2. Projects

Projects are the primary organizational unit within Mosaic. Typically, a project will represent an individual case, which could be a single patient, a family (for example, a family trio consisting of a proband and parents), or any other family structure. The project consists of the following pages, each accessible from the left menu:

2.1. Project Home

The Project Home acts as a dashboard for the project where important information can be aggregated. If the project is included in any collections, they will be listed at the top of the page. Which collections a project is in can be managed by clicking the +/- icon here.

The Recent Documents card at the top of the page provides quick links to project documents, e.g. pdf files. This makes it easy to view documents like clinical reports for a case.

Important attributes, conversations, charts, or variants can be pinned to the Project Home to provide a curated set of information immediately available upon entering the project. How to pin these objects is covered in the documentation sections dedicated to them.

The Project Home also displays the Variant Watchlist — any variants that have been flagged for the project (for example, candidate variants under active review or the flagged diagnostic variant). The watchlist is described in Variants. Conversations for the project can be opened directly from here using the Conversations button next to Dashboard.

2.2. Samples

Project samples refer to individual samples, typically a proband or family member. The Samples page (also present in collections) shows the project pedigree and provides a list of all the samples in the project along with any selected sample attributes associated with the sample. Default columns may include the sample name, Read Coverage, the Pedigree position, Kindred Name, Affected Status, Sex, and Relation (how the sample is related to the proband). As with other tables, the displayed columns can be edited by clicking the Edit Columns button at the top right of the table to include any other sample information. Default columns can also be modified using templates. See Templates.

Check boxes to the left of each sample allow individual or groups of samples to be selected, and then the Actions button provides a number of options, or the Launch App button allows different web apps to be launched. For more detail on the information attached to each sample, see Sample Attributes.

2.3. Project Attributes

Project Attributes displays all the project-level (as opposed to sample-level) attributes associated with a project. From here, you can create new attributes, import, edit, or pin them to Project Home. Project attributes are discussed here.

2.4. HPO Terms

Human Phenotype Ontology (HPO) terms provide a standardized vocabulary for describing the clinical features of a sample. Recording phenotype as structured HPO terms — rather than free text — allows Mosaic to relate a patient's clinical presentation to the genes and variants most likely to be relevant, and underpins features such as variant prioritization and the ClinVar Reanalysis process.

HPO terms are found under Ontologies in the left menu. The Ontologies page is organized into tabs — HPO Terms, MONDO Terms, and OMIM — and the HPO Terms tab lists every term currently attached to the samples in the project. Terms are typically assigned to the proband, but can be recorded for any sample.

To add terms, click the Actions button and choose Add HPO Terms to Samples. In the dialog you can search for terms individually or paste a list of terms into the text box, choose which samples the terms should apply to, and optionally record a Source for the phenotype information. You can search by term name (for example, seizure) or by HPO identifier (for example, HP:0001250). Terms can be removed at any time using the check boxes and the Actions menu.

Tip: Because HPO terms drive variant prioritization, it is good practice to record the proband's phenotype as completely as possible before beginning variant analysis. Where HPO terms are supplied as part of the case data on import, they will already be populated here for review.

2.5. Variants

The project Variants page is where annotated genetic variants for the case are viewed, filtered, prioritized, and discussed. Because variant analysis is central to Mosaic and shares the same tools in both projects and collections, it is documented in full in its own section. See Variants for a complete description of the variants table, annotations, filtering, the variant watchlist, and variant-level conversations.

2.6. Conversations

The Conversations page lists every discussion thread within the project. Conversations keep case discussion — on clinical presentation, a specific variant, available data, or next steps — in one shared, searchable location rather than in email. Conversations created in a project are visible only within that project.

From this page you can create a conversation, start or stop watching a conversation to control your notifications, pin a conversation to Project Home, or delete a conversation. The full set of conversation tools, including the cross-project conversation inbox, is described in Communication.

2.7. Documents

The Documents page stores files attached to the project, such as clinical reports, consent forms, requisition forms, or supporting correspondence. Storing documents alongside the genomic data helps keep a complete case record in a single location.

To add a document, use the Actions button and choose to upload a file. Uploaded documents appear in the table, where they can be opened, downloaded, or removed by users with appropriate permissions. Recently added documents also surface in the Recent Documents card on Project Home for quick access.

Warning! Documents may contain protected health information. Access to a document follows the access controls of the project it belongs to, and can be further restricted using Policies. Only upload documents to projects whose membership is appropriate for the information they contain. :::

2.8. Analytics

The Analytics page lets you generate charts from the attributes recorded in the project. Charts are a quick way to visualize and quality-check the data captured for a case. The same charting tools are available at the collection level, where they are most powerful for reviewing data across an entire cohort. Charting is described in full in Analytics and Charts.

2.9. Analyses

The Analyses page lists the analytical workflows that have been run on the project's data and provides access to their results. An analysis groups a set of inputs (for example, the relevant data files and parameters) with the output it produces, so that results remain reproducible and traceable back to the data they came from.

Each entry shows the analysis type and its status. Click an analysis to view its outputs. The analyses available to a project depend on the applications enabled for it; see Applications below and contact the Frameshift team if a workflow you expect is not available.

2.10. Settings & More

A lot of project information is stored under Settings & More in the left menu. Expanding this section reveals the project's settings together with management pages for data files, applications, and genes. These are all addressed below.

2.10.1. Settings

Project Information
The project information section allows basic information about the project to be edited. This includes the name, nickname, and description, as well as the privacy level of the project. The privacy level can be set to Public, Protected, or Private; the meaning of each level is described in Creating Projects and Collections.

Project Members
This section of the settings lets you look at who has access to the project, what their roles are, as well as invite people or edit their roles. Exactly what you are allowed to do here depends on your own role in the project. Only people with Admin access or above can modify users of a project. The top of this section shows a table of all current members and their roles (Figure 2.1). To edit a user's role (if you have permission), select the role dropdown next to the user's name and change their role.

To grant access to the project for new users, scroll down to the Invite a Collaborator table and search for the user name. Only users with active Mosaic accounts can be added. When the user has been selected, choose a role and add the user to the project. Typically users are added as Members. If the new user should be authorised to grant project access to other users, they can be given the Admin role.

The roles available, in increasing order of privilege, are:

• Viewer — can see project data and conversations but cannot make changes.
• Member — can edit project data, add attributes and HPO terms, work with variants, and take part in conversations. This is the typical role for most collaborators.
• Admin — everything a Member can do, plus the ability to manage members and their roles and to edit project settings.
• Owner — full control of the project, including the most sensitive settings.

The exact actions available to each role may be further shaped by Policies.

Project Tasks
Tasks are outstanding items that require attention in the project — for example, required attributes that have not yet been given a value, or variants flagged for review by ClinVar Reanalysis. This area lets you review the project's tasks and manage which task notifications you receive. Tasks are covered in detail in Tasks.

Project Templates
A template defines a standard set of attributes, conversations, and dashboard layout that can be applied to a project. The dropdown here shows the template currently applied to the project (if any) and lets you apply a different one. Applying a template never overwrites existing project content. Templates are described in Templates.

2.10.2. Data Files

The Data Files page lists the genomic data associated with the project — for example, alignment files (BAM/CRAM) and variant files (VCF) — together with the sample each file belongs to. This is where you can confirm that the expected data is present and correctly linked before launching applications or beginning analysis.

Each row shows the file, its type, and the sample it is attached to. Correct attribution of files to samples is important: it ensures that when an application such as a genome browser is launched, the right data is loaded for the right sample. If you experience errors or if files are missing or attributed to the wrong sample, contact the Frameshift team, as data loading is typically managed during onboarding.

2.10.3. Applications

The Applications page controls which web applications are available within the project and how they are configured. Mosaic integrates a range of client applications for visualizing and interrogating data, including the genome browser IGV and the iobio family of tools. Once enabled, these can be opened from the Launch App button on the Samples and Variants pages.

For documentation on the individual applications, see the Client Applications section.

2.10.4. Genes

For information on genes, see the dedicated section in the docs: Genes. In brief, the Genes page lets you browse the genes defined for the project's reference genome and build Gene Sets (panels) that can then be used to filter variants.