The Promise of Pathology Informatics

The Promise of Pathology Informatics

James J. Cimino, M.D.Department of Medical Informatics

Columbia University

Questions You WouldLike Answered

• How can we link patient record information to pathology specimens to support clinical research?

• If we can do this, what will be possible?

The Question I ThinkYou Need to Answer

• How can pathology information be represented to support data reuse?

What is “Data Reuse”?

In contrast to the primary use of health data (“show it to the doctor”)…

…any secondary use of the data for tasks ranging from direct patient care, to financial purposes, to research

My Goal for this Talk

• Expand upon the notion of data reuse

• Discuss representational issues needed for reuse

• Propose a challenge

First Admission: August, 1983

In August, 1983, a 50 year old male presented to the St. Vincent’s Hospital (NY) emergency room with a scalp laceration due to a falling paint can. The wound was cleaned and sutured, and the patient was give a follow up appointment for surgery clinic. Two weeks later, the patient was seen at the scheduled clinic visit and was found to have delayed healing of one portion of the wound. After several weekly visits, the poorly-healing area was excised and the wound was closed. The patient had a good result and was discharged from further follow up.

Second Admission - March, 1984

The patient was brought to the emergency room for recent increasing lethargy. Laboratory evaluation was remarkable only for a calcium of 17 mg/dl. The patient was treated aggressively with hydration and diuretics, but expired shortly after admission. A diagnostic report was received.

Prologue as Epilogue

The pathology report from the wound revision the previous September included the following phrase:

“Metastatic adenocarcinoma of uncertain origin is noted at the tissue margins”

What Happened?

• The primary use of the data was to produce a report

• An information system could have managed that report

• High-quality data representation could have supported the reuse of the data by a decision support system

Pathology Information Today

• Narrative reports

• Structured reports

• Coded data (ICD9-CM vs. SNOMED vs. Local Codes)

Potential for Reuse of Pathology Information

• Direct use by care providers• Billing• Quality assurance/Case management• Clinical research (including Outcomes)• Automated decision support• Integration with other information systems

ResearchDatabase

Example:Retrospective Clinical ResearchPathology System

Financial System

Laboratory System

Pharmacy System

Data Monitor

Repository

ResearchDatabase

Example:Prospective Clinical Research

Pathology System

Financial System

Laboratory System

Pharmacy System

Data Monitor

Repository

DecisionSupport KB

Example:Prospective Clinical Research

• Data monitor checks eligibility criteria

• Alert sent to subject recruiter

• Example: Biphosphonate Study

Example:Automated Decision Support

• Data monitor checks for triggering conditions

• Medical Logic Modules decide if warning conditions are present

• Message sent to appropriate channel

• Example: Tuberculosis culture result

Caveats: TB Example

• Monitors for delayed culture results

• Sends message if result not equal to the code “No growth”

• One day, dozens of alerts about positive results but no organism was reported

• What happened?

How the Lab Fooled the Alert

• Alert looked for results “No Growth”

• Lab started reporting “No Growth to Date”

• “No Growth to Date” “No Growth”

• Solution: Use the controlled terminology to map all No-Growth-like lab terms into a single class, and have the alert logic refer to the class.

No Growth after ...

How we Outsmarted the Lab

No Growth

No Growth after 48 Hours

No Growth after 72 Hours

“No Growth” Results

No Growth after 24 Hours

No Growth to Date

Example:Linking to On-line Resources

• Clinician reviewing reports will have information needs

• On-line information sources can satisfy that need

• Data from report can be used to automate the query

Linking Text Reports to On-line Information Sources

• Natural Language Processing

• Data representation to support reuse

• Codification of information needs

How does CPMC Support Data Reuse?

• Natural Language Processing

• High-quality controlled terminology ( “codes”)

High-Quality Terminology

• Concept oriented - with concept permanence

• Multiple synonyms

• Multiple hierarchies

• Semantic network of interconcept relations

• Integration of low-level (clinical) terminology with high-level (aggregation) terminology

LaboratoryTest

Medical Entities Dictionary

HasIngredient

Measures

Chemical

AminoglycosideAntibiotic

Gentamicin

Serum Gentamicin

Test

Drug

Injectable GentamicinTrade-Name: Garamycin"Has-Ingredient: GentamicinMeasures

Random Gentamicin Level

Main-MeSH:

Supplementary-MeSH: "Gentamicin/bl"

Measures: Gentamicin

Pathology Informatics“Grand Challenges”

• Representing the concepts in reports

• Represent the relationships among concepts in reports

• Representing the concepts for aggregation and retrieval

• Integration of the concepts

What Will Be Possible

• Data retrieval

• Data mining

• Improvements in report quality

• Improved reuse of data…

…including patient care

My Challenge to You

Ask not what informatics can do for you.

Ask what you can do for informatics.

Questions?