INBIOMEDvision Workshop at MIE 2011. Ferran Sanz

INBIOMEDvision

Ferran Sanz (UPF) @ MIE 2011

Ferran Sanz

Research Programme on Biomedical Informatics (GRIB)IMIM – Hospital del Mar Research Institute

Universitat Pompeu FabraBarcelona Biomedical Research Park (PRBB)

Barcelona

Promoting and Monitoring

Biomedical Informatics in Europe

INBIOMEDvision


Workshop programme

• Ferran Sanz. IMIM-Hospital del Mar. Pompeu Fabra University. General introduction on INBIOMEDvision concepts and activities.

• Søren Brunak. Center for Biological Sequence Analysis. Dept. of Systems Biology. Technical University of Denmark. Perspectives in Medical Informatics in the interface to genomics and systems biology.

• Victoria López-Alonso. Carlos III Institute of Health (ISCIII). Madrid. Bioinformatics challenges in a personalised medicine pipeline.

INBIOMEDvision


Bridging gaps between Bioinformatics and MI

Bioinformaticsin biomedical research

(molecular, “omics”,systems biology)

Medical informaticsIn health care &clinical research

(EHR)

INBIOMEDvision





(EHR)

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MU

TU

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INBIOMEDvision





(EHR)

TranslationalBioinformatics


INBIOMEDvision





(EHR)


Research re-use ofclinical information


INBIOMEDvision





(EHR)


Research re-use ofclinical information


BIO

ME

DIC

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INF

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INBIOMEDvision


Biomedical Informatics

BMI deals with the integrative management and synergic exploitation of the wide and inter-related scope of information that is generated and needed in healthcare settings, biomedical research institutions and health-related industry.

IT and computational approaches in Biomedicine

(integrativeapproaches)


Integrative Biomedical Informatics in Pharmacovigilance

EHRDb ivEHR

Db iiiEHRDb iiEHR

db i

Data extraction and integration

Signal detection

Signal substantiation

In silico pharmacology

Mining of BDs andbiomedical literature

Systems biology

Text mining(Terminology mapping)

Statistical analysis


Possible drug – AE relationship

to be assessed

Biological

pathways

Genetic variants (SNPs)

Drug Adverse event

Similardrugs-ligands

Drugmetabolit

es

Involved proteins

Workflows for chemo-bioinformatics signal substantiation

INBIOMEDvision


For the effective development of the integrative Biomedical Informatics concept, from both the scientific and applied points of view, several key challenges have to be addressed:

• Synergic integration between the computational methods and technologies used in life sciences research (Bioinformatics) and the computer sciences and applications supporting healthcare and clinical research (Medical Informatics).

• This integration requires a more intense interaction between the Bioinformatics and the Medical Informatics scientific communities.

Challenges in Biomedical Informatics (1)

INBIOMEDvision


Development of effective translational approaches that facilitate a better and quicker application of:

a) knowledge resulting from the basic biomedical research in the disease prevention and treatment,

b) experience accumulated in the clinical practice in the basic biomedical research.

This bidirectional knowledge translation includes:

c) the extension of the electronic healthcare record (EHR) concept in order to incorporate and exploit new information types, such as these resulting from the “omics” technologies, which contribute to the development of a more personalized medicine.

d) a more intense and automated incorporation of phenotypic information generated in the healthcare settings into “omics” and molecular research.


INBIOMEDvision


• Integration and joint exploitation of heterogeneous information stored in widespread repositories and diverse formats, which requires further progress in systems interoperability, as well as the development of more effective techniques for automatic knowledge extraction, especially from documents in free-text and multi-lingual format.

• This aspect implies a focus on all the aspects related to the development, adoption and dissemination of appropriate standards and ontologies. Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support.


INBIOMEDvision


• Development of innovative methods for the simulation and modelling of complex biological phenomena, as well as the corresponding computational applications, able to operate on a wide range of data types, as well as diverse length dimensions and time scales.

• These computational methods and tools have to show reliable predictive capabilities, demonstrating their usefulness for the biomedical scientists and the healthcare professionals.


INBIOMEDvision


Basic characteristics

• Coordination Support Action (CSA) (it is not a standard research project, it is devoted to the organisation and execution of a series of activities to support a specific research field)

• Start date: 1-Feb-2011

• End date: 31-Jan-2013

• Partners: Universitat Pompeu Fabra (coordination)• Fundació IMIM (managing)• Danish Technical University• Erasmus University Medical Center• Universidad Politécnica de Madrid• Instituto de Salud Carlos III• University College London

• +30 additional experts committed to participate

INBIOMEDvision


To promote Biomedical Informatics by means of:

• permanent monitoring of the scientific state-of-the-art and existing activities in the theme,

• prospective analysis of the emerging challenges and opportunities, and

• dissemination of the knowledge in the field.

General objective

INBIOMEDvision


• Re-use of Clinical Information for Research. June 24, 2011. London.

• Genotype-phenotype resources. October 5, 2011. Brussels.

• Translational Bioinformatics. October 18, 2011. Barcelona.

Think Tanks

INBIOMEDvision


Think Tank on Research Reuse of Clinical Information

Held in London on June 24, 2011.

Some conclusions (I):• The issues around the re-use of clinical data for research purposes are

complex; finding optimum solutions will require a multi-disciplinary approach, including IT and data security specialists, clinicians, biomedical researchers and bioethics experts among others.

• The roles of patients and their carers are crucial. These people must be listened to and empowered.

• Patients can be encouraged to share their data, but this must never be made compulsory, and it should always be possible for them to opt out of and/or withdraw their data from studies.

• Clinicians and healthcare centres should be on their hand encouraged to share their completely anonymised or permitted to share data.

• Industry – not only the pharmaceutical and biotech industries, but also the IT industry – is an important player. IT system suppliers for hospitals must be informed about research needs.

INBIOMEDvision


Think Tank on Research Reuse of Clinical Information

Held in London on June 24, 2011.

Some conclusions (II):• Hospital IT systems should be developed to include data needed in research, and

should be flexible enough to allow the frequent and simple incorporation of new data types.

• Provided that standardisation is seen as a priority, it may be best for standards to be allowed to evolve pragmatically rather than trying to impose too many in advance.

• Health data raises issues of security, privacy and ethics beyond those of other types of data.

• It is important to raise awareness about the current problems regarding IT security, information governance, and legal issues with particular regard to clinical data.

• Developing and maintaining the highest possible standards for data collection is essential.

• Analysis of retrospective clinical data is likely to be of great value, but this poses particular challenges, especially in the area of quality assurance.

• Preventive medicine is an important priority and is becoming increasingly more so. The re-use of clinical data research can certainly be useful for research in this field.

INBIOMEDvision


More information at ...

www.inbiomedvision.eu

INBIOMEDvision


Workshop programme

• Ferran Sanz. IMIM-Hospital del Mar. Pompeu Fabra University. General introduction on INBIOMEDvision concepts and activities.

• Søren Brunak. Center for Biological Sequence Analysis. Dept. of Systems Biology. Technical University of Denmark. Perspectives in Medical Informatics in the interface to genomics and systems biology.

• Victoria López-Alonso. Carlos III Institute of Health (ISCIII). Madrid. Bioinformatics challenges in a personalised medicine pipeline.

Health & Medicine

INBIOMEDvision Workshop at MIE 2011. Ferran Sanz