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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

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

WP5: Methods, Technologies & Tools

Work in the 1st year

… work presented during the 1st APR


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

1st year

SoA review

on Methods, Systems and Tools

in BMI


Wp5 methods technologies tools

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).


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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 !!!


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools (1st year)

WP5 SOA: Bioinformatics

Genomics  Post/Functional Genomics


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools (1st year)

WP5 SOA: Medical Informatics

Clinics  Post/Functional Genomics


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools (1st year)

WP5 SOA: Biomedical Informatics (BMI)

Toward Integrated Clinico-Genomics


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

Work in the 2nd year

… achieved & on-going


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

2nd year

SoA review D13

First report on systems interoperability

for data analysis, information retrieval

and decision support


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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 


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

2nd year

WP5  WP6.1


Wp5 methods technologies tools

WP5 in support of WP6 pilots (2nd year)

WP5  WP6.1:Pharmainformatics

Biomedical

Text Mining

Data Analysis:

Clustering

MI-EMC (Erasmus)  AstraZeneca


Wp5 methods technologies tools

WP5 in support of WP6 pilots (2nd year)

WP5/WP4  WP6.1:Pharmainformatics

Molecular Pathways:

Model, Represent,

Reason & Visualize

WP4

(standards)


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

2nd year

WP5  WP6.2


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

2nd year

WP5  WP6.4


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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


Hl7 v 3 message specification

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


Hl7 v 3 message implementation

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


Hl7 v 3 basic concepts classes attributes

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


Wp5 methods technologies tools

WP5 in support of WP6 pilots (2nd year)

WP5  WP6.4:HL7 workplan


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

1stand 2ndyears

Dissemination:

Scientific Community

Other Stakeholders


Wp5 methods technologies tools

Medical Informatics

Bioinformatics

WP5: Methods, Technologies & Tools (1st & 2nd year)

Dissemination to Scientific Community (papers)


Wp5 methods technologies tools

Biomedical Informatics

WP5: Methods, Technologies & Tools (1st & 2nd year)

Dissemination (continued - 1)


Wp5 methods technologies tools

Other stakeholders

WP5: Methods, Technologies & Tools (1st & 2nd year)

Dissemination (continued - 2)


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

WP5:

next 12 months

(~ March 2006)

… also with relation to foreseen FORTH activities


Wp5 methods technologies tools

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’


Wp5 methods technologies tools

Advancing Clinico-Genomic Trials

A new Integrated project on BMI


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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


Wp5 methods technologies tools

Concertation

activities

Partnership


Wp5 methods technologies tools

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)


Wp5 methods technologies tools

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)


Wp5 methods technologies tools

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


Wp5 methods technologies tools

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


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools

Next 12 months Schedule


Wp5 methods technologies tools

WP5: Methods, Technologies & Tools


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