Presenter: Marc Hadfield (917) 991-9685 www.alitora.com Building Innovation Networks in the Life Sciences http://en.wikipedia.org/wiki/Collaborative_Innovation_Networks

Presenter:

Marc Hadfield

(917) 991-9685

www.alitora.com

Marc Hadfield, President and CTO Creator of Alitora Technology Semantic Database Natural Language Processing applied to Life Sciences Alitora Systems Semantic Software co. Software-as-a-Service/Platform-as-a-Service

Marc Hadfield, President and CTO

Creator of Alitora Technology

Semantic Database

Natural Language Processing applied to Life Sciences

Alitora Systems

Semantic Software co.

Software-as-a-Service/Platform-as-a-Service

How can we: Surface & Distribute Insights from Unstructured Data? Or: How do we deliver to you the interesting bits of knowledge out of a lot of text?

Problem: Insights from Data Silos Case Study: Eli Lilly / Life Science

Solution: Natural Language Processing? Transform a pile of Documents into A pile of Facts . We still have a pile.

Solution: Natural Language Processing + Linked Relationships via Ontologies? What in the network is important ?

Solution: Natural Language Processing + Linked Relationships + Relevancy? Relevant to whom?

Solution: Natural Language Processing + Linked Relationships + Relevancy + Collaboration. Ah Ha! Relevant information can find me via my context. My colleagues can help.

Then we can Surface & Distribute Insights Deploy solution as a service so Insights can be embedded anywhere.

People Databases, Ontologies News, PR, Documents, Reports Innovation Network

Innovation Network - DEMO Web Application Application Plug-In

Alitora Systems Architecture Interface Web, Cytoscape ASAPI Webservice Search, Collaborate Annotate Process Documents kHarmony Semantic DB Semantic / Graph DB Alitora Foundry NLP Components

Interface

Web, Cytoscape

ASAPI Webservice

Search, Collaborate

Annotate

Process Documents

kHarmony Semantic DB

Semantic / Graph DB

Alitora Foundry

NLP Components

Collaboration, Entitlement Scope: User, Colleague, Team, Organization, Database Segment Entitlements are Semantic Statements Cross-Department Single Organization Independent Segments for Departments and Databases Cross Organization (“in the Cloud”) Multiple Organization Deployment Secure Shared Segments Example: Pharmaceutical and CRO Web Service accessed by Enterprise Applications i.e. Documentum, Sharepoint, LDAP

Scope: User, Colleague, Team, Organization, Database Segment

Entitlements are Semantic Statements

Cross-Department

Single Organization

Independent Segments for Departments and Databases

Cross Organization (“in the Cloud”)

Multiple Organization Deployment

Secure Shared Segments

Example: Pharmaceutical and CRO

Web Service

accessed by Enterprise Applications

i.e. Documentum, Sharepoint, LDAP

Innovation Network kHarmony™ Data Representation: Each Object has Properties “ chunks” of RDF Unique URI “ Core” RDFs Model

Innovation Network kHarmony™ HyperEdges: Statements about Statements Track Provenance Difficult in RDF alone (everything “reified”)

kHarmony™ Relevancy Function[] Graph Topology Metrics Paths to User Time Properties including “certainty” Neighbor Properties Confidential

Function[]

Graph Topology Metrics

Paths to User

Time

Properties

including “certainty”

Neighbor Properties

Semantic Collaborative Statements

Semantic Knowledge Statements Domain Ontology + Instance Statements

Semantic Knowledge Statements Direct or Inferred

Text Mine Unstructured Data: Semantic Parse Graph Representation “ Suppression of endogenous Bim greatly inhibits Gadd45a induction of apoptosis.” [action, inhibit, [action, suppress, [unknown], [gp, endogenous Bim] ], [action, induce, [gp, Gadd45a], [process, apoptosis] ], ]

“ Suppression of endogenous Bim greatly inhibits Gadd45a induction of apoptosis.”

[action, inhibit,

[action, suppress,

[unknown],

[gp, endogenous Bim]

],

[action, induce,

[gp, Gadd45a],

[process, apoptosis]

],

]

Entity and Relationship Normalization Heuristics Bayesian String Similarity Abbreviation Expansion Species Context Output a “score” Confidential Copyright Alitora Systems, Inc. 2009

Heuristics

Bayesian

String Similarity

Abbreviation Expansion

Species Context

Output a “score”

Innovation Network Current Platform Applications for Customers & Partners: Life Science BI and R&D Social Network, Contextual Content Media, Real Time Web Brand Tracking, Real Time Web “ Semantics-as-a-Service” “ Platform-as-a-Service”

Current Platform Applications for Customers & Partners:

Life Science BI and R&D

Social Network, Contextual Content

Media, Real Time Web

Brand Tracking, Real Time Web

Innovation Network - DEMO Demo Semantic Mash-Up: Alitora Systems API Alitora Foundry Biomedical Parser Yahoo News Feeds OpenCalais API 10 Biomedical Data sources, Freebase data GWT-based Web Interface Cytoscape-based Graph Visualization

Demo Semantic Mash-Up:

Alitora Systems API

Alitora Foundry Biomedical Parser

Yahoo News Feeds

OpenCalais API

10 Biomedical Data sources, Freebase data

GWT-based Web Interface

Cytoscape-based Graph Visualization

Innovation Network - DEMO Web Application Application Plug-In … including OpenCalais

Contact Information Alitora Systems 155 Water Street New York, NY 11201 (917) 463-4776 [email_address]

Alitora Systems

155 Water Street

New York, NY 11201

(917) 463-4776

[email_address]

Innovation Network Interface

Innovation Network

Alitora Foundry Toolkit Test and Train Annotators

Test and Train Annotators

Alitora Foundry Toolkit Other Annotators: OpenCalais (Business Relationships) Oscar3 (Chemical Names) http://sourceforge.net/projects/oscar3-chem Nico Adams, et al. University of Cambridge

Other Annotators:

OpenCalais (Business Relationships)

Oscar3 (Chemical Names)

http://sourceforge.net/projects/oscar3-chem

Nico Adams, et al.

University of Cambridge