Lung - Tier 2 metadata definitions

	A	B	C	D	E	F	G	H	I	J	K
1		Field name	Field programmatic name	Description	Data type	Categorical values (ontology and enum)	Examples	Required	Imported from bionetwork	Encoded by sample, cell, donor, dataset, library (or combination)	Public / DB side

2	1	Age value	age_value	Age of donor at the time of sample collection. Specify the age unit (week, month, year) in age_unit.	integer	N/A	20; 32; 56	PRIORITISED	Genetic Diversity	donor	controlled access available
3	2	Age unit	age_unit	Age unit (week, month, year) for the age_value.	string	day; week; month; year	day; week; month; year	PRIORITISED	Genetic Diversity	donor	controlled access available
4	3	Gender identity selfreported	genderidentity_selfreported	Donor self-reported gender identity.	string	N/A	Female Gender; Male Gender; Non-Binary Gender; Other Gender; Agender; Gender Fluid; Gender Identifier X; Genderqueer; Transgender; Two-spirit	PRIORITISED	Genetic Diversity	donor	controlled access available
5	4	Body mass index	bmi	Body mass index of the donor at the time of collection.	integer	N/A	36.4; 19.2; 27	PRIORITISED	Genetic Diversity	donor	controlled access available
6	5	Height	height	Height of donor in cm at the time of collection.	integer	N/A	160; 137; 203	PRIORITISED	Genetic Diversity	donor	controlled access available
7	6	Weight	weight	Weight of donor in kilograms at the time of collection.	integer	N/A	50; 80	PRIORITISED	Genetic Diversity	donor	controlled access available
8	7	Ethnicity self reported	ethnicity_selfreported_freetext	Donor self-reported ethnicity (or ethnicities) in free-text; can include tribe, dialect group, etc. If race information is submitted under this field, please ensure that the question(s) and response options posed to donors are included in the next metadata category (“ethnicity_question_text”). Separate multiple entries with a comma.	string	N/A		PRIORITISED	Genetic Diversity	donor	controlled access available
9	8	Ethnicity question text	ethnicity_question_text	Question and response options posed to donors for collecting metadata on donor self-reported ethnicity and / or tribe and / or dialect group and / or race etc.	string	N/A	“What is your ethnicity?”; “Are you Hispanic/Latino?”; Example from All of Us “Which categories describe you? Select all that apply. Note You may select more than one group. American Indian or Alaska Native (for example, Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) Prefer not to answer” not collected, not available	PRIORITISED	Genetic Diversity	donor	controlled access available
10	9	Smoking status	smoking_status	If the donor smokes/smoked or not.	string	active; former; never	active; former; never	PRIORITISED	Genetic Diversity	donor	controlled access available
11	10	Years since smoking cessation	years_since_smoking_cessation	If smoking status is "former", specify the number of years since smoking cessation, if available.	integer	N/A	1; 4; 12	PRIORITISED		donor	controlled access available
12	11	Smoking pack years	smoking_pack_years	Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years subject was smoking.	integer	N/A	4.55; 12; 49.5	PRIORITISED		donor	controlled access available
13	12	Household smoking exposure	household_smoking_exposure	If the donor is exposed to passive smoking in their household or not (excluding if they are the ones smoking).	string	yes; no	yes; no	PRIORITISED		donor	controlled access available
14	13	Vaping status	vaping_status	If the donor vapes/vaped or not.	string	active; former; never	active; former; never	PRIORITISED		donor	controlled access available
15	14	Inhaled marijuana status	marijuana_inhaled_status	If the donor inhales or smokes marijuana, in the present, past or never.	string	active; former; never	active; former; never	PRIORITISED		donor	controlled access available
16	15	Comorbidities	comorbidities_ontology_term_id	Indicate all comorbidities/ secondary diagnoses of the donor (primary diagnosis was asked in disease_ontology_term_id field of tier 1 metadata). This must be a MONDO term. Separate multiple entries with a comma.	string	MONDO ontology term	MONDO:0005044; MONDO:0005148	PRIORITISED		donor	controlled access available
17	16	Medication in last month	medication_within_last_month_pre_sample	Please indicate the last known therapy, as drug categories from the NCIT ontology, administered to the patient within the last month prior to sample collection. If this information is not shareable due to data privacy restrictions, please indiciate "not_shareable".	string	NCIT ontology term	NCIT:C389; NCIT:C71534; NCIT:C78113; not_shareable	PRIORITISED		donor	controlled access available
18	17	Diet meat consumption	diet_meat_consumption	Dietary patterns of donor – meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet – at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat.	string	yes; no	yes; no	PRIORITISED	Genetic Diversity	donor	controlled access available
19	18	Primary language	language_donor_primary_language	Primary language(s), spoken by donor. Can include dialects (for example, Hokkien).	string	N/A	Mandarin Chinese; Hokkien; Bahasa Melayu; Tamil; Hausa; Yoruba; Swahili	PRIORITISED	Genetic Diversity	donor	controlled access available
20	19	Current residence location country state	geography_currentresidence_location_country_state	Country and state of donor’s current residence at time of sample collection.	string	N/A	Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria	PRIORITISED	Genetic Diversity	donor	controlled access available
21	20	Current residence location granular	geography_currentresidence_location_granular	Nearest city, town, or village to location of donor’s current residence at time of sample collection.	string	N/A	Singapore; Cambridge; Boston; Kingston	PRIORITISED	Genetic Diversity	donor	controlled access available
22	21	Collection site latitude longitude	geography_collectionsite_latitude_longitude	Latitude and longitude GPS coordinates of collection site in decimal degrees. Please specify latitude followed by longitude separated with a comma.	string	N/A	1.3,103.8; not_sharable	PRIORITISED	Genetic Diversity	donor	controlled access available
23	22	Sample collection time point	sample_collection_time_point	Time point when the sample was collected, indicated as YYYY/MM/DD. If this information is not sharable, please indiciate "not_shareable".	date	N/A	2022/10/29; not_shareable	PRIORITISED		sample	controlled access available
24	23	Tissue dissociation protocol	protocol_tissue_dissociation	The dissociation process that was used for the dissociation.	string	Collagenase D + DNAse; Dispase + collagenase; Cold protease 1h; Collagenase + Elastase + DNAse; Cold protease overnight; Collagenase A + DNAse; Mechanical dissociation (chilled) + detergent-based nuclei isolation; Mechanical dissociation (frozen) + citric-acid based nuclei isolation; other	Collagenase D + DNAse; Dispase + collagenase; Cold protease 1h; Collagenase + Elastase + DNAse; Cold protease overnight; Collagenase A + DNAse; Mechanical dissociation (chilled) + detergent-based nuclei isolation; Mechanical dissociation (frozen) + citric-acid based nuclei isolation; other	PRIORITISED		sample	controlled access available
25	24	Tissue dissociation protocol free text	protocol_tissue_dissociation_free_text	A free text option to describe dissociation process if not listed in available options.	string	N/A	Collagenase IV and I at 37°C for 8h	PRIORITISED		sample	controlled access available
26	25	Pft method	PFT_method	Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed.	string	spirometry; plethysmography; DLCO_KCO_test	spirometry; plethysmography; DLCO_KCO_test	PRIORITISED		donor	controlled access available
27	26	Age at pft	age_at_PFT	Indicate the age of the subject at the time point of pulmonary function parameter assessment in years, if known.	integer	N/A	45; 77; 32	PRIORITISED		donor	controlled access available
28	27	Pft time point	PFT_time_point	Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'.	string	N/A	2024-11-14; 2019-01-31; not_shareable	PRIORITISED		donor	controlled access available
29	28	Pft relative time point	PFT_relative_time_point	If timepoint of sample collection (sample_collection_time_point) and/or timepoint of PFT recording (PFT_time_point) is not available, indicate how many days prior or after sample collection the pulmunary function parameters were assessed if available. E.g. if PFT recording 5 days prior to sample collection corresponds to "-5", on the day of sample collection "0" and three days after sample collection "3".	integer	N/A	0; -5; 12	PRIORITISED		donor	controlled access available
30	29	Fev1 milliliters predicted	FEV1_milliliters_predicted	Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available.	integer	N/A	3500; 4200; 2800	PRIORITISED		donor	controlled access available
31	30	Fev1 milliliters prebd	FEV1_milliliters_preBD	Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available.	integer	N/A	3500; 4200; 2800	PRIORITISED		donor	controlled access available
32	31	Fev1 milliliters postbd	FEV1_milliliters_postBD	Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available.	integer	N/A	3500; 4200; 2800	PRIORITISED		donor	controlled access available
33	32	Fev1 percent of predicted prebd	FEV1_percent_of_predicted_preBD	Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available.	integer	N/A	80; 78; 105	PRIORITISED		donor	controlled access available
34	33	Fev1 percent of predicted postbd	FEV1_percent_of_predicted_postBD	Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available.	integer	N/A	80; 78; 105	PRIORITISED		donor	controlled access available
35	34	Fvc milliliters predicted	FVC_milliliters_predicted	Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available.	integer	N/A	4500; 5000; 3800	PRIORITISED		donor	controlled access available
36	35	Fvc milliliters prebd	FVC_milliliters_preBD	Indicate the measured FVC in milliliters before bronchodilator administration if available.	integer	N/A	4000; 4800; 3600	PRIORITISED		donor	controlled access available
37	36	Fvc milliliters postbd	FVC_milliliters_postBD	Indicate the measured FVC in milliliters after bronchodilator administration if available.	integer	N/A	4200; 5000; 3700	PRIORITISED		donor	controlled access available
38	37	Fvc percent of predicted prebd	FVC_percent_of_predicted_preBD	Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available.	integer	N/A	89; 96; 95	PRIORITISED		donor	controlled access available
39	38	Fvc percent of predicted postbd	FVC_percent_of_predicted_postBD	Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available.	integer	N/A	93; 100; 97	PRIORITISED		donor	controlled access available
40	39	Fev1 fvc ratio prebd	FEV1_FVC_ratio_preBD	Indicate the ratio of FEV1 to FVC before bronchodilator administration if available.	integer	N/A	0.75; 0.79; 0.72	PRIORITISED		donor	controlled access available
41	40	Fev1 fvc ratio postbd	FEV1_FVC_ratio_postBD	Indicate the ratio of FEV1 to FVC after bronchodilator administration if available.	integer	N/A	0.76; 0.80; 0.73	PRIORITISED		donor	controlled access available
42	41	Frc abs milliliters	FRC_abs_milliliters	Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available.	integer	N/A	3000; 3500; 2700	PRIORITISED		donor	controlled access available
43	42	Frc percent of predicted	FRC_percent_of_predicted	Indicate the percentage of the predicted FRC, based on patient demographics, if available.	integer	N/A	95; 88; 102	PRIORITISED		donor	controlled access available
44	43	Rv milliliters	RV_milliliters	Indicate the Residual Volume (RV) in milliliters if available.	integer	N/A	1500; 1800; 1400	PRIORITISED		donor	controlled access available
45	44	Rv percent of predicted	RV_percent_of_predicted	Indicate the percentage of the predicted RV, based on patient demographics, if available.	integer	N/A	80; 90; 85	PRIORITISED		donor	controlled access available
46	45	Ic milliliters	IC_milliliters	Indicate the Inspiratory Capacity (IC) in milliliters if available.	integer	N/A	3500; 4000; 3200	PRIORITISED		donor	controlled access available
47	46	Ic percent of predicted	IC_percent_of_predicted	Indicate the percentage of the predicted IC, based on patient demographics, if available.	integer	N/A	92; 85; 97	PRIORITISED		donor	controlled access available
48	47	Dlco milliliters	DLCO_milliliters	Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available.	integer	N/A	25; 30; 22	PRIORITISED		donor	controlled access available
49	48	Dlco percent of predicted	DLCO_percent_of_predicted	Indicate the percentage of the predicted DLCO, based on patient demographics, if available.	integer	N/A	88; 95; 82	PRIORITISED		donor	controlled access available
50	49	Kco mmol min kpa l	KCO_mmol_min_kPa_L	Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available.	integer	N/A	5; 6; 4.5	PRIORITISED		donor	controlled access available
51	50	Kco percent of predicted	KCO_percent_of_predicted	Indicate the percentage of the predicted KCO, based on patient demographics, if available.	integer	N/A	90; 98; 85	PRIORITISED		donor	controlled access available
52	51	Gold stage	GOLD_stage	If donor has COPD, indicating current GOLD stage.	string	1; 2; 3; 4	1; 2; 3; 4	PRIORITISED		donor	controlled access available
53	52	Mmrc grade	mMRC_grade	If donor has COPD, indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade if available.	string	0; 1; 2; 3; 4	0; 1; 2; 3; 4	PRIORITISED		donor	controlled access available
54	53	Cat score	CAT_score	If donor has COPD, indicate the COPD Assessment Test (CAT) score if available.	string	N/A	2; 5; 37	PRIORITISED		donor	controlled access available
55	54	Gold abe assessment	GOLD_ABE_assessment	If donor has COPD, indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available.	string	A; B; E	A; B; E	PRIORITISED		donor	controlled access available
56	55	Copd phenotype	COPD_phenotype	If donor has COPD, indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor	string	COPD not otherwise specified; COPD with emphysema; COPD with bronchitis; COPD with history of asthma; COPD with >300 eos in blood; COPD with allergy; COPD with Chronic Mucus; Hypersecretion; COPD with frequent exacerbations	COPD not otherwise specified; COPD with emphysema; COPD with bronchitis; COPD with history of asthma; COPD with >300 eos in blood; COPD with allergy; COPD with Chronic Mucus; Hypersecretion; COPD with frequent exacerbations	PRIORITISED		donor	controlled access available
57	56	Percentage of emphysema	percentage_of_emphysema	If donor has COPD, Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan.	integer	N/A	18; 37; 63	PRIORITISED		donor	controlled access available
58	57	Current residence duration	geography_currentresidence_duration	Duration of residence, in years, rounded up to the nearest whole number, at time of sample collection.	integer	N/A	20; 37; 45-65	RECOMMENDED	Genetic Diversity	donor	controlled access available
59	58	Current residence type urbanrural	geography_currentresidence_urbanrural	Urban, suburban, or rural descriptor of current residence.	string	urban; suburban; rural	urban; suburban; rural	RECOMMENDED	Genetic Diversity	donor	controlled access available
60	59	Place of birth location - country state	geography_placeofbirth_location_country_state	Country and state of place of birth.	string	N/A	Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria	RECOMMENDED	Genetic Diversity	donor	controlled access available
61	60	Place of birth location - granular	geography_placeofbirth_location_granular	Nearest city, town, or village to location of place of birth.	string	N/A	Singapore; Cambridge; Boston; Kingston	RECOMMENDED	Genetic Diversity	donor	controlled access available
62	61	Place of birth duration	geography_placeofbirth_duration	Duration of residence, in years, rounded up to the nearest whole number.	integer	N/A	20; 37; 45-65	RECOMMENDED	Genetic Diversity	donor	controlled access available
63	62	Place of birth type urbanrural	geography_placeofbirth_urbanrural	Urban, suburban, or rural descriptor of place of birth.	string	urban; suburban; rural	urban; suburban; rural	RECOMMENDED	Genetic Diversity	donor	controlled access available
64	63	Ethnicity parents selfreported	ethnicity_parents_selfreported_freetext	Donor’s parents’ self-reported ethnicity (or ethnicities) in free-text; can include tribe, dialect group, etc. Separate multiple entries with a comma.	string	N/A	Singaporean Chinese; Singaporean Malay; Singaporean Indian; Haitian; Nigerian Hausa; Ghana Hausa; Benin Kanuri; Nigerian Kanuri; Igbo; Luo; Herero; Garifuna; Kalinago	RECOMMENDED	Genetic Diversity	donor	controlled access available
65	64	Mother father tongue	language_mother_father_tongue	Ancestral language(s), spoken by parents (“mother tongue” and / or “father tongue”) and / or grandparents. Can include dialects (for example, Hokkien).	string	N/A	Mandarin Chinese; Hokkien; Bahasa Melayu; Tamil; Hausa; Yoruba; Swahili	RECOMMENDED	Genetic Diversity	donor	controlled access available
66	65	Menarche age	menarche_age	Age at menarche, rounded to nearest whole number.	integer	N/A	13; 12; 16	RECOMMENDED	Genetic Diversity	donor	controlled access available
67	66	Menopause status	reproductive_menopause	Menopausal status of donor at time of sample collection.	string	pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced); not applicable	pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced); not applicable	RECOMMENDED	Genetic Diversity	donor	controlled access available
68	67	Number children	reproductive_number_children	Number of children (full-term pregnancies) the donor has given birth to at time of sample collection.	integer	N/A	0; 2; 3	RECOMMENDED	Genetic Diversity	donor	controlled access available
69	68	Number pregnancies	reproductive_number_pregnancies	Number of pregnancies the donor has had at time of sample collection.	integer	N/A	2; 3; 5	RECOMMENDED	Genetic Diversity	donor	controlled access available
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100