presentation
TRANSCRIPT
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
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
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
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
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
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
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
Text miningText mining the PCD literature
PCD validity
Text mining
May 2013 Uses and Validity of Primary Care Database studies
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Text miningText mining the PCD literature
PCD validity
Text mining the PCD literature
May 2013 Uses and Validity of Primary Care Database studies
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
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
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
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
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
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
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
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
Text miningText mining the PCD literature
PCD validity
Broad scope of topics in PCD studies
A network graph of PCD topics of investigation
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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
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
Text miningText mining the PCD literature
PCD validity
. . . as are analysis methods
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Bayesian etc. Descriptives only Misc
Mixed−effects RCT comparisons Regression models
Simulations Survival analysis
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May 2013 Uses and Validity of Primary Care Database studies
Text miningText mining the PCD literature
PCD validity
PCD validity
May 2013 Uses and Validity of Primary Care Database studies
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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