Table 1 We collect the results of each call to OLS API in a table that contains: raw value (input value to the program, before parsing—not shown here); parsed value (input value after parsing the raw value); ontology (used to annotate the input value—not shown here); ontology_id (id of the term in the ontology used for annotating the parsed value); pref_label (preferred label of the ontological term used for the annotation); synonym (a list of synonyms associated to the term corresponding to the ontology id); match_score (where (P) and (S) respectively indicate that the score was calculated subtracting a penalty from the 10 or 9 initial match scores); onto_suitability; onto_acceptance; annotation_score. The table shows an excerpt of our results, ordered by descending annotation score

creatinine meas.

NCIT_C64547

Creatinine Measurement

Creatinine, Creatinine Level, ...

10 (P)

4.39

0.86

5.23

creatinine meas.

NCIT_C61048

Urine Creatinine Measurement

Urine Creatinine Measurement

9 (P)

4.39

0.86

4.71

mean arterial pressure

NCIT_C120935

Mean Pulmonary Arterial Pressure

MPAP, Mean Pulmonary Arterial Pressure

9 (P)

4.39

0.86

4.71

diverticulitis

EFO_1001460

diverticulitis

digestive tract diverticulum inflammation, ...

10 (P)

3.40

0.32

3.36

survival time

EFO_0000714

survival time

survival, time of survival

10 (P)

3.40

0.32

3.36

diastolic blood pressure

EFO_0006336

diastolic blood pressure

DIABP, diastolic pressure

10 (P)

3.40

0.32

3.36

viral load

EFO_0010125

viral load

viral titer, viral titre, viral burden

10 (P)

3.40

0.32

3.36

mean corpuscular hemoglobin

EFO_0004527

mean corpuscular hemoglobin

MCH, mean corpuscular haemoglobin

10 (P)

3.40

0.32

3.36

calcium measurement

EFO_0004838

calcium measurement

calcium levels

10 (P)

3.40

0.32

3.36

autoimmune disease

EFO_0005140

autoimmune disease

autoimmunity

10 (P)

3.40

0.32

3.36

moderate albuminuria

HP_0012594

Moderate albuminuria

High urine albumin levels, Microalbuminuria

10 (P)

3.40

0.32

3.36

glomerular filtration rate

EFO_0005208

glomerular filtration rate

GFR

10 (P)

3.40

0.32

3.36

anxiety

EFO_0005230

anxiety

10 (P)

3.40

0.32

3.36

diaphragmatic hernia

EFO_0007216

congenital diaphragmatic hernia

CDH, congenital diaphragmatic hernia, ...

9 (P)

3.40

0.32

3.02

sarcoidosis

EFO_0010723

ocular sarcoidosis

9 (P)

3.40

0.32

3.02

sneeze

EFO_0007887

autosomal dominant compelling helio...

photic sneeze reflex, Peroutka sneeze

8 (S)

3.40

0.32

2.69

anorexia nervosa

HP_0002039

Anorexia

Anorexia

8 (P)

3.40

0.32

2.69

lean body mass

NCIT_C139219

Lean Body Mass to Total Body Mass Ratio

Lean Body Mass to Total Body Mass Ratio, ...

5 (P)

4.39

0.86

2.62

fasting blood insulin meas.

EFO_0004465

fasting blood glucose meas.

fasting glucose-related traits, ...

7.5 (P)

3.40

0.32

2.52

protozoal diseases

MONDO_0001955

protozoal dysentery

7.5 (P)

3.40

0.26

2.43

primary sclerosing

EFO_0004268

sclerosing cholangitis

fibrosing cholangitis, cholangitis, sclerosing, ...

7 (P)

3.40

0.32

2.35

event free survival time

EFO_0004919

metastasis free survival

metastasis free survival time

6.5 (S)

3.40

0.32

2.18

response to vancomycin

NCIT_C76312

Vancomycin Resistant Enterococcus

Vancomycin-Resistant Enterococcus, VRE, ...

4 (P)

4.39

0.86

2.09

fish oil supplement exposure meas.

EFO_0009116

vitamin supplement exposure measurement

vitamin use exposure measurement

5.5 (P)

3.40

0.32

1.85

magnesium:creatinine ratio meas.

EFO_0007635

concentration dose ratio

CDR measurement

4.5 (S)

3.40

0.32

1.51

other and unspecified

EFO_0009734

unspecified juvenile idiopathic arthritis

unspecified JIA, ...

4 (S)

3.40

0.32

1.34

pre-eclampsia

DOID_10591

pre-eclampsia

gestational hypertension, ...

10 (P)

0.14

0.39

0.89

bipolar disorder

DOID_3312

bipolar disorder

bipolar depression, manic disorder, ...

10 (P)

0.09

0.39

0.85

binocular movement

MP_0006148

binocular blindness

7.5 (P)

0.59

0.28

0.77

asthma

HP_0002099

Asthma

Bronchial asthma, Asthma

10 (P)

0.16

0.31

0.75

stroke

SYMP_0000734

stroke

cerebral accident, brain attack, apoplexy, ...

10 (P)

0.10

0.25

0.58

schizophrenia

OMIT_0013465

Schizophrenia, Paranoid

9 (P)

0.27

0.18

0.52

schizophrenia

OMIT_0013464

Schizophrenia, Disorganized

9 (P)

0.27

0.18

0.52

creatinine measurement

MAXO_0000832

serum creatinine measurement

9 (P)

0.31

0.13

0.46

bipolar disorder

NBO_0000258

bipolar disorder

BD, manic depression, bipolar affective disorder

10 (P)

0.08

0.19

0.44

postydysenteric arthropathy

MPATH_684

arthropathy

8 (P)

0.05

0.19

0.34

inflammatory biomarker meas.

MAXO_0000554

interleukin-1 beta biomarker measurement

IL-1 beta assessment

6.5 (P)

0.31

0.13

0.33