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Text mining Text mining the PCD literature PCD validity Uses and Validity of Primary Care Database studies May 2013 David Springate, Evan Kontopantelis, Ivan Olier, David Reeves May 2013 Uses and Validity of Primary Care Database studies

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Page 1: Presentation

Text miningText mining the PCD literature

PCD validity

Uses and Validity of Primary Care Database studies

May 2013

David Springate, Evan Kontopantelis, Ivan Olier, David Reeves

May 2013 Uses and Validity of Primary Care Database studies

Page 2: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature

2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 3: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 4: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 5: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 6: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding

4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 7: Presentation

Text miningText mining the PCD literature

PCD validity

Outline

1 Use of text-mining to explore the scientific literature2 Text-mining the PCD literature

What is being studied using PCD’s?

Changes in topics of investigation over time

3 Validity of Clinical coding4 ClinicalCodes.org : A new repository for clinical code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 8: Presentation

Text miningText mining the PCD literature

PCD validity

Text mining

May 2013 Uses and Validity of Primary Care Database studies

Page 9: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 10: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 11: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 12: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 13: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 14: Presentation

Text miningText mining the PCD literature

PCD validity

What is it?

The process of extracting high-quality structured informationfrom unstructured text (e.g. Scientific literature).

Uses a variety of computational and statistical methods tofind patterns and trends in text

Text mining consists of:

1 Information extraction

Automatically extracting structured information fromunstructured text

2 Semantic searching

Improves search accuracy by including context into a search

3 Knowledge discovery

Identifying relationships in extracted data

May 2013 Uses and Validity of Primary Care Database studies

Page 15: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 16: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 17: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 18: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 19: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 20: Presentation

Text miningText mining the PCD literature

PCD validity

Why do we need it?

The scientific literature is rapidlyincreasing in size

Humans can’t keep up to date withthe literature

75 trials and 11 Systematicreviews published per day!Bastian et al. (2010) PLoSMedicine

It is increasingly difficult to hone inon relevant papers

More of the literature is being heldonline in machine-readable archives

TM can reduce processing time forsystematic reviews by 80%(NCTM)

May 2013 Uses and Validity of Primary Care Database studies

Page 21: Presentation

Text miningText mining the PCD literature

PCD validity

Text-mining is not a magic bullet

Many publications are not openaccess

Often need to rely onabstractsGrey literature is ofteninaccessable

Still need plenty of humaninput!

TM algorithms can be verycomplex

Breadth at the expense of depth

May 2013 Uses and Validity of Primary Care Database studies

Page 22: Presentation

Text miningText mining the PCD literature

PCD validity

Text-mining is not a magic bullet

Many publications are not openaccess

Often need to rely onabstractsGrey literature is ofteninaccessable

Still need plenty of humaninput!

TM algorithms can be verycomplex

Breadth at the expense of depth

May 2013 Uses and Validity of Primary Care Database studies

Page 23: Presentation

Text miningText mining the PCD literature

PCD validity

Text mining the PCD literature

May 2013 Uses and Validity of Primary Care Database studies

Page 24: Presentation

Text miningText mining the PCD literature

PCD validity

UK Primary Care Databases

GPRD / CPRD

The General Practice Research Database / The Clinical PracticeResearch Datalink

˜ 900 papers

THIN

The Health Improvement Network

˜ 360 papers

QResearch

˜ 75 papers

May 2013 Uses and Validity of Primary Care Database studies

Page 25: Presentation

Text miningText mining the PCD literature

PCD validity

The Dataset

All articles reported by CPRD, THIN, QResearch in Pubmed

1185 Abstracts with metadata

141 full-text articles for validation

How are PCD’s being used by researchers?

May 2013 Uses and Validity of Primary Care Database studies

Page 26: Presentation

Text miningText mining the PCD literature

PCD validity

The Dataset

All articles reported by CPRD, THIN, QResearch in Pubmed

1185 Abstracts with metadata

141 full-text articles for validation

How are PCD’s being used by researchers?

May 2013 Uses and Validity of Primary Care Database studies

Page 27: Presentation

Text miningText mining the PCD literature

PCD validity

The Dataset

All articles reported by CPRD, THIN, QResearch in Pubmed

1185 Abstracts with metadata

141 full-text articles for validation

How are PCD’s being used by researchers?

May 2013 Uses and Validity of Primary Care Database studies

Page 28: Presentation

Text miningText mining the PCD literature

PCD validity

The Dataset

All articles reported by CPRD, THIN, QResearch in Pubmed

1185 Abstracts with metadata

141 full-text articles for validation

How are PCD’s being used by researchers?

May 2013 Uses and Validity of Primary Care Database studies

Page 29: Presentation

Text miningText mining the PCD literature

PCD validity

The Dataset

All articles reported by CPRD, THIN, QResearch in Pubmed

1185 Abstracts with metadata

141 full-text articles for validation

How are PCD’s being used by researchers?

May 2013 Uses and Validity of Primary Care Database studies

Page 30: Presentation

Text miningText mining the PCD literature

PCD validity

PCD studies are a growth area!

Number of publications is rapidly increasing. . .

1990 1995 2000 2005 2010

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PCD articles in pubmed

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May 2013 Uses and Validity of Primary Care Database studies

Page 31: Presentation

Text miningText mining the PCD literature

PCD validity

PCD studies are a growth area!

. . . and there is global interest in UK PCD research

Institutions affiliated with UK PCD publications

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May 2013 Uses and Validity of Primary Care Database studies

Page 32: Presentation

Text miningText mining the PCD literature

PCD validity

Broad scope of topics in PCD studies

A network graph of PCD topics of investigation

●●

Cancer1

Fractures/osteo

VTE

antipsychotics/smi

Diabetes

Asthma

NSAID's

HRT

Flu vaccination

Pregnancy

CHD/antihypertensives

Stroke

Pneumonia

Statins

Psoriasis

Antibiotics

Steroids

Atrial/warfarin

Epilepsy

AntidepressantsParacetamol

Heart attack

IBS

BMI/obesity

Kidney disease

Cancer2

Seizures

Auto−immune

COPD

Healthcare costs

Beta blockers

May 2013 Uses and Validity of Primary Care Database studies

Page 33: Presentation

Text miningText mining the PCD literature

PCD validity

Study types are changing. . .

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Associations Benefits Effectiveness

Epidemiology Harms and risks Healthcare costs

Misc Predictions Validity

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May 2013 Uses and Validity of Primary Care Database studies

Page 34: Presentation

Text miningText mining the PCD literature

PCD validity

. . . as are analysis methods

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Mixed−effects RCT comparisons Regression models

Simulations Survival analysis

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May 2013 Uses and Validity of Primary Care Database studies

Page 35: Presentation

Text miningText mining the PCD literature

PCD validity

PCD validity

May 2013 Uses and Validity of Primary Care Database studies

Page 36: Presentation

Text miningText mining the PCD literature

PCD validity

Threats to validity

Unmeasured confounding

Correlation does not equal causation

GP recording

Clinical coding

May 2013 Uses and Validity of Primary Care Database studies

Page 37: Presentation

Text miningText mining the PCD literature

PCD validity

Threats to validity

Unmeasured confounding

Correlation does not equal causation

GP recording

Clinical coding

May 2013 Uses and Validity of Primary Care Database studies

Page 38: Presentation

Text miningText mining the PCD literature

PCD validity

Threats to validity

Unmeasured confounding

Correlation does not equal causation

GP recording

Clinical coding

May 2013 Uses and Validity of Primary Care Database studies

Page 39: Presentation

Text miningText mining the PCD literature

PCD validity

Threats to validity

Unmeasured confounding

Correlation does not equal causation

GP recording

Clinical coding

May 2013 Uses and Validity of Primary Care Database studies

Page 40: Presentation

Text miningText mining the PCD literature

PCD validity

Clinical Coding in PCD’s

All clinical events are entered by GP’s as clinical codes:

Symptoms, signs & diagnoses (READ codes)

Referrals to external care centres

Immunisation records

Prescription information

Diagnostic test records and results

Everything recorded by a GP can be identified (if you knowwhich codes to look for and where to look for them!)

e.g.

H331.00 - Asthma diagnosis

H33z011 - Severe asthma attack

33G1 - Spirometry testing

May 2013 Uses and Validity of Primary Care Database studies

Page 41: Presentation

Text miningText mining the PCD literature

PCD validity

Clinical Coding in PCD’s

All clinical events are entered by GP’s as clinical codes:

Symptoms, signs & diagnoses (READ codes)

Referrals to external care centres

Immunisation records

Prescription information

Diagnostic test records and results

Everything recorded by a GP can be identified (if you knowwhich codes to look for and where to look for them!)

e.g.

H331.00 - Asthma diagnosis

H33z011 - Severe asthma attack

33G1 - Spirometry testing

May 2013 Uses and Validity of Primary Care Database studies

Page 42: Presentation

Text miningText mining the PCD literature

PCD validity

Clinical Coding in PCD’s

All clinical events are entered by GP’s as clinical codes:

Symptoms, signs & diagnoses (READ codes)

Referrals to external care centres

Immunisation records

Prescription information

Diagnostic test records and results

Everything recorded by a GP can be identified (if you knowwhich codes to look for and where to look for them!)

e.g.

H331.00 - Asthma diagnosis

H33z011 - Severe asthma attack

33G1 - Spirometry testing

May 2013 Uses and Validity of Primary Care Database studies

Page 43: Presentation

Text miningText mining the PCD literature

PCD validity

Clinical Coding in PCD’s

All clinical events are entered by GP’s as clinical codes:

Symptoms, signs & diagnoses (READ codes)

Referrals to external care centres

Immunisation records

Prescription information

Diagnostic test records and results

Everything recorded by a GP can be identified (if you knowwhich codes to look for and where to look for them!)

e.g.

H331.00 - Asthma diagnosis

H33z011 - Severe asthma attack

33G1 - Spirometry testing

May 2013 Uses and Validity of Primary Care Database studies

Page 44: Presentation

Text miningText mining the PCD literature

PCD validity

Clinical codes in PCD studies

Diagnoses are made by reference to a set of clinical codes

Workflow

1 Researchers decide on a rough set of codes for a condition

By searching lookup tables for matching terms

By reference to an external source (e.g. QOF)

2 Clinicians go through this draft list by hand and select therelevant codes

3 The database is searched for events matching the finalisedcode list

4 The correct combination of events in the timeframe of interestgives a diagnosis

e.g. For Asthma: Need at least 1+ clinical event 1+ drugevent in the last year to qualify

May 2013 Uses and Validity of Primary Care Database studies

Page 45: Presentation

Text miningText mining the PCD literature

PCD validity

Code list? What code list?

Currently no obligation to publish code lists

No centralised repository for clinical codes

The vast majority of PCD studies do not publish their codes

No way of knowing if a condition diagnosis is valid

No way to replicate the research

For example. . .

In 45 UK case-control PCD studies (diabetes):

Only 5 reported ANY clinical codes. . .

Only 2 of these published codes in appendix

Only 1 provided full set of code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 46: Presentation

Text miningText mining the PCD literature

PCD validity

Code list? What code list?

Currently no obligation to publish code lists

No centralised repository for clinical codes

The vast majority of PCD studies do not publish their codes

No way of knowing if a condition diagnosis is valid

No way to replicate the research

For example. . .

In 45 UK case-control PCD studies (diabetes):

Only 5 reported ANY clinical codes. . .

Only 2 of these published codes in appendix

Only 1 provided full set of code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 47: Presentation

Text miningText mining the PCD literature

PCD validity

Code list? What code list?

Currently no obligation to publish code lists

No centralised repository for clinical codes

The vast majority of PCD studies do not publish their codes

No way of knowing if a condition diagnosis is valid

No way to replicate the research

For example. . .

In 45 UK case-control PCD studies (diabetes):

Only 5 reported ANY clinical codes. . .

Only 2 of these published codes in appendix

Only 1 provided full set of code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 48: Presentation

Text miningText mining the PCD literature

PCD validity

Code list? What code list?

Currently no obligation to publish code lists

No centralised repository for clinical codes

The vast majority of PCD studies do not publish their codes

No way of knowing if a condition diagnosis is valid

No way to replicate the research

For example. . .

In 45 UK case-control PCD studies (diabetes):

Only 5 reported ANY clinical codes. . .

Only 2 of these published codes in appendix

Only 1 provided full set of code lists

May 2013 Uses and Validity of Primary Care Database studies

Page 49: Presentation

Text miningText mining the PCD literature

PCD validity

Validity of Clinical coding

Clinical codes should be held to scrutiny and peer-review (eitherpre- or post-publication)

This would allow for:

replication of studies

validation of diagnoses

incremental improvements to clinical definitions

May 2013 Uses and Validity of Primary Care Database studies

Page 50: Presentation

Text miningText mining the PCD literature

PCD validity

Validity of Clinical coding

Clinical codes should be held to scrutiny and peer-review (eitherpre- or post-publication)

This would allow for:

replication of studies

validation of diagnoses

incremental improvements to clinical definitions

May 2013 Uses and Validity of Primary Care Database studies

Page 51: Presentation

Text miningText mining the PCD literature

PCD validity

Validity of Clinical coding

Clinical codes should be held to scrutiny and peer-review (eitherpre- or post-publication)

This would allow for:

replication of studies

validation of diagnoses

incremental improvements to clinical definitions

May 2013 Uses and Validity of Primary Care Database studies

Page 52: Presentation

Text miningText mining the PCD literature

PCD validity

ClinicalCodes.org

. . . Is an online repository for PCD researchers to upload theircodes upon publication.

Deposit code-lists forpublished studies

Download historicalcode-lists

Archive for all Quality andOutcomes Frameworkbusiness rules (2004 -current)

Database-specificinformation (e.g.consultation types)

May 2013 Uses and Validity of Primary Care Database studies

Page 53: Presentation

Text miningText mining the PCD literature

PCD validity

ClinicalCodes.org

Allows for validation /replication of PCD studies

Tracking of diseasedefinitions through time

Comparitive studies ofclinical codes

Don’t reinvent the wheel!

Currently in development on campus:

medcodes.ls.manchester.ac.uk:8080/codesdb

May 2013 Uses and Validity of Primary Care Database studies

Page 54: Presentation

Text miningText mining the PCD literature

PCD validity

Summary

Publish open access!

Upload your codes!

Thank you

May 2013 Uses and Validity of Primary Care Database studies

Page 55: Presentation

Text miningText mining the PCD literature

PCD validity

Summary

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Upload your codes!

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May 2013 Uses and Validity of Primary Care Database studies

Page 56: Presentation

Text miningText mining the PCD literature

PCD validity

Summary

Publish open access!

Upload your codes!

Thank you

May 2013 Uses and Validity of Primary Care Database studies