Darrell provides the workshop an overview of the key semantic applications that are being utilized today.

1. Semantic Applications in Science
Darrell W. Gunter EVP / CMO
May 13, 2010
www.collexis.com

2. 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!

3. The Facts
• 90 – 100 hours to
write an article
Researchers
• 2 – 3 Peer Review 3 –
6 hrs
• Articles 154 vs. 83
• # pages/article 12.4 vs.
Journal Growth 7.4
• Total pages 2,216 vs.
820
23,000 Jnls / 90%
electronic /Articles –
800K+
The Author is under great pressure!
1,2,3

4. Collexis Fingerprint Engine
Collexis Technology
Text KnowledgeBase Fingerprint

5. Collexis Knowledge Engine 7.0
Abbreviation
Tokenizer Normalizer
expansion
Language Coordination
Dehyphenation
detection expansion
Part-of-Speech Entity recognition Noun phrase
tagging based on regular expressions detection
Part-of-speech Exclude known
Concept finding based disambiguation of
thesaurus concepts idioms
Fingerprint
aggregation

6. Collexis Knowledge Engine 7.0
• Modular NLP workbench – processing and analyzing of
text documents
• Retrieval and aggregation engine – serving the
application layer

7. Collexis – selected references
Dana Farber Cancer Institute Asklepios Kliniken Johnson & Johnson
Harvard University
National Institutes of Health Johns Hopkins University University of California, San
Franciscio
Bundesministerium für Bildung Mayo Clinic Stanford University
und Forschung
The Wellcome Trust California Institute for DKFZ
Quantitative Biosciences (QB3),

8. Explore instead of Searching!

9. Creating expert profiles from documents
using semantic technologies
Document fingerprints aggregated to expert profiles!

10. 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

12. • Co-author based
networks

13. Geographical
mapping of the
co-author network

16. 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

21. Same Application for the NIH

22. 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

23. Why Knowledge
Management?
Guide Workflows Optimize Workflows Distribute
(e.g. Care Plans, Expert-Task (e.g. Avoid interruptions caused Expert Knowledge
Context Allocation) by knowledge search, retrieval, (across multiple locations,
and application) time zones, medical
conditions)
Stimulate new
Help Asklepios to know
Knowledge Acquisition Usage
“what Asklepios knows”
Models

24. Use Case 1 – Expert
profiles
• 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)

25. Asklepios Research
Profiles

26. Expert Profile of Prof.
Grifka

27. Make Internal Expertise
available!

28. Provide a single point of
search for all relevant content
from publishers!
Link internal expertise /
experience and external
knowledge sources!

29. Use Case 4 - External Resources and
Internal Experience Use Case 4 - External
Resources and Internal Experience
• 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?

30. Asklepios Intelligent
Digital Library
Search - Cisplatin shows
the relevant publications
from Springer, Elsevier,
Thieme, OVID and other
publishers

31. Link External Knowledge and
Internal Expertise
Opening an journal article…
…shows immediately similar
publications colleagues
… and the names
and expert profiles

32. 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)

33. 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

38. Key Benefits Reviewer Finder
• Fingerprint of manuscript - Clarity
• Determine the best reviewer
• Free of conflicts
• More efficient and effective process
• Ultimately increases profitability

39. 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

40. Thank you for your attention!
www.collexis.com
Darrell W. Gunter, EVP / Chief Marketing Officer
gunter@collexis.com, cell +1-973-454-3475