Feb 19, 2026

SOP BGE7.2a: PUBLICATION OF PROTOCOLS V.1

DOI
https://dx.doi.org/10.17504/protocols.io.q26g77wq1gwz/v1
SOP BGE7.2a: PUBLICATION OF PROTOCOLS
  • 1SciLifeLab Data Centre;
  • 2SciLifeLab
  • Biodiversity Genomics Europe
Angela Fuentes Pardo
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DOI: https://dx.doi.org/10.17504/protocols.io.q26g77wq1gwz/v1
External link: https://biodiversitygenomics.eu/
Protocol Citation: Angela Fuentes Pardo, Joanna Sendecka, Olga Vinnere Pettersson 2026. SOP BGE7.2a: PUBLICATION OF PROTOCOLS. protocols.io https://dx.doi.org/10.17504/protocols.io.q26g77wq1gwz/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this SOP
Created: February 11, 2026
Last Modified: February 19, 2026
Protocol  Integer ID: 243055
Keywords: Biodiversity Genomics Europe, protocol publication, SOP, whole genome sequencing, protocol publication on this platform, protocol publication, publishing protocol, publication of protocol, scilifelab protocol, novel protocols from bge, biodiversity genomics europe, protocol, genome sequencing work stream, protocol submitter, standardised biodiversity data, publication, novel protocol, genome sequencing, protocols within the scope, publishing research method, private protocol, consortium, genomic method, bge, scientific article, report, persistent unique identifier, dna barcoding, web, standard operating procedure, based platform
Funders Acknowledgements:
European Union's Horizon Europe Research and Innovation Action
Grant ID: 101059492
Abstract
This Standard Operating Procedure (SOP) provides general guidance on publishing protocols within the scope of the Biodiversity Genomics Europe (BGE) consortium. BGE is a pan-European consortium that uses genomic methods (e.g., DNA barcoding and whole-genome sequencing) to generate standardised biodiversity data that supports monitoring and conservation action.

This SOP specifically describes how novel protocols from BGE’s Genome Sequencing work stream are documented, curated, and published on SciLifeLab Protocols powered by protocols.io, a web-based platform for sharing and publishing research methods.

In brief, protocol publication on this platform begins with the creation of a private protocol in the BGE workspace. The protocol submitter then requests review and approval from a workspace administrator (admin) using the signing flow. If the protocol is ready, the admin proceeds with publication; otherwise, the admin returns it to the submitter for revision.

Once published, the protocol is assigned a DOI (Digital Object Identifier), a persistent unique identifier that should be cited in relevant project outputs (e.g., scientific articles, presentations, reports). The detailed workflow is shown in Figure 1.

Figure 1. BGE protocol publication workflow in protocols.io.

Guidelines

Purpose


The purpose of this SOP is to ensure that novel protocol contributions become permanent, citable, and FAIR-complaint research outputs, while ensuring:

  • High scientific quality
  • Consistent and complete documentation
  • Public visibility and accessibility
  • Appropriate attribution for method development
  • Compliance with the FAIR principles and open science practices
  • Alignment with institutional and funder requirements

Who should use this SOP


This SOP applies to all BGE consortium members who contribute protocols for publication, such as:

  • Principal investigators
  • Laboratory staff
  • Research engineers
  • Graduate students
  • Project coordinators
  • External collaborators

When this SOP should be used


This SOP should be followed when a protocol:

  • Has been experimentally validated
  • Represents a novel BGE contribution
  • Is ready for publication

Protocol novelty criteria


A novel protocol contribution within BGE, for the purposes of publication, includes:

  • New methods
  • Substantial modifications to existing protocols
  • Validated adaptations for new organisms, sample types, or sequencing platforms

Only protocols that meet any of these novelty criteria should be deposited and published in the BGE workspace. When in doubt, contact Olga Vinnere Pettersson and Tulli Lundbäck-Larva for support.

Protocols that do not meet the criteria are captured by the BGE Work Package 7 (WP7) partners when completing the Cognito-based Genome Report template and are made publicly available alongside the corresponding genomic data.

Workspace setup and membership


Administrative controls for publication

To ensure appropriate control over protocol publication from the BGE workspace, administrators must:


Joining the BGE workspace


To publish protocols in the BGE workspace, you must be a workspace member. If you are not currently a member and do not have a protocols.io account, follow these steps:


Workspace organisation


The BGE workspace is organised into Work Packages (WPs). Protocols derived from the genome sequencing work package must be placed in the WP7 folder and in the corresponding subfolder. This folder contains three subfolders:
  • DNA extraction
  • Size Selection
  • Library Preparation

Role definitions and responsabilities


Protocol submitter:

  • Drafts the protocol using the suggested format and structure
  • Ensures the protocol is complete, accurate, and experimentally validated
  • Includes appropriate protocol documentation and metadata
  • Requests review prior to publication via the signing flow

Reviewer (workspace administrator):

  • Invites members to join the BGE workspace
  • Assesses scientific quality, clarity, and completeness
  • Confirms that the protocol represents a novel BGE contribution
  • Request revisions where needed
  • Approves or rejects the protocol through the signing flow
  • Completes the final publication step in protocols.io

General administrator:

  • Invites members to join the BGE workspace
  • Manages BGE workspace profile and organisational collections (folders/collections)
  • Manages publication permissions in the BGE workspace
  • Enables and enforces the signing flow
  • Ensures compliance with institutional and funder requirements

In Table 1, you find a list of the current administrators of the BGE workspace, their contact information, and their roles.

RoleNameE-mailDescription
General administratorOlga Vinnere Pettersson[email protected]Contact between SciLifeLab and BGE; WP7; T7.2
General administratorChristian de Guttry[email protected]BGE manager; WP3
Reviewer (workspace administrator)Tuuli Lundbäck- Larva[email protected] WP7 (Reference genome sequencing)
Reviewer (workspace administrator)Wiesia Johnson[email protected]WP7 (Reference genome sequencing)
Table 1. Administrators of the BGE workspace

Post-publication responsibilities


After protocol publication, BGE members should:

  • Cite the protocol DOI in relevant project outputs (e.g., scientific articles, presentations)
  • Monitor feedback and address request for clarification when needed
  • Coordinate with workspace administrators for major updates or corrections, as applicable

Protocol updates


If a published BGE protocol is refined, corrected, or customised, BGE members must maintain a clear and permanent link to the original protocol on protocols.io. Refer to the guidance on reusing and adapting existing protocols using versions or forks.

General recommendations:

Published protocols should be managed using versioning in protocols.io, and all previous versions must remain accessible via the version history.

When to use a new version:

Use a new version when substantive changes are made to an existing protocol. New versions are typically created and published by the protocol submitter (the protocol owner on the platform). Substantive changes include, but are not limited to:

  • Correcting an error in a step
  • Adding optimisation details to improve efficiency

When to use a fork:

Use a fork for smaller changes or adaptations, such as:

  • Adapting a protocol from single-sample to multi-sample processing
  • Using alternative kits or equipment
  • Creating variants for different sample types

Before start
If you have not already done so, review the Guidelines & Warnings tab of this SOP for background information, including its purpose, when it should be used, and who the workspace administrators are.

To familiarise yourself with protocols.io, consult the summary instructions on the SciLifeLab Protocols page. For more detailed guidance, refer to the protocols.io Help Center documentation.
Prepare the protocol document
Draft the protocol in an accepted text-based format (e.g., DOCX, PDF, or TXT). It should include:
  • Step-by-step instructions of the research methods
  • Contextual information of the protocol (metadata), such as title, authors, materials, references, safety notes, troubleshooting, among others. Refer to the Protocol Documentation Checklist for further details:
Download SOP_BGE7.2a_v.1.0_Protocol_Documentation_Checklist.docxSOP_BGE7.2a_v.1.0_Protocol_Documentation_Checklist.docx4.7MB
Import the protocol into protocols.io
Import the document into protocols.io as a private protocol (see guidance). Start by adding the steps of the protocol and add the contextual information in the respective tabs.
Revise and edit
Review the protocol for completeness, clarity, and scientific accuracy. Update as needed.
Confirm readiness for review
Determine whether the protocol is ready for administrator review.
  • If revisions are still required, return to Step 3
  • If ready, proceed to Step 5
Submit for administrator review
Use the signing flow to sign and submit the protocol for administrator review. Refer to the guidance on signing and requesting signatures as part of the protocol review and approval process.
Administrator review
A workspace administrator reviews the submitted protocol to verify completeness, accuracy, and compliance with BGE requirements. Refer to the Workspace Administrator Approval Checklist for further details:
Download SOP_BGE7.2a_v1.0_Workspace_Administrator_Approval_Checklist.docxSOP_BGE7.2a_v1.0_Workspace_Administrator_Approval_Checklist.docx4.8MB
Review decision
The administrator determines whether the protocol is ready for publication.
  • Not ready: The protocol is rejected with an explanation and suggested revisions. The submitter revises the protocol and resubmits (return to Step 3).
  • Ready: Proceed to Step 8.
Administrator approval and publishing
The administrator approves the protocol by signing it. Once signed:
  • The submitter is notified (via email and protocols.io's profile).
  • The administrator publishes the protocol following the protocol publication guidance.
Confirm publication and persistent identifier
The published protocol is assigned a DOI (a permanent, unique identifier) and becomes publicly accessible. Verify in a web browser that:
  • The protocol record is publicly accessible as intended.
  • The DOI is visible and correct.

Record the protocol DOI for citation and use in project materials and reports.
Acknowledgements
We thank EU Horizon Europe and Biodiversity Genomics Europe, Grant Agreement No 101059492.

We thank Science for Life Laboratory (SciLifeLab), Sweden, for providing BGE with premium access to SciLifeLab Protocols, powered by protocols.io.