Extend GECKO to include more categories from Maelstrom

[beckyjackson]

Maelstrom includes some categories that have no matches in GECKO such as lifestyle and the already-added reproduction.

I'll make a full list of the new categories in the corresponding PR. Full list of new terms below.

[beckyjackson]

I'm going to make a PR for these changes, but I want to list them all here so we can discuss.

Imports from external ontologies

ID	Browser Label	Browser Category	Ontology Label	Maelstrom Term
EUPATH:0000147	cause of death	other questionnaire/survey data	cause of participant death	Cause of death
EUPATH:0000308	hospitalizations	healthcare information	hospitalization information	Hospitalizations
EUPATH:0000359	occupation	socio-demographic and economic characteristics	occupation	Labour force and retirement
EUPATH:0000374	marital status	socio-demographic and economic characteristics	marital status	Marital/partner status
EUPATH:0000451	healthcare information	questionnaire/survey data	healthcare information	Health and community care services utilization
EUPATH:0010032	physical environment	questionnaire/survey data	environment associated with human dwelling	Physical environment
MF:0000041	personal beliefs and values	other questionnaire/survey data	belief	Beliefs and values
MONDO:0002051	skin and subcutaneous tissue	diseases	integumentary system disease	Diseases of the skin and subcutaneous tissue
MONDO:0002081	musculoskeletal system	diseases	musculoskeletal system disease	Diseases of the musculoskeletal system and connective tissue
MONDO:0003900	connective tissue	diseases	connective tissue disease	Diseases of the musculoskeletal system and connective tissue
MONDO:0005550	infectious disease	diseases	infectious disease	Certain infectious and parasitic diseases
MONDO:0021178	injury	diseases	injury	Injury, poisoning and certain other consequences of external causes
MONDO:0024458	visual system	diseases	disease of visual system	Diseases of the eye and adnexa
MONDO:0024623	diseases of the ear, nose, and/or throat	diseases	otorhinolaryngologic disease	Diseases of the ear and mastoid process
MONDO:0029000	poisoning	diseases	poisoning	Injury, poisoning and certain other consequences of external causes
OBI:0002415	exposure to carcinogens	physical environment	exposure to environmental and workplace carcinogens history	Biological exposure, Chemical exposure, Radiation exposure
OMRSE:00000501	income and possessions	socio-demographic and economic characteristics	income data	Income, possessions, and benefits

Potential requests for EUPATH

(if they don't want these, we can add them to GECKO instead)

Browser Label	Browser Category	Ontology Label	Ontology Parent	Maelstrom Term
housing characteristics	physical environment	human dwelling environment	environment associated with human dwelling	Housing characteristics
neighbourhood characteristics	physical environment	human neighborhood environment	environment associated with human dwelling	Built environment/neighbourhood characteristics
workplace characteristics	physical environment	human workplace environment	environment associated with human dwelling	Workplace characteristics
routine visits to health professionals	healthcare information	routine clinical visit information	information	Visits to health care professionals

New terms for GECKO

Note that "perception of health and quality of life" has no ontology parent - I don't plan to put this in GECKO, but it will appear as a grouping category in the IHCC view.

Browser Label	Browser Category	Ontology Label	Ontology Parent	Maelstrom Term
perception of health and quality of life	questionnaire/survey data			Perception of health, quality of life, development and functional limitations
cognitive and psychological measurements	questionnaire/survey data	psychological measurement	measurement datum	Cognition, personality and psychological measures and assessments
cognitive functioning	cognitive and psychological measurements	cognitive measurement	psychological measurement	Cognitive functioning
personality	cognitive and psychological measurements	personality measurement	psychological measurement	Personality
psychological distress and emotions	cognitive and psychological measurements	emotion	biological process	Psychological distress and emotions
oral health and hygiene	lifestyle and behaviours	oral health history	lifestyle history
psychological interventions	non-pharmacological interventions	psychological treatment history	non-pharmacological treatment history	Cognitive, psychological and sensory interventions
radiological interventions	non-pharmacological interventions	radiological treatment history	non-pharmacological treatment history	Radiological interventions
physical therapy interventions	non-pharmacological interventions	physical therapy history	non-pharmacological treatment history	Physical therapy interventions
perception of health	perception of health and quality of life	perception of health measurement	psychological measurement	Perception of health
quality of life	perception of health and quality of life	quality of life measurement	psychological measurement	Quality of life
functional limitations	perception of health and quality of life	information about functional limitations	information	Functional limitations
use of assistive devices	perception of health and quality of life	information about use of assistive devices	information	Use of assistive devices
religion	socio-demographic and economic characteristics	religious affiliation	information	Ethnicity, race and religion
social environment	other questionnaire/survey data	human social environment	immaterial entity	Social environment and relationships

[jamesaoverton]

@mcourtot We'd really appreciate your thoughts on this, and then we plan to reach out to the developers of these ontologies to coordinate more widely.

[mcourtot]

This is amazing, thank you! I didn't quite understand the comment:

Note that "perception of health and quality of life" has no ontology parent - I don't plan to put this in GECKO, but it will appear as a grouping category in the IHCC view.

Shouldn't all the IHCC grouping categories correspond to something in the ontology?

[beckyjackson]

We excluded some terms that didn't really make sense ontologically, such as "other biosample type". These still appear as classes in the IHCC view itself.

"perception of health and quality of life" combines categories from both "information" and "physiological measurement" parents, so I think this would be kind of difficult to place within the true "ontology" version of GECKO, and I think it's closer to a "subset" than it is an actual ontology class.

Hopefully that made sense... please let me know if you have any other questions or ideas!

[mcourtot]

For Maelstrom let's hold for a couple of days and see if we are able to create an OWL version after talking to them further. Then we can directly reuse the right Maelstrom IRIs. What do you think?