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WP5 : Methods, Technologies & Tools

WP5 : Methods, Technologies & Tools. Work in the last 2 years. Costas Marias Yannis Tollis Manolis Tsiknakis George Potamias Institute of Computer Science (ICS) FORTH. WP5 : Methods, Technologies & Tools. Work in the 1 st year. … work presented during the 1 st APR.

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WP5 : Methods, Technologies & Tools

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  1. WP5: Methods, Technologies & Tools Work in the last 2 years Costas Marias Yannis Tollis Manolis Tsiknakis George Potamias Institute of Computer Science (ICS) FORTH

  2. WP5: Methods, Technologies & Tools Work in the 1st year … work presented during the 1st APR

  3. WP5: Methods, Technologies & Tools 1st year SoA review on Methods, Systems and Tools in BMI

  4. Audience -Communities • Computer Scientist • Bioinformatician • Medical Informaticians • Biologists • Physicians Web-site WP5 Leader WP5: Methods, Technologies & Tools (1st year) WP5 SoA on Systems, Methods & Tools in BMI Rational • To informthe related communities about advances in BioMedical Informatics (links with WP2: Dissemination). • Educate them about BMI SoA methods in order to tackle related biomedical problems and tasks (links with WP3: Education). • Single-stop reference to BMI tasks, methods, technologies and tools. • As a ‘consultation’ service for INFOBIOMED pilots (links with WP6: Pilots). • Special focus on biomedical knowledge discovery. • Enabling clinico-genomics research and clinical-trials. • Integrated Clinico-Genomics Environment(links with WP4: Standards).

  5. WP5: Methods, Technologies & Tools (1st year) WP5 SoA on Systems, Methods & Tools in BMI Structure … oriented around ‘biomedical-tasks’ Description Linksto methods, technologies, SW tools, Web-sites, databases, … References

  6. TOTAL BI MI BMI LINKS ~ 400 ~ 250 ~ 100 ~ 50 REFERENCES ~ 500 ~ 300 ~ 170 ~ 35 TERMS ~ 350 WP5: Methods, Technologies & Tools (1st year) WP5 SoA on Systems, Methods & Tools in BMI Contents … in its infancy !!!

  7. WP5: Methods, Technologies & Tools (1st year) WP5 SOA: Bioinformatics Genomics  Post/Functional Genomics

  8. WP5: Methods, Technologies & Tools (1st year) WP5 SOA: Medical Informatics Clinics  Post/Functional Genomics

  9. WP5: Methods, Technologies & Tools (1st year) WP5 SOA: Biomedical Informatics (BMI) Toward Integrated Clinico-Genomics

  10. WP5: Methods, Technologies & Tools Work in the 2nd year … achieved & on-going

  11. WP5: Methods, Technologies & Tools 2nd year SoA review D13 First report on systems interoperability for data analysis, information retrieval and decision support

  12. WP5: Methods, Technologies & Tools (2nd year) Deliverable D13 (months 13-21) v1.0 Pre-Final • Collaborative effort between all INFOBIOMED partners • Based on WP5 SoA review on ‘Systems, methods & Tools for BMI’ (main effort of the 1st year). • Special focus and material onClinico-Genomic Trials

  13. WP5: Methods, Technologies & Tools 2nd year WP5 in support of WP6 pilots WP5 SoA/D13 references … on partners’ bilateralcollaboration … exploit SoA methods, technologies, tools 2 examples 

  14. WP5: Methods, Technologies & Tools 2nd year WP5  WP6.1

  15. WP5 in support of WP6 pilots (2nd year) WP5  WP6.1:Pharmainformatics Biomedical Text Mining Data Analysis: Clustering MI-EMC (Erasmus)  AstraZeneca

  16. WP5 in support of WP6 pilots (2nd year) WP5/WP4  WP6.1:Pharmainformatics Molecular Pathways: Model, Represent, Reason & Visualize WP4 (standards)

  17. WP5: Methods, Technologies & Tools 2nd year WP5  WP6.2

  18. WP5 in support of WP6 pilots (2nd year) WP5  WP6.2:Genomics & Infection UEDIN /GTI  FORTH • Martin Reczko (FORTH) delivered a presentation to the UEDIN/GTI covering his work on the development of algorithms for the prediction of miRNA coding sequences To provide an update on miRNA (and target) identification The basic Task Overlap of predicted miRNA target networks onto the interferon network in order to understand how miRNAs may act to control the expression of interferon-related proteins in vivo. • BioInformaticsSystems, Methods and Tools for miRNA prediction • Prediction of host target sites for viral miRNA binding • Prediction of viral target sites for host miRNA binding • Prediction of viral target sites for viral miRNA binding • Prediction of host interferon-related target sites for predicted host miRNA binding

  19. WP5 in support of WP6 pilots (2nd year) WP5  WP6.2:miRNA prediction Energy + structural features 2 851 352 871 bases Inverted repeats, composition Cross-species conservation SVM HMM RNA secondary structure prediction • Novel microRNAs • Microarray verification … involved in interferon and herpes virus pathways … the pipeline

  20. WP5 in support of WP6 pilots (2nd year) WP5  WP6.2:miRNA prediction Preliminary results:All miRNA targets (in IFN map) with high score miRNA-ID HUGO Ensembl-ID miranda- Score -------------------------------------------------- Single targets: miRUL22A-1_3p HSPA5 ENSG00000044574 119 miRUL22A-1_3p CTSS ENSG00000163131 127 miRUL112-1_3p CBFB ENSG00000067955 113 miRUL112-1_3p DAP ENSG00000112977 132 miRUL148D-1_3p SOCS3 ENSG00000184557 113 miR-US5-1_3p CASP8 ENSG00000064012 124 miR-US5-2_3p PSMD12 ENSG00000197170 111 miRUS33-1_5p PRKCA ENSG00000154229 112 miRUL36-1_5p BCL6 ENSG00000113916 123 Double target: miRUL36-1_5p CAMK2A ENSG00000070808 115 miRUS25-2_3p CAMK2A ENSG00000070808 114 Collaboration with: Artemis Hatzigeorgiou, Praveen Sethupathy, Molly Megraw, Karol Szafranski Center for Bioinformatics, School of Medicine, University of Pennsylvania, USA

  21. WP5: Methods, Technologies & Tools 2nd year WP5  WP6.4

  22. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:Genomics & Hereditary Colon-cancer FUNEN/HNPCC  FORTH • Various communications/contacts – meeting on November 2005 Specify, define & develop HL7 based message standards to enable and support the communication between HNPCC Danish central colon-cancer disease registry (and other registries) with genetic consulting departments, DNA-laboratories and surgery-departments • The basic Tasks • FUNEN and HNPCC have agreed on contents of 4 standards: Family, Individual, Laboratory and the Surgery message. • The aim is to get these standards adapted to HL7 in order to support seamless communication and access to relative information and data  FORTH • Medical InformaticsSystems, Methods and Tools for standardised • communication and messaging between heterogeneous clinico-genomic feeder • systems • HL7 (Health Informatics) standard methodology (version 3) • HL7 (v.3) Message Specification & Implementation technology • HL7 fundamental concepts/classes  extension to cover HNPCC domain

  23. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:Building HL7 models Application Trigger RIM Role Event Derive Information Modeling Storyboard D-MIM Sender Receiver Restrict Triggers References Interaction R-MIM Serialize Example Interaction Modeling HMD Restrict Message Design Storyboard Message Content Example Type Use Case Modeling … based on HL7 v.3Methodology Standard Reference Models Actors

  24. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:Building HL7 models Chapter-Specific Specs Message Model Information Model Use Case Model Interaction Model 2-nd Order 1 choice of 0-n Drug 0-1 Nursing HL7 v.3Message Specification HL7 Reference Model Common Specs Implementable Message Specification XML/ER7/… Implementable Message Specification OLE/CORBA Implementable Message Specification EDIFACT

  25. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:Building HL7 models Hierarchical Message Definition And CMET Specifications XML Schema Specification HL7 Message Data Parsing HL7 Message HL7-Conformant Message Data Instance Application Creation HL7-Conformant Application HL7 v.3 Message Implementation

  26. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:Building HL7 models • Observation • Procedure • Supply • Medication • Financial • ... • Performer • Author • Witness • Subject • Destination • ... • Living Subject • Person • Organization • Material • Place • ... Entity Class Code Participation Type Code Act Class Code 1 1 1 1 0..* 0..* 0..* 0..* Entity Role Participation Act classCode determinerCode id code statusCode classCode id code statusCode effectiveTime typeCode time classCode moodCode id code statusCode effectiveTime • Patient • Provider • Employee • Specimen • Practitioner • ... • Definition • Intent • Order • Event • Criterion • ... • Kind • Instance • (QualifiedGroup) Entity Determiner Code Role Class Code Act Mood Code HL7 v.3Basic Concepts/Classes - Attributes plays scopes

  27. WP5 in support of WP6 pilots (2nd year) WP5  WP6.4:HL7 workplan

  28. WP5: Methods, Technologies & Tools 1stand 2ndyears Dissemination: Scientific Community Other Stakeholders

  29. Medical Informatics Bioinformatics WP5: Methods, Technologies & Tools (1st & 2nd year) Dissemination to Scientific Community (papers)

  30. Biomedical Informatics WP5: Methods, Technologies & Tools (1st & 2nd year) Dissemination (continued - 1)

  31. Other stakeholders WP5: Methods, Technologies & Tools (1st & 2nd year) Dissemination (continued - 2)

  32. WP5: Methods, Technologies & Tools WP5: next 12 months (~ March 2006) … also with relation to foreseen FORTH activities

  33. The Final target … towards System Medicine - Specialty - Organ Radiology - Imaging - Tissue Histopathology - Laboratory - Organ Modeling - Simulations - Cell Immunochemistry e-Cell modeling Molecular imaging Mol. Pathway Gene/Protein Interactions Proteomics RNA Functional Genomics DNAACGTTCGCT Genomics ‘virtual human’

  34. Advancing Clinico-Genomic Trials A new Integrated project on BMI

  35. User Applications and services layer in support of Clinical trials … U U The ACGT Integration Layer, the ACGT Tools and Services U Simulation and Visualization Tools D U D Knowledge Discovery Tools D U D U D Ontologies and mediation tools D D D D D Basic GRID technology and security D User Data and Public Databases Layer Distributed Biomedical Data The Vision

  36. WP5 / WP4 2D/3D visualization for in silico models Multi-level data mining analyses,simulation ACGT experiment topology will follow the example of the Virtual Lab project Microarray data processing/clustering for molecular classification of disease Integration … Workflows

  37. Concertation activities Partnership

  38. MineGene: An Integrative microarray data analysis tool FORTH in INFOBIOMED WP5-related activity/effort Integrated intelligent microarray data analysis tool for the discovery of molecular/gene markers and the discovery of families of co-regulated genes (metagenes) based on clustering approaches To be exploited within INFOBIOMED partners (… March 2006)

  39. MineGene: An Integrative microarray data analysis tool FORTH in INFOBIOMED WP5-related activity/effort ……..also Tools for Biomedical data visualisation (January 2006) Tools for standardised MA data analysis (end of 2006) To be exploited within INFOBIOMED partners (… March 2006)

  40. ICGE: Integrated Clinico-Genomics Environment FORTH in INFOBIOMED External Clinical (Cancer) Information Sources PACS Images Patient ClinicalInformation HistoPathIS LabIS OncoIS 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 Information Modeling Genomic Data Models Data Analysis DSS Visualization Prognochip project GeneIS Genomic Information DNA-sequences Gene-Expression profiles Differential Gene - Markers Patient GenomicInformation WP5 WP5 WP4 WP5 WP4 … work in progress Building-Blocks WP5

  41. Exploitation & Concertation FORTH in INFOBIOMED Symbiomatics Special Support Action – Synergy between Bioinformatics and Medical Informatics (EU-IST, 2005-2007) Beyond The Horizon(BTH) ‘Bio-ICT Synergies’ Coordinated Action, EU-FP6-FET ERCIM ‘WG on BMI’ ERCIM News, Special issue on BMI January 2005 http://www.ercim.org/publication/Ercim_News/enw60/EN60.pdf

  42. WP5: Methods, Technologies & Tools Next 12 months Schedule

  43. WP5: Methods, Technologies & Tools

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