Age of donor at the time of sample collection. Specify the age unit (week, month, year) in age_unit.

Age unit (week, month, year) for the age_value.

day; week; month; year

day; week; month; year

genderidentity_selfreported

Female Gender; Male Gender; Non-Binary Gender; Other Gender; Agender; Gender Fluid; Gender Identifier X; Genderqueer; Transgender; Two-spirit

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.

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.

“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

socioeconomic_status

Specify the socioeconomic status of the donor.

Should be mapped to OccO Occupation Ontology OCCO:00000001

Specify the education level of the donor.

no formal education; primary education; secondary education; technical education; bachelor's degree; master's degree; doctoral degree

no formal education; primary education; secondary education; technical education; bachelor's degree; master's degree; doctoral degree

Height of donor in cm at the time of collection.

Weight of donor in kilograms at the time of collection.

Body mass index of the donor at the time of collection.

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.

language_donor_primary_language

Primary language(s), spoken by donor. Can include dialects (for example, Hokkien).

Mandarin Chinese; Hokkien; Bahasa Melayu; Tamil; Hausa; Yoruba; Swahili

geography_currentresidence_location_country_state

Country and state of donor’s current residence at time of sample collection.

Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria

geography_currentresidence_location_granular

Nearest city, town, or village to location of donor’s current residence at time of sample collection.

Singapore; Cambridge; Boston; Kingston

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.

1.3,103.8; not_sharable

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. These could include periodontal diseases, dental caries (cavities), tooth loss, oral infection or inflammation, lesions or mucosal conditions, neoplastic or desquamative conditions, systemic conditions affecting oral health, or any other pathological condition not described in the disease field.

MONDO ontology term

gingivitis, periodontitis, decay, trauma, abscesses, leukoplakia, lichen planus, aphthous ulcers, herpetic lesions, benign tumors, malignant tumors, cysts, granulomas, pemphigus vulgaris, pemphigoid, linear IgA disease

Diseases that have previously affecting donor, but are not considered active for now.

MONDO ontology term

disease_family_history

Diseases that have been affecting donor's family.

MONDO ontology term

Does the donor have drink/ drank/ never drank alcohol?

active; former; never

active; former; never

Specify the alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000)

alcohol_usage_duration

Duration of donor's alcohol consumption in years

beer; liquor; wine

active; former; never

active; former; never

smoking_pack_years

Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years subject was smoking.

years_since_smoking_cessation

If smoking status is "former", specify the number of years since smoking cessation, if available.

smoking_product_type

Type of smoking product the donor used.

cigarettes; cigars; pipe; e-cigarettes; smokeless tobacco; betel nut chewing; other

cigarettes; cigars; pipe; e-cigarettes; smokeless tobacco; betel nut chewing; other

household_smoking_exposure

If the donor is exposed to passive smoking in their household or not (excluding if they are the ones smoking).

active; former; never

active; former; never

marijuana_inhaled_status

If the donor inhales or smokes marijuana, in the present, past or never.

active; former; never

active; former; never

substance_use.substance_type

Specify any drug or substance the donor use/used.

marijuana; cocaine; heroin; methamphetamine; prescription drugs (non-medical use); other

marijuana; cocaine; heroin; methamphetamine; prescription drugs (non-medical use); other

substance_use.substance_status

If the donor uses/used or never used substance described in substance type.

active; former; never

active; former; never

substance_use.frequency

Number of donor's substance usage per year.

substance_use.duration_of_use

Duration of donor's substance usage in years.

substance_use.duration_since_last_use

If donor is no longer using, specifiy the number of years since substance usage cessation, if available.

List of prescription medication consumed by the donor at time of sample collection. Should be an NCIT ontology term

NCIT ontology term

atorvastatin; brevicon; chlorthalidone

Treatments the individual has undergone prior to biomaterial collection.

Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer

dental_visits_frequency

Specify the number of donor's dental visits in a year.

dental_treatment_type

Specify any previous dental treatments of the donor, like dental surgeries, orthodontic treatments, dental restorations or use of dental prosthetics.

cleaning; filling; crown; bridge; implant; root canal; extraction; orthodontic treatment; denture; veneer

brushing_frequency

Specify the number of brushings per day.

dental_care_types

Specify the dental care type(s) the donor has applied.

brushing; flossing; mouthwash; water flosser; interdental brushes; tongue scraper; professional cleaning; dental sealants; fluoride treatment

brushing; flossing; mouthwash; water flosser; interdental brushes; tongue scraper; professional cleaning; dental sealants; fluoride treatment

Specify the donor's description of pain.

no pain; mild pain; moderate pain; severe pain; persistent pain

no pain; mild pain; moderate pain; severe pain; persistent pain

Specify the occlusion class of the donor. Should be one of Class I (Normal); Class II Division 1 (Retrognathism with Overjet); Class II Division 2 (Retrognathism with Overbite); Class III (Prognathism);

Class I; Class II Division 1; Class II Division 2; Class III

Class I; Class II Division 1; Class II Division 2; Class III

chewing_efficiency

Specify the donor's chewing efficiency.

normal; mildly reduced; moderately reduced; severely reduced

normal; mildly reduced; moderately reduced; severely reduced

dental_preventive_measures

Specify the donor's preventive measures.

regular dental check-ups; fluoride treatments; dental sealants; oral prophylaxis; oral health education

regular dental check-ups; fluoride treatments; dental sealants; oral prophylaxis; oral health education

desquamative_type

If donor has a desquamative condition, please specify the type.

lichen planus, pemphigus vulgaris, mucous membrane pemphigoid (cicatricial pemphigoid), erythema multiforme, lupus erythematosus, chronic ulcerative stomatitis, paraneoplastic pemphigus, linear iga disease, dermatitis herpetiformis, epidermolysis bullosa, and stevens-johnson syndrome/toxic epidermal necrolysis

lichen planus, pemphigus vulgaris, mucous membrane pemphigoid (cicatricial pemphigoid), erythema multiforme, lupus erythematosus, chronic ulcerative stomatitis, paraneoplastic pemphigus, linear iga disease, dermatitis herpetiformis, epidermolysis bullosa, and stevens-johnson syndrome/toxic epidermal necrolysis

gross_description

If donor has any oral pathologies, please specify any histopathological findings.

caries_tooth_number

Specify the tooth number that has caries (cavities). If multiple teeth, separate by comma.

Specify the decay type of the caries described in "Caries Tooth Number". If multiple caries, separate by comma.

enamel; dentin; cementum/root; recurrent

enamel; dentin; cementum/root; recurrent

Specify the Decayed, Missing due to caries, and Filled Teeth (DMFT) index of the donor

Specify the Decayed, Missing due to caries, and Filled Surfaces (DMFS) index of the donor

Specify the International Caries Detection and Assessment System (ICDAS) score of the donor. Available options are 0: No Evidence of Caries; 1: First Visual Change in Enamel; 2: Distinct Visual Change in Enamel; 3: Localized Enamel Breakdown; 4: Underlying Dark Shadow from Dentin; 5: Distinct Cavity with Visible Dentin; 6: Extensive Distinct Cavity with Visible Dentin

periodontal_tooth_number

Specify the tooth number that is afected by periodontitis. If multiple teeth, separate by comma.

Specify the Community Periodontal Index (CPI) of the donor. Available options are 0: Healthy; 1: Bleeding on Probing; 2: Calculus; 3: Shallow Pocket (4-5 mm); 4: Deep Pocket (6 mm or more)

Specify the Pocket Probing Depth (PPD) of the donor in mm.

Specify the Clinical Attachment Loss (CAL) of the donor in mm.

Specify the Bleeding on Probing (BOP) of the donor.

Specify the Gingival Index (GI) of the donor. Available options are 0: Normal Gingiva; 1: Mild Inflammation; 2: Moderate Inflammation; 3: Severe Inflammation;

Specify the Plaque Index (PI) of the donor. Available options are 0: No Plaque; 1: A Film of Plaque Adhering to the Free Gingival Margin and Adjacent Area of the Tooth; 2: Moderate Accumulation of Soft Deposits within the Gingival Pocket, or the Tooth and Gingival Margin; 3: Abundance of Soft Matter within the Gingival Pocket and/or on the Tooth and Gingival Margin;

periodontal_exudate

Specify if donor presents exudate or not.

periodontal_mobility

Specify the donor's periodontal mobility. Available options are 0: No Mobility; 1: Slight Mobility (less than 1 mm horizontal displacement); 2: Moderate Mobility (greater than 1 mm horizontal displacement); 3: Severe Mobility (vertical as well as horizontal displacement);

periodontal_malocclusion

Specify the donor's periodontal malocclusion.

normal; crowding; spacing; deep bite; open bite; crossbite; midline discrepancy

normal; crowding; spacing; deep bite; open bite; crossbite; midline discrepancy

Specify the tumor size of the donor's Head and Neck Squamous Cell Carcinoma. Available options are: T0: No Evidence of Primary Tumor; T1: Tumor ≤ 2 cm; T2: Tumor > 2 cm but ≤ 4 cm; T3: Tumor > 4 cm; T4: Tumor Involves Adjacent Structures.

T0; T1; T2; T3; T4

T0; T1; T2; T3; T4

Specify the node involvement of the donor's Head and Neck Squamous Cell Carcinoma. Available options are: N0: No Regional Lymph Node Involvement; N1: Metastasis in 1 to 3 Regional Lymph Nodes; N2: Metastasis in 4 or More Regional Lymph Nodes; N3: Metastasis in Distant Lymph Nodes.

Specify the metastasis of the donor's Head and Neck Squamous Cell Carcinoma. Available options are: M0: No Distant Metastasis; M1: Distant Metastasis Present.

sjogren_focus_score

Specify the focus score of the Sjögren's diseased donor in foci / 4 mm2.

sjogren_salivary_flow_rate

Specify the salivary flow rate of the Sjogren's diseased donor in mL/min.

sjogren_salivary_ph

Specify the salivary pH of the Sjogren's diseased donor.

sjogren_ocular_staining_score

Specify the ocular staining score of the Sjogren's diseased donor.

periimplantitis_material

Specify the material of the implant of the peri-implantitis diseased donor.

periimplantitis_age

Specify the age of the implant of the peri-implantitis diseased donor.

periimplantitis_pocket_depth

Specify the pocket depth of the implant of the peri-implantitis diseased donor.

periimplantitis_bone_graft_type

Specify the bone graft type of the implant of the peri-implantitis diseased donor.

autografts; allografts; xenografts; alloplasts; growth factor enhanced graft

autografts; allografts; xenografts; alloplasts; growth factor enhanced graft

periimplantitis_probing_depth

Specify the probing depth of the implant of the peri-implantitis diseased donor.

periimplantitis_bop

Specify the bleeding on probing (BOP) of the peri-implantitis diseased donor.

periimplantitis_bone_loss

Specify the length of the radiographic bone loss around the implant of the peri-implantitis diseased donor in mm.

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).

Mandarin Chinese; Hokkien; Bahasa Melayu; Tamil; Hausa; Yoruba; Swahili

geography_currentresidence_duration

Duration of residence, in years, rounded up to the nearest whole number, at time of sample collection.

geography_currentresidence_urbanrural

Urban, suburban, or rural descriptor of current residence.

urban; suburban; rural

urban; suburban; rural

geography_placeofbirth_location_country_state

Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria

geography_placeofbirth_location_granular

Nearest city, town, or village to location of place of birth.

Singapore; Cambridge; Boston; Kingston

geography_placeofbirth_duration

Duration of residence, in years, rounded up to the nearest whole number.

geography_placeofbirth_urbanrural

Urban, suburban, or rural descriptor of place of birth.

urban; suburban; rural

urban; suburban; rural

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.

Singaporean Chinese; Singaporean Malay; Singaporean Indian; Haitian; Nigerian Hausa; Ghana Hausa; Benin Kanuri; Nigerian Kanuri; Igbo; Luo; Herero; Garifuna; Kalinago

Age at menarche, rounded to nearest whole number.

reproductive_menopause

Menopausal status of donor at time of sample collection.

pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced); not applicable

pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced); not applicable

reproductive_number_children

Number of children (full-term pregnancies) the donor has given birth to at time of sample collection.

reproductive_number_pregnancies

Number of pregnancies the donor has had at time of sample collection.