aap/psp semantic publishing workshop

www.collexis.com

Semantic Applications in Science

Darrell W. Gunter EVP / CMO

May 13, 2010

Our Agenda For Today

• The Challenges of Scientific Research

• The Collexis Technology

• Case Studies

o Professional Networks

o Institutional Networks Johns Hopkins & Asklepios

o Managing the Peer Review Process

• The Future… Oh, that’s right Thane is covering that

next!

The Facts

• 90 – 100 hours to

write an article

• 2 – 3 Peer Review 3 –

6 hrs

Researchers

• Articles 154 vs. 83

• # pages/article 12.4 vs.

7.4

• Total pages 2,216 vs.

820

Journal Growth

23,000 Jnls / 90% electronic /Articles –

800K+

1,2,3

The Author is under great pressure!

Collexis Technology

KnowledgeBaseText Fingerprint

Collexis Fingerprint Engine

Collexis Knowledge Engine 7.0

Tokenizer NormalizerAbbreviation

expansion

DehyphenationLanguage

detection

Coordination

expansion

Part-of-Speech

taggingEntity recognition based on regular expressions

Noun phrase

detection

Concept findingPart-of-speech based disambiguation of

thesaurus concepts

Exclude known

idioms

Fingerprint

aggregation

Collexis Knowledge Engine 7.0

• Modular NLP workbench – processing and analyzing of

text documents

• Retrieval and aggregation engine – serving the

application layer

Collexis – selected references

Bundesministerium für Bildung

und ForschungStanford University

Asklepios Kliniken Johnson & Johnson

Johns Hopkins University University of California, San

Franciscio

Dana Farber Cancer Institute

Harvard University

National Institutes of Health

Mayo Clinic

California Institute for

Quantitative Biosciences (QB3),

The Wellcome Trust DKFZ

Explore instead of Searching!

Creating expert profiles from documents

using semantic technologies

Document fingerprints aggregated to expert profiles!

BiomedExperts – more than

297,000 registered users

• Prepopulated network – based on PubMed

• 1.8 million precalculated experts

• More than 24 million co-author relations between them

• Representing over 3,500 institutions

• From 190 countries

• Growing each day between 500 and 1000 users

• BME data used in other applications

• Co-author based

networks

Geographical

mapping of the

co-author network

Johns Hopkins: The Issue

Connecting Experts• Fall retreat main issue how do they take advantage of

the university’s expertise and build collaboration

• First solution – Repurpose a parking lot to be a coffee

shop for the JH community to grab a cup of Joe and

find new collaborators.

• Outcome – Great coffee, great conversation but

collaboration did not take off.

• The Collexis Solution – Expert Institutional Dashboard

Same Application for the NIH

Asklepios

Facts and Figures

• Asklepios - Europe‘s largest health care

provider– 500.000 patients for inpatient care per year, 95 hospitals,

21.000 beds

– 34.500 employees

– Asklepios owns medical nursing and allied health schools

– Home care programs and residential care programs

• Asklepios International – Pacific Health System – California

– Greece, Athens Medical Center

– University hospital in Shanghai: Joint Venture with

Siemens and Tongji University

Optimize Workflows

(e.g. Avoid interruptions caused

by knowledge search, retrieval,

and application)

Distribute

Expert Knowledge

(across multiple locations,

time zones, medical

conditions)

Guide Workflows

(e.g. Care Plans, Expert-Task

Context Allocation)

Help Asklepios to know

“what Asklepios knows”

Stimulate new

Knowledge Acquisition Usage

Models

Why Knowledge

Management?

• Patient, male, age of 62, needs a knee joint prosthesis

due to Rheumatoid Arthritis

• Where is the best place to get it?

• Criteria which will be taken into account:

– Geographical aspects

– Recommendation of his GP

– Publicly available information - mostly via Internet

• Strongest competitors: university hospitals (within the

region)

Use Case 1 – Expert

profiles

Asklepios Research

Profiles

Expert Profile of Prof.

Grifka

Make Internal Expertise

available!

Provide a single point of

search for all relevant content

from publishers!

Link internal expertise /

experience and external

knowledge sources!

• Patient with lung cancer and reduced renal function

• Decision in chemotherapeutic drug is pending

• Preferred choice: Cisplatin as chemotherapeutic agent

• Open questions: can Cisplatin be used which has

nephrotoxicity as a side effect?

Use Case 4 - External Resources and

Internal Experience Use Case 4 - External

Resources and Internal Experience

Search - Cisplatin shows

the relevant publications

from Springer, Elsevier,

Thieme, OVID and other

publishers

Asklepios Intelligent

Digital Library

Opening an journal article…

…shows immediately similar

publications colleagues

… and the names

and expert profiles

Link External Knowledge and

Internal Expertise

Key Issues in STM Industry

• Publishers / Editors

o Finding the right reviewer

o Expanding their pool of reviewers

• Institutions

o Determining what grants they should go after

o Determining who within their organization is best to apply

• Grant Funding Organizations

o Analyzing the vast amount of grant applications submitted.

o Determining who within the organization is best qualified to review the

grant application (known and unknown)

The Challenge for STM

Publishers• Receive thousands of manuscripts annually

• Timely process to conduct the Peer Review Process

• Timely process to determine who should review it.

• Important for reviewer to free of conflicts of interest

• Ethics of review process are paramount

Key Benefits Reviewer Finder

• Fingerprint of manuscript - Clarity

• Determine the best reviewer

• Free of conflicts

• More efficient and effective process

• Ultimately increases profitability

Some thoughts…..

• Get started with a practical project

• Engage your user community before, during & after

• Seek out the best practices and adopt them

• Develop an application that achieves the following:

o Improves productivity

o Solves a problem

o Enhances the value chain

• Build, partner or buy the technology

www.collexis.com

Thank you for your attention!

Darrell W. Gunter, EVP / Chief Marketing Officer

gunter@collexis.com, cell +1-973-454-3475