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Our goal is to create a system that describes research study designs in a machine-readable format to facilitate rapid study development; higher quality research; easier replication; and sharing of methods between researchers, institutions, and countries.

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Concepts

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vs. Working Sets

A "concept" is the definition of a single entity that will be used in a research project. It may be a disease ("type 2 diabetes"), a treatment ("metformin"), a test result ("HbA1c"), or anything else that may be defined within the data. The definition is typically tied to the data source, so different coding systems would need different definitions (diabetes in primary care and diabetes in a hospital setting would be two separate concepts, defined in Read codes and ICD10 codes, respectively). In addition, different concepts may be created for different purposes. One researcher may want to tightly define diabetes with high specificity, while another might want to capture everyone with possible diabetes; these would be represented as two different concepts. Different users may have different definitions, simply because the correct definition is a matter of opinion. Creating multiple concepts to define the same thing is not a problem (though of course it is best to use a single, shared definition, unless there is a good reason not to). Currently, the system stores simple concepts, which can simply be defined as a set of clinical codes. It will be further developed in the future to allow more complex definitions, such as rule-based algorithms, to be stored and shared.

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All concepts within a working set can be referenced as a unit, and included within analysis as a unit via the API.

Search for concepts

Click on "concepts" to view the main list of concepts. A standard search interface is provided. One can also look for concepts that have specific tags associated them, using the tags box (which has autocomplete to discover tags). A tick box enables finding only concepts that you have created.

Content is never deleted from the system permanently–the "delete" function makes a concept invisible by default, but it is still present in the system. Deleted concepts can be included in the search by clicking the appropriate tick box.

You can only see content that has been shared with you (either because a concept has been made public, or because you are part of a group within which a concept has been shared). 

View a concept

Clicking on the magnifying glass icon to the far right of a concept in the results allows you to view it. The top portion of the page shows documentation and permission information. 

The "Components" section is where the clinical codes that make up a concept are actually defined. Each component matches a certain set of codes, and there are several types of components which implement several ways of adding codes:

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Components can be defined as "inclusion" or "exclusion". The codes matched by an "exclusion" component will be excluded from the concept, even if they appear in other "inclusion" components.

A full history of all changes made to a concept is stored, and that history is shown at the bottom of the concept page. The old versions can be viewed using the magnifying glass symbol.

Getting Started: Creating and Editing Concepts

To create a new concept, click the "Add new concept" button, or an existing concept (which you have permission to edit) may be edited by clicking the pencil button in its row, or clicking the edit button after viewing the concept.

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Any user who has permission to view a concept can copy it to a new, identical concept using the "fork" button (this can be done either to the latest version or an older version of a concept).

Creating and editing working sets

Working sets can be created in much the same way as concepts; they have a similar documentation section, and permissions, history, etc. work in the same way. See the above section on creating and editing concepts for more information.

To add concepts to a working set, click on "add concept", which adds a new row. You can then enter a concept in the field that is created; there is autocomplete functionality to help you find the concept you are looking for. To remove the concept and replace it with a different one, click the circular arrow icon. To delete a row completely, click the red X icon.

You can also click "add attribute" to add a new column that allows setting a value for each concept included in the working set.

• You must enter a name for each attribute added. Requirements for names follow typical database naming conventions (case insensitive, must start with a letter, can be followed by any combination of letters, numbers, and underscores). Attribute names must be unique.
• For each attribute, you can specify int, float, or string as the type. The values entered in a field will be validated against this type (blank is allowed for any type of attribute).

Any number of attributes is allowed, but currently the user interface does not work well for more than 3-4 attributes. This is a known issue and will be resolved in the near future.

Added concepts and attributes are not saved to the working set until you click the Save button.

Concept Library and the SAIL Gateway

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