a framework for clinical e-science

A Framework for A Framework for Clinical e-ScienceClinical e-Science

Welcome to our Industrial Steering Group Partners

Today’s MeetingToday’s Meeting

• Get to know each other• Tell you something about CLEF• Start to find out

– How we can best work together – What you would find of most value– What you have that would help us– Who else we should be talking to

Project ParticipantsProject Participants

University of Sheffield

University College London

University of Brighton

Judge Institute

Royal Marsden NHS Trust

University of Manchester

Industrial Steering GroupIndustrial Steering Group

Who is CLEF ?Who is CLEF ?

Why is CLEF needed ?Why is CLEF needed ?What is CLEF ?What is CLEF ?

A Convergence of NeedA Convergence of Need

Post genomic research Need for more Need for more

and better and better clinical clinical

informationinformation

Clinical Practice, Audit &

Governance

Management& Policy

Evidence based

health care

Clinical trials recruitment

Problems with Accessing Problems with Accessing Clinical information ?Clinical information ?

Medicolegal, ethical and practical barriers

prevent large scale data sharing between

institutions

STOP STOP

STOP STOP

Much useful clinical information is still only in free text (clinic letters) that computers can’t read

Date-ordered view of record is too comprehensive and only records what happened, not why

UNION SELECT COUNT Patient_ID FROM Patients, Narrative, Diagnosis, Intervention WHERE ((Patients.Patient_ID=Narrative.Patient_ID AND Patients.Patient_ID=Diagnosis.Patient_ID AND Patients.Patient_ID=Intervention.Patient_ID) AND (Diagnosis.Name=“cancer” AND Diagnosis.Locus=“head of the pancreas” AND Intervention.Name= NOT “pancreaticduodenectomy”)AND (Patients.YearOfDeath BETWEEN Diagnosis.Year AND Diagnosis.Year+5)GROUP BY Patients.Date_of_death

SetA.Def {All unique patient& experience[[event.surgery:pancreaticoduodenectomy

treats[event.problem:cancer hasLocus[head of pancreas]]]& timedAt[time_point starts[time_interval:more than 5 years endedBy[time_point

timeOf[now]]]]]}SetB.Def {SetA

& experience[event.intervention.drug administration hasDrug[gemcitabine]& NOT timedAt[(time_point similarTimeAs[time_point

timeOf[event.intervention.drug administration hasDrug[chemotherapy drug]])]& occursBefore[time_point timeOf[event.intervention.drug administration hasDrug[gemcitabine]

occursJustBefore [time_point timeOf [event.intervention.Radiotherapy]]]}SetC.Def {SetA minus SetB} SetD.Def {SetB

& experience[event.problem:death & timedAt[time_point starts[time_interval:less than 5 years

& endedBy[time_ point timeOf[event.surgery:pancreaticoduodenectomy treats[event.problem:cancer hasLocus[head of pancreas]]]]}

SetE.Def {SetC& experience[event.problem:death

& timedAt[time_point starts[time_interval:less than 5 years & endedBy[time_ point timeOf[event.surgery:pancreaticoduodenectomy

treats[event.problem:cancer hasLocus[head of pancreas]]]]}Query.Def {(Size(SetB) - Size(SetD)) / Size(SetB)} Query.Def {(Size(SetC) - Size(SetE)) / Size(SetC)}

UNION SELECT COUNT Patient_ID FROM Patients, Narrative, Diagnosis, Intervention WHERE ((Patients.Patient_ID=Narrative.Patient_IDAND Patients.Patient_ID=Diagnosis.Patient_ID AND Patients.Patient_ID= Intervention.Patient_ID) AND (Diagnosis.Name=“cancer” AND Diagnosis.Locus=“head of the pancreas” AND Intervention.Name=“pancreaticduodenectomy”) AND (Patients.YearOfDeath BETWEEN Diagnosis.Year AND Diagnosis.Year+5) GROUP BY Patients.Date_of_death)

Query interfaces for interrogating

databases about temporal relationships

are complex

‘Huge variations in cancer care’BBC News 22nd May 2003

Why start with Why start with cancer ?cancer ?Major priority for NHS and Research

High public interest and concern

Clinical care and gene research strongly linked in cancer

Cancer patient EPR is information rich>100 letters per patient over lifetime

‘Breast cancer at

record levels’

BBC News 2nd June 2003

‘Wheat may prevent

colon cancer’

BBC News 23 rd February 2002

‘Vitamin cocktail cuts cancer deaths’BBC News 4th August 2003‘Vitamin D boosts

cancer treatment’

BBC News 14th June 2003

‘Direct-to-Consumer Marketing of

Genetic Tests for Cancer: Buyer

Beware’Journal of Clinical Oncology 21st July 2003

‘Gene to halt ovarian

cancer found’

New Scientist 23rd June 2003

‘Gene test may show if cancer will respond to chemotherapy’The Independent 1st August 2003‘Scientists stunned as

pioneering British research

cuts death rate by 30 per cent’

The Independent 1st June 2003

Who is CLEF ?Who is CLEF ?Why is CLEF needed ?Why is CLEF needed ?

What is CLEF ?What is CLEF ?

CLEF’s GoalsCLEF’s Goals

GRID

GRID

• Collect clinical information from multiple sitesCollect clinical information from multiple sites

• Analyse, structure and integrate itAnalyse, structure and integrate it

• Make it available using GRID tools (e.g. Make it available using GRID tools (e.g. mymyGrid)Grid)

• To authorised clinicians and e-Health scientistsTo authorised clinicians and e-Health scientists

• In a secure and ethical collaborative frameworkIn a secure and ethical collaborative framework

Ethical oversight committee

ReidentifyBy Hospital

PseudonymiseIn Hospital

Depersonalise

ExtractInformation

Integrate &Aggregate

Construct‘Chronicle’

Chronicle

Ethical oversightcommittee

Obvious patient names & identifiers masked by source hospital

PseudonymisedRepository

Hazardmonitoring

Knowledgeenrichment

Summarise& Formulate

Queries

Significant clinical information identified in text (e.g. diagnoses, drugs, clinical findings etc)…

Less obvious identifiers removed from text (e.g. occupation)

…and integrated with structured information (e.g. lab tests, theatre records)…

…and federated in a single secure data

repository

Individual Summaries& Queries

PrivacyEnhancementTechnologies

References reconstructed between information (e.g. Problem X was discovered during Investigation Y)…

…and ‘Chronicle’ view added to repository

Clinicians from original hospital can view summaries and query the repository…

…and reidentify specific patients, only with permission

Hospital exports its electronic records of regular clinical practice

Information extraction informed by data

already in repository

Clinical e-Scientists connected by Grid…query the repository

for e.g. numbers of patients with specific diseases.

…but answers are monitored to prevent

reidentification of patients by cross reference or data

mining.

Researchers reqired to notify possible reidentification risks

…and also contribute additional information (e.g. adding never stated diagnosis of anaemia if blood results suggest it)

All interactions between e-Scientists and repository approved and monitored

by ethical oversight committee.

ArchitectureArchitectureOutline Outline



Depersonalise

ExtractInformation



Chronicle



Hazardmonitoring

Knowledgeenrichment


Queries





Depersonalise

ExtractInformation



Chronicle



Hazardmonitoring

Knowledgeenrichment


Queries



ArchitectureArchitectureOutline Outline

Data Acquisition Cycle

Data Access Cycle

CLEF Data CycleCLEF Data Cycle

Data AcquisitionData Acquisition

ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE 324A621F:MRS Dorothy Smith

DOB: 12/05/44 21, Park Crescent

Basingstoke B12 Q13 16 Dec 1992 Seen in General Surgical This lady who has had a mastectomy and left open capsulotomy and removal of her prosthesis was seen by me in the clinic today on behalf of Mr Peterson. She has extensive bony lymphoedema in her left arm which does not seem to be getting any better although she is more or less reconciled to the problem. The original problem was that she complained of shooting pain in the direction of ulna nerve and although there does not seem to be any evidence of local, regional or distant recurrence the pain itself warrants management in a pain clinic. Mrs Smith could be seen in the pain clinic at the Marsden but as this would involve a lot of travelling would like to be treated nearer her home. I wonder whether it would be possible for you to investigate if there is a pain clinic available at Basingstoke as I am sure Dotty could be treated and benefit from its management. I have otherwise arranged for her to be seen in the clinic again in a year's time. There are no signs of recurrence at this time.

Mr Thomas Partridge

Reports dictated Reports dictated For hospital use: For hospital use:

ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE 324A621F:MRS Dorothy Smith

DOB: 12/05/44 21, Park Crescent

Basingstoke B12 Q13 16 Dec 1992 Seen in General Surgical This lady who has had a mastectomy and left open capsulotomy and removal of her prosthesis was seen by me in the clinic today on behalf of Mr Peterson. She has extensive bony lymphoedema in her left arm which does not seem to be getting any better although she is more or less reconciled to the problem. The original problem was that she complained of shooting pain in the direction of ulna nerve and although there does not seem to be any evidence of local, regional or distant recurrence the pain itself warrants management in a pain clinic. Mrs Smith could be seen in the pain clinic at the Marsden but as this would involve a lot of travelling would like to be treated nearer her home. I wonder whether it would be possible for you to investigate if there is a pain clinic available at Basingstoke as I am sure Dotty could be treated and benefit from its management. I have otherwise arranged for her to be seen in the clinic again in a year's time. There are no signs of recurrence at this time.

Mr Thomas Partridge

Pseudonymisation Pseudonymisation at hospitalat hospital

Carer pseudonymised

Clinic date blurredpreserving sequence

Mrs SmithXXXXXXXXX

324A621F:MRS Dorothy Smith

21, Park CrescentBasingstoke B12 Q13

########:######### ####### Obvious mentions of patient name

ROYAL MARSDEN##### #######

MarsdenXXXXXXX

BasingstokeXXXXXXXXXXX

CLEF-RMH-Entry-Key: 52A4F6DB2B46E

or hospital name removed

Overt identifying information removed in hospital & ID replaced by CLEF Entry Key

Mr Thomas Partridge

16 Dec 1992

5213A4F612F1

AB 1992

12/05/441944

Date of birth reduced to year

Depersonalisation Depersonalisation by CLEF Language by CLEF Language Technology…Technology…

Non-obvious identifyinginformation removedusing languagetechnology

##### ####### NHS TRUST - PATIENT CASE NOTE ########:######### ####### DOB: 1944 CLEF-RMH-Entry-Key: 52A4F6DB2B46E

AB 1992 Seen in General Surgical This lady who has had a mastectomy and left open capsulotomy and removal of her prosthesis was seen by me in the clinic today on behalf of Mr Peterson. She has extensive bony lymphoedema in her left arm which does not seem to be getting any better although she is more or less reconciled to the problem. The original problem was that she complained of shooting pain in the direction of ulna nerve and although there does not seem to be any evidence of local, regional or distant recurrence the pain itself warrants management in a pain clinic. XXXXXXXXX could be seen in the pain clinic at the XXXXXXX but as this would involve a lot of travelling would like to be treated nearer her home. I wonder whether it would be possible for you to investigate if there is a pain clinic available at XXXXXXXXXXX as I am sure Dotty could be treated and benefit from its management. I have otherwise arranged for her to be seen in the clinic again in a year's time. There are no signs of recurrence at this time.

5213A4F612F1

Nick-name “Dotty”spotted by language software & removedXXXXX

XXXXXXXXXXX

Carer name spotted & pseudonymised

##### ####### NHS TRUST - PATIENT CASE NOTE ########:######### ####### DOB: 1944 CLEF-RMH-Entry-Key: 52A4F6DB2B46E

AB 1992 Seen in General Surgical This lady who has had a mastectomy and left open capsulotomy and removal of her prosthesis was seen by me in the clinic today on behalf of XXXXXXXXXXX. She has extensive bony lymphoedema in her left arm which does not seem to be getting any better although she is more or less reconciled to the problem. The original problem was that she complained of shooting pain in the direction of ulna nerve and although there does not seem to be any evidence of local, regional or distant recurrence the pain itself warrants management in a pain clinic. XXXXXXXXX could be seen in the pain clinic at the XXXXXXX but as this would involve a lot of travelling would like to be treated nearer her home. I wonder whether it would be possible for you to investigate if there is a pain clinic available at XXXXXXXXXXX as I am sure XXXXX could be treated and benefit from its management. I have otherwise arranged for her to be seen in the clinic again in a year's time. There are no signs of recurrence at this time.

5213A4F612F1

Extraction of keyExtraction of keyinformation from textinformation from text

Information Extraction identifies events and relationships between them from the text, based on templates & knowledge resources

recurrence

no signs of recurrence

bony lymphoedema

shooting pain in thedirection of ulna nerve

pain

Interventions

Problems

Problem Site

Locations

left arm

local, regional or distant

a year’s time

today

at this time

Time

pain clinic

clinic

pain clinic

General Surgical

pain clinic

mastectomy left open capsulotomyremoval of her prosthesis

management

management

Extraction of keyExtraction of keyinformation into Data information into Data StructureStructure

Extracted information collected…

Interventions

Problems

Problem Site

Locations

Time

recurrence


bony lymphoedema


pain

left arm


a year’s time

today

at this time

pain clinic

clinic

pain clinic

General Surgical

pain clinic

mastectomy left open capsulotomyremoval of her prosthesis

management

management

recurrence


bony lymphoedema


pain

left arm


a year’s time

today

at this time

pain clinic

clinic

pain clinic

General Surgical

pain clinic

mastectomyleft open capsulotomy

removal of her prosthesis

management

management

recurrence

no signs of recurrencebony lymphoedema


pain

left armlocal, regional or distant

a year’s timetoday

at this time

pain clinicclinic

pain clinicGeneral Surgical

pain clinic

mastectomy

left open capsulotomy


managementmanagement

across multiple documents

radiology, pathology and other narrative reports

Information from laboratory and pharmacy systems

Extraction of keyExtraction of keyinformation into Data information into Data StructureStructure

Information extraction also collates repeated reporting of same event

Interventions

Problems

Problem Site

Locations

Time

Provenance of information linked to original texts…

recurrenceno signs of recurrence

bony lymphoedema


pain



at this time

pain clinicclinic

pain clinicGeneral Surgical

pain clinic

mastectomy



managementmanagement

..including multiple source documents

management

pain clinic

The CLEFThe CLEFChronicleChronicle

Internal links between events added by information extraction:What happened & why ?What was done & why ?

Interventions

Problems

Problem Site

Locations

Time

recurrenceno signs of recurrence

bony lymphoedema


pain



at this time

pain clinic

General Surgical

pain clinic

mastectomy



management

pain clinic

mastectomy

caused_by

bony lymphoedemaevi

dence

Including the links to original texts, this is the CLEF Chronicle

CLEF-RMH-Entry-Key: 52A4F6DB2B46E Female 66 with radiation induced leukaemia since 1931 Onset age 63. Thirty three appointments to date. Problems: Aplastic anaemia, cataract, astheniaTx:imatinibMeds: unclear

Hospital EPREPR Drugs Refer Tools Help

Protocol 354Staging CT

BP

Haem Chem Immu Bact Xray ECG USS

12.10.20 Coryza: chest NAD: reassure13.10.20 URTI: wheezy: amoxycillin20.10.20 Anxiety: lump under arm: staging scan24.10.21 PEFR : 300 :10.11.21 PEFR : 400: CXR requested12.11.21 CXR Basal Consolidation: : erythromycin27.11.21 : Chest clear :07.03.30 Depression: recurrence: Paroxetine19.04.30 WCC OK01.06.31 : : rpt Rx paroxetine18.10.31 Pain L arm: : coproxamol03.03.31 Viral URTI: PEFR 350: salbutamol04.03.34 WCCAbnormal : :30.05.34 : BP, ECG NAD :

Results Letters ApptDrugs

Summarisation forSummarisation forPatient CarePatient Care

Very brief summaryof chronicle for recordheader and front sheet is available to source hospital …

can be incorporated within the hospital system

CLEF-RMH-Entry-Key: 52A4F6DB2B46E Female 66 with radiation induced leukaemia since 1931 Onset age 63. Thirty three appointments to date. Problems: Aplastic anaemia, cataract, astheniaTx:imatinibMeds: unclear

Summary for top of screen/page for allpatient interactions

Patient reidentifiable only by source hospital, with permission

CLEF-RMH-Entry-Key: 52A4F6DB2B46EMaria Sklodowska-Curie

CLEF Data CycleCLEF Data Cycle

Data AccessData Access

CLEF e-Scientist LOGINLogin Query OMIM Exit

User ID:Password:

Users of this site are bound byCLEF Privacy PolicyCLEF Security PolicyData Protection ActMedical Records Act

Use is monitored by the CLEFEthics oversight board.

Access for e-Access for e-Scientists Scientists

Cumulative repository is made accessible for remote querying by e-Scientists…

******************

IdentityConfirmed

Possible physical identification of users by biometric readers or smartcard

Digital certificates issued per session

…under control of oversight committee.

Once user is authenticated, level of access authority is retrieved from oversight committee.

CLEF User IDCL-00236F

AuthorisationLEVEL 2

CLEF WYSIWYM Query Writer – L2Login Query OMIM Exit

Relevant Subjects

Treatment Profiles

Outcome Measures

Patients with [this type of tumour] at [this site]

Percentage of patients in [this condition] after [this interval of time].

Patients who received [this type of treatment], compared with patients who received [this type of treatment].

AND [another characteristic].

E-Scientist E-Scientist formulates queriesformulates queries

e-Scientists construct queries using structured query writer

Percentage of patients [alive] after [1 year] and after [2 years] and after [5 years].

Patients who received [radiotherapy] [daily], compared with patients who received [radiotherapy] [every other day] and those who received [no radiotherapy].

carcinomacarcinoma-in-situsarcomaneuroma

nothing elsethis clinical stagethis gradethis genetic marker---------------------------this symptomhas had this treatmentthis complication

AND [this genetic marker].

Links out to other bioscience resources e.g. OMIM, PubMed, Gene Ontology

AND [BRCA1 (OMIM 113705)].Patients with [this type of carcinoma ] at [this site]adenocarcinoma

basal carcinomasquamous carcinomatransitional carcinoma

Patients with [adenocarcinoma] at [this site]bladderbloodbrainbreastcervixcolonendometriumkidneylarynxlunglymphnodeoesophagusovarypancreasprostaterectumskinstomachtestistongue

Patients with [adenocarcinoma] of [this laterality] of [this part] of [breast]

…or graphically

For all patients with adenocarcinoma of the breast, compare the survival at 1, 2 and 5 years for those patients who had daily radiotherapy, those who had radiotherapy on alternate days, and those who had no radiotherapy

Feedback TextQUERY RESULT1792 patients diagnosed with adenocarcinoma of the breast were found. 788 had radiotherapy daily, 513 had it on alternate days and 491 had no radiotherapy.

After 5 years, 20% (n=158) of patients who had a daily treatment were alive. After 5 years, 10% (n=49) who had alternate day treatment were alive. After 5 years, 5% (n=27) of the patients who had no treatment were alive.

Result of running query displayed as generated text…

Generated text confirms the nature of the query

Privacy EnhancementPrivacy Enhancement& authorisation& authorisation

Queries logged,threats to confidentiality monitored.

CLEF WYSIWYM Query WriterLogin Query OMIM Exit

Relevant Subjects

Treatment Profiles

Outcome Measures

[Male] patients with [adenocarcinoma] of of [this laterality] of [this part] of [breast]AND [age] at [diagnosis] was [less than 30].



WARNINGLess than 20 male patients diagnosed with adenocarcinoma of the breast were found.

Further subanalysis on small groups increases the risk that a patient may be identifiable.

Your CLEF security authorisation does not permit your query to be processed.

Queries on small patient groups are blocked or the figures blurred.

malefemale

[Female] patients with [adenocarcinoma] of of [this laterality] of [this part] of [breast]

QUERY RESULT1792 patients diagnosed with adenocarcinoma of the breast were found. 788 had radiotherapy daily, 513 had it on alternate days and 491 had no radiotherapy.


With special authorisation researchers may examine individual records in anonymised form.

CLEF Patient Chronicle Viewer – L2Exit

#12345678910111213141516171819202122232425262728293031

17

1974

Grade III infiltrating ductal carcinoma left breast

7/22 sampled nodes positive

Radical Mastectomy Left Breast

Insertion Left Breast Prosthesis

MEFUP Chemotherapy

1982/3

Recurrence Left supraclavicular nodes

Excision biopsy of nodes

Radiotherapy

1992

Replacement of Left Breast Prosthesis

Removal of replacement to left breast prosthesis

1994

Recurrence inside chest (confirmed biopsy)

VAC Chemotherapy aborted (toxicity)

Radiotherapy completed

L5/S1 degeneration

Left phrenic nerve paralysis

1996

Multiple pulmonary emboli

Post-radiation fibrosis left upper lung

Prior rib fractures

Frontal lobe ischaemic atrophy

Teflon injection vocal cord

1997

Recurrence in chest

Pleural effusions

VAC Chemotherapy 6 cycles

1998

Recurrence in chest

Radiotherapy

Normal Left Shoulder Xray

1999

No evidence of recurrence

Congestive cardiac failure

Died June 1999

19 75 19 80 19 85 19 90 19 95 20 00

D i edG rad e I I I i n fi l tr ati n g

d u c ta lc ar c i n om a l e f t b reas t

RR ecu rr e n ce

R R R

TAMOXIFEN ARIMIDEX

RA D IO

C H E M O

SSSSSS S S S SS SSS t ag in g C T

T 1N 3 cM 0

T 1 >N 3 cM 1

S tag e IIA S tag e I II c S tag e IV

N o d e sL iv erS p l ee nK id n e yB o n e

N o d e sL iv erS p l ee nK id n e yB o n e

T 1 >N 1 >M 0

Textual summary of CLEF Chronicle for patient #17

Graphical ‘time line’ view of CLEF

Chronicle

1975 1980 1985 1990 1995 2000

DiedGrade III infiltrating

ductal carcinoma left breast

RRecurrence

R R R

TAMOXIFEN ARIMIDEX

SSSSSSS S S SS SSStaging CT

NodesLiverSpleenKidneyBone

NodesLiverSpleenKidneyBone

T1>N1>M0

T1N3cM0

T1>N3cM1

>Stage IIA Stage IIIc Stage IV

RADIO

CHEMO

Data Summarisation &Data Summarisation &VisualisationVisualisation

Hazard Monitoring Hazard Monitoring

Automated anonymisation unlikely to be perfect.

Users can report possible hazards they encounter.


Relevant Subjects

Treatment Profiles

Outcome Measures

[Female] patients with [adenocarcinoma] of of [this laterality] of [this part] of [breast]AND [age] at [diagnosis] was [less than 30].






#12345678910111213141516171819202122232425262728293031

17

Lab

Higher security authorisation, more detail visible…

ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE

########:######### #######DOB: 1944CLEF-RMH-Entry-Key: 52A4F6DB2B46E

AD 1997 Seen in Pain Clinic

Dear XXXXX,

Thankyou for referring XXXXXXXXX to me. I know her quite well, as she is captain of my local ladies’ golf team.

As you say, her tumour is responding satisfactorily at the moment to Arimidex. She does not complain of any severe symptoms now, except continuing lymphoedema of the arm.

I will see her again in 3 months time.

5213A4F612F4

Report Hazard

Knowledge Knowledge Enrichment Enrichment

Authorised users can also augment chronicle with additional information.


Relevant Subjects

Treatment Profiles

Outcome Measures

[Female] patients with [adenocarcinoma] of of [this laterality] of [this part] of [breast]AND [age] at [diagnosis] was [less than 30].






#12345678910111213141516171819202122232425262728293031

17

Lab Report HazardLab

0 5 10 15 20

WCC

Hb

0 5 10 15 20

LFT

0 5 10 15 20

Period of clinical anaemia, not recorded in chronicle

+

+

+

+

CLEF Knowledge Editor – L1Exit

Hb

0 5 10 15 20

Evidence

Event:

Yes No Cancel

ID(5627) ID(5645) ID(5685)

anaemiaProblem Type: diagnosisDate: 6F to 9B

UMLS CUI:C0002871

NB. Research access to depersonalised narratives will be highly restricted

Knowledge ResourcesKnowledge Resources• Internal knowledge sources

– Clinical significance – what’s clinically obvious”• “only osteoporosis” “No bony metastases”• Leukopaenia possible cause to stop treatment• Tamoxifen is used in breast cancer

may cause menopausal symptoms sometimes treated with HRT

– Linguistic resources and corpora

• External knowledge sources– Pubmed, UMLS, other literature …– OMIM, GO, other databases…

• Standards– HL7, CEN EHR, NCICB CaCore, …

Links & Related projectsLinks & Related projects• Bioinformatics

– GO, GONG, MGED, EBI

• Post-genomic research & cancer– NCRI/NTRAC/NCTR/NCRN– BioBank

• NHS & Healthcare– Cancer Networks & National Programme

• International– NCICB, Mouse/Human Anatomy projects

• E-Science & Standards– myGrid, CO-ODE/HyOntUse, ESNW, DTI, Semantic

Web/Grid– HL7, CEN TC251, ISO TC215– Semantic Mining NoE in 6th Framework

DeliverablesDeliverables• Privacy policies and framework

– A steering group hopefully in collaboration with others

• Information extraction– Clinical information from semi-parallel texts from

parallel records

• EHR/Chronicle/Repository– Specification and demonstrator of integrated

populated

• Workbench and Language Generation– Demonstration useful and usable interface for clinical

bioscientist to access repository– Query methods for specification longitudinal chronicle

• E-Science Implementation– Technical– Knowledge, metadata standards

• Tools from CO-ODE, myGrid, E-Science

Project Plan from 20K ftProject Plan from 20K ft

Design Prototype Revise & Integrate

Year 1 Year 2 Year 3

Policy & ethics

Information flow

Internal links

External links

first joined up demonstration

Info Extraction /depersonalisation demo

WorkbenchPrototype

Repository/Chronicles architecture & simulation

Internal Knowledge resources

Basic Engineering & architecture

Robust Info Extraction /depersonalisation

Integrated Workbench &Privacy Enhancement

Populated integratedRepository/Chronicles

Links to external knowledge & standards

Integration, E-Science Web services

Demonstrator & Evaluation

Vision& Plan

Thank you for comingThank you for coming

www.clinical-escience.orgwww.clinical-escience.org

Empowering the e-ScientistEmpowering the e-Scientist

Removing barriers to data sharingRemoving barriers to data sharing

Enriching clinical knowledge basesEnriching clinical knowledge bases

2003- 20052003- 2005

a framework for clinical e-science

Documents