An Enriched Repository of Patient Chronicles Linking Clinical Care and Biomedical Research

An Enriched Repository of Patient Chronicles Linking Clinical Care and Biomedical Research Alan RectorBioHealth Informatics GroupDepartment of Computer ScienceAlan.Rector@Manchester.ac.ukwww.clinical-escience.org

Management & Policy Evidence based health care Clinical Practice, Audit & Governance Clinical trials recruitment A Convergence of Need Post genomic research Need for more and better clinical information

CLEF & CLEF-Services • CLEF • One of initial MRC E-Science Projects • Prototypes and technologies • Focused at the Royal Marsden • A special opportunity - the best data for development & testing • An unrepeatable situation - canot generalise • CLEF Servicesfrom removing barriers to “doing it” • Adding new partners to strengthen Privacy & Clinical Resources • Making software generic and grid enabled • Chronicle as a semantic grid application • Implement on myGrid and Grid security • Interacting with standards, NCRI, EU, US, … • Implementation in less specialised centres • London Genetics (and Cancer Networks)

Knowledgeenrichment Knowledgeenrichment HazardMonitoring Integrate &Aggregate Integrate &Aggregate PseudonymisedRepository PseudonymisedRepository ExtractInformation ExtractInformation Ethical oversightcommittee Ethical oversightcommittee Depersonalise Depersonalise Chronicle Chronicle PrivacyEnhancementTechnologies Summarise & FormulateQueries Summarise & FormulateQueries Construct‘Chronicle’ Construct‘Chronicle’ PseudonymiseIn Hospital PseudonymiseIn Hospital Individual Summaries & Queries Individual Summaries & Queries PrivacyEnhancementTechnologies ReidentifyBy Hospital HazardMonitoring ReidentifyBy Hospital Data Access Cycle Data Acquisition Cycle Focus on Information capture, organisation, and presentation

The CLEF Technologies • Privacy • Policy, Security of access and storage, Statistical disclosure control, monitoring & oversight • Information extraction from text • Because Doctors dictate • “Getting the information other projects can’t reach” • Information organisation & fusion • The EHR, Chronicle, & provenance • What was done & why • How we know? Who has used it? What have they found? • Usability for research • The query formulation tools and workbench • “What you get is what you meant”

Clinical Records ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE ######:MRS ##### ####### 27 Aug 1998 Seen in the Follow Up Staging Clinic This 65 year old lady has been reviewed in the Breast staging clinic. As you know, she was originally diagnosed with a carcinoma of the left breast in 1974 and treated with a total mastectomy. This was followed with MEFUP chemotherapy. In 1982 she noticed a lump in the infraclavicular region which was excised and this was followed by radiotherapy. In 1994 she developed a tumour in the chest cavity that was diagnosed with a CT guided biopsy and this was treated with VAC chemotherapy and radiotherapy to the mediastinum. Since 1994 she had noticed a slight deterioration and earlier this year she had problems with occasional episodes of vomiting, nausea and general lethargy. She was found to have lymphadenopathy in the right supraclavicular fossa and was treated with Arimidex. Since being on Arimidex there was originally stablisation of her disease but recently it appears that the node has started to enlarge. On examination today, she has a 1.5x1cm lymph node in the right supraclavicular fossa and an essence of thickening probably due to previous therapy in the left supraclavicular fossa. She also has radiation changes in the lung which produced some physical sign at both bases and there was no evidence of abdominal organomegaly. Her recent staging investigations show that she has C5 carcinoma cells present in the lymph node fine needle aspirate. A right mammogram is unremarkable. An ultrasound of the liver was normal and a chest x-ray showed some soft tissue thickening present in the left axilla due to previous therapy. There is also some loss of volume in the left upper zone but no lung nodules seen. A bone scan shows evidence of degenerative changes but no specific evidence of bony metastases. Her thyroid function tests show that the TSH is 0.12 and her free T3 are 4 which indicates that the TSH is slightly low. This does not amount to primary hypothyroidism but it would be worth repeating the thyroid function tests in three months time. Overall, it appears that the patient has stable disease on Arimidex apart from in the right supraclavicular fossa. The Arimidex is not holding the disease completely and we feel that the best approach to management would be to consider some radiotherapy to the right supraclavicular fossa. She has previously had radiation therapy to the left clavicular region and mediastinum. We have discussed performing a CT scan of the thorax but she was unable to lie flat for the duration of the investigation some months ago. We shall ask our radiotherapy colleagues to review her and consider her for therapy. We shall review her again in the follow up clinic in six weeks time. 28/03/2003, 10:50:25 ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE ######:MRS ##### ####### 15 Dec 1993 General Surgical I reviewed this patient in clinic today. She has been followed up for a left breast carcinoma for which she was treated with a mastectomy. She had a prosthesis removed last year and has had some improvement in the symptoms of chest wall discomfort since then although she still gets quite sharp pains intermittently. She has been reviewed in the pain clinic local to where she lives but has not had much relief of her symptoms. She feels though that she can bear with these and does not want any further intervention at present. On examination today there is no sign of recurrence of her disease. Chest and abdominal examination were unremarkable. We will see her again in a year's time. 28/03/2003, 10:35:26 ROYAL MARSDEN NHS TRUST - DIAGNOSTIC RADIOLOGY - CT REPORT ######:#######,MRS ##### Exam 18 Dec Examination LIVER/THORAX/ABDOMEN/PELVIS Exam Number [NUM] Date of Birth 17 May 1933 Ref [HCA1] OUTPATIENT Clinical BR Verified by [HCA2] DIAGNOSIS: Carcinoma of breast. CT scans have been obtained through chest, abdomen and pelvis with oral contrast only. There is thickening in the left clavicular fossa and small- volume residual abnormalities in the mediastinum. Comparison is made with the most recent scan (21.7.95) and there is no discernible change by CT criteria. Lung changes, which may have been related to radiotherapy, are now less extensive. There are no abnormally-enlarged nodes in the retroperitoneum or pelvis. There are no focal hepatic masses. CONCLUSION: No CT evidence of disease progression. 28/03/2003, 12:35:06 ROYAL MARSDEN NHS TRUST - PATIENT CASE NOTE ######:MRS ##### ####### 24 Jan 1997 Seen in the Chemotherapy Clinic (TPFRIDAY) I saw ##### today in clinic. I am very pleased to say that she has had a complete response in her superior mediastinum and right supraclavicular fossa lymphadenopathy. There is some minimal thickening remaining in the soft tissues around the superior mediastinum and in fact it is felt that this might now be related to previous radiotherapy. To be honest, however, symptomatically there has been little in the way of benefit with overall palliative response of no change. She is tolerating the treatment fairly well. Interestingly she has had virtually complete alopecia with the treatment. She has been on warfarin for about the same amount of time and I wonder whether this may be partly responsible. We have given her a fourth cycle of treatment today and we will see her in three weeks for consideration of her fifth. 28/03/2003, 10:44:20

R R R R Grade III infiltrating ductal carcinoma left breast Died RADIO CHEMO TAMOXIFEN ARIMIDEX Nodes Liver Spleen Kidney Bone Nodes Liver Spleen Kidney Bone Staging CT S S S S S S S S S S S S S T1>N1>M0 T1N3cM0 T1>N3cM1 >Stage IIA Stage IIIc Stage IV Recurrence 1975 1980 1985 1990 1995 2000 The CLEF Chronicle:Inferred best view of the patient history

…and a natural easy way to query them

Human:1382 Pain:5735 Ulcer:1945 locus locus attends reason locus reason finding attends attends time time time time time time time time Breast:1492 Clinic:1024 Clinic:2010 Clinic:4096 plans plans reason plans plans plans reason reason Biopsy:1066 Radio:1812 Chemo:6502 locus target finding treats reason treats Mass:1666 Cancer:1914 locus What happened… And why What was done…

Other Feature Status Name Status Laterality Name Name Goal LOCUS INVESTIGATION Age PATIENT INTERVENTION Sex Race REGIME Name Occupation Doctor Dose Form DRUG Route TIME Name CONSULT PROBLEM Name Size Clinical Course LOCATION PATHOLOGY Diagnostic Status Family History Name Type Evidence for Presence / absence Status Other Feature compare target partOf has-locus has-locus subpart has-locus indication involves recommend about treats/indicates recommend finding causes after indicatedBy causes about partOf locatedAt Draft Schemafor Chronicle

To link Grid & NHS computing NHS Information (NPfIT) Research Information genetics biosciences clinical trials and longitudinal studies knowledge management decision support data mining health improvement patient centred medicine clinical service framework clinical governance outcome: effectiveness/ efficiency evidence Information forpatients & public Security Images, Language, GenomicsArchitecture, Web/Grid Services, Terminology, Standards To realise the research potential of the nhs

CLEF ethical approach • Organisational • Ethical Oversight Committee • Possibly joint with others? • PIAG, “XRec” approval • Data sharing initiatives – MRC, Digital curation, … • Technical • CLEF • De-identification • Pseudonymisation • Depersonalisation • Access control • Usage monitoring • Statistical disclosure control • GRID security • Links to Ning Zhang and David Chadwick

University of Sheffield University of Brighton Judge Institute Royal Marsden NHS Trust Project Participants University College LondonCHIME London Institute for Genetic Medicine University of ManchesterComputer Science ISBE Cathie Marsh Centre

Linked projects on Knowledge ManagementCo-ode HyOntUse • Cooperative ontology developmentThe Web Ontology Language (OWL) meets real users • Making OWL useful and usable • Joint with Stanford and Southampton/AKT • US effort funded through NCI • Much effort on tutorial material and teaching • Matthew’s tutorial is the de facto text on OWL • Three levels • Migration/neophyte’s interface • Bulk developer’s interface • Logician’s interface • Aiming for multi-user and web based development • Consulting with NHS on tools for NPfIT

Come and see us if: • You need help with or can help us with: • Electronic health records for care or research • Text based information • Query interfaces • Information fusion • HL7, Archetypes, SNOMED-CT, UMLS,… …Links to Decision support… • Knowledge management • Ontologies, Classifications, Terminologies, The Semantic Web

An Enriched Repository of Patient Chronicles Linking Clinical Care and Biomedical Research