Medical Data

The Tasks of Medicine

• Clinical• Diagnosis• Prognosis• Therapy

• Public Health• Prevention• Detection

• Research• Quality Improvement• Cost Containment• Biomedical Research

• Understanding• Therapies

• Education

The Medical Cycle

interpret

plan

integratepatient

data information

diagnosistherapy

initial presentation

Settlement

Membership

Care Team

Int. Med

Rad

Lab

Pharm

Surgery

Account

Plan Design

Discharge Dismiss

Episode Activation Authorization

Health Status Mgt.

Community Care

Self Care

Evaluate

Assess

Plan

Act

Schedule

Refer Visit Activation

Mgt. Team

Health Mgt.

Health Record

Measure

Enterprise-level Clinical Process Automation...

figure from David Margulies

The “Learning Health Care System”

Membership

Care Team

Int. Med

Rad

Lab

Pharm

Surgery

Account

Plan Design

Discharge Dismiss

Episode Activation Authorization

Health Status Mgt.

Community Care

Self Care

Evaluate

Assess

Plan

Act

Schedule

Refer Visit Activation

Mgt. Team

Health Mgt.

Health Record

MeasureObserve/Measure

Analyze

Model Plan Intervene

•Process •Medical content

DogmaPhenotype = f(Genotype , Environment)Traits Diseases Behaviors …

Gene sequence SNP’s, CNV’s RNA sequence Expression (proteins) …

Diet, smoking, drugs, … Insults and injuries Exposures …

• What is the functional form? • How do we investigate these relationships? • Can we take advantage of the exponential growth

of genomic data?

Clinico-Genomic Research

• Identify a highly specific clinical population, and controls• Gene-wide association studies (GWAS)• Hope that notable differences appear between those with/those without disease• Disease models:

• Mendelian• Single-nucleotide polymorphisms• Private variation• ?

Why Keep Records?

• Basis for historical record• Communication among providers• Anticipate future health problems• Record standard preventive measures• Identify deviations from the expected• Legal record• Basis for clinical research

• Who?• Doctor• Nurse• Office staff, admissions• Administrator• physical therapist• lab personnel• radiologist• pharmacist• patient

Forms of Clinical Data

– Numerical Measurements– Lab data– Bedside measurements– Home instrumentation

– Recorded signals (e.g., ECG, EEG, EMG)

– Images (X-ray, MRI, CAT, Ultrasound, Pathology, …)

– Genes (SNPs, expression arrays, pedigrees, …)

– Coded (?) discrete data – Family history – Patient’s medical history

– Current complaint – Symptoms (patient) – Signs (doc)

– Physical examination – Medications

– Narrative text – Doctor’s, nurse’s notes – Discharge summaries – Referring letters

Organization of Data

• Doctor’s journal (traditional)• Time order of collection, per patient (Mayo)• Source of data• Problem-Oriented Medical Record (POMR) (L. Weed, 1969)

• Notes organized by problems• SOAP: subjective, objective, assessment, plans

POMR

Data Base Problem List

Plans(by problem)

Progress Notes(by problem)

diagnostic, therapeutic,patient education

The Data Base

• Identifying information (name, age, sex, race, religion, insurance info, etc.)

• Patient profile (occupation, education, marital status, children, hobbies, worries, moods, sleep patterns, habits, etc.)

• Medical history• Chief complaints• History of present illness• Past medical history• Review of systems• Family history• Medications

• Physical examination• Laboratory data and physiologic tests (complete blood count,

electrocardiogram, chest x-ray, creatinine, urinalysis, vital capacity, tonometry, etc.)

The Problem List

• “those features in the patient’s psychobiological makeup that require continuing attention”• Social history• Risk factors• Symptoms• Physical findings• Lab tests

• Causally organized; e.g., GI bleeding caused by duodenal ulcer appears under the ulcer

Example Problem ListNo Active Date Inactive Date

1 Hypertension 19532 Recurrent bronchitis 19583 Penicillin allergy 19584 S/P pyelonephritis 19605 Gallstones Oct 1972 àCholecystectomy Mar 1973

6 Arthralgias Mar 1973 à#9 June 1973

7 Pleurisy Mar 1973 à#9 June 1973

8 Proteinuria Apr 1973 à#9 June 1973

9 SLE June 1973

10 Unemployment Nov 1973

Problem-Related Plans

• Diagnostic: lab tests, radiology studies, consultations, continued observations, …

• Therapeutic: medications, diet, psychotherapy, surgery, …• Patient education: instruction in self-care, about goals of therapy,

prognosis, …

Plans per problem

1. DiarrheaDx:

• stool for occult blood, culture, ova, and parasites, microscopic fat; and muscle fibers

• Sigmoidoscopy• Barium enema if persistent

Rx: Avoid foods that exacerbateEd: Informed that more info is needed to make a

diagnosis, will aim for symptomatic therapy for now.

Plans per problem (cont.)

1. PyuriaDx:

• BUN• Repeat urinalysis• Urine culture

2. ObesityRx: 1500 kcal diet, Weight WatchersEd: Dangers of obesity cited. Goal: 170 lbs.

Progress Notes

• Subjective: interval history, adherence to program• Objective: physical findings, reports of lab, x-ray, other tests• Assessment: Appraisal of progress, interpretation of new findings, etc.• Plan: Dx, Rx, Ed.

Example SOAP Note

#3 RHD with mitral stenosis S: 2 flight dyspnea, mild fatigue. No orthopnea, hemoptysis, ankle

edema. Child has strep throat. O: BP 120/70. P 78 regular

Neck veins normal, lungs clear. Grade iii diastolic rumble, wide opening snap, P2 slightly ↑

A: Stable. Catheterization still not indicated. Risk of strep throat present.

P: Dx:Cardiac fluoroscopy Rx:Continue chlorothiazide and penicillin V 250mg b.i.d.—2

weeks Ed:Reinstructed about antibiotic coverage for tooth extractions,

sched. for next month. (Will contact oral surgeon.)

POMR characteristics

• Augment with data flow sheets• Importance of clinical judgment• Benefits:

• Communication among team members, explicitness• Education and audit• Clinical research

POMR evidence

• Difficult adoption• Some duplication• Some doctors liked it• Paper-based POMR slow, computer-based maybe faster• Demand-oriented MR: by time, by source, by problem, etc. Dynamic

arrangement.

Mayo experience

• Paper records, mostly• Pneumatic tube delivery, therefore limited size• Formal procedures for reaping and organizing records at discharge• Comprehensive index

The Computer-basedPatient Record

• IOM Study: Dick, R. S. and Steen, E. B., Eds. (1991). The Computer-Based Patient Record: An Essential Technology for Health Care. Washington, D.C., National Academy Press.• Made strong case for CPR• Recommended CPRI (Institute), but it never caught on

• Resurrected in today’s Patient Centered Outcomes Research Institute (PCORI)

• Today’s standards grow more out of communication standards: HL7 (labs) and DICOM (digital images)

Paper record: Strengths

• Familiar; low training time• Portable to point of care• No downtime• Flexibility; easy to record subjective data• Browsing and scanning

• Find information by unanticipated characteristics (e.g., Dr. Jones’ handwriting)

Paper record: Weaknesses

• Content: missing, illegible, inaccurate• E.g., one hospital study: 11% of tests were repeats to replace lost

information• Too thick (1.5 lbs avg.)• Fail to capture rationale• Incomprehensible to patients and families

Sample paper record defects

• 75% of face sheets had no discharge disposition, 48% no principal Dx• Agreement between encounter (witnessed) and record: 29% med hx,

66% Rx, 71% info re current illness, 72% tests, 73% impression/Dx, 92% chief complaint

• 20.8% of Medicare discharges coded incorrectly (DRG inflation)• Unavailable at up to 30% of patient visits

• Two clinic visits in a day• Docs keep records in their office• Failure to deliver• Misfiled in file room

• Discontinuity across institutions• In/outpatient records separate

Ethnographic Design

• Xerox PARC analysis of office work• Sociologists, Anthropologists, Engineers• Much of work is

• communication, • assignment of responsibilities, • problem solving

Medicine is an Information Industry

• 35-39% of hospital operating costs due to professional and patient communications

• Physicians spend 38%, nurses 50% of their time charting• Exponential growth of medical knowledge and literature

Individual Usersof Patient Records

• Providers• Chaplains• Dental hygienists• Dentists• Dietitians• Lab technicians• Nurses• Occupational therapists• Optometrists• Pharmacists• Physical therapists• Physicians• Physician assistants• Podiatrists• Psychologists• Radiology technologists• Respiratory therapists• Social workers

• Management – Administrators – Financial managers and accountants – Quality assurance managers – Records professionals – Risk managers – Unit clerks – Utilization review managers

• Reimbursement – Benefit managers – Insurers (Fed, State, private)

• Other – Accreditors – Gov’t policymakers, legislators – Lawyers – Health care researchers, clinical investigators – Health Sciences journalists and editors – Patients, families

Institutional Usersof Patient Record

• Healthcare Delivery• Alliances, associations, networks, systems of

providers• Ambulatory surgery centers• Donor banks (blood, tissue, organs)• HMO’s• Home care agencies• Hospices• Hospitals• Nursing homes• PPO’s• Physician offices, group practices• Psychiatric facilities• Public Health Departments• Substance abuse programs

• Management and Review• Medicare peer review organizations• Quality assurance companies• Risk management companies• Utilization review/management comp.

• Reimbursement – Business Health coalitions – Employers – Insurers

• Research – Disease registries – Health data organizations – Health care technology developers and

manufacturers – Research Centers

• Education – Allied health professional schools, medical,

nursing, public health schools • Accreditation

– Accreditation organizations – Inst. licensure agencies – Prof. Licensure agencies

• Policymaking – Fed, State, Local gov’t agencies

Primary Uses of Patient Record• Patient care delivery (Patient)

– Document services received– Constitute proof of identity– Self-manage care– Verify billing

• Patient care delivery (Provider)– Foster continuity of care– Describe diseases and causes– Support decision making about Dx and Rx– Assess and manage risk– Facilitate care via Clin. Practice Guidelines– Document patient risk factors– Assess and document patient expectations and

satisfaction– Generate care plans– Determine preventive advice– Remind clinicians– Support nursing care– Document services provided

• Patient care management – Document case mix – Analyze severity of illness – Formulate practice guidelines – Manage risk – Characterize use of services – Basis for utilization review – Perform quality assurance

• Patient care support – Allocate resources – Analyze trends and develop forecasts – Assess workload – Communicate between departments

• Billing and reimbursement – Document services for payment – Bill for services – Submit insurance claims – Adjudicate insurance claims – Determine disabilities (workmen’s comp) – Manage & report costs – Perform actuarial analysis

Secondary Uses of Patient Record

• Education– Document health care professional experience– Prepare conferences and presentations– Teach students

• Regulation– Evidence in litigation– Foster postmarketing surveillance– Assess compliance with standards– Accredit professionals and hospitals– Compare health care organizations

• Policy– Allocate resources– Conduct strategic planning– Monitor public health

• Research – Develop new products – Conduct clinical research – Assess technology – Study patient outcomes – Study effectiveness and cost-

effectiveness of care – Identify populations at risk – Develop registries and databases – Assess cost-effectiveness of record

systems • Industry

– Conduct R&D – Plan marketing strategy

User Requirements

• Record Content• Uniform core data elements• Standardized coding systems

and formats• Common data dictionary• Information on outcomes of

care and functional status

• Record Format• “Front-page” problem list• Ability to “flip through” the

record• Integrated among disciplines

and sites of care• System Performance

• Rapid retrieval• 24/7• Available @ convenient

places• Easy data input

User Requirements (cont.)

• Linkages• To other info systems (e.g., radiology,

lab)• Transferability of information among

specialties and sites• With relevant literature• Other registries and institutional

databases• To records of other family members• E-billing

• Training and Implementation• Minimal training required• Graduated implementations

• Intelligence – Decision support – Clinician reminders – “Alarm” systems, customized

• Reporting – “Derived documents”, e.g., insurance

forms – Easily customized output, UI – Standard clinical reports, e.g.,

discharge summary – Custom and ad hoc reports – Trend reports and graphics

• Control and Access – Easy patient access – Safeguards of confidentiality

MIMIC2 Data Structure (Clinical Data)

Figure 2.1: Major MIMIC II clinical database components. The patient table D PATIENTS is central to the database model,other information such as admission, dempgraphics, procedures or medications can be readily accessed once a particular patientis identified. The tables above show the relationship between the major components in the database.

19

Additives

ICD9

Admissions ChartEvents

NoteEvents

D_Patients

TotalBalEventsChartDurations IODurations

MedEvents IOEvents

MedDurations

CensusEvents

Deliveries

D_Patients

Figure 2.1: Major MIMIC II clinical database components. The patient table D PATIENTS is central to the database model,other information such as admission, dempgraphics, procedures or medications can be readily accessed once a particular patientis identified. The tables above show the relationship between the major components in the database.

19

mysql> select * from d_patients limit 10; +------------+------+---------------------+---------------------+---------------------+ | subject_id | sex | dob | dod | hospital_expire_flg | +------------+------+---------------------+---------------------+---------------------+ | 56 | F | 2553-05-26 00:00:00 | 2644-01-23 00:00:00 | Y | | 3 | M | 2606-02-28 00:00:00 | 2683-05-02 00:00:00 | N | | 21 | M | 3051-05-22 00:00:00 | 3139-03-28 00:00:00 | Y | | 12 | M | 2803-05-14 00:00:00 | 2875-10-09 00:00:00 | Y | | 26 | M | 3007-03-02 00:00:00 | 3080-12-22 00:00:00 | N | | 37 | M | 3195-09-11 00:00:00 | 3265-12-31 00:00:00 | N | | 31 | M | 2606-05-17 00:00:00 | 2678-08-29 00:00:00 | Y | | 61 | M | 3297-10-27 00:00:00 | 3353-02-09 00:00:00 | Y | | 78 | M | 2729-08-08 00:00:00 | 2781-03-11 00:00:00 | N | | 67 | M | 2903-06-04 00:00:00 | 2976-11-29 00:00:00 | Y | +------------+------+---------------------+---------------------+---------------------+ 10 rows in set (0.00 sec)

mysql> select hospital_expire_flg, count(*) from d_patients group by hospital_expire_flg; +---------------------+----------+ | hospital_expire_flg | count(*) | +---------------------+----------+ | N | 2347 | | Y | 1653 | +---------------------+----------+ 2 rows in set (0.00 sec)

mysql> select 1653/(1653+2347); +------------------+ | 1653/(1653+2347) | +------------------+ | 0.4133 | +------------------+

Admissions

mysql> select * from admissions limit 10; +---------+------------+---------------------+---------------------+ | hadm_id | subject_id | admit_dt | disch_dt | +---------+------------+---------------------+---------------------+ | 28766 | 56 | 2644-01-17 00:00:00 | 2644-01-23 00:00:00 | | 2075 | 3 | 2682-09-07 00:00:00 | 2682-09-18 00:00:00 | | 20666 | 21 | 3138-10-29 00:00:00 | 3138-11-11 00:00:00 | | 20882 | 21 | 3139-03-19 00:00:00 | 3139-03-28 00:00:00 | | 12532 | 12 | 2875-09-26 00:00:00 | 2875-10-09 00:00:00 | | 15067 | 26 | 3079-03-03 00:00:00 | 3079-03-10 00:00:00 | | 18052 | 37 | 3264-08-14 00:00:00 | 3264-08-19 00:00:00 | | 15325 | 31 | 2678-08-21 00:00:00 | 2678-08-29 00:00:00 | | 7149 | 61 | 3352-06-23 00:00:00 | 3352-07-26 00:00:00 | | 5712 | 61 | 3353-01-10 00:00:00 | 3353-02-09 00:00:00 | +---------+------------+---------------------+---------------------+

> library(RMySQL) Loading required package: DBI > conn = dbConnect(MySQL(),

host="mendel.csail.mit.edu", dbname="mimic2", user="mimic2", password="XXX")

> adm = dbReadTable(conn, "admissions") > adm.dur = as.numeric(as.Date(adm$disch_dt)

- as.Date(adm$admit_dt)) > hist(adm.dur, breaks="Scott",

main="Durations of ICU Admissions", xlab="Days")

Durations of ICU Admissions

Days

Frequency

0 50 100 150 200 250 300

0200

400

600

ICD9 codes

mysql> select * from icd9 limit 10; +------------+---------+----------+--------+----------------------------------------------------+ | subject_id | hadm_id | sequence | code | description | +------------+---------+----------+--------+----------------------------------------------------+ | 56 | 28766 | 1 | 198.3 | SECONDARY MALIGNANT NEOPLASM OF BRAIN AND SPINAL C | | 56 | 28766 | 2 | 162.8 | MALIGNANT NEOPLASM OF OTHER PARTS OF BRONCHUS OR L | | 56 | 28766 | 3 | 531.40 | CHRONIC OR UNSPECIFIED GASTRIC ULCER WITH HEMORRHA | | 56 | 28766 | 4 | 276.1 | HYPOSMOLALITY AND/OR HYPONATREMIA | | 56 | 28766 | 5 | 428.0 | CONGESTIVE HEART FAILURE UNSPECIFIED | | 56 | 28766 | 6 | 780.39 | OTHER CONVULSIONS | | 56 | 28766 | 7 | 272.0 | PURE HYPERCHOLESTEROLEMIA | | 56 | 28766 | 8 | 401.9 | UNSPECIFIED ESSENTIAL HYPERTENSION | | 37 | 18052 | 1 | 410.71 | SUBENDOCARDIAL INFARCTION INITIAL EPISODE OF CARE | | 37 | 18052 | 2 | 428.0 | CONGESTIVE HEART FAILURE UNSPECIFIED | +------------+---------+----------+--------+----------------------------------------------------+

> icd = dbGetQuery(conn, "select subject_id, count(*) c from icd9 group by subject_id") > dicd = dbGetQuery(conn, "select subject_id, count(distinct code) c from icd9 group by subject_id") > hist(icd$c, breaks="Scott") > hist(icd[icd$c<=50,][,"c"], breaks="Scott", main="# ICD9 codes/patient (<=50)", xlab="# of codes")

# ICD9 codes/patient

# of codes

Frequency

0 50 100 150 200 250 3000

200

600

1000

# distinct ICD9 codes/patient

# of codes

Frequency

0 20 40 60 80 100

0200

600

1000

# ICD9 codes/patient (<=50)

# of codes

Frequency

0 10 20 30 40 50

0200

600

1000

0 50 100 150 200 250 300

020

4060

80100

icd$c

dicd$c

ChartEvents> hct = dbGetQuery(conn, "select charttime, value1 from chartevents where itemid='813' and subject_id='21280'") > hct$t = as.POSIXct(hct$charttime) > plot(hct[,"t"], hct[,"value1"], main="HCT for patient 21280", xlab="time", ylab="HCT")

2504 2505 2506 2507 2508 2509

1520

2530

3540

HCT for patient 21280

time

HCT

Nov Jan Mar May

1520

2530

35

HCT for patient 21280

time

HCT

> hct1 = hct[hct$t<as.POSIXct("2504-06-01 00:00:00"),] > plot(hct1[,"t"], hct1[,"value1"], main="HCT for patient 21280", xlab="time", ylab="HCT")

NoteEventsmysql> select category, count(*) c from noteevents group by category order by c desc; +-------------------+--------+ | category | c | +-------------------+--------+ | Nursing/Other | 101934 | | RADIOLOGY_REPORT | 65884 | | DISCHARGE_SUMMARY | 3930 | | MD Notes | 179 | +-------------------+--------+

DATE: [**2644-1-19**] 12:09 PM CHEST (PORTABLE AP) Clip # [**Clip Number (Radiology) 12570**] Reason: aspiration pna? Admitting Diagnosis: HEAD BLEED ______________________________________________________________________________ UNDERLYING MEDICAL CONDITION: [**Age over 90 **] year old woman with ICH and nmoe with increased secretions REASON FOR THIS EXAMINATION: aspiration pna? ______________________________________________________________________________ FINAL REPORT This is a portable semierect chest that is dated [**2644-1-19**] compared to [**2644-1-17**]. CLINICAL INDICATION: Question aspiration pneumonia. Nasogastric tube terminates below the diaphragm. The cardiac silhouette appears enlarged, but stable. There is a large mass-like opacity overlying the left hilum, which has slightly lobulated margins. This measures about 6 cm in greatest diameter. Bilateral pleural effusions are noted, moderate on the left and small on the right. No pneumothorax is identified. As compared to the previous study, alveolar opacities adjacent to the perihilar mass have resolved. IMPRESSION: Marked improvement in left perihilar alveolar process with residual well-marginated mass-like opacity, concerning for neoplasm. This could be initially confirmed with PA and lateral chest radiographs, but CT may be considered for more complete characterization. Findings communicated to clinical service caring for the patient.

A Nursing Note

NSG Admit noteB: Please refer to careview and remarks for details.

Pt arrived from the ED at 0400 with Nipride gtt off and Dilatin IV infusing.

Pt arousable to voice and able to answer last name "[**Known patient lastname 243**]", but unable to determin if oriented to place or date. Speach slurred/garbled. Impaired gag, strong cough.Initially, moving RUE and RLE spontanously, withdrawing LLE to nailbed, nothing from LUE. Next exam pt moved all extremities, LUE to nailbed. OU PERL 2mm/2mm. Pt does not appear to be in discomfort.

Temp on arrival 95.7. Heated blankets applied. Unable to place aline at this time. Following cuff to keep SBP 90-140. NS 250cc bolus admin x1 for SBP 85 with good effect, ^103. Palp bilat pedal pulses.

RESP Pox wave form dampened at times. LS dimily CTA. NC 3L on.

BS hypoactive. Abd S/NT/ND. Dr. [**Last Name (NamePattern4) 244**] placed NGT in (R) nare. Placement verified by auscultation. CXR to be done. Foley insitu, draing small amounts of clear yellow urine.

Bilat wrist restraints applied to prevent pt from pulling NGT out.

PLANL: Admin K-excelate. 3% NS with q2h Na levels. Neuro exam q1h. Monitor I/O, resp status. MRI today after questionaire completed. Call H.O. with changes.

Can we formalize the medical record?

• It’s hard:• “Sometime before his 5th birthday, Johnny had scarlet fever, which caused

changes in his heart sounds.”• QMR: LEG <S> WEAKNESS PROXIMAL ONLY• PIP: (EDEMA with

LOCATION = FACIAL or PERI-ORBITAL, PAINFULNESS = not PAINFUL,  SYMMETRY = not ASYMMETRICAL, ERYTHEMA = not ERYTHEMATOUS)

• Uncertainly is ubiquitous• Explicit: “... may be consistent with ...”• Implicit: “... a week before hospitalization ...”

• ... next lecture

Minimum Clinical Dataset

• Demographics• Name, address, phone number• Family contacts• Insurance details• Employer

• Problem list• Current problems• Significant past problems

• Current and recent medications• Recent past visit history• Allergies• Lab data• Clinical measurements (e.g., vitals)• Radiology, pathology, ... studies

• Children: • Growth curves• Immunizations

Lotte Record

Immunizations

Labs Summary

Lab Studies

Thyroxine Weight

The I2B2 Data Model (Star-shaped) https://www.i2b2.org/software/files/PDF/current/CRC_Design.pdf

observation_fact

encounter_num

patient_numconcept_cd

provider_id

start_datemodifier_cd

instance_numvaltype_cd

tval_charnval_num

valueflag_cd

quantity_numunits_cd

end_datelocation_cd

observation_blob

confidence_numupdate_date

download_dateimport_date

sourcesystem_cd

upload_idtext_search_index

patient_dimension

patient_num

vital_status_cd

birth_date

death_date

sex_cd

age_in_years_num

language_cd

race_cd

marital_status_cd

religion_cd

zip_cd

statecityzip_path

income_cd

patient_blob

update_date

download_date

import_date

sourcesystem_cd

upload_id

concept_dimensionconcept_path

concept_cdname_char

concept_blob

update_datedownload_date

import_datesourcesystem_cd

upload_id

Examples of patient_dimension & concept_dimension

+-------------+-------+---------------------+------------+--------+------+-------------+--------------------+---------+-------------------------+--------+ | patient_num | vital | birth_date | death_date | sex_cd | age | language_cd | race_cd | marital | religion_cd | zip_cd | +-------------+-------+---------------------+------------+--------+------+-------------+--------------------+---------+-------------------------+--------+ | 1 | N | 1983-07-01 00:00:00 | NULL | M | 29 | ENGLISH | NULL | NULL | Unable To Collect | 02045 | | 2 | N | 1987-10-31 00:00:00 | NULL | M | 25 | ENGLISH | W-White | S | Jewish | 19810 | | 3 | N | 1990-05-03 00:00:00 | NULL | F | 23 | ENGLISH | W-White | S | No Religious Preference | 01905 | | 4 | N | 1990-07-17 00:00:00 | NULL | F | 23 | ENGLISH | W-White | S | Declined to Answer | 02148 | | 5 | N | 1986-08-06 00:00:00 | NULL | F | 26 | ENGLISH | Declined to Answer | NULL | NULL | 01746 | | 6 | N | 1988-07-11 00:00:00 | NULL | F | 24 | ENGLISH | Declined to Answer | S | Unable To Collect | 02492 | | 7 | N | 1992-02-11 00:00:00 | NULL | M | 22 | ENGLISH | W-White | S | Catholic-Baptized | 02148 | | 8 | N | 1991-10-10 00:00:00 | NULL | F | 21 | ENGLISH | W-White | S | Unable To Collect | 01821 | | 9 | N | 1992-02-06 00:00:00 | NULL | F | 21 | ENGLISH | W-White | S | Catholic-Baptized | 01001 | | 10 | @ | 1990-08-02 00:00:00 | NULL | F | 22 | ENGLISH | W-White | S | NULL | 02368 | +-------------+-------+---------------------+------------+--------+------+-------------+--------------------+---------+-------------------------+--------+

+------------------------------------------------------------------------+-----------------------------------------------+------------------------------------------+ | concept_path | concept_cd | name_char | +------------------------------------------------------------------------+-----------------------------------------------+------------------------------------------+ | \i2b2\Reports\Pathology\PATH:Addendum Report (All Pathology)\ | PATH:Addendum Report (All Pathology) | Addendum Report (All Pathology) | | \i2b2\Reports\Pathology\PATH:Autopsy Final Report\ | PATH:Autopsy Final Report | Autopsy Final Report | | \i2b2\Reports\Pathology\PATH:Cardiac Registry Report (Autopsy)\ | PATH:Cardiac Registry Report (Autopsy) | Cardiac Registry Report (Autopsy) | | \i2b2\Reports\Pathology\PATH:Cytology (Gyn) Final Report\ | PATH:Cytology (Gyn) Final Report | Cytology (Gyn) Final Report | | \i2b2\Reports\Pathology\PATH:Cytology (Non-Gyn) Final Report\ | PATH:Cytology (Non-Gyn) Final Report | Cytology (Non-Gyn) Final Report | | \i2b2\Reports\Pathology\PATH:Flow Cytometry (Pathology) Report\ | PATH:Flow Cytometry (Pathology) Report | Flow Cytometry (Pathology) Report | | \i2b2\Reports\Pathology\PATH:Genetics History Addendum Report\ | PATH:Genetics History Addendum Report | Genetics History Addendum Report | | \i2b2\Reports\Pathology\PATH:Genetics History Final Report\ | PATH:Genetics History Final Report | Genetics History Final Report | | \i2b2\Reports\Pathology\PATH:Neuropathology Addendum\ | PATH:Neuropathology Addendum | Neuropathology Addendum | | \i2b2\Reports\Pathology\PATH:Neuropathology Addendum Report (Autopsy)\ | PATH:Neuropathology Addendum Report (Autopsy) | Neuropathology Addendum Report (Autopsy) | | \i2b2\Allergy\Drug Allergy\A\A & D topical ointment\Ag:8504363\ | Ag:8504363 | A & D topical ointment | | \i2b2\Allergy\Drug Allergy\A\A-Cillin\Ag:931890\ | Ag:931890 | A-Cillin | | \i2b2\Allergy\Drug Allergy\A\A/B Otic\Ag:931911\ | Ag:931911 | A/B Otic | | \i2b2\Allergy\Drug Allergy\A\A/Fish Oil\Ag:931924\ | Ag:931924 | A/Fish Oil | | \i2b2\Allergy\Drug Allergy\A\ABACAVIR\Ag:8526008\ | Ag:8526008 | ABACAVIR | | \i2b2\Allergy\Drug Allergy\A\abacavir\Ag:931206\ | Ag:931206 | abacavir | | \i2b2\Allergy\Drug Allergy\A\Abelcet\Ag:13891\ | Ag:13891 | Abelcet | | \i2b2\Allergy\Drug Allergy\A\Abilify\Ag:1477636\ | Ag:1477636 | Abilify | | \i2b2\Allergy\Drug Allergy\A\Abilify\Ag:19623575\ | Ag:19623575 | Abilify | +------------------------------------------------------------------------+-----------------------------------------------+------------------------------------------+

Example of observation_fact+---------------+-------------+-------------------+-------------+---------------------+-------------+--------------+------------+------------------------------------------+------------------+--------------+--------------+--------------------+---------------------+ | encounter_num | patient_num | concept_cd | provider_id | start_date | modifier_cd | instance_num | valtype_cd | tval_char | nval_num | valueflag_cd | quantity_num | units_cd | end_date | +---------------+-------------+-------------------+-------------+---------------------+-------------+--------------+------------+------------------------------------------+------------------+--------------+--------------+--------------------+---------------------+ | 19742386 | 1993740 | AMED:15586958 | 14030735 | 2013-07-02 08:00:00 | @ | 2109943806 | NULL | Parenteral Nutrition Pharmacy | NULL | NULL | 1.00000 | mL | 2013-07-02 08:00:00 | | 646660 | 40346 | LAB:1450 | 1059643 | 2007-01-18 17:53:00 | 0 | 1 | N | E | 3.00000 | @ | NULL | NULL | 2007-01-18 17:53:00 | | 16682842 | 1711379 | AMED:3682905 | 1004436 | 2010-10-22 09:57:00 | @ | 1012979661 | NULL | morphine | NULL | NULL | 0.70000 | mg | 2010-10-22 09:57:00 | | 15740451 | 1724107 | LAB:1338 | 1097272 | 2009-11-08 01:30:00 | 0 | 1 | N | E | 82.10000 | @ | NULL | fL | 2009-11-08 01:30:00 | | 16801472 | 1783565 | MED:3671784 | 1102586 | 2011-02-08 13:00:00 | @ | 374714423 | NULL | NULL | NULL | NULL | 100.00000 | mg | 2011-02-08 13:00:00 | | 4663517 | 654758 | ICD9:564.00 | 1095766 | 2007-07-02 10:30:00 | 2 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2007-07-02 10:30:00 | | 11260486 | 425178 | LAB:10210 | 1000180 | 2001-03-21 03:13:00 | 0 | 1 | T | SEE NOTE | NULL | @ | NULL | NULL | 2001-03-27 14:27:00 | | 3756977 | 3858 | Note:15611692 | 1005846 | 2007-11-24 16:05:00 | @ | 290446477 | B | ICU Note Medications | NULL | NULL | NULL | | 2007-11-26 15:09:42 | | 10804273 | 591943 | Note:8022198 | 2017755 | 2008-11-24 20:18:00 | @ | 500928149 | B | Genitourinary Additional Info | NULL | NULL | NULL | | 2008-11-24 20:18:27 | | 11966472 | 838754 | LAB:1361 | 1116006 | 2007-11-03 09:30:00 | 0 | 1 | N | E | 2.00000 | H | NULL | NULL | 2007-11-03 09:30:00 | | 3319592 | 648239 | MED:3681486 | 1003577 | 2008-12-21 19:00:00 | @ | 155876193 | NULL | NULL | NULL | NULL | 3.00000 | mg | 2008-12-21 19:00:00 | | 8735843 | 1071418 | Clinic:GI/WM(674) | 1105877 | 2007-04-09 09:30:00 | @ | 1 | NULL | NULL | 6103361870.00000 | NULL | NULL | NULL | NULL | | 2175321 | 453326 | LAB:6629 | 2000556 | 2008-01-09 01:10:00 | 0 | 1 | N | E | 203.70000 | H | NULL | mmHg | 2008-01-09 01:10:00 | | 19703075 | 1885753 | AMED:15586958 | 9446910 | 2013-06-04 17:00:00 | @ | 2077231252 | NULL | Parenteral Nutrition Pharmacy | NULL | NULL | 12.00000 | mL | 2013-06-04 17:00:00 | | 17640826 | 1875403 | AMED:3682905 | 2033935 | 2011-10-29 02:57:00 | @ | 1390182189 | NULL | morphine | NULL | NULL | 0.80000 | mg | 2011-10-29 02:57:00 | | 17520284 | 1687756 | MED:3670855 | 2023386 | 2011-09-28 00:00:00 | @ | 445002729 | NULL | NULL | NULL | NULL | 1.00000 | appl | 2011-09-28 00:00:00 | | 17305364 | 455483 | PATH:EEG Report | 1112333 | 2011-07-22 10:45:45 | 1 | 1931400 | B | I | NULL | NULL | NULL | NULL | 2011-07-28 08:18:00 | | 11753316 | 677336 | AMED:3670983 | 1090767 | 2007-08-04 04:00:00 | @ | 230224584 | NULL | sodium bicarbonate | NULL | NULL | 5.20000 | mEq | 2007-08-04 04:00:00 | | 16686953 | 1780747 | AMED:3656336 | 2030000 | 2011-03-26 06:00:00 | @ | 1142934772 | NULL | budesonide | NULL | NULL | 0.25000 | mg | 2011-03-26 06:00:00 | | 3408931 | 781235 | AMED:3687862 | 1002593 | 2007-10-28 06:00:00 | @ | 274811581 | NULL | sildenafil | NULL | NULL | 1.50000 | mg | 2007-10-28 06:00:00 | | 7440139 | 1179677 | Clinic:GEN/S(323) | 1068547 | 2009-02-25 00:00:00 | @ | 1 | NULL | NULL | 6105767628.00000 | NULL | NULL | NULL | NULL | | 4630515 | 860837 | CPT4:71010 | 1071529 | 2005-09-12 05:15:00 | 1404 | -3 | B | PORT CHEST 1 VIEW | NULL | NULL | NULL | NULL | NULL | | 6065320 | 905528 | LAB:1307 | 1004485 | 2007-01-22 16:28:00 | 0 | 1 | T | Yes | NULL | @ | NULL | NULL | 2007-01-22 16:28:00 | | 16474267 | 1777632 | Note:15610746 | 1003262 | 2010-07-30 09:46:00 | @ | 951566890 | B | NICU Note ID Assess. and Plan | NULL | NULL | NULL | | 2010-07-30 09:46:48 | | 16958192 | 487063 | Note:67621144 | 1002236 | 2011-02-19 17:55:00 | @ | 1105108845 | B | Infectious Diseases Inpatient MD | NULL | NULL | NULL | | 2011-02-20 10:19:03 | | 17615503 | 1870055 | Note:8022054 | 1002593 | 2011-11-08 17:13:00 | @ | 1403075690 | B | Prior Anesthetic/Sedation Considerations | NULL | NULL | NULL | | NULL | | 15778070 | 36481 | AMED:3670659 | 1003838 | 2010-02-18 12:12:00 | @ | 828223971 | NULL | diazepam | NULL | NULL | 0.90000 | mg | 2010-02-18 12:12:00 | | 8511289 | 505746 | LAB:8900 | 1122829 | 2007-01-18 14:09:00 | 1 | 1 | NULL | NULL | NULL | NULL | NULL | NULL | 2007-01-18 14:09:00 | | 17532954 | 1204331 | MED:3653201 | 1080643 | 2011-09-12 11:00:00 | @ | 440510489 | NULL | NULL | NULL | NULL | 1.00000 | mL | 2011-09-12 11:00:00 | | 18357499 | 1814239 | MED:3671073 | 2004663 | 2012-04-13 21:00:00 | @ | 510098264 | NULL | NULL | NULL | NULL | 1.00000 | mg | 2012-04-13 21:00:00 | | 17019687 | 1823510 | LAB:1335 | 1080649 | 2011-03-18 16:35:00 | 0 | 1 | N | E | 3.32000 | L | NULL | M cells/uL | 2011-03-18 16:35:00 | | 8720830 | 78046 | AMED:3671024 | 1026678 | 2008-03-11 00:00:00 | @ | 349960040 | NULL | metoclopramide | NULL | NULL | 1.00000 | mg | 2008-03-11 00:00:00 | | 19599686 | 1044015 | AMED:3682717 | 5840803 | 2013-03-31 17:45:00 | @ | 2000051254 | NULL | milrinone | NULL | NULL | 0.00000 | mg | 2013-03-31 17:45:00 | | 17109200 | 1831298 | LAB:1342 | 2022224 | 2011-04-26 05:35:00 | 0 | 1 | N | E | 3.12000 | @ | NULL | g/dL | 2011-04-26 05:35:00 | | 570833 | 1185858 | Note:3268562 | 1005251 | 2008-06-01 08:06:57 | @ | 397448718 | B | Preliminary Report | NULL | NULL | NULL | 000002008152000426 | 2008-06-01 08:06:57 | | 11475781 | 23805 | ICD9:299.00 | 1057817 | 2000-07-14 00:00:00 | 1 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2000-07-14 00:00:00 | | 20204446 | 1751233 | SER:PHA | 2013627 | 2013-08-15 11:15:00 | O | 1 | NULL | NULL | 6113558053.00000 | NULL | NULL | NULL | NULL | | 19365586 | 1965860 | Vital:Weight | 1102586 | 2013-06-30 08:26:00 | @ | 2107738484 | N | E | 3.87000 | Female | NULL | cm | 2013-06-30 08:26:00 | | 8917455 | 1395838 | ICD9:343.9 | 1004157 | 1992-08-26 12:57:00 | 2 | 1 | F | NULL | NULL | NULL | NULL | NULL | 1992-08-26 12:57:00 | | 2697974 | 608411 | ICD9:518.89 | 1004626 | 2005-12-28 16:43:00 | 4 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2005-12-28 16:43:00 | | 16739263 | 694681 | MED:3684505 | 2004229 | 2010-12-18 21:00:00 | @ | 360100366 | NULL | NULL | NULL | NULL | 5.00000 | mL | 2010-12-18 21:00:00 | | 6675653 | 10432 | LAB:1175 | 1002746 | 2007-09-08 12:00:00 | 0 | 1 | N | E | 39.00000 | H | NULL | mg/dL | 2007-09-08 12:00:00 | | 646336 | 1042434 | LAB:1333 | 1071809 | 2008-12-08 10:11:00 | 0 | 1 | N | E | 5.13000 | L | NULL | K cells/uL | 2008-12-08 10:11:00 | | 19624653 | 41353 | LAB:1595 | 2043573 | 2013-04-04 22:15:00 | 0 | 1 | T | Negative | NULL | N | NULL | NULL | 2013-04-04 22:15:00 | | 18487343 | 1734400 | LAB:7055 | 1027504 | 2012-05-31 17:00:00 | 0 | 1 | T | NULL | NULL | NULL | NULL | NULL | 2012-05-31 17:00:00 | | 2078272 | 1583350 | MED:3677365 | 1109192 | 2008-05-30 14:00:00 | @ | 112712896 | NULL | NULL | NULL | NULL | 6.50000 | mg | 2008-05-30 14:00:00 | | 20289238 | 1014791 | MED:3682615 | 2015499 | 2013-09-11 08:00:00 | @ | 743942369 | NULL | NULL | NULL | NULL | 1.00000 | appl | 2013-09-11 08:00:00 | | 10715181 | 72769 | Note:8022797 | 1011283 | 2009-01-15 07:37:00 | @ | 554705315 | B | Pre-Anesthetic Evaluation | NULL | NULL | NULL | | 2009-01-28 08:48:57 | | 20054974 | 415711 | SER:NLS | 1018717 | 2013-06-17 09:30:00 | O | 1 | NULL | NULL | 6112453877.00000 | NULL | NULL | NULL | NULL | | 18413641 | 1906706 | LAB:1010 | 2013005 | 2012-05-07 15:10:00 | 0 | 1 | N | E | 9.80000 | N | NULL | mg/dL | 2012-05-07 15:10:00 | | 16722404 | 1667701 | LAB:15037 | 1003917 | 2010-11-19 14:31:00 | 1 | 1 | NULL | NULL | NULL | NULL | NULL | NULL | 2010-11-19 14:31:00 | | 17750397 | 1858365 | MED:3681486 | 1003047 | 2013-03-11 05:00:00 | @ | 635801900 | NULL | NULL | NULL | NULL | 0.10000 | mg | 2013-03-11 05:00:00 | | 17926628 | 1888091 | Note:2820578 | 2035771 | 2012-02-24 16:00:00 | @ | 1525224304 | B | Ophthalmology Consultation | NULL | NULL | NULL | | 2012-02-24 16:34:34 | | 12840127 | 147792 | LAB:6634 | 1002593 | 2004-03-29 10:19:00 | 0 | 1 | N | E | 3.60000 | L | NULL | mmol/L | 2004-03-29 10:21:00 | | 19823554 | 2007497 | LAB:1367 | 1105850 | 2013-07-02 03:30:00 | 0 | 1 | T | 1+ | NULL | NA | NULL | NULL | 2013-07-02 03:30:00 | | 1198111 | 1053939 | ICD9:V20.2 | 1000477 | 2001-03-15 00:00:00 | 1 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2001-03-15 00:00:00 | | 16072670 | 1390509 | MED:3677766 | 1112333 | 2010-04-01 08:00:00 | @ | 283541241 | NULL | NULL | NULL | NULL | 2.00000 | puff | 2010-04-01 08:00:00 | | 18429836 | 1867562 | Note:187605823 | 2017815 | 2012-05-04 03:51:00 | @ | 1611333143 | B | Cardiovascular System | NULL | NULL | NULL | | 2012-05-04 06:24:33 | | 17189217 | 70562 | AMED:3670670 | 1057505 | 2011-05-08 11:00:00 | @ | 1191974841 | NULL | DOPamine | NULL | NULL | 0.00000 | mg | 2011-05-08 11:00:00 | | 17763757 | 850740 | ICD9:315.32 | 1004342 | 2011-11-29 15:30:00 | 4 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2011-11-29 15:30:00 | | 17645001 | 41022 | LAB:1335 | 1124571 | 2011-10-31 09:15:00 | 0 | 1 | N | E | 3.08000 | L | NULL | M cells/uL | 2011-10-31 09:15:00 | | 3654566 | 1274342 | LAB:8900 | 1002480 | 2001-12-27 21:51:00 | 1 | 1 | NULL | NULL | NULL | NULL | NULL | NULL | 2001-12-27 21:51:00 | | 15423650 | 1657103 | MED:3670573 | 2003402 | 2009-09-29 08:00:00 | @ | 229987270 | NULL | NULL | NULL | NULL | 350.00000 | mg | 2009-09-29 08:00:00 | | 18339549 | 1910155 | AMED:130873247 | 1106028 | 2012-03-21 22:00:00 | @ | 1560497880 | NULL | heparin flush | NULL | NULL | 20.00000 | unit | 2012-03-21 22:00:00 | | 17837658 | 460758 | ICD9:785.6 | 2004860 | 2012-01-20 11:00:00 | 1 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2012-01-20 11:00:00 | | 15923178 | 1734652 | Note:15612553 | 1102586 | 2010-04-14 09:59:00 | @ | 870866040 | B | ICU Note Problem List | NULL | NULL | NULL | | 2010-04-14 10:02:37 | | 4776568 | 1262801 | Note:3268565 | 1060705 | 2006-03-29 10:44:02 | @ | 39277557 | B | Final | NULL | NULL | NULL | 000002006085000738 | 2006-03-29 10:44:02 | | 17936233 | 1896866 | AMED:3684456 | 2001553 | 2012-04-21 08:00:00 | @ | 1595948272 | NULL | norepinephrine | NULL | NULL | 0.00000 | mg | 2012-04-21 08:00:00 | | 2799866 | 503084 | ICD9:787.91 | 1019637 | 2004-12-09 11:00:00 | 2 | 1 | F | NULL | NULL | NULL | NULL | NULL | 2004-12-09 11:00:00 | | 19324399 | 1088711 | MED:3687826 | 2017343 | 2012-12-27 14:00:00 | @ | 607660829 | NULL | NULL | NULL | NULL | 25.00000 | mg | 2012-12-27 14:00:00 | +---------------+-------------+-------------------+-------------+---------------------+-------------+--------------+------------+------------------------------------------+------------------+--------------+--------------+--------------------+---------------------+

> 300M rows in CH database, for ~2.8M patients