Creating & Sharing Collections

About Collections

Pathogenwatch collections are a way of creating meaningful groups of genomes for comparing and sharing with collaborators and the communities.

• Collections are the easiest way of sharing data with colleagues or the general public. Some Collections are pre-built, and accessible from the Collections page.

• Collections you create are shown in the "My Collections" section on the Collections page.

• You can explore a Collection using the Interactive Collection View. Each Collection's URL is permanent, so you can bookmark it in your browser to return later. The "name" text is optional and doesn't affect navigation (see note).

Typical uses of collections include:

• Supplementing publications (see How to cite),

• Providing an interactive public interface to a large-scale survey,

• Storing the results of a particular study or investigation for future reference,

• Highlighting an observation and sharing with public health colleagues.

Creating A Collection

Collections can be created in one of two ways - The genome selection basket - The Interactive Collection View ( See: Creating sub-collections)

Genome selection basket

Collections are created by first selecting genomes on the Genomes page (or from a Folder, as when you have just uploaded genomes).

Select genomes using the tickboxes. You can select "All in this search" if the Search returned <5000 genomes, but only up to 2000 genomes can go into a Collection. You can select genomes from multiple searches before creating a collection.

When you have (1) selected a set of desired genomes, (2) open the "Selected Genomes" basket and click the (3) "Create Collection" button. (4) Give your Collection a name and description (perhaps to explain its purpose to others), and (5) click Submit. This brings up the Interactive Collection View.

Selecting Genomes & Creating a Collection on the Genomes page

Explore your Collection in the Interactive Collection View, including generating a tree if that is supported for the species in your Collection.

Collection URLs

The URL of the collection is permanent, and is composed of a unique unpredictable identifier (required) and the title of the collection (optional, for readability). The only part that affects navigation is the part before the "name" text. Thus, you can change the title of the Collection, and although that may be reflected in the URL, that does not change navigation or bookmarks. The following three URLs would all point to the same Collection.

• /2SzTQfQ6TPMadzqvRoVY5c

• /2SzTQfQ6TPMadzqvRoVY5c-50-s-enterica-genomes

• /2SzTQfQ6TPMadzqvRoVY5c-new-name-for-the-collection

Sharing your collection

By default, collections are private and can only be viewed by the creator of the collection.

The owner of a collection can share it by changing access settings and then sharing the URL. This process is reversible.

Steps to sharing a collection

1. In the Interactive Collection View, click the "share" icon in the top right. This opens the "Share Collection" dialog box.
2. Choose who should have access to the collection:

   1. "Public" access gives access to anyone who has the URL.

   2. "Private" limits access to people you specifically add in the "Invite" box, and you can choose what kind of access they should each have (Viewer, Editor, Manager).

3. Copy the URL and share it. Regardless of the settings above, nobody will be able to get to your collection without knowing the URL.

To un-share a collection, open the "Share collection" dialog, set access back to Private, and revoke access for each of the invited collaborators.