IBD16S_samp

Bundled with HMP2Data · exported, loads via data()

Class

data.frame

Dimensions

178 × 490

Missing

63,005

Format

rda · xz

File

data/IBD16S_samp.rda

Fingerprint

597d03ae

About this object

A list of equal-length columns presented as a table. Almost everything rectangular in R inherits from it, which is why the class column so often has more than one entry. R object catalogue

Columns

Column

Type

Distinct

Missing

Summary

Project

character

178

–

sample_id

character

178

–

subject_id

character

–

site_sub_coll

character

178

–

data_type

character

–

week_num

numeric

0 – 53

date_of_receipt

Date

178

–

interval_days

numeric

178

1 values

visit_number

integer

1 – 32

Research Project

character

–

PDO Number

character

178

–

GSSR IDs

character

178

–

Product

character

178

–

LCSET

character

178

–

Aggregated Lanes

character

178

–

WR ID

character

178

–

# Lanes in Aggregation

character

178

–

reads_raw

character

178

–

reads_filtered

character

178

–

reads_qc_fail

character

178

–

reads_human

character

178

–

reads_ribosomal

character

178

–

reads_viral

character

178

–

Delta

character

178

–

IntervalName

character

–

IntervalSequence

integer

1 – 32

ProjectSpecificID

integer

2008 – 6033

site_name

character

–

Age at diagnosis

numeric

5 – 74

Has the subject had a cholecystectomy?

character

178

–

Has the subject had a prior abdominal surgery (other)?

character

178

–

Has the next visit been scheduled?

character

178

–

Has the subject been given new stool kits?

character

178

–

Has the subject completed the FFQ/YAQ?

character

178

–

Education Level

character

–

Occupation

character

–

Scanned FFQ/YAQ document:

character

178

–

FFQ/YAQ results:

character

178

–

Has the subject had an appendectomy?

character

178

–

Has the subject had a tonsillectomy?

character

178

–

biopsy_location

character

–

Were study bloods drawn?

character

178

–

Whole blood received at Broad:

character

–

Serum tube #1 received at CSMC:

character

–

Serum tubes #2-4 received at MGH:

character

–

Whole Blood (DNA)

character

178

–

Serum #1

character

178

–

Serum #2

character

178

–

Serum #3

character

178

–

Serum #4

character

178

–

Number of flora tubes collected:

numeric

1 – 4

Rectum Flora:

numeric

206538 – 224844

Ileum flora:

numeric

206534 – 224845

Other inflamed flora:

numeric

165

206564 – 219659

Non-inflamed flora:

numeric

155

206536 – 215067

Have samples been sent for histopathology?

character

–

Number of tubes collected for epithelial cell biopsies:

numeric

0 – 3

Rectum cell biopsy:

numeric

126

203657 – 206981

Ileum cell biopsy:

numeric

128

203656 – 206980

Other inflamed cell biopsy:

character

178

–

Other non-inflamed cell biopsy:

numeric

173

206863 – 206868

FLora received at MGH:

character

–

RNA/DNA received at Broad:

character

–

ECP received at Washington U:

character

–

Number of DNA/RNA tubes collected:

numeric

1 – 4

Rectum DNA/RNA:

character

–

Ileum DNA/RNA:

character

–

Other Inflamed DNA/RNA:

character

137

–

Non-inflamed DNA/RNA:

character

107

–

consent_age

numeric

6 – 76

diagnosis

character

–

Soft drinks, tea or coffee with sugar (corn syrup, maple syrup, cane sugar, etc)

character

178

–

Diet soft drinks, tea or coffee with sugar (Stevia, Equal, Splenda etc)

character

178

–

Fruit juice (orange, apple, cranberry, prune etc.)

character

178

–

Water

character

178

–

Alcohol (beer, brandy, spirits, hard liquor, wine, aperitif, etc.)

character

178

–

Yogurt or other foods containing active bacterial cultures (kefir, sauerkraut)

character

178

–

Dairy (milk, cream, ice cream, cheese, cream cheese)

character

178

–

Probiotic

character

178

–

Fruits (no juice) (Apples, raisins, bananas, oranges, strawberries, blueberries

character

178

–

Vegetables (salad, tomatoes, onions, greens, carrots, peppers, green beans, etc)

character

178

–

1) In the past 2 weeks, have you received any of the following medications

character

178

–

Beans (tofu, soy, soy burgers, lentils, Mexican beans, lima beans etc)

character

178

–

Whole grains (wheat, oats, brown rice, rye, quinoa, wheat bread, wheat pasta)

character

178

–

Starch (white rice, bread, pizza, potatoes, yams, cereals, pancakes, etc.)

character

178

–

Eggs

character

178

–

Processed meat (other red or white meat such as lunch meat, ham, salami, bologna

character

178

–

Red meat (beef, hamburger, pork, lamb)

character

178

–

White meat (chicken, turkey, etc.)

character

178

–

Shellfish (shrimp, lobster, scallops, etc.)

character

178

–

Fish (fish nuggets, breaded fish, fish cakes, salmon, tuna, etc.)

character

178

–

Sweets (pies, jam, chocolate, cake, cookies, etc.)

character

178

–

Antibiotics

character

–

Chemotherapy

character

–

Immunosuppressants (e.g. oral corticosteroids)

character

–

2) In the past 2 weeks, have you undergone a colonoscopy or other procedure

character

178

–

3) In the past 2 weeks, have you used an oral contrast

character

178

–

4) In the past 2 weeks, have you had diarrhea?

character

178

–

5) In the past 2 weeks, have you been hospitalized?

character

178

–

6) Have you ever had bowel surgery?

character

178

–

Tea or coffee no sugar and no sugar replacement

character

178

–

Did you grow up on a farm?

character

178

–

Did you attend daycare as a child?

character

178

–

Were you exposed to cigarette smoke as a child?

character

178

–

Were you born prematurely (more than 3 weeks early)?

character

178

–

Do you currently smoke marijuana?

character

178

–

If yes, how many times per month do you smoke marijuana on average?

character

178

–

In the past 2 months, have you used any acid reducing medication

character

178

–

If yes, how frequently do you take them?

character

178

–

In the past 2 months, have you used any medications modifying bile production

character

178

–

Do you use non-steroidal anti-inflammatory medications

character

178

–

Were you born in a hospital?

character

178

–

If yes, how frequently do you take them?.1

character

178

–

If you are female, do you use hormonal contraception?

character

178

–

If yes, what type of contraception?

character

178

–

Please list your current hormonal contraceptive:

character

178

–

If yes, for how many months have you been taking hormonal contraception?

character

178

–

Have you changed your hormonal contraceptive regimen in the past two months?

character

178

–

In the past 6 months, have you used antibiotics?

character

178

–

In the past 3 months, have you consumed any probiotics (other than yogurt)

character

178

–

In the past 3 months, how often have you consumed yogurt or other foods containi

character

178

–

Were you born via C-section?

character

178

–

What are your dietary preferences with respect to meat?

character

178

–

How often do you consume alcoholic beverages?

character

178

–

In the past 7 days, my sleep quality was...

character

178

–

In the past 7 days, my sleep was refreshing...

character

178

–

I had a problem with my sleep...

character

178

–

I had difficulty falling asleep...

character

178

–

My sleep was restless...

character

178

–

I tried hard to get to sleep...

character

178

–

I worried about not being able to fall asleep...

character

178

–

I was satisfied with my sleep...

character

178

–

Were you born in the United States?

character

178

–

In the past 7 days, I felt worthless...

character

178

–

I felt helpless...

character

178

–

I felt depressed...

character

178

–

I felt hopeless...

character

178

–

I felt like a failure...

character

178

–

I felt unhappy...

character

178

–

I felt that I had nothing to look forward to...

character

178

–

I felt that nothing could cheer me up...

character

178

–

In the past 7 days, I felt fearful...

character

178

–

I found it hard to focus on anything other than my anxiety...

character

178

–

If no, where were you born?

character

178

–

If no, in what year did you come to the United States?

numeric

178

1 values

Were you breastfed as an infant?

character

178

–

My worries overwhelmed me...

character

178

–

I felt uneasy...

character

178

–

I felt nervous...

character

178

–

I felt like I needed help for my anxiety...

character

178

–

I felt anxious...

character

178

–

I felt tense...

character

178

–

When was the last time you saw a dentist (generalist, prosthodontist, periodonti

character

178

–

When was the last time you had a dental cleaning? Choose the most recent option.

character

178

–

Manual toothbrush

character

178

–

Electric toothbrush

character

178

–

Alcohol-based mouthwash

character

178

–

Non alcoholic mouthwash

character

178

–

Floss

character

178

–

Water-based pick/jet

character

178

–

Tongue cleaner

character

178

–

Tooth-whiteners

character

178

–

Were you treated with antibiotics before the age of one?

character

178

–

Were you hospitalized before the age of five?

character

178

–

Did you have pets growing up?

character

178

–

Subject is unwilling or unable to provide biopsy, blood, and stool samples:

character

178

–

Subject has an immune mediated disease (i.e. rheumatoid arthritis, lupus, T1DM):

character

178

–

Subject is pregnant:

character

178

–

Subject has a known bleeding disorder:

character

178

–

Subject has an acute gastrointestinal infection:

character

178

–

Subject is actively being treated for a malignancy with chemotherapy:

character

178

–

Subject has been diagnosed with indeterminate colitis:

character

178

–

Subject has a stoma or pouch:

character

178

–

Subject has an acute gastrointestinal illness:

character

178

–

Subject has an acute gastrointestinal infection or IBD:

character

178

–

Behavior (B)

character

178

–

For UC and CD, has the disease classification changed since baseline?

character

178

–

Extent (E)

character

178

–

For months 3, 6, and 9 ONLY: Has the subject been given 6 new stool collection k

character

178

–

Location (L) prior to first surgery

character

178

–

Has the subject experienced a flare since the last study visit?

character

178

–

If yes, how many times?

numeric

178

1 values

Weight

numeric

178

1 values

Has the subject had a colonoscopy since the last visit?

character

178

–

Has the subject been hospitalized for any reason since the last study visit?

character

178

–

Has the subject had any accute diarrheal illnesses since the last study visit?

character

178

–

Has the subject used any antibiotics since the last visit?

character

178

–

fecalcal_ng_ml

character

178

–

Parents

character

178

–

Mother

character

178

–

Father

character

178

–

Siblings

character

178

–

Male sibling 1

character

178

–

Male sibling 2

character

178

–

Male sibling 3

character

178

–

Female sibling 1

character

178

–

Female sibling 2

character

178

–

Female sibling 3

character

178

–

Children

character

178

–

Male child 1

character

178

–

Male child 2

character

178

–

Male child 3

character

178

–

Female child 1

character

178

–

Female child 2

character

178

–

Female child 3

character

178

–

Grandparents

character

178

–

Male grandparent 1

character

178

–

Male grandparent 2

character

178

–

Female grandparent 1

character

178

–

Female grandparent 2

character

178

–

Distant Relative

character

178

–

Male distant relative 1

character

178

–

Male distant relative 2

character

178

–

Male distant relative 3

character

178

–

Female distant relative 1

character

178

–

Female distant relative 2

character

178

–

Female distant relative 3

character

178

–

Uveitis

character

–

Erythema nodosum

character

–

Aphthous ulcers

character

–

Pyoderma gangrenosum

character

–

Anal fissure

character

–

New fistula

character

–

Abscess

character

–

Was HBI completed?

character

173

–

General wellbeing

character

173

–

Abdominal pain

character

173

–

Number of liquid or very soft stools in the past 24 hours:

numeric

173

0 – 3

Abdominal mass

character

173

–

Arthralgia

character

–

hbi

numeric

173

2 – 9

Hispanic or Latino Origin

character

–

BMI

numeric

178

1 values

Height

numeric

178

1 values

Weight.1

numeric

178

1 values

Cancer - breast

character

–

Cancer - cholangiocarcinoma

character

–

Cancer - colon or rectum

character

–

Cancer - Hodgkin's lymphoma

character

–

Cancer - liver

character

–

Cancer - lung

character

–

Cancer - lymphoma (not otherwise specified)

character

–

Cancer - Non-Hodkin's lymphoma

character

–

Cancer - ovarian

character

–

Cancer - prostate

character

–

Other immune mediated diseases

character

178

–

Celiac sprue

character

–

Chronic bronchitis

character

–

Dermatitis herpetiformis

character

–

Familial Mediterranean fever

character

–

Grave's disease

character

–

Guillian-Barre Syndrome

character

–

Hashimoto's (autoimmune) thyroiditis

character

–

Idiopathic pulmonary fibrosis

character

–

Idiopathic thrombocytopenia purpura

character

–

Irritable bowel syndrome

character

–

Alopecia areata

character

–

Multiple sclerosis

character

–

Myasthenia gravis

character

–

Myocarditis

character

–

Neuropathy

character

–

Pericarditis

character

–

Pemphigus vulgaris

character

–

Pernicious anemia

character

–

Polymyositis or dermatomyositis

character

–

Primary biliary cirrhosis

character

–

Primary sclerosing cholangitis

character

–

Ankylosing spondylitis

character

–

Psoriasis

character

–

Rheumatoid arthritis

character

–

Sarcoidosis

character

–

Scleroderma (systemic sclerosis)

character

–

Sjogren's syndrome

character

–

Systemic lupus erythematosis

character

–

Temporal arteritis

character

–

Thyroid disease (uncertain diagnosis, not cancer)

character

–

Type I Diabetes (Juvenile Diabetes)

character

–

Vitiligo

character

–

Arthritis (uncertain diagnosis)

character

–

Wegener's granulomatosis

character

–

Asthma

character

–

Autoimmune hemolytic anemia

character

–

Autoimmune hepatitis

character

–

Bechet's syndrome

character

–

Did the patient sign informed consent?

character

–

Did the subject withdraw from the study?

character

–

Was subject terminated by investigator?

character

–

Reason for withdrawal or termination:

character

174

–

Subject is 18 years of age or older:

character

178

–

Subject is 17 years of age or younger:

character

178

–

Subject has a confirmed diagnosis of IBD:

character

178

–

Subject was diagnosed within the last 6 months:

character

178

–

Subject is NOT on an anti-TNF inhibitor:

character

178

–

Subject has had IBD for 5 years or more:

character

178

–

is_inflamed

character

–

Have the following labs been drawn within +/- 2 weeks?

character

–

CRP (mg/L)

numeric

0.02 – 999

ESR (mm/hr)

numeric

2 – 999

Location

character

136

–

What is the endoscopic grading of severity?

character

136

–

Showing the first 300 of 490 columns.

Version history

Version	Released	Rows × Cols	Change	Stored as	Confidence
3.23	2026-04-28	178 × 490	Unchanged	rda · xz	exact
3.22	2025-10-29	178 × 490	Unchanged	rda · xz	exact
3.21	2025-04-15	178 × 490	Unchanged	rda · xz	exact
3.20	2024-10-29	178 × 490	Unchanged	rda · xz	exact
3.19	2024-04-30	178 × 490	Unchanged	rda · xz	exact
3.18	2023-10-24	178 × 490	Unchanged	rda · xz	exact
3.17	2023-04-25	178 × 490	Unchanged	rda · xz	exact
3.16	2022-11-01	178 × 490	Unchanged	rda · xz	exact
3.15	2022-04-26	178 × 490	Unchanged	rda · xz	exact
3.14	2021-10-26	178 × 490	Unchanged	rda · xz	exact
3.13	2021-05-19	178 × 490	Unchanged	rda · xz	exact
3.12	2020-10-27	178 × 490	Unchanged	rda · xz	exact
3.11	2020-04-27	178 × 490	Unchanged	rda · xz	exact
3.10	2019-10-29	178 × 490	–	rda · xz	exact