Tree of Life Profile

In COPO, a Tree of Life (ToL) [1] work profile [2] is required to submit research objects [3] such as samples, barcoding manifests, sequence annotations, reads, assemblies and files.

A ToL profile can be used to create one of the following biodiversity projects:

Aquatic Symbiosis Genomics (ASG)
Darwin Tree of Life (DTOL)
Darwin Tree of Life Environmental (DTOL_ENV)
European Reference Genome Atlas (ERGA)

Steps to Create a Tree of Life Profile

1. Choose Profile Type

Important

The profile type dropdown menu is displayed beside the Work Profiles page title. By default, it will only display the Genomics profile option.

If your desired profile type is not displayed in the dropdown menu, please indicating the type of profile group that you would like to be granted access to. Thereafter, the desired profile type option will be displayed in the dropdown menu (along with the default Genomics profile type).

Please ensure that you select the correct profile type from the dropdown menu when creating a new profile record.

Hint

Please see the Projects brokered through COPO section for an overview of the projects i.e. profile types that are brokered through COPO.

Choose the desired profile type from the dropdown menu.

See the following screenshot for possible Tree of Life (ToL) profile type options.

Please refer to the important note above if the desired profile type is not displayed in the dropdown menu.

ToL Profile: Dropdown menu showing all profile types; including the default option, ‘Genomics’

After you have chosen a profile type option, click the Add new profile record button to view the Add Profile form for the desired profile type

ToL Profile: Add new profile record button

2. Provide Profile Details in the Add Profile Form

In the Add Profile form dialogue, provide details for the new profile.

See the following sections for more information:

Title & Description

Choose Associated Profile Type (if applicable)

Choose Sequencing Centre (if applicable)

Input Locus Tag

Save Profile Details

Title & Description

Hint

Both profile Title and profile Description are mandatory form fields.

Meaningful field values are recommended in the form boxes because the information will appear in submissions of the research objects associated with the profile, in public remote repositories.

ToL Profile Form: Provide profile title and description

Select Associated Profile Type (if applicable)

Note

The Associated Profile Type dropdown menu will only display if the European Reference Genome Atlas (ERGA) profile type is selected.

It is mandatory to choose an associated profile type or subproject when creating an ERGA profile.

More than one associated type also known as subproject or child project can be chosen.

ERGA Profile Type Form: Choose associated profile type or a subproject [5]

Select Sequencing Centre (if applicable)

Note

The Sequencing Centre dropdown menu will only display if the European Reference Genome Atlas (ERGA) profile type is selected.

It is mandatory to choose a sequencing centre when creating an ERGA profile.

If Sanger Institute is selected as the sequencing centre, the Associated Profile Type field will automatically be set to Sanger Institute Approval Needed (SANGER).

See the Sequencing Centres that utilise COPO FAQ for additional information.

ERGA Profile Type: Choose sequencing centre

Input Locus Tag (if applicable)

ToL Profile form: Input locus tag

If applicable, input the ENA [4] Locus Tag in the form box. Please refer to the Locus tag prefix creation FAQ for guidelines.

3. Save Profile Form

Click the Save button to save the profile details entered in the Add Profile form.

4. Profile created

The new profile will be displayed in the Profile list

ToL Profile: ‘Work Profiles’ web page displaying the created profile

Hint

The list of profiles or profile records on the Work Profiles web page can be sorted by date created, profile title or profile type.

Choose the desired sort type from the Sort by dropdown menu (at the top-right of the profile record).

See more information in the Sorting Profiles section.

Tree of Life Profile Components

A COPO profile [2] defines a set of component types from which instances of research objects can be created.

The following component types are currently defined:

Tree of Life Profile Components

Component instances defined within a profile will only be visible within that profile.
To access a component within a profile, click the component button displayed within the popup after the button was clicked (see the screenshot above).

Footnotes