Annotation Schema for Indexing Clinical Conditions from ED Reports
May 17, 2005
Num Variables
otati Example
Medical Concepts
Single clinical condition
EXCEPTION to Y: Multiple, Multiple clinical conditions that share
inextricable clinical
Conditions that share
adjectives and other
Annotate each
condition and its
relevant modifiers
separately, using
disjoint spans where
Historical findings
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
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
Included in clinical
Non-specific clinical words
EXCEPTION to N: with
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
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
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
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


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