Immune Exposure Model Instructions

Please follow these instructions to fill out the immune exposure template.

Required Columns

These four columns are always required for every row:

Given a certain event type, other columns may be required, optional, or excluded. If a column is required, it may be restricted to a subset of the terminology. If a cell of this table is empty, then the column is excluded, and any value will result in an validation error.

Event Group Event Type Exposure Material Type Disease Type Disease Stage Specimen Type Specimen ID
life process birth
death
healthcare process patient visit
hospital admission
hospital discharge
study process study enrollment
study exit
specimen collection required required
administration vaccination required: vaccine
infectious challenge required: infectious agent optional: infectious disease optional
transplantation required: anatomical entity
occurrence of disease infectious disease required: infectious agent required: infectious disease required
allergic disease required: allergen required: allergic disease required
autoimmune disease required: autoimmune disease required
cancer required required
exposure without disease asymptomatic infection required: infectious agent
exposure with immune reactivity required: allergen
documented exposure required: material entity
exposure to ubiquitous agent required: infectious agent

1. Subject ID

The Subject ID is your own identifier for a single subject. Any non-blank value is allowed. This column is used to link multiple rows about the same subject.

2. Event Type

See the table above for the allowed event types. The event type column is required for every row. Based on the event type, other columns may be required, optional, or excluded. The event type can also restrict the allowed values for other columns. This column should be filled with the primary label of the term. If a synonym is used, the validator will recommend replacing it with the primary label.

3. Start Time

The start time and end time are always required. They can be provided as ISO8601 standard calendar dates or datetimes, or they can be provided as study days. Examples:

4. End Time

The end time is always required, and has the same format as the start time.

5. Exposure Material Type

When the event type indicates that the subject has been exposed to some material, then this column is required. It is usually restricted to a relevant type, such as a vaccine, infectious agent, translant material, or allergen. When this column is required, it should be filled with the primary label of the term. If a synonym is used, the validator will recommend replacing it with the primary label.

6. Disease Type

For disease types we use the Disease Ontology. When this column is required, it should be filled with the primary label of the term. If a synonym is used, the validator will recommend replacing it with the primary label.

The diseas type should correspond to the exposure material type. For instance, if the disease is dengue hemorrhagic fever then the exposure material type should be Dengue virus.

7. Disease Stage

When a diease type is specified, the disease stage must also be specified. Choose one of:

8. Specimen Type

For specimen types we use the Ontology for Biomedical Investigations. When this column is required, it should be filled with the primary label of the term. If a synonym is used, the validator will recommend replacing it with the primary label.

9. Specimen ID

When the specimen type is required, the specimen ID is also required. Like the Subject ID, the Specimen ID is your own identifier for a single subject. Any non-blank value is allowed.