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Semantic Applications in Science


Darrell W. Gunter   EVP / CMO


May 13, 2010


www.collexis.com
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
                    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
Collexis Fingerprint Engine

Collexis Technology




    Text          KnowledgeBase   Fingerprint
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
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

 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),
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
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
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)
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!
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?
Asklepios Intelligent
Digital Library




                        Search - Cisplatin shows
                        the relevant publications
                        from Springer, Elsevier,
                        Thieme, OVID and other
                        publishers
Link External Knowledge and
Internal Expertise


                       Opening an journal article…




                              …shows immediately similar
                               publications colleagues




                                       … and the names
                                         and expert profiles
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
Thank you for your attention!




                  www.collexis.com


    Darrell W. Gunter, EVP / Chief Marketing Officer
       gunter@collexis.com, cell +1-973-454-3475

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AAP/PSP Semantic Publishing Workshop

  • 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
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  • 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
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  • 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)
  • 26. Expert Profile of Prof. Grifka
  • 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
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  • 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