Sharing and Permissions

Overview

OpenCGA Catalog provides an authenticated environment to manage data. It counts with a powerful mechanism of custom-built and secure permission system defined by a mechanism of Access Control Lists (ACLs).

The system enables to define a list of permissions at any entity level. The permissions are granted to members, being a member either a isolate user or a defined group of users.

Users

A User is generally a person who will be using OpenCGA. The idea in OpenCGA is that every single person have its corresponding user created in OpenCGA. Every user should be authenticated (see Authentication section) to be able to perform any action. However, to be able to perform any actions, users will need to be granted some specific permissions or to have a specific category within the Study (see Sharing and Permissions section).

There are two default types of user accounts:

• full: these users have permission to create projects and studies.

• guest: users that will not have the possibility to create their own projects and studies. Despite this, these users will still be able to collaborate (view, write...) in other user's studies as long as they have been granted the proper permissions.

Groups

You can create group of users, this will simplify data permission management. Groups are defined at study level, i.e. each study contains different groups. Groups can only be created by the study owner or the study admins. A Group of users will generally bring together users that have something in common. Groups are strongly related to permissions in Catalog (see Sharing and Permissions section). For example, let's imagine that we have 5 different departments in our institution and each department requires different permissions to the data. In that case, we could think of creating as many groups of users as different departments we have in our institution and give the specific permissions to those groups (not to the users) that have been created in OpenCGA. Doing it this way have lots of benefits:

• A user belonging to different departments (groups) will have the permissions from all the groups he/she belongs to.

• If one user leaves the department, we would just need to remove that user from the corresponding group. That user will automatically lose the permissions the group has*.

• If one user starts in the department, we would just need to add that user to the corresponding group. That user will automatically gain the permissions the group has.

* Unless the user had some or all the permissions granted to the group defined in a different group he/she might still belong to or assigned directly to the user.

All studies have always two administrative groups that cannot be deleted or renamed, these are admins and members.

Projects

Any full user can create any number of projects (and studies). A Project is a piece of planned work or an activity that is finished over a period of time and intended to achieve a particular purpose (Cambridge dictionary definition). A Project in Catalog is understood as a scientific project for one concrete species. Any project in Catalog will contain at least a name, an alias (project identifier) and the species organism. But it can also contain the organisation and a description of the project.

Projects are used as the central piece for variants storage.

Studies

Projects are composed by a set of studies. A Study is the activity of examining a subject in detail in order to discover new information (Cambridge dictionary definition) Any project owner can create as many studies as necessary. Most of the Catalog data models, except for User and Project belong to a particular Study, so it can be seen as the central piece in OpenCGA Catalog. A Study contains, similarly to Project, a name and an alias (study identifier). Optionally, it can have a description as well.

Groups in a Study

Despite the explanation of Groups from a previous section, Groups are actually defined within a Study. Different studies can have different groups of users that are basically defined by the Study owner or administrators. By default, every Study is created with two reserved groups (admins and members). The roles of these two groups is described in Sharing and Permissions section.

Variable Sets and Annotation Sets

One of the most outstanding features of OpenCGA Catalog is the ability to not only store any type of data in the database, but also filter and query by any of the values populated by the researchers. This can be achieved with what we have called Variable Sets and Annotation Sets.

A Variable Set is a set of Variables, understanding as a Variable the complete definition of a field that need to be populated. In other words, a Variable Set could be seen as a template of a form that is given to the patient containing the points the patient should fill in. A Variable Set will look similar to the table shown above. That Variable Set is composed of four well described Variables:

Variable	Sex	Categorical	Yes	MALE, FEMALE, UNKNOWN
Variable	Age	Integer	Yes	NA
Variable	Mother name	Text	Yes	NA
Variable	Affected	Boolean	Yes	NA

Every Study can have as many different Variable Set definitions as necessary.

The values defined for each of the Variables are called Annotations, and the population of a whole Variable Set is called Annotation Set. This means that an Annotation Set only makes sense and is always related to one concrete Variable Set.

There are four Annotable data models: Sample, Individual, Family and Cohort. Each entry from these data models can have Annotation Sets as can be seen in the diagram in the right margin. An Annotation Set will look to something similar to:

Annotation	Sex	MALE
Annotation	Age	60
Annotation	Mother name	Jane
Annotation	Affected	Yes

OpenCGA allows querying by any of these key-value pairs.

Files

OpenCGA Catalog keeps track of all the files and folders containing the relevant data. Every File registry contains the physical path where the files/folders are stored in the file system (uri). Besides this, Catalog creates a virtual file structure so no matter what the real location of the files are, users can organise and work with those files differently. Everything related to Files can be found in the File Management section.

Individuals and Families

We understand an Individual as a subject (typically a person) for which some analysis will be made. A group of Individuals with any parental or blood relationship is called Family. Any of these two data models can have Annotation Sets defined.

Samples and Cohorts

A Sample is any biological material, normally extracted from an Individual, that is used for a particular analysis. Cohorts contains groups of samples sharing some particular conditions such as "healthy" vs "infected". Any of these two data models can also have Annotation Sets defined.

Clinical Analysis

A Clinical Analysis contains all the information of the Individuals and Samples involved to perform a real clinical analysis. It also allows storing the interpretations derived from the results.

Jobs

OpenCGA Catalog allows running different tools. This tools can be any of the ones built in OpenCGA, but also any external tool the user might need to use. Every time the user calls to a analysis web service to run anything, a new Job is created. This jobs contain the essential information of the task that needs to be run. A daemon is in charge of checking whether there are any prepared, queued or running jobs and update the information.

OpenCGA supports SGE (Sun Grid Engine) that accepts, schedules, dispatches, and manages the remote and distributed execution of large numbers of standalone or parallel jobs.