Table 3 Named entity categories with definitions, examples, and relevant UMLS semantic types

Named entity categories from [12]

anatomy

Includes organs, body parts, and

head, neck, gum

Body System,

tissues.

Anatomical Structure

cellular_entity

Includes anatomical entities at the

hemoglobin,

Cell,

molecular or cellular level.

giant cell

Cell Component

diagnostic_

Includes tests and procedures used

biopsy, hemoglobin,

Diagnostic Procedure,

procedure

for diagnosis

iron levels

Laboratory Procedure

drug_supplement

Includes substances used for

atenolol,

Clinical Drug,

therapeutic purposes.

atenolol 50 mg,

Vitamin

campho-phenique

food

Refers to specific nutritional

eggs, breads, meat

Food

substances.

gene_protein

Includes specific genes and gene

BRCA1,

Gene or Genome,

products.

BRCA1 gene,

Enzyme

GLUT4 protein

geographic_

Includes countries, cities, etc.

India, Singapore

Geographic Area

location

lifestyle

Refers to daily and recreational

smoking, yoga

Daily or Recreational

activities.

Activity

measurement

A quantity that is a core attribute of a named entity, such as dosage of a drug.

10mg, 2%

Quantitative Concept

organization

Includes institutions as well as their

navy, California

Organization

subparts.

Hospitals

person_

Includes individuals (gender, age

daughter, female,

Age Group,

population

group, etc.) and population groups.

war veteran,

Population Group

16 year old

problem

Includes disorders, symptoms,

HIV, cholesterol,

Disease or Syndrome,

abnormalities, and complications.

broke,

Neoplastic Process

autoimmune disease

procedure_device

Refers to procedures or medical

shingles treatment,

Medical Device,

devices used for therapeutic

nephrolithotomy,

Therapeutic or

purposes as well as unspecific

implants

Preventive Procedure

interventions.

profession

Includes occupations, disciplines, or

dermatologist, dr,

Professional or

areas of expertise.

surgeon

Occupational Group

substance

Includes chemicals, hazardous

iron, cholesterol,

Inorganic Chemical,

substances, and body substances.

blood, alcohol

Biologically Active

Substance

other

Includes entities that are relevant to

more than once

Temporal Concept

question understanding, but do not

fit in one of the categories above.

Named entity categories added in the present study

organism_function

Refers to physiological functions of the organism.

pregnancy

Organism Function

research_cue

Indicates that consumer is interested in research information.

new, latest information

Qualitative Concept