Visual Knowledge ® Software Inc. Visual Knowledge BioCAD Case Study Parallels to Other Domains VK Semantic Web Server

Visual Knowledge ® Software Inc. Life Science Needs History of researcher investing a lifetime to discover one gene or protein or drug Trend towards thinking about biology more as a system of systems rather than focus on individual parts Integrated cycle from Hypothesis, Simulation, Observation Make sense of an explosion in data exceeding Moore’s Law

Life Science Challenges Even a vertical slice of cell biology crosses many disciplines of knowledge Knowledge / Data is distributed globally across thousands of databases, taxonomies and ontologies Observational science with large body of clinical and research knowledge trapped in millions of publications Visual Knowledge ® Software Inc.

Private vs Public Tension Systems of Private and Public knowledge Evolve rapidly Evolve rapidly Feed each other Feed each other Cannot be compromised Cannot be compromised Visual Knowledge ® Software Inc.

System Thought Model “Pathway” is a common word in medicine and biology Can be drawn as a picture to explain a complex process A cascade of events where a “signal” is sent from one point in a cell/organism that creates a response A drug effects a reaction A drug effects a reaction A dysfunctional pathway effects a disease A dysfunctional pathway effects a disease Visual Knowledge ® Software Inc.

Ontologies to the Rescue Seamless formalism from the abstract to the concrete Open world assumption embraces federated modeling Models can be independent from solution Direct mapping between concept and solutions Constructs that can support context Visual Knowledge ® Software Inc.

Visual Knowledge ®

Data Asset Inventory - ontology driven conversion integration of dozens of online community databases Visual Knowledge ®

real time inferencing for pathway analysis of cause and effect >27 million concepts hyper-integrated Visual Knowledge ®

Pathway Editor/Simulator ontologies built by visual metaphor ontologies built by visual metaphor easy to use drag / drop interface easy to use drag / drop interface international curation international curation gene regulatory nets, protein signaling and metabolic pathways gene regulatory nets, protein signaling and metabolic pathways chemical to cellular concepts chemical to cellular concepts map experimental results onto visual pathways map experimental results onto visual pathways Visual Knowledge ®

live production transactional system integrated data warehousing, mining, with real time supply chain OLTP on top of 27M ontology Visual Knowledge ®

semantic simulation – in the case above VK ® is simulating the affect of a host cell reacting to the attack of a pathogen Visual Knowledge ®

n-tier semantic publication private collaboration servers role/team based security role/team based security semantic change control semantic change control develop/test/revise proprietary hypothesis develop/test/revise proprietary hypothesis multiple experimental protocols multiple experimental protocols micro array, PCR, blots, mass spec micro array, PCR, blots, mass spec publish to private or public collaboration network publish to private or public collaboration network Public Knowledge Server Private Research Server Peer Review Visual Knowledge ®

Visual Knowledge ® Software Inc. Parallels in other Domains A vertical slice of a government or large organization crosses many disciplines of knowledge

Parallels in other Domains Knowledge / Data is distributed globally across thousands of databases, taxonomies and ontologies A great deal of operational procedures, doctrine and technical knowledge is locked up inside unstructured text Publications Publications Messages Messages Wikis Wikis Visual Knowledge ® Software Inc.

Parallels in other Domains Economies, Organizations and other complex systems can have non-linear, adaptive and context sensitive meaning and behavior Improve the transparency and governance of business Visual Knowledge ® Software Inc.

15 year Commitment to Semantic Technology 15 year focus on our vision 5 th generation technology Visual Knowledge ® Software Inc.

R&D through real world implementations Visual Knowledge ® Software Inc.

What is our technology? Large scale multi-agent software systems Visual Knowledge ® Software Inc.

Addressed semantic tech Challenges to create practical value to the enterprise and systems that work Addressed semantic tech Challenges to create practical value to the enterprise and systems that work

What is our technology? Agents that are rapidly modeled and evolved by millions of people Visual Knowledge ® Software Inc.

What is our technology? Systems of agents that can be federated and can create executable systems Systems of agents that can be federated and can create executable systems Visual Knowledge ® Software Inc.

What is our technology? Agent systems that cope with conflicting ideas, causality and context Agent systems that cope with conflicting ideas, causality and context Visual Knowledge ® Software Inc.

Visual programming leading high performance execution in C++ semantic database kernel. Faster than system coded in Java or C#. 1. Visual Gesturing of Model 2. Phantom objects in Java 3. High throughput execution in our own semantic database

Agents model the most concrete instances of a domain Agents also model the meta meta meta Is OWL DL and Full compliant, is UML / MOF compliant, and other standards because these are just implementations of a standard Agents can be inferencing agents We have implemented a OWL tableaux reasoner Agents can be algorithmic processing units The societies create computation or domain reactivity and execution Fuzzy, Bayesian and other inferencing methods would be new agents Visual Knowledge ® Software Inc. What is our technology?

Take Aways Life sciences are attacking the problem of understanding how life works Life science is trailblazing community knowledge integration and are adopting ontologies to transform health and evironment Scale, change management and executing knowledge are fundamental challenges Platforms like Visual Knowledge exemplify the order of technology needed Visual Knowledge ® Software Inc.