Annotation_schema_condition_spans
Annotation Schema for Indexing Clinical Conditions from ED Reports
May 17, 2005
Num Variables
Definition
Annotate
Annotation
otati Example
Medical Concepts
Single clinical condition
EXCEPTION to Y: Multiple, Multiple clinical conditions that share
inextricable clinical
conditions
EXCEPTION to Y:
Conditions that share
adjectives and other
Annotate each
modifiers
condition and its
relevant modifiers
separately, using
disjoint spans where
necessary
Historical findings
Procedures
Symptoms
Common risk factors
taking illegal drugs. These risk factors
Drinking alcohol: 1)
alcohol; 2)
drinks
Taking drugs: 1)
drug; 2) drug names
Qualitative physical findings
Annotate all relevant §
Has good perfusion
words even if they are
disjoint
Quantitative physical findings
EXCEPTION to Y: with
qualitative modifier
Prefer the qualitative
over the quantitative
Qualitative radiological findings A radiological finding that does not
Qualitative diagnostic test results A diagnostic test result (e.g., lab test,
Quantitative lab test results
A lab test result with a numeric value –
Diagnoses
Demographics
Medications
EXCEPTION to N:
Included in clinical
condition
Non-specific clinical words
EXCEPTION to N: with
Trauma/Accident
Vague causes of a clinical
A cause for a clinical condition that is
condition
Therapeutic interventions
Linguistic Form
Noun phrase or verb phrase
Clauses or verb phrases modifying Parts of a clause or verb phrase
EXCEPTION to N: verb
phrase ends in -ing
clinical condition ends in
–ing
EXCEPTION to N: clinical Nominal clinical condition is
condition alone is
meaningless
Ambiguous adjective
Unambiguous adjective
Section headings
Lexicalized expression
Lexicalized expressions are phrases or sentences
(contiguous by definition)
that would not normally be annotated because of
their linguistic form but that can actually be treated
§
Regular rate and rhythm §
Extraocular muscles are
as single words, because they occur so frequently.
Lexicalized expressions can be annotated in any
linguistic form, regardless of other rules. The
relevant body part or organ should be annotated as
part of the lexicalized expression, if it is
- pupils equally round and reactive to light and
- chest/lung sounds clear and equal bilaterally (to
- abdomen soft, non-tender, and non-distended
Lexicalized expression that is not The lexicalized expression is not contiguous in the
contiguous
Determiners used with nominal A definite or indefinite article, possessive
clinical condition
adjective, or demonstrative adjective used with a
EXCEPTION to N:
Determiner is contained within the phrase being
determiner is internal to
Coordinated modifiers
Modifiers separated from the clinical condition by
Modifier Types
Integral to meaning
A modifier that changes the meaning of the clinical
condition and is necessary for correct interpretation
Void of clinical meaning
A modifier that does not add any clinical meaning
Anatomic location
A modifier indicating the anatomic location of the
§
tenderness at McBurney’s §
tenderness over the
EXCEPTION to Y: vague
Anatomic locations that don’t provide any useful
anatomic locations
Sidedness
A modifier indicating the sidedness of the
Verticality
A modifier indicating the verticality of the
A modifier indicating the quality of the condition
Non-numeric severity quantifiers A non-numeric quantifier indicating the severity of
Numeric quantifiers
A numeric quantifier of a clinical condition
“otherwise” modifiers
Modifiers that indicate a condition in contrast to a
previously mentioned condition by using a word
Causal/association
An entity or action that caused or is associated
with the clinical condition being annotated. Both
Consequence modifiers without A modifier indicating that the clinical condition is
the causality
resulting or associated with a cause that is not
Uncertainty
A modifier indicating uncertainty of the condition
Negation
A modifier indicating the absence of the clinical
Time of onset
A modifier indicating the time of onset for the
§
previous ingrown toenails §
new arm redness
EXCEPTION to N: integral Time of onset modifier is not meant to indicate
to meaning of phrase
time of onset but is integral to the meaning of the
clinical condition. True for the following
Acute myocardial infarction, acute coronary
syndrome, acute sinusitis, chronic sinusitis, acute
Change over time
A modifier indicating a change over time for the
EXCEPTION to N: required A clinical condition would not exist without the
to be a clinical concept
change over time modifier – the change over time
Non-numeric duration
A non-numeric modifier indicating the temporal
Numeric duration
A numeric modifier indicating the temporal
Non-numeric Continuity/
A non-numeric modifier indicating that the clinical
episodic
Numeric Continuity/episodic
A numeric modifier indicating the clinical
Observer’s perception
A modifier indicating the observer’s perception of
Evidence
A modifier indicating evidence or signs of a
Source: http://blulab.ucsd.edu/sites/default/files/Annotation_Schema_condition_spans.pdf
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