HCA Data Portal

Tier 2 Metadata

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Donor

FieldDescription
Age Value
Recommended

integer

Description
Example
20
32
56
Rationale
Source
HCA
BioNetworks
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Age Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Rationale
Source
HCA
BioNetworks
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BMI
Recommended

integer

Description
Example
36.4
19.2
27
Rationale
Source
HCA
BioNetworks
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Height
Recommended

integer

Description
Example
160
137
203
Rationale
Source
HCA
BioNetworks
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Weight
Recommended

integer

Description
Example
50
80
Rationale
Source
HCA
BioNetworks
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Gender Identity Self-Reported
Recommended

string

Description
Example
Female Gender
Male Gender
Non-Binary Gender
Other Gender
Agender
Gender Fluid
Gender Identifier X
Genderqueer
Transgender
Two-spirit
Rationale
Source
HCA
BioNetworks
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Ethnicity Self-Reported Free Text
Recommended

string

Description
Rationale
Source
HCA
BioNetworks
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Ethnicity Question Text
Recommended

string

Description
Example
"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
Rationale
Source
HCA
BioNetworks
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Language Donor Primary Language
Recommended

string

Description
Example
Mandarin Chinese
Hokkien
Bahasa Melayu
Tamil
Hausa
Yoruba
Swahili
Rationale
Source
HCA
BioNetworks
Show more
Geography Current Residence Location Country State
Recommended

string

Description
Example
Singapore
United Kingdom
Massachusetts USA
New South Wales Australia
Bauchi State
Nigeria
Rationale
Source
HCA
BioNetworks
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Geography Current Residence Location Granular
Recommended

string

Description
Example
Singapore
Cambridge
Boston
Kingston
Rationale
Source
HCA
BioNetworks
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Occupation
Recommended

string

Description
Allowed Values
Example
Should be mapped to OccO Occupation Ontology OCCO:00000001
Source
HCA
BioNetworks
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Comorbidities
Recommended

string

Description
Allowed Values
Example
MONDO:0005044
MONDO:0005148
Source
HCA
BioNetworks
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Genotype
Recommended

string

Description
Example
DRB1 0401 protective allele
HLA-B*3901 allele
Source
HCA
BioNetworks
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Medication
Recommended

string

Description
Allowed Values
Example
atorvastatin
brevicon
chlorthalidone
Rationale
Source
HCA
BioNetworks
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Diet Meat Consumption
Recommended

string

Description
Allowed Values
Example
yes
no
Rationale
Source
HCA
BioNetworks
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Medical Test Results
Recommended

string

Description
Example
lipid panel shows normal level of LDL (124 mg/dL)
HIV, HBV, HCV: Negative
Source
HCA
BioNetworks
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Treatments
Recommended

string

Description
Example
Patient treated with antibiotics for a urinary tract infection
Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer
Source
HCA
BioNetworks
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Previous Surgery
Recommended

string

Description
Source
HCA
BioNetworks
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Previous Surgery Relative Time Point
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
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Previous Surgery Relative Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
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History of Injury Type
Recommended

string

Description
Example
ankle injury
burn
spinal cord injury
Source
HCA
BioNetworks
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History of Injury Type Relative Time Point
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
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History of Injury Type Relative Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
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Alcohol Status
Recommended

string

Description
Allowed Values
Example
active
former
never
Source
HCA
BioNetworks
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Alcohol Type
Recommended

string

Description
Allowed Values
Example
beer
liquor
wine
Source
HCA
BioNetworks
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Alcohol Usage Duration
Recommended

integer

Description
Example
3
14
21
Source
HCA
BioNetworks
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Alcohol Units
Recommended

numeric

Description
Example
0.4
7
14.9
Source
HCA
BioNetworks
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Smoking Status
Recommended

string

Description
Allowed Values
Example
active
former
never
Rationale
Source
HCA
BioNetworks
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Years Since Smoking Cessation
Recommended

integer

Description
Example
1
4
12
Source
HCA
BioNetworks
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Smoking Pack Years
Recommended

integer

Description
Example
4.55
12
49.5
Source
HCA
BioNetworks
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Nutritional State
Recommended

string

Description
Allowed Values
Example
normal
fasting
feeding tube removed
Source
HCA
BioNetworks
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Physical Activity / Physical Exposure
Recommended

string

Description
Example
active - football, tennis
sedentary
Source
HCA
BioNetworks
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Handedness
Recommended

string

Description
Allowed Values
Example
left
right
ambidextrous
unknown
Source
HCA
BioNetworks
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Microanatomical Region
Recommended

string

Description
Example
myotendinous junction, trabecular, enthesis
Source
HCA
BioNetworks
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Geography Collectionsite Latitude Longitude
Recommended

string

Description
Example
1.3, 103.8
not_sharable
Rationale
Source
HCA
BioNetworks
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Geography Currentresidence Duration
Recommended

integer

Description
Example
20
37
45-65
Rationale
Source
HCA
BioNetworks
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Geography Currentresidence Urban Rural
Recommended

string

Description
Allowed Values
Example
urban
suburban
rural
Rationale
Source
HCA
BioNetworks
Show more
Geography Place of Birth Location Country State
Recommended

string

Description
Example
Singapore
United Kingdom
Massachusetts USA
New South Wales Australia
Bauchi State
Nigeria
Rationale
Source
HCA
BioNetworks
Show more
Geography Place of Birth Location Granular
Recommended

string

Description
Example
Singapore
Cambridge
Boston
Kingston
Rationale
Source
HCA
BioNetworks
Show more
Geography Place of Birth Duration
Recommended

integer

Description
Example
20
37
45-65
Rationale
Source
HCA
BioNetworks
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Geography Place of Birth Urban Rural
Recommended

string

Description
Allowed Values
Example
urban
suburban
rural
Rationale
Source
HCA
BioNetworks
Show more
Ethnicity Parents Self-Reported Freetext
Recommended

string

Description
Example
Singaporean Chinese
Singaporean Malay
Singaporean Indian
Haitian
Nigerian Hausa
Ghana Hausa
Benin Kanuri
Nigerian Kanuri
Igbo
Luo
Herero
Garifuna
Kalinago
Rationale
Source
HCA
BioNetworks
Show more
Language Mother Father Tongue
Recommended

string

Description
Example
Mandarin Chinese
Hokkien
Bahasa Melayu
Tamil
Hausa
Yoruba
Swahili
Rationale
Source
HCA
BioNetworks
Show more
Menarche Age
Recommended

integer

Description
Example
13
12
16
Rationale
Source
HCA
BioNetworks
Show more
Reproductive Menopause
Recommended

string

Description
Allowed Values
Example
pre-menopausal
peri-menopausal
post-menopausal
post-menopausal (induced)
not applicable
Rationale
Source
HCA
BioNetworks
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Reproductive Number Children
Recommended

integer

Description
Example
0
2
3
Rationale
Source
HCA
BioNetworks
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Reproductive Number Pregnancies
Recommended

integer

Description
Example
2
3
5
Rationale
Source
HCA
BioNetworks
Show more

Sample

FieldDescription
Collected Tissue Processing
Recommended

string

Description
Example
tissue collected in DMEM/F12 containing 10% FCS and washed in PBS. Frozen within 2h of surgery after all fat trimmed off.
Source
HCA
BioNetworks
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Tissue Transportation
Recommended

string

Description
Example
snap frozen tissue shipped from Argentina to the UK on dry ice.
Source
HCA
BioNetworks
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Time to Laboratory
Recommended

integer

Description
Example
1.5
2
Source
HCA
BioNetworks
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Side of Tissue Collected
Recommended

string

Description
Allowed Values
Example
left
right
main-axis
unknown
Source
HCA
BioNetworks
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Sample Storage Method
Recommended

string

Description
Allowed Values
Example
ambient temperature
cut slide
fresh
frozen at -70C
frozen at -80C
frozen at -150C
frozen in liquid nitrogen
frozen in vapor phase
paraffin block
RNAlater at 4C
RNAlater at 25C
RNAlater at -20C
Source
HCA
BioNetworks
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Sample Storage Relative Time Point
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
Show more
Sample Storage Relative Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
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Sample Dissociation Relative Time Point
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
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Sample Dissociation Relative Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
Show more
Digestion Temperature
Recommended

string

Description
Example
42
37
cold
Source
HCA
BioNetworks
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Dissociation Description
Recommended

string

Description
Source
HCA
BioNetworks
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Dissociation DOI
Recommended

string

Description
Example
10.1073/pnas.2404775131
10.1016/j.ajog.2016.07.031
Source
HCA
BioNetworks
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Cell Suspension Storage Time
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
Show more
Cell Suspension Storage Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
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Library Prep Relative Time Point
Recommended

integer

Description
Example
4
37
58
Source
HCA
BioNetworks
Show more
Library Prep Relative Time Unit
Recommended

string

Description
Allowed Values
Example
day
week
month
year
Source
HCA
BioNetworks
Show more
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