description
3. Reduced reusability

4.Data Quality Checks Before Submission

Section titled 4.Data Quality Checks Before Submission

Perform these checks:

1. Any value biologically impossible? (e.g., TKW = 0)
2. Any experiment listed but no observed data?
3. Are missing values empty or zero?
4. All Sample Names unique?
5. All ontologies filled?
6. All studies referenced?

5.Final Pre-Submission Checklist

Section titled 5.Final Pre-Submission Checklist

Before uploading:

 ☐ ISA structure complete
 ☐ Investigation file fully filled
 ☐ All ontologies listed
 ☐ Study names consistent
 ☐ Coordinates in decimal format
 ☐ Sample Name present
 ☐ Replicates uniquely identified
 ☐ Passport data included
 ☐ ORCID and emails included
 ☐ No duplicated columns
 ☐ No empty referenced studies