Annotation

Here we present an overview of all the annotations of E3C. Please refer to the annotation guidelines for more detailed descriptions and examples.

Temporal Information

 Annotation of temporal information includes the following span-based annotations and attributes:

TIMEX3: time expressions (e.g. "10 days", “3 years ago”)
Attributes:

• timex3Class (possible values: "DATE", "DURATION", "PREPOSTEXP", "QUANTIFIER", "SET", "TIME")

• function InDocument (possible values: "DOCTIME", "SECTIONTIME", "NONE")

• value (e.g. "10D" for "10 days"; for dates and times we follow the ISO 8601 standard)

EVENT: events (e.g. “history”, “diagnosed”, “ITP”, “splenectomy”)
Attributes:

• eventType (possible values: "ASPECTUAL", "EVIDENTIAL", "N/A")

• docTimeRel (possible values: "AFTER", "BEFORE", CONTAINS", "IS-CONTAINED", "OVERLAP")

• degree (possible values: "LITTLE", "MOST", "N/A")

• contextualAspect (possible values: "INTERMITTENT", "NOVEL, "N/A")

• contextualModality (possible values: "ACTUAL", "GENERIC", "EDGED", "HYPOTHETICAL-IF", "HYPOTHETICAL-OTHER")

•  permanence (possible values: "FINITE, "PERMANENT")

• polarity (possible values: "NEG", "POS")

Annotation of temporal information includes the following relations:

• ALINKS: aspectual relations that are created between an aspectual event, the source of the relation, and its subordinated non-aspectual event, the target of the relation (relation types are CONTINUES, INITIATES, REINITIATES, and TERMINATES).

• TLINKS: temporal relations that can hold between two events, between two time expressions or between an event and a time expression (relation types are CONTAINS, BEFORE, BEGINS-ON, ENS-ON, SIMULTANEOUS, and OVERLAP)

Clinical Information

Annotation of clinical entities includes the following span-based annotations and attributes:

CLINICAL ENTITY: disorders, defined in UMLS as "a definite pathologic process with a characteristic set of signs and symptoms" (e.g.  "ulcer", “nausea”)
Attributes: 

• • entityID: the UMLS concept unique identifier (CUI) of the entity to which the annotation can be mapped (e.g.  "C0041582" for "ulcer"]

ACTOR: any person or animal mentioned in the text (e.g. “A 54-year-old female patient”, “she”, “the patient”)
Attributes:

• age (e.g. "54")

• role (possible values: "H-PROFESSIONAL", "PATIENT", "OTHER")

BODYPART: parts of the human body (e.g.  “duodenum")
Attributes:

• eventiveValue (possible value: "EVENT", "N/A")

RML: (often numeric) results and measurements (e.g. “3000-8000/μL”)

Annotation of clinical information includes the following type of relation:

• PERTAINS-TO: links an RML (source) to the appropriate test EVENT (target) (e.g. "3000-8000/μL” PERTAINS-TO “platelets”)