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Why do I need to register a project?

The Research Registry has been designed with the following aims in mind:

Contents

Why do I need to register a project?

The Research Registry has been designed with the following aims in mind:

1. To promote collaboration and to reduce duplication of effort within the Research Environment: Registering a project will allow researchers within your domain and throughout all of GeCIP and the Discovery Forum to be aware of the work that is carried out within the Research Environment. 
2. To provide a mechanism to assess adherence to the Genomics England Publication Policy: Authorship and co-authorship of any publication or output should be defined in accordance with the guidelines issued by the International Committee of Medical Journal Editors (ICMJEImage Added) and outlined in the Genomics England Publication Policy. Note that a registered research project should comprise research aimed to result in a publication, such as a journal article, or a piece of work within a
3. To provide a mechanism to enact the Publication Moratorium: Disease-facing domains have a protected time period for analysis and publication on participant data pertaining to their domain in recognition of the efforts of the domain members who have assisted in recruiting participants to the project.
4. To provide a mechanism to assess adherence to the Genomics England Publication Policy: Authorship and co-authorship of any publication or output should be defined in accordance with the guidelines issued by the International Committee of Medical Journal Editors (ICMJEImage Removed) and outlined in the Genomics England Publication Policy. Note that a registered research project should comprise research aimed to result in a publication, such as a journal article, or a piece of work within a student thesis. Hence, multiple projects can be registered within a single domain. For a full definition of a project see here.
5. To assess that the proposed research adheres to acceptable uses of data for which the Access Review Committee has granted data access approval: Genomics England will be able to review whether a proposed research project falls within the scope of the detailed research plan submitted by the domain and as such that no additional data access requests need to be considered.
6. To promote collaboration and to reduce duplication of effort within the Research Environment: Registering a project will allow researchers within your domain and throughout all of GeCIP to be aware of the work that is carried out within the Research Environment. To allow export of allow export of analysis results: The Research Registry provides a page for collaborative development of a manuscript within the Research Environment. Use of this page to prepare a manuscript is not compulsory; manuscripts can be written outside the Research Environment. However, the Airlock Review Team will be reviewing requests for export of analysis results and manuscripts against the Research Registry information, so your project still needs to be registered. Manuscripts and analysis results will be allowed to leave the Research Environment only if they adhere to the criteria outlined above (ie i.e. if they abide by the Publication Policy, relevant Acceptable Uses of Data and the Publication Moratorium).
7. To provide a mechanism to enact the Publication Moratorium: Disease-facing domains have a protected time period for analysis and publication on participant data pertaining to their domain in recognition of the efforts of the domain members who have assisted in recruiting participants to the project.

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What is considered a research project?

A research project is considered to be any set of analyses or investigations that would ordinarily be the subject of a single research article, or piece of work within a student thesis. In some cases this may change during the research period; for example, a project may grow to encompass more than one planned publication. For this reason, you can add more than one publication to a record in the Research Registry. Preliminary searches of the data for the purposes of hypothesis generation or, for example, to generate pilot data for a funding proposal, would not be considered a research project.

The projects submitted to the Research Registry will be reviewed by Genomics England to ensure that they are within the bounds of valid Access Review Committee approval from the research lead’s domain. The Research Registry also provides Genomics England with an overview of the research activity being undertaken in the Research Environment; as such, any files moved out through the Airlock must be associated with activities covered by a registered and approved research project.

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A project can be registered by anyone who wishes to lead on a involved in a study that is aimed to result in one or more publications and would otherwise be considered . You do not need to be the lead author on a publication, or a student/supervisor of a student project.

Remember to contact the relevant domain lead before registering a new project.

leading the project to register it but you should discuss it with the project lead if not. 

If you have not spoken to your domain lead about the project you are registering, we suggest that you do so before submitting the form. 

Outlined below are the most likely scenarios when registering a project:

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Please note, you can use genomes protected under another domain's moratorium as controls or to investigate a disease unrelated to the domain they fall within.

Who can join a project?

When a project lead registers a project, they provide a summary of the work they plan to carry out. This abstract is visible to all GeCIP members, regardless of their involvement in a given project. A list of all current and completed research projects is available within the Research Registry and can be reviewed by all GeCIP members accessing the Research Environment. Project status is given for each entry, indicating the progress of the project through the Research Environment.

Any GeCIP member can request to join a project listed in the Research Registry. Below are the likely scenarios:

1. A GeCIP member is interested in joining a project within their domain. While each project lead is encouraged to positively consider applications to join a research project, the decision on whether to accept or reject an application is entirely theirs.
2. A GeCIP member is interested in joining a project outside their domain. As above, the project lead may decide whether to accept the applicant. If accepted, the applicant is collaborating with the domain in question and is not restricted by the moratorium period.

How do I review the status of a project?

To view the Research Registry, you need to navigate to the Research Registry. To do so, log into the Research Environment. Click the icon "Research Environment Documentation", then click "GeCIP" and navigate to "Research Registry" on the side menu.

You will be able to view all projects that have been registered and their status:

• Under review – being reviewed by Genomics England, not yet approved
• Approved – project has been approved by Genomics England and can begin work
• Publication in draft – research team has created a publication and are writing up their project
• Publication under review – project has been completed and is waiting export via ‘Airlock’
• Published – project has been published in a journal.

Using the Research Registry at a glance

The flowchart below outlines a series of steps necessary to register a project and use the Project Registry for collaboration purposes. For detail on specific items, please go to the subheadings below.

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To enable the greatest research value to be extracted from the 100,000 Genomes Project, and to ensure that all research is carried out under a valid ARC approval, we require that all research projects carried out within GeCIP are logged and summary details are openly available. A registered project is also a prerequisite for associated airlock exports and publication submissions.

The system by which this will be administered is the Research Registry, a form which is built into Confluence within the Research Environment.

By entering your research project into the Research Registry, you and your co-researchers are provided with a private Confluence space where you can collaborate on analyses and documents.

Our definition of what constitutes a research project is:

a set of analyses that cumulatively would be within the scope of a single research paper. It may either be a small focused analysis using a small amount of data, or a large more complex project involving multiple researchers from multiple domains. In both cases there should be a single overarching, well-defined research question, and detailed aims, objectives and methods.

If, as the research project progresses, it becomes clear that it may be more appropriate to make it the subject of multiple publications, it is recommended that the original project be split into multiple project accordingly. Preliminary searches of the data for the purposes of hypothesis generation or, for example, to generate pilot data for a funding proposal, would not be considered a research project.

How to register your project

Register your project

Navigate to the Research Registry Project Submission Form page. Log into the Research Environment. Click the icon "Research Environment Documentation", then click "GeCIP" and navigate to "Research Registry" on the side menu, then the subpage "Research Registry Project Submission Form".

Complete the “Register a project” form

How to complete the "Register a project" form

• Date
• Project title
• Project lead
  • You can search for and add a project lead. You will only be able to find profiles for GeCIP members who have accounts and have completed their Information Governance training. Those who haven't can be added as external contributors below.
• Co-researchers
  • You should include all researchers who are expected to be authors on any publication resulting from this project as co-researchers. For GeCIP members who have received account details for the Research Environment, you will be able to add them by searching for their name.
  • If anyone working on the project does not have an account for the Research Environment (yet), or hasn't completed their Information Governance training, you will not be able to find them by searching for their name. Instead you can add them as ‘external contributors’ on the page after you have selected co-researchers; you will need their full name and email address in order to do this.
• External collaborators

• Project contact email
  Please provide the email any queries about the project or requests to join should be sent to
• Research area
• Rare disease  group (if applicable)
• Rare disease subgroup (if applicable)
• Cancer type (if applicable)
• Cancer subtype (if applicable
• Funding

• Name of funder

  • If you are applying for funding or have received funding for your project, you should state this here. This will be used to determine who owns the intellectual property for your project.

• Abstract and lay summary

  • You must provide an abstract and lay summary of your project. These will be visible to anyone looking at the Research Registry. The lay summary may be used to describe your project on the Genomics England public website, if permission is granted by the project lead, and should be understandable by patients and the general public

• GeCIP domains (you can select multiple domains)

  • Please list the domains you are interested in researching data from.
  • You will need to select the GeCIP domain(s) that the project pertains to. You should be a member of this domain.
  • If your project is part of more than one domain, you can add addition domains in the ‘Other GeCIP Domain(s)’ section. You can select multiple domains by holding CTRL/CMD and clicking the domain name.

• Related project

  • If any related projects have been submitted to the Research Registry, please provide their Registry ID

• Are any of the genomes that you want to use currently under moratorium?

  • You should check in the 'domain_assignment' table in LabKey to see which genomes are under moratorium

Check the box to accept that Genomics England reserves the right to refuse this project.

When you are ready, click “Register”.

The status of your project will be 'blank’. If you do not do this, your project is not registered with Genomics England, so has not been approved and no one can request to join it.

A member of the GeCIP team at Genomics England will review your project, and change the status to "UNDER REVIEW". A GeCIP team member will ensure the project is in line with your domain’s ARC-approved research plan. You will receive a notification when it has been approved by Genomics England and the status of your project will change to 'APPROVED'.

Your research project will have its own space within confluence, which the GeCIP team will create on your behalf. This space is where all members of the project can create and edit pages. You can use this space for writing updates on your project, problem solving, writing up your methods/results, etc. The home page is automatically created when you submit your project and you can customise this in any way you like. Only those who are listed as co-researchers can edit the pages within your project’s space, but all GeCIP members can view them.

If you have any queries please contact [email protected] or contact us via RocketChat.

How to join an existing project

All projects submitted to the Research Registry are visible. The contact email address for the project lead is present. Please contact the lead directly to request to join the project. Anyone can request to join a project, but while each research lead is encouraged to positively consider applications to join a research project, the decision on whether to accept or reject an application is entirely theirs.

You will receive a notification of the outcome of your application.

You cannot request to join a research project once it reaches ‘PUBLICATION IN DRAFT’ status as at this point it is expected that all research on the project is complete and the project team are working on writing up their results for publication, so you would not meet the ICMJE authorship criteria.

Your Research Project Space

Your research project will have its own space within confluence, which the GeCIP team will create on your behalf. This space is where all members of the project can create and edit pages. You can use this space for writing updates on your project, problem solving, writing up your methods/results, etc. The home page is automatically created when you submit your project and you can customise this in any way you like. Only those who are listed as co-researchers can edit the pages within your project’s space, but all GeCIP members can view them. This space and any pages it contains will only be accessible to those with access to the Research Environment.

If you want to make the page private then you can edit the page restrictions by clicking on the 3 dots menu in the top right hand corner. Then navigating to "Restrictions". Here you can name the users that you want to be able to view and edit the space.

You should include all researchers who are expected to be authors on any publication resulting from this project as co-researchers. For GeCIP members who have received account details for the Research Environment, you will be able to add them by searching for their name. If anyone working on the project does not have an account for the Research Environment (yet), you can add them as ‘external contributors’ on the page after you have selected co-researchers; you will need their full name and email address in order to do this.

Note, external collaborators will not be able to view and interact with the project space in Confluence as they will not have the necessary credentials to log into the Research Environment.

Creating Publications

There is the option to use Confluence to prepare your publication draft. Although it may not have all the formatting options available in word processors, Confluence is ideal for collaborating on text and will allow you to:

• Have complete version control: to view the history of a page click on the 3 dots menu in the top right and select Page History
• Import and Export from Word: click on the 3 dots menu and select either Import from Word, or Export to Word.
• Add comments to a page or inline: add a comment at the bottom of the page, or select some text and click on the comment icon above it.
• Link to articles: Pubmed has been whitelisted in the Research Environment, so links to any pages on http://www.ncbi.nlm.nih.gov/pubmed/ will be accessible from Confluence.

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How to register your project

Navigate to the Research Registry Project Submission Form page. Log into the Research Environment. Click "Research Registry" then the subpage "Research Registry Project Submission Form" on the side menu.

A member of the GeCIP team at Genomics England will review your project, and change the status to "UNDER REVIEW", and ensure the project is in line with your domain or company's ARC-approved research plan. You will receive a notification when it has been approved by Genomics England and the status of your project will change to 'APPROVED'.

If you have any queries, or if you want to edit or change the status of your project (e.g. to "publication under review"), please contact [email protected].

How do I review the status of a project?

A list of all current and completed research projects is available within the Research Registry and can be reviewed by all researchers accessing the Research Environment. To view the Research Registry, log in to the Research Environment and click the icon "Research Registry". Please note that because the Research Registry is inside the Research Environment, one needs to be a researcher with an active Research Environment account to be able to view it.

You will be able to view all projects that have been registered and their status:

• Under review – being reviewed by Genomics England, not yet approved.
• Approved – project has been approved by Genomics England and can begin work.
• Not Approved – project has not been approved by Genomics England. Where this happens, we will contact the project lead.
• Publication under review – project has been completed and is waiting export via ‘Airlock’.
• Published – project has been published in a journal.

Collaborating on a Project

Any researcher can request to join a project listed in the Research Registry by using the contact email provided for the project to get in touch with the lead researcher. If they are happy to collaborate, the lead can email [email protected] and we will add any co-researchers or external contributors to the project. While each project lead is encouraged to positively consider applications to join a research project, the decision on whether to accept or reject an application is entirely theirs. If you are accepted to collaborate on a project outside your domain you will be collaborating with that domain and not be restricted by the moratorium period.

You can request a Research Space within the Research Environment for your project by emailing [email protected]. This is a JIRA page where researchers can share notes and updates on their projects. These pages are only accessible from within the Research Environment and you will be able to edit who has permissions to view and edit the page by clicking the 3 dots menu in the top right hand corner. Then navigating to "Restrictions". 

Creating Publications

There is the option to use Confluence to prepare your publication draft. Although it may not have all the formatting options available in word processors, Confluence has some useful features for collaborating on text and will allow you to:

• Have complete version control: to view the history of a page click on the 3 dots menu in the top right and select Page History
• Add comments to a page or inline: add a comment at the bottom of the page, or select some text and click on the comment icon above it.
• Link to articles: Pubmed has been whitelisted in the Research Environment, so links to any pages on http://www.ncbi.nlm.nih.gov/pubmed/ will be accessible from Confluence.