Helping scientists collaborate BioCAD. ©2003 All Rights Reserved

Helping scientists collaborate

BioCAD

©2003 All Rights Reserved


Researcher “Data” Overload

Exponential growth of Data

Tens of millions of publications

Multi-disciplinary Collaboration

Proteomics, functional genomics, “…ics”

Disease involving multiple pathways

Home grown computing tools

Investigator Community

Hypothetical Pathways

Lab Books

Public Databases


Informatics Challenge

Is there a better way to explain a complex biological process than using prose?

Can we create fully integrated models that combine knowledge of: Geneticists Pathologists Immunologists Cell Signaling Researchers Clinicians, Chemists, Physicists, Mathematicians…

How do we find appropriate experimental evidence and downgrade obsolete evidence?

How can we make sense of thousands of statistically relevant high throughput data points?


The Need To Enable…

Tools/Methods for researchers to create integrated biological models

Multi-disciplinary models with millions of concepts

Represent all possible contexts that a gene, protein or cell system can function under

Computer applications that can understand these concepts


Semantic Networks

Artificial Intelligence concept from the 1960’s Formalize, Capture and Communicate Meaning Influenced object-oriented technology and relational

databases Robust, Efficient and Flexible Basis for many A.I. efforts for last 30 years Previously Beyond the Power of Hardware / Networks


Female

Male

Son

Mother

Male

Brother

Son

Model of a Family

All Relationships are Represented in the NetworkNot In Code or Queries


Sally

Robert Charles

mother

mother

brother

Joe

GWB

?

Smith Family


Ask the network…

How are Robert and Charles Related?

Who is my second cousin third removed?

Which six people connect me to the President of the United States (GWB)?


Ask the network…

How is Protein A related to Protein B?

If this gene is mutated what pathways are affected and how?

Which six drug targets will down-regulate the expression of this Gene?

What dysfunctional pathways model this disease?


Semantic Web

Announced by Tim Berners-Lee (inventor of WWW)Scientific American May 2002

“A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities”

Science and The Semantic WebJames Hendler

Science, Jan 24, 2003

“The current World Wide Web … is insufficient for the needs of collaboration across scientific disciplines.”


Visual Knowledge

Highly scaleable semantic database platform

12 years of intense/focused R&D

6 years delivering real systems to complex problems

Absorbs knowledge of large multi-disciplinary cultures

Domain expertise driven

Very large scale Adaptive Schema


Visual Knowledge

Servers, each containing millions of Semantic Agents Each Agent is a proxy for gene, protein, cell, researcher

or experiment Each Agent is “aware” of relationships that it holds with

all other agents in the network Agents organize into complex societies that give rise to

adaptive behaviour Versions of Semantic Agents can be packaged and

distributed into other servers


Visual Knowledge Specialty

Systems driven by knowledge of many experts Integration of Social, Economic and Scientific Models Cause and Effect Modeling systems that rapidly evolve and change

shape


BioCAD Semantic Database

Interactive Pathway Editor

2 Tier Server Architecture

Cell System modeling

Experimental Management

High Throughput

Research Community

Private Servers

Research Operations

Lab Books

CuratedKnowledge

Base


Semantic Models

PublicDatabases

Genomic/Proteomic

Experiments

Inference Hypothesis Discovery

Pathway Editors


Interactive Pathway Editor

Easy to use drag and drop interface

Gene regulatory, protein signaling and metabolic pathways

Different conceptual levels

Hypothetical cause and effect compared to experimental results


2 Tier Architecture

Web based

XML interaction

Public Collaboration Server(s)

Hypothetical normal and pathological pathways

Curated and connected to experimental evidence

Peer review and release process

Public Knowledge

Server

Private Research

Server

Private Research

Server

Private Research

Server

Peer Review


2 Tier Architecture

Private Collaboration Server(s)

Role/Team based security

Semantic Change control (Model Versioning)

Develop proprietary hypothesis and test

Multiple Experimental Protocols

Micro Array, PCR, Western, Mass Spect

Publish results to private or public collaboration network

Public Knowledge

Server

Private Research

Server

Private Research

Server

Private Research

Server

Peer Review


Summary

Life Science Research now involves millions of multi-disciplinary concepts

Large scale Internet Wide Semantic Networks can help us communicate biological processes

Visual Knowledge is a mature powerful technology for Semantic Networks

[email protected]

www.visualknowledge.com


Helping scientists collaborate

BioCAD

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Helping scientists collaborate BioCAD. ©2003 All Rights Reserved