3. Collections

Projects can be aggregated into collections. The structure of a collection largely mirrors that of a project, but there is important functionality unique to collections. Of note, collections allow: 1) easy access to attributes across all constituent projects, largely removing the need to maintain spreadsheets for data cohorts, and 2) the ability to query variants and attributes across the entire cohort.

A collection is the natural home for a cohort that shares a common theme — for example, all cases referred for a particular disease area, all cases enrolled in a research study, or all cases handled by a given laboratory. Each case remains its own project; the collection sits above those projects and lets you view and analyze them together. A project can belong to more than one collection.

The pages within a collection parallel those within a project, and are accessed from the left menu. In the home table of projects and collections, collections are shown in green and carry a badge indicating how many projects they contain, making them easy to distinguish from individual projects (see Getting Started).

3.1. Collection Home

The Collection Home is the dashboard for the cohort, where various high-level information about the collection is brought together — for example, Collection Info, Recent Documents, and recent Activity, alongside any pinned charts. As with a project, important attributes, conversations, charts, and variants can be pinned here so that the most relevant cohort-level information is immediately visible.

3.2. Projects

The Projects page lists every project (case) contained in the collection. To view all projects within a collection, click Projects in the left menu; a Search bar lets you find a specific project within the collection by name. From here you can open any constituent project, and — with appropriate permissions — create a new project directly inside the collection.

Creating projects from within the collection is recommended: a project created here is automatically made available to all collection members with the same role they hold on the collection, and any template and scopes of work associated with the collection are applied automatically. See Creating Projects and Collections for the full project-creation workflow.

3.3. Samples

The collection Samples page aggregates the samples from every project in the collection into a single table. Selected sample attributes can be displayed as columns (using Edit Columns), allowing you to review, sort, and compare values such as relation, affected status, sex, and quality metrics across the entire cohort at once. As in a project, check boxes and the Actions and Launch App buttons let you act on individual or multiple samples. See Sample Attributes for more on the information.

3.4. HPO Terms

The collection HPO Terms page brings together the phenotype terms recorded across all probands in the cohort. This provides a cohort-level view of the clinical features represented in the collection, which is useful for understanding the composition of a study population and for identifying samples that share particular phenotypes. The mechanics of viewing and assigning HPO terms are the same as in a project; see HPO Terms.

3.5. Variants

One of the most powerful features of a collection is the ability to query variants across every individual in the cohort at once, rather than project by project. The collection Variants page uses the same table, annotation, and filtering tools described in Variants, but applies them across the whole cohort. This makes it straightforward to ask cohort-level questions — for example, which individuals carry a variant in a particular gene, or how often a given variant appears across the population of cases. Filtering on a Gene Set is especially useful at this level. If the collection variants table is empty, please contact the Frameshift team and we can enable this feature for your collection.

3.6. Conversations

The collection Conversations page holds discussion threads that belong to the cohort as a whole, separate from the conversations inside each individual project. Use collection conversations for cohort-wide topics — study coordination, shared protocols, or decisions that affect multiple cases. The conversation tools (watching, pinning, mentions, and notifications) work the same as described in Communication.

3.7. Documents

The collection Documents page stores files relevant to the cohort rather than to a single case — for example, a study protocol, a data-sharing agreement, or summary reporting. Documents are uploaded and managed in the same way as in a project (see Documents).

3.8. Analytics

Charting at the collection level is where Mosaic's analytics are most valuable. Because a collection aggregates attribute values from every constituent project, a single chart can summarize the entire cohort — for example, the distribution of diagnostic status, sample sex, or a quality-control metric across all cases. This is an efficient way to monitor data quality and track progress across a program. Charting is described in full in Analytics and Charts.

3.9. Analyses

The collection Analyses page lists analytical workflows run at the cohort level and provides access to their results, mirroring the project Analyses page.

3.10. Settings & More

As in a project, Settings & More in the left menu gathers the collection's administrative pages.

3.10.1. Settings

The collection settings mirror those of a project. Collection Information lets you edit the collection's name, description, and privacy level. Collection Members lets you review who has access to the collection and, if you have Admin permission or above, invite members and adjust their roles; roles granted on the collection propagate to projects created within it. This area also includes Subscriptions, where you can choose to receive notifications about tasks across the collection — see ClinVar Reanalysis and Tasks. Member roles and the actions they permit are described in Project Members.

3.10.2. Applications

The Applications page controls which web applications are enabled and how they are configured for the collection. See Client Applications for documentation on the individual tools.

3.10.3. Genes

The Genes page lets you browse genes for the collection's reference genome and define Gene Sets (panels) for use in cohort-wide variant filtering. Gene Sets are described in Genes.