INFOBIOMED / Kick-off meeting 9-10 February 2004, IMIM, Barcelona, Spain

1. INFOBIOMED / Kick-off meeting 9-10 February 2004, IMIM, Barcelona, Spain Manolis Tsiknakis George Potamias Institute of Computer Science (ICS) Foundation for Research and Technology – Hellas (FORTH) Center of Medical Informatics & Health Telematics Applications (CMI-HTA) BioInformatics Division (ICS-IMBB / FORTH) HYGEIAnet WP5 - METHODS, TECHNOLOGIES AND TOOLS: ACTIVITIES, SCHEDULE, ASSIGNMENTS

2. INFOBIOMED NoE Activity objectives: Development of new technology & Careful study 5.1.Research on the computational tools available and required for data analysis and information retrieval from complex and heterogeneous databases will be carried out. This activity will consider techniques for database querying, data and text mining and machine learning algorithms, among others. The field of microarray-based gene expression data is a good example of the need to improve methods for knowledge extraction, and it will take advantage from the availability of clinical data to annotate and validate biological results. 5.2. Research & study: (a) Medical imaging , (b) Microarray image analysis , (c) ….. 5.3. Methods and tools for automatic and on-demand extraction of knowledge from the heterogeneous data structures that will result from the integration of information obtained at the molecular, cell, tissue, individual and population levels, with the aim of using it in research, healthcare or management activities. The need of new models and systems to computerize clinical practice guidelines that can integrate medical genetic knowledge will be a must in the future and deserves a sound exploration. This task will analyze the possibilities of extension and integration of decision support tools currently existing in the BI and MI domains and the basic functionalities required for further developments in the field.

3. Patient ClinicalInformation Supporting Technology Clustering Classification GeneSelection Visualization ……….. CLIS LIS HPIS Clinical Information Demographics History Physiological Laboratory Information Indicators Hematological Biochemical Pathologo- Anatomical Information Tumor Sample/Tissue Genomicsworld Clinicalworld Group-Χ vs. Group-Υ Focused/Interesting Clinical Profiles Group-A vs. Group-B Focused/Interesting GE profils GIS Genomic Information DNA-sequences Gene-Expression profiles Differential Gene - Markers Supporting Technology Clustering Classification Discr. Analysis DST ….. Patient GenomicInformation Integrated Clinico-Genomics: A Use-Case Scenario X -- A Y -- B

4. External Clinical (Cancer) Information Sources PACS Images Patient ClinicalInformation LIS HPIS CLIS HistoPathology Information Tumor Sample/Tissue Clinical Information Demographics History Physiological Laboratory Information Indicators Hematological Biochemical External Genomic Information Sources Information Modeling Clinical Data Models Ontology Data Extraction Gateways Medical Informatics Clinical Practice BioInformatics Functional Genomics Info. Modeling Gene Ontology Genomic Data Models Data Analysis DSS Visualization GIS Genomic Information DNA-sequences Gene-Expression profiles Differential Gene - Markers Building-Blocks Patient GenomicInformation Towards an Integrated Clinico-Genomics Environment POPULATION REGISTRIES

5. UMLS SNOP ICD COAS HL7 REGISTRIES GIS CLIS LIS HPIS PACS Images CLINICAL Information Systems Wrappers Clinical Data Model(s) Clinical Ontology DAS Data Analysis Suite Data Mining DSS …… XML <?xml version="1.0" encoding="UTF-8"?> <!– XML Use For Clinical Observations Model Programmer : Kwstas Christofis --> <!DOCTYPE Query [ <!ELEMENT Query(Observation)*> <!ATTLIST Query TimeOfQuery CDATA #REQUIRED WhoAsk CDATA #REQUIRED SelectedQuery CDATA #REQUIRED GeographicRegion CDATA #REQUIRED TimeRange CDATA #REQUIRED Gender CDATA #REQUIRED Age CDATA #REQUIRED> <!ELEMENT Observation (AtomicObservation | CompositeObservation)> <!ATTLIST Observation Patient_Id CDATA #REQUIRED Information_System CDATA #REQUIRED Visit_Id CDATA #REQUIRED> <!ELEMENT CompositeObservation((AtomicObservation | CompositeObservation)* ,ObservationReference*, ObservationQualifier*)> <!ATTLIST CompositeObservation ObservationType CDATA #REQUIRED ObservationTime CDATA #IMPLIED> <!ELEMENT AtomicObservation(ObservationValue,ObservationReference*, ObservationQualifier*)> <!ATTLIST AtomicObservation ObservationTypeCDATA #REQUIRED ObservationTime CDATA #IMPLIED> ……………………………………………………………………. RESULTS HCI / Web-based Human Computer Interface USER Query Formulation Documents Genomic Data Model Genomic Ontology Information System Wrapper GENOMIC Operations & Workflow GO Gene Ontology MGED MIAME ICGE: Integration Issues & Enabling Technology RDF/ XML Generator & Filters

6. WP5: 1 to 12 months INFOBIOMED PARTNERS & SCIENTIFIC COMMUNITY …contribute SERVICES  SYSTEMS  TOOLS  METHODS  TECHNIQUES  STANDARDS INFOBIOMED ICGE Architecture NEEDS & REQUIREMENTS …contribute PILOTS INFOBIOMED

7. INFOBIOMED NoE Activity work plan - first 12 months Activity code and title: 5.1. Data Analysis and Information Retrieval 5.2. Image Visualization and Analysis 5.3. Information Systems & DST Responsible partner: FORTH(WP5, 5.1) – UAVR (5.2) – MI-EMC (5.3) Activity objectives: Development of new technology & Careful study 5.1.Research on the computational tools available and required for data analysis and information retrieval from complex and heterogeneous databases will be carried out. This activity will consider techniques for database querying, data and text mining and machine learning algorithms, among others. The field of microarray-based gene expression data is a good example of the need to improve methods for knowledge extraction, and it will take advantage from the availability of clinical data to annotate and validate biological results. 5.2. Research & study: (a) Medical imaging , (b) Microarray image analysis , (c) ….. 5.3. Methods and tools for automatic and on-demand extraction of knowledge from the heterogeneous data structures that will result from the integration of information obtained at the molecular, cell, tissue, individual and population levels, with the aim of using it in research, healthcare or management activities. The need of new models and systems to computerize clinical practice guidelines that can integrate medical genetic knowledge will be a must in the future and deserves a sound exploration. This task will analyze the possibilities of extension and integration of decision support tools currently existing in the BI and MI domains and the basic functionalities required for further developments in the field. Expected results (at least one to be delivered within first 6 months; include contributions to WP deliverables as set on page 61 of DOW): Month 6: (i) Services, Systems, Tools, Methods, Techniques, StandardsREGISTRY specs & design (ii) Filled-in Questionnaire about: ‘Services’ / ‘Enabling Technology’  ‘Technology-Provider’ (iii)Input from related national initiatives/projects/… Month 12: (i)Web-Enabled REGISTRY INFOBIOMED Web-Site (ii) Scientific Workshop Relationships with other activities (input/output): WP4 , WP6  

8. INFOBIOMED NoE Activity code and title: Indicate the expected involvement of partners in the table below, describing role and estimated effort, expressed in person-months. *: Code as follows: L - Activity Leader. W - Works. I - Provides input. R - Reviews. O - Other (please specify).