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From Bench to Bedside: Applications to Drug Discovery and Development . Eric Neumann W3C HCLSIG co-chair Teranode Corporation HCLSIG F2F Cambridge MA. Knowledge “ --is the human capacity (both potential and actual) to take effective action in varied and uncertain situations. ”.

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from bench to bedside applications to drug discovery and development

From Bench to Bedside:Applications to Drug Discovery and Development

Eric Neumann W3C HCLSIG co-chair Teranode Corporation

HCLSIGF2F

Cambridge MA

slide2
Knowledge“--is the human capacity (both potential and actual) to take effective action in varied and uncertain situations.”
slide4

Drug R&D Trends

from Innovation or Stagnation, FDA Report March 2004

new regulatory issues confronting pharmaceuticals

Tox/Efficacy

New Regulatory Issues Confronting Pharmaceuticals

ADME Optim

from Innovation or Stagnation, FDA Report March 2004

translational medicine
Translational Medicine
  • Enable physicians to more effectively translate relevant findings and hypotheses into therapies for human health
  • Support the blending of huge volumes of clinical research and phenotypic data with genomic research data
  • Apply that knowledge to patients and finally make individualized, preventative medicine a reality for diseases that have a genetic basis
role of informatics
Role of Informatics

John Glaser, CIO Partners Healthcare

  • Providing high quality and efficient health care isn't possible anymore without a sophisticated marriage of information technology and state-of-the-art science.
  • Bringing these together to inform patient care is a tremendous undertaking… the full array of new information provided by genomic research must be harnessed and made real for doctors and patients
  • A Framework for conducting clinical research in and across large multidisciplinary academic medical centers is designed to establish a "new" biomedicine to "fully exploits the fruit of the genomic revolution for clinical practice and allows clinical care to be leveraged to advance basic biological research.
challenges for drug d d
Challenges for Drug D&D
  • Counteracting the legacy of “Silos”
  • How to break away from the DD “conveyor belt model” to the “Translation model”
    • gaining and sharing insights throughout the process
  • The Benefit of New Targets for New Diseases
  • How to best identify safety and efficacy issues early on, so that cost and failure are reduced
  • A D3 Knowledge-base: Drugability and Safety
drug discovery development knowledge

Qualified Targets

Lead Generation

Lead Optimization

Toxicity & Safety

Biomarkers

Molecular Mechanisms

Pharmacogenomics

Clinical Trials

Drug Discovery & Development Knowledge

KD

drug discovery development knowledge11
Drug Discovery & Development Knowledge

Qualified Targets

Molecular Mechanisms

Lead Generation

Toxicity & Safety

Lead Optimization

Pharmacogenomics

Biomarkers

Clinical Trials

Launch

communities and interoperability
Communities and Interoperability

Semantic interoperability is directly tied to CoP:

  • “Within a community or domain, relative homogeneity reduces interoperability challenges.  Heterogeneity increases as one moves outside of a focal community/domain, and interoperability is likely [to be] more costly and difficult to achieve” Moen, 2001
  • Meanings encoded in a schema are usually useful for only one (original) community - difficult to extend to others!
  • Database utility more difficult if group is heterogeneous
multiple ontologies used together

DiseasePolymorphisms

Disease

Group

Protein

Person

Chemicalentity

Multiple Ontologies Used Together

UMLS

OMIM

SNP

Drug target

ontology

FOAF

UniProt

BioPAX

PubChem

Patent

ontology

Extant ontologies

Under development

Bridge concept

potential linked clinical ontologies

DiseaseDescriptions

Clinical Obs

Applications

Mechanisms

IRB

Molecules

Potential Linked Clinical Ontologies

SNOMED

CDISC

ICD10

Clinical Trials

ontology

RCRIM

(HL7)

Disease

Models

Pathways(BioPAX)

Tox

Genomics

Extant ontologies

Under development

Bridge concept

drug safety knowledge

Toxicity Indication

Drug Safety Knowledge
  • Genomic Profile Standards set by Regulatory Agencies
  • To be part of NDA (New Drug Applications)
  • How will Reviewers be empowered to handle such large amaount sof new data?

Human Hepato-Toxicity Study

Hepato-Toxicity Lens

cdisc and the semantic web
CDISC and the Semantic Web?
  • Reduce the need to write data parsers to any CDISC XML Schema
  • Make use of ontologies and terminologies directly using RDF
  • Easier inclusion of Genomic data
  • Use Semantic Lenses for Reviewers
  • Easier acceptance by industry with their current technologies
developing standards
Developing Standards

Exchange

Implementation

Design

support full information integration
Support Full Information Integration
  • Integration: integrate and manage data from sources, EDC systems, Clinical Data Management Systems , labs and CROs
  • Analysis and reporting: Accurately and timely analytical reports from study data, for use in decision making; easier results sharing with researchers and reviewers
  • Discovery: Use expanding research information as a knowledge base for rapid investigations into critical drug safety issues, new marketing claims, and identify product-line extensions.