ICPD Submission Guide

How to prepare and deposit crop phenotyping data in the Indian Crop Phenome Database (ICPD). Written for external data submitters. Read this page first: it shows the whole route on one page and what to have ready.

Start with registration Web-based submission

Three tags are used throughout this guide: MANDATORY the submission cannot be completed without this field. RECOMMENDED the submission can be completed without this field but it is recommended to be filled. NEW IN v3.0 introduced in this version of the guide.

Complete submission flow #

The route, step by step #

If the web interface cannot be used, the template-based route is available, but it takes longer because the metadata has to be checked by hand.

How ICPD records are connected #

A submission is organised into three linked record types. A phenoproject may contain one or many studies, and each study holds one or more data files. The accession numbers (PPJ_, PST_, PDT_) are assigned by ICPD, are permanent, and must be quoted in full without spaces. Section 3 explains the model.

Submission checklist #

Tick each item before you open the submission forms. Submissions usually stall because one of these was not available at registration.

Keep names and IDs consistent #

Most returned submissions have a mismatch between two files or two fields. These are the places where the same value must be identical.

Document information

Revision history #

1. How to use this guide

This guide explains how to prepare and deposit crop phenotyping data in the Indian Crop Phenome Database. It is written for the submitter. It is not a procedural document for IBDC staff; the internal procedures for validation, curation, release and withdrawal are held in separate SOPs listed above.

Three conventions are used throughout.

• MANDATORY the submission cannot be completed without this field.
• RECOMMENDED the submission can be completed without this field but its recommended to be filled
• NEW IN v3.0 introduced in this version of the guide.

2. About ICPD

The Indian Crop Phenome Database (ICPD), developed by the Indian Biological Data Centre (IBDC) at the Regional Centre for Biotechnology, Faridabad, is an open-access platform for the archiving, management, analysis, and sharing of crop phenome data. Although a large volume of crop phenotyping data is generated through agricultural trials worldwide, much of it remains unpublished and inaccessible to the wider research community. ICPD addresses this gap by providing a centralized, user-friendly platform, open to researchers everywhere, that organizes and preserves multi-crop phenome data in compliance with the MIAPPE standard and the FAIR principles — findable, accessible, interoperable, and reusable. Each submitted dataset undergoes curation and is assigned a unique, persistent IBDC accession, and the platform supports both open and managed access submission modes. ICPD operates under a CC BY-NC-SA licensing framework that ensures proper attribution while supporting ethical, non-commercial reuse. ICPD is a member database of the AgBioData Consortium and is registered in FAIRsharing.Data deposited in ICPD receive persistent IBDC accession numbers. The portal is available at https://ibdc.dbt.gov.in/icpd/.

3. The ICPD data model

3.1 Record types #

A submission to ICPD is organised into three linked record types. Understanding this hierarchy before you start will save considerable time, because the boundaries between a phenoproject and a study, and between one study and the next, determine how your data can later be found and combined with other people's data.

3.2 Accession number format #

Accession numbers are assigned automatically by ICPD and are permanent. Once issued, an accession number is never reassigned to a different record, even if the original record is later suppressed or withdrawn.

3.3 One study per site and season #

This follows the convention used internationally for multi-environment trials. It keeps the environmental description, the experimental design and the observation units unambiguous for each environment, and it allows others to select exactly the environments they need when reusing your data. The phenoproject record is what holds the set together.

3.4 Relationship to MIAPPE #

The ICPD metadata model is aligned with MIAPPE, the Minimum Information About a Plant Phenotyping Experiment standard (www.miappe.org). ICPD targets MIAPPE v1.2. The ICPD phenoproject corresponds to the MIAPPE investigation, the ICPD study to the MIAPPE study, and the ICPD data file to the MIAPPE observation and observed variable sections.

Trait, developmental stage, plant anatomy and treatment terms are drawn from the Planteome ontologies (planteome.org) and from Crop Ontology (cropontology.org), which are the ontologies MIAPPE recommends for these fields.

4. Before you begin

4.1 What to gather first #

Assemble the following before opening the submission forms. Submissions that stall usually do so because one of these was not available at the time of registration.

4.2 Formatting conventions #

These conventions apply to every field and every file you submit.

4.3 Choosing ontology terms #

ICPD records traits, developmental stages, plant anatomy and treatments using ontology terms rather than free text, so that a search for a trait returns data from every submitter who measured it, regardless of the words they happened to use.

Work in this order.

1. Search the existing term in the Browse Ontology tool.
2. If your exact term is absent, consider whether an existing broader term is scientifically adequate. In most cases it is.
3. Only if no suitable term exists, propose a new term through Create Ontology Term.

5. Getting started

The overview of steps required for the initiate and complete the phenome data submission to ICPD are summarised in Figure 4.

5.1 User registration #

Select User Registration at the top of the ICPD home page. Your email address is your primary identifier and cannot be changed later without contacting support, so use an institutional address that will remain valid. After sign-up, an activation link is sent to that address; the account becomes usable once you confirm it.

5.2 User login #

Log in with the username and password set at registration. Forgot Password, Register Now and Resend Activation Link are available on the login page.

5.3 User dashboard #

The dashboard lists your submission links on the left and your submission statistics in the centre, together with a summary of phenoprojects, studies and data files you have already submitted. Start a new submission with Submit New Data. The left panel also provides:

• Discussion Forum, for suggestions and questions about the submission process.
• Browse Ontologies, to search terms for traits, developmental stages, plant anatomy and methods.
• Create Ontologies, to propose a new term.
• Download User Manual, this guide.
• Download ICPD Submission Template, for the template-based route.

6. Web-based submission

The web-based route is recommended. It offers guided selection of ontology terms, validates entries as you go, and generates a pre-filled data template so that you only need to enter observations. The route has five steps.

Step 1. Register a phenoproject

Click Submit New Data on the dashboard. The phenoproject registration form consists of several fields required to comprehensively define a new phenoproject. All the fields marked with asterisk are mandatory and others are optional for the users to provide. The form has a project section and a crop section.

Project section #

Crop section #

List the scientific name and NCBI Taxonomy identifier of every crop studied in the project. Just type the scientific name of the crop and the NCBI taxon ID will be automatically fetched from NCBI taxonomy. User can add multiple crop in one project.

On submission, the phenoproject accession is issued and displayed at the top of the page and will get updated on “My project” page.

Step 2. Register a study

A phenoproject may contain one or many studies. Click Register New Study to add a study to a new or existing phenoproject. Remember the rule in section 3.3: one study covers one site in one season.

Step 2.0 Basic information #

Growth and environmental conditions #

Record the conditions under which the trial was grown. Every value requires a unit. Where a condition varied over the season, record the range.

Step 2.1 Treatments #

A treatment is the experimental factor deliberately imposed on the plants. It is not something you measured. Record the factor, the levels it took, and how it was applied.

Step 2.1 Traits #

Declare every trait recorded in the study. A trait declaration in ICPD has five components, all of which are required for the data to be reusable.

Author list #

Provide first name, last name, email, organisation, designation and ORCID iD for each person who contributed to the study, together with their role, for example principal investigator, data curator or field technician. Press Submit. The study accession is issued on success.

Step 3. Generate and download the template

Once the study is registered, click Step 3: Generate and Download Template. Provide:

• the study accession;
• the full list of genotype names to be tested, including the tolerant and susceptible checks;
• the number of biological and technical replicates;

Click Generate Template CSV. The template downloads immediately with the identifying columns pre-filled. You can print it and use it as a field book, then enter the values on return.

Before you fill the template

• Do not add, remove, rename or reorder columns, and do not change the file format.
• Each genotype name must appear once in the genotype list you provide. Duplicated names cannot be resolved and the submission will be rejected.
• Use the same spelling of a genotype name everywhere. N22 and N-22 are treated as two different genotypes.
• Enter NA for a value that was not recorded. Do not leave a cell blank.

Step 4. Upload data

Click Step 4: Upload Data, select the study, browse to the completed file and upload. The file is checked automatically on arrival. If checks fail, the errors are reported with row and column references so that you can correct and re-upload. On success a data file accession is issued and your dashboard updates immediately.

Step 5. Supporting data

Step 5 accepts the additional files that make a study interpretable. Download the relevant template, select the study, complete the file and upload it.

9. Passport and environment data

Passport data identifies the genetic material you evaluated. It is what allows a user in another institute to obtain the same material, or to recognise that your genotype and theirs are the same accession under different local names. The passport template follows the FAO and Bioversity Multi-Crop Passport Descriptors.

7. Template-based submission

Where the web interface cannot be used, ICPD accepts a completed workbook by email. This route receives the same curation as the web route but takes longer, because metadata that the web forms would validate on entry has to be checked by hand.

1. Click Download ICPD Submission Template on the dashboard.
2. Complete the phenoproject, study and data sheets, following the conventions in section 4.2.
3. Attach the plant passport sheet.
4. Email the workbook to ICPD support at icpdsupport@ibdc.rcb.res.in.

10. After you submit

Upload is not the end of the process. Every submission passes through automated validation and curator review before it becomes part of the archive.

11. Release, embargo and licence

You declare a release date when you register a phenoproject. Until that date the record is held privately and is visible only to you and to IBDC curators. On that date it is released publicly.

12. Correcting, updating and withdrawing data

Data in the archive can be corrected. Accession numbers, however, are permanent, and public records are not deleted. IBDC follows the data availability model used internationally, under which a record that should no longer be consulted is given a defined status rather than being erased.

Requests are made on form IBDC-DWS-01, Data Withdrawal and Suppression Request Form, available from the ICPD support team. Note that data which have been publicly available for any period may already have been downloaded by others, and IBDC cannot recall those copies.

13. Citing ICPD data

Cite the accession in the data availability statement of any publication that uses ICPD data, whether the data are yours or someone else's.

Suggested form. Author(s). Title of the study. Indian Crop Phenome Database, Indian Biological Data Centre. Accession PST_100118.

If you deposited the data yourself, cite your own accession in the paper that reports it. This is what makes the deposit findable and creditable, and journals increasingly require it.

14. Finding and reusing data

My Data #

Phenoprojects, studies and data files you have submitted appear under My Data on your dashboard. Metadata and data files can be viewed and downloaded at any time.

Browse Data #

Released phenoprojects, studies and data files can be browsed by any visitor from Browse Data on the home page, without registration.

15. Ontology browse and create

Consistent trait vocabulary is what makes phenotype data comparable across studies, so ICPD records traits, developmental stages, plant structures and methods as ontology terms.

• Browse Ontology searches meta-trait, developmental stage, trait and plant structure terms.
• Create Ontology Term proposes a new term where no suitable term exists.

Terms you propose are accepted immediately as provisional so that your submission is not held up. Provisional terms carry a local ICPD identifier, are displayed as provisional in your record, and are then reviewed against the Plant Trait Ontology, Plant Ontology, Plant Experimental Conditions Ontology and Crop Ontology. A provisional term is either mapped to an existing ontology term, in which case your record is updated and you are notified, or promoted to a permanent ICPD term.

16. Support

For questions, suggestions and help with a submission, write to the ICPD support team at icpdsupport@ibdc.rcb.res.in

Introductory material is also available on video:

• ICPD webinar: https://youtu.be/Grx973vAelM
• Short introduction to ICPD: https://youtu.be/B-WjgpD57ag