search

EBISPOT / efo

Github repo for the Experimental Factor Ontology (EFO)
https://www.ebi.ac.uk/efo/
56 stars 13 forks source link

Request terms for UK Biobank Fields #1285

Closed smlmbrt closed 2 years ago

smlmbrt commented 3 years ago

Preferred term label

time spent outdoors

Synonyms

NA

Textual definition

Measurement of time an an individual spends outside

Suggested parent term

environmental exposure measurement EFO_0008360

Suggested child term

sunlight exposure measurement EFO_0010729

Source

Appears in UK Biobank questionnaire:

Attribution

0000-0001-8222-008X

smlmbrt commented 3 years ago

Preferred term label

Insulin use measurement

Synonyms

NA

Textual definition

Quantification of some aspect of the use of insulin.

Suggested parent term

drug use measurement EFO:0007010

Suggested links

_isabout some insulin

Source

Appears in UK Biobank questionnaire:

Attribution

0000-0001-8222-008X

smlmbrt commented 3 years ago

Preferred term label

family history of prostate cancer

Synonyms

NA

Textual definition

A reported family history of prostate cancer in one or more family members.

Suggested parent term

family history of cancer EFO_0009640

Suggested links

_isabout some prostate cancer

Source

UKB Category 100034 (Family History) https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=100034

Attribution

0000-0001-8222-008X

smlmbrt commented 2 years ago

Preferred term label

bowel opening frequency

Synonyms

From Frequency of bowel action (SNOMED:249521002):

Textual definition

Number of times bowels opened per day

Suggested parent term

measurement

Suggested links

_isabout digestive health (perhaps https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008460)

Source

UKB Field 21044 "Average number of times bowels opened per day" https://biobank.ndph.ox.ac.uk/ukb/field.cgi?id=21044

Attribution

0000-0001-8222-008X

smlmbrt commented 2 years ago

Request import of PP Interval (CMO_0000278)

Details can be extracted from the CMO

Suggested parent term

electrocardiography (EFO_0004327)

Source

UKB Field 22334 "PP interval" https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=22334

smlmbrt commented 2 years ago

Request PQ interval as a synonym for PR Interval

Synonym to be added

PQ interval

Sources for the synonym

https://en.ecgpedia.org/wiki/Conduction https://en.wikipedia.org/wiki/PR_interval

Related Source Data

PQ Interval in UKB https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=22330

kallia-p commented 2 years ago

@smlmbrt EFO_0600081 time spent outdoors measurement EFO_0600082 insulin use measurement. Another parent term has been inferred by the reasoner which is insulin measurement EFO_0004467 (according to the definition this refers to the insulin measurement typically done for the diagnosis of patients so it is slightly distinct term from the insulin use measurement). EFO_0600083 family history of prostate cancer EFO_0600084 bowel opening frequency
EFO_0600085 PP interval PQ interval added as a synonym for PR Interval

Source added https://doi.org/10.1101/2021.09.02.21262942

smlmbrt commented 2 years ago

Sounds good, but don't think EFO_0004467 (insulin measurement) is a good parent for insulin use measurement (EFO_0600082), because this measures how long after diagnosis insulin was used as a drug/treatment.

kallia-p commented 2 years ago

@smlmbrt You are right about this but the reasoner has made the inference which I cannot easily change. It's not entirely off as they both refer to an insulin measurement; drug use measurement is an asserted parent of insulin use measurement.