Contact: +1 (302) 660-3275, PIUGinfo@piug.org

PIUG 2013 Biotechnology Meeting

Meeting Challenges in Biotechnology Patent Searching

Tuesday, February 26, 2013

Amgen Inc. 360 Binney Street One Kendall Square, Building 1000
Cambridge, Massachusetts 02141
+1 (617) 444-5000

Program

7:30 AM
Registration and Vendor Exhibits
8:30 AM

Welcome to the PIUG 2013 Biotechnology Meeting

Session 1
Chair: Helen Oen, Eisai Inc.

8:45 AM Update on Sequence Listings in Patent Applications- Dave Nguyen (USPTO)
9:15 AM An Attorney's Perspective on Biotech-Related International FTO Searches - Anita Varma, Ropes & Gray LLP
9:45 AM Getting the right message: Following real-time translation of patent information by partnering with patent attorneys - Tobias Pawliczek (Novartis Pharma AG)
10:15 AM
Product Reviews
10:25 AM
Break & Vendor Exhibits

Session 2
Chair: Alison Taylor, Abbott

11:00 AM Trees Lost In the Forest- Using Visualization Tools to Interpret Sequence Search Results  - Denis Bayada (GenomeQuest), Joe Terlizzi (Questel, Inc.)
11:30 PM Creating Reports from Patent and Sequence Databases with the BizInt Smart Charts Product Family - John Willmore (BizInt)
12:00 PM
Product Reviews
12:10 PM
Lunch & Vendor Exhibits

Session 3
Chair: Kim Spytek, Novartis Institutes of Biomedical Research

1:30 PM Lossy Data Compression in Patent Informatics - Kristine Atkinson (Boston Scientific)
2:00 PM DIY Searching - Seth Mendelson (Novartis Institutes of Biomedical Research)
2:30 PM
Product Reviews
2:45 PM Break & Vendor Exhibits

Session 4
Moderator: Ruben Diaz, Genentech

3:15 PM Panel: Assisting Information Professionals 
4:45 PM Concluding Remarks
5:00 PM Adjourn
  Evening Networking & Dinner

Meeting Abstracts

Update on Sequence Listings in Patent Applications
Dave Nguyen
USPTO
Abstract

The presentation provides a brief overview of USPTO current sequence business process. The presentation then covers frequently asked questions related to sequence listings in patent applications.

Biography

Mr. Nguyen is a graduate of the Virginia Polytechnic Institute and State University and Johns Hopkins University. He works at the U.S. Patent & Trademark Office, where he served as the supervisory patent examiner of Art Unit 1633 and TC 1600 Quality Assurance Specialist from 2004-2009. He currently manages the Patent Examination Art Unit 1634 directed to personalized medicine and pharmacogenetics, and serves as a specialist and coordinator for the Sequence Business Process.

  • Mr. Nguyen's current assignments in the agency include:
  • Supervisory Patent Examiner, Art Unit 1634
  • Workgroup 1630 Hiring Program Coordinator
  • TC 1600 Externship Program Coordinator
  • Member of the WIPO ST.25 Revision Task Force
  • Co-Lead of TC 1600 Automation Working Group
  • Member of the Enhancing Technical Knowledge Between Examiners Working Group - Patents Process Reengineering Team
An Attorney's Perspective on Biotech-Related International FTO Searches
Anita Varma
Ropes & Gray LLP
Abstract

Freedom-to-Operate is fundamental to the success of pharmaceutical and biotechnology companies. This presentation will cover strategies for developing and executing successful and cost-effective FTO searches and analyses, as well as explore challenges that arise in international FTO searches and outline strategies to overcome them.

Biography

Anita is co-head of Ropes & Gray's Intellectual Property Rights Management Practice Group and has over 20 years of experience in intellectual property law as a lawyer and as a Patent Examiner at the United States Patent and Trademark Office (USPTO). Her experience as a Patent Examiner provides unique insights into the workings of the USPTO and as a UK Solicitor she is qualified to practice before the European Patent Office. Anita focuses her practice on developing, analyzing, and managing patent portfolios in diverse areas of technology for life sciences companies. She leverages this broad patent experience to counsel clients on transactional matters in connection with financial investments, mergers and acquisitions, and collaborations. Anita combines her patent experience with an understanding of regulatory exclusivities to help clients evaluate target portfolios and conduct worldwide due diligence assessments. She has conducted numerous pre-litigation assessments and rendered opinions regarding patentability, validity, non-infringement, freedom-to-use, Orange Book listing and delisting matters, and advised clients regarding the follow-on biologics legislation.

Getting the right message: Following real-time translation of patent information by partnering with patent attorneys
Tobias Pawliczek
Novartis Pharma AG
Abstract

Genomic information is transcribed into messenger RNAs (mRNAs) by RNA polymerases. Ribosomes translate mRNAs into functional proteins. Both processes are interdependent, highly regulated and coordinated.

Global information is distilled to selected patent/scientific information by patent searchers. Patent attorneys translate patent/scientific information into legal opinions or actions. But how well coordinated are those processes?

This presentation will highlight a pilot initiative in which a patent searcher partners with several patent attorneys to follow the translation of patent/scientific information into legal opinions or actions. Key messages will be presented that ultimately increased mutual understanding, legal awareness and search quality.

Biography

Tobias studied molecular biotechnology at the University of Lübeck (Germany) and completed his graduate research at Yale University (USA). He conducted his doctoral studies at the University of Cambridge (UK), whilst also completing a postgraduate certificate in patent law in Germany. Since May 2010 he has been working as a Patent & Scientific Analyst at Novartis, Basel (Switzerland).

Trees Lost In the Forest- Using Visualization Tools to Interpret Sequence Search Results
Denis Bayada, GenomeQuest, Joe Terlizzi, Questel, Inc.
Abstract

When comparing sequences from patent databases, one does not always know beforehand the number of hits that one will get.  Choosing the right algorithm and the appropriate filters can reduce the number of hits to a reasonable size, but this is not always the case.  In those hard to solve cases, thousands of hits can occur and some form of visual aid is critical.  The ability to analyze very large sets of documents, to drill down selected data, and to position concepts in the data by similarity will be explored. GenomeQuest and Questel will show how visualization can provide tremendous help in focusing on the few important patents - the trees lost in the middle of the forest.

Biographies

Denis Bayada
Senior Field Application Scientist, GenomeQuest

Dr. Denis Bayada is a senior field application scientist at GenomeQuest, applying his extensive chemoinformatics and genomics-based drug discovery experience to the solution of problems faced by research organizations in IP as well as molecular biology.Dr. Bayada’s PhD. in Chemistry centered on the computational analysis of molecules, an experience he was able to leverage as a senior researcher at NV Organon/Akzo Nobel, where he was an integral member of their early bioinformatics team. Dr. Bayada was also a senior researcher at the French national sequencing center, Genoscope/CEA where his work focused on the sequencing and analysis of bacterial DNA.With an extensive background in chemoinformatics and genomics-based drug discovery spanning nearly two decades, Dr. Bayada transforms customer feedback into effective workflow refinements, especially in variant detection and IP.

Joe Terlizzi
IP Specialist- Training Manager, Questel, Inc.

Joe Terlizzi is Questel’s chemical information specialist and training manager. He has been involved with chemical search and retrieval systems since 1975, when he joined the Central Abstracting and Indexing Service (CAIS) of the American Petroleum Institute. At CAIS, Joe worked until 1999 as an indexer, product manager, editor of the API Thesaurus, and chief trainer, and helped develop their machine-aided indexing system. Joe joined Questel in 2000 as an IP specialist and sales representative and became their head trainer for the Merged Markush Service. Joe holds a Bachelor of Science degree from Stevens Institute of Technology in Hoboken, NJ.

Creating Reports from Patent and Sequence Databases with the BizInt Smart Charts Product Family
John Willmore
BizInt
Abstract
Creating reports from gene sequence databases in addition to patent databases presents some interesting challenges. This paper will discuss using tools in the BizInt Smart Charts product family to create reports and visualizations from gene sequence and patent databases, including new features, limitations, and suggestions for future enhancements. Key features under development include:
  • create reports combining data from different patent and gene sequence databases and identify related records across databases, using BizInt Smart Charts for Patents;
  • clean-up, normalize, and transform data (such as Assignees) from different databases using tools in VantagePoint - BizInt Smart Charts Edition and filter patent families by authorities of interest;
  • summarize data from related records into a single row using BizInt Smart Charts Reference Rows, including the ability to group records based on Sequence ID or Publication Number rather than Common Patent Family, and creating summary subtables of query parameters in a Reference Row;
  • export reports in HTML, Word, Excel, and Acrobat, with links to backing records and related information;
  • analyze and visualize your normalized and de-duplicated data in VantagePoint - BizInt Smart Charts Edition.
Biography

John Willmore is Vice President, Product Development, for BizInt Solutions, Inc. and manages the development of all aspects of the BizInt Solutions product line. John has a B.S. in Electrical Engineering from Rice University and over 20 years experience in software development. He was the head of the TRW Smart Charts development team at TRW, Inc. and along with Diane Webb, founded BizInt Solutions in 1996. John has over 15 years of experience in processing, analyzing and integrating patent and drug pipeline information, and has worked closely with patent and drug pipeline publishers over that period.

Lossy Data Compression in Patent Informatics
Kristine Atkinson
Boston Scientific
Abstract:

With increasing mechanization of data processing and interpretation, the potential for error via data extrapolation or algorithmic editing rises. We will explore the path taken by original data to content sharing in patent and genetic databases. Data compression of large sequence files is of particular concern for accurate information retention over time on various platforms; there are also considerations of algorithm operation during transfers among devices and through complex protocol environments. For these information challenges we consider how patent data are serially processed and construed, with attention to sources and procedures that may lead to information loss or reconfiguration.

Biography

Kristine Atkinson is an early adopter and beta tester of many hardware and software innovations in electronic data retrieval, Kristine Atkinson's doctoral thesis in genetics was a treatise on proteomic and karyotype speciation driven by continental drift and host/parasite coevolution. She also holds an M.S. degree in cell biology, a bachelor's in foreign languages, and has enjoyed incarnations as a protein chemistry laboratory director, electron microscopist, biomanufacturing trainer, business analyst, medical editor, medical device and vaccine inventor, and discovery paralegal. She is a registered U.S. patent agent specializing in patentability, freedom-to-operate and technology landscape searches. She cochaired the Training Working Group of the PIUG Education task force from 2008 to 2012.

DIY Searching
Seth Mendelson
Novartis Institutes of Biomedical Research
Abstract

If you have ever watched a home improvement show and then tried a DIY project, you know that it often looks much easier on TV.  Patent searching, analyzing and reporting strategies are much like a DIY project.  Done well, methodologies for getting from request to report look downright easy.

Preparing for a search takes the same effort as preparing to tile your bathroom.  You take measurements and collect information on the tile, adhesive and grout.  We’ll consider some good preparation techniques for uncovering keywords and exemplar sequences, how to re-focus the search request when you get a thousand hits, as well as selecting appropriate databases and sequence search settings.  Performing a well-executed search is as deceptively simple as laying tile.  Proper implementation can make the difference between a beautiful wall and a crooked, lumpy backsplash.

We’ll discuss some good implementation strategies and how post processing can smooth the path to an attractive final report.  Finally, you may love to watch the DIY disaster shows, but you don’t want to be in one.  You want to show off your job well done.  We’ll consider how to present what you found.  The format of the report should tell a clear story to the client, highlighting the things they need to know without drowning them in irrelevant details and records.  This is where you can include useful information that can save the client time and show them how invaluable your skills are.

Biography

Seth Mendelson is a Patent and Scientific Analyst in the NIBR Patents group at Novartis Institutes for Biomedical Research.  He has a BS in animal science and an MS in physiology, both from the University of Rhode Island.  He has held several positions, beginning at the bench in a microarray lab at the Genetics Institute, spending two years in the bioinformatics group at Wyeth and finally moving into patent searching.  Seth began working as a patent analyst in 2004 and has been at Novartis since 2008.

Panel: Assisting Information Professionals

Panelists will share their expertise in helping solve challenges in biotechnology patent searching, integrating, post processing and delivery. Each panelist will have an introductory speaking spot. The panelist will have five minutes per question and five minutes for questions. Panelists will select two of the following questions to be answered in the introductory speaking spot:

  1. What common difficult biotechnology/biosequence questions do you receive and   how do you resolve them?

  2. Do you have an interesting story from your experiences?

  3. How do you see your role changing in the next five years?

Panelists will also answer questions from the audience.

Panelist Biographies

Denis Bayada, GenomeQuest

Dr. Bayada is a senior field application scientist at GenomeQuest, applying his extensive chemoinformatics and genomics-based drug discovery experience to the solution of problems faced by research organizations in IP as well as molecular biology.Dr. Bayada’s PhD. in Chemistry centered on the computational analysis of molecules, an experience he was able to leverage as a senior researcher at NV Organon/Akzo Nobel, where he was an integral member of their early bioinformatics team. Dr. Bayada was also a senior researcher at the French national sequencing center, Genoscope/CEA where his work focused on the sequencing and analysis of bacterial DNA.With an extensive background in chemoinformatics and genomics-based drug discovery spanning nearly two decades, Dr. Bayada transforms customer feedback into effective workflow refinements, especially in variant detection and IP.

Jim Brown, FIZ Karlsruhe

Jim Brown is presently the Senior Account Manager for FIZ Karlsruhe in the U.S.  Jim joined FIZ Karlsruhe, Inc. in 2008 as a Regional Sales Manager after working at IFI Patent Intelligence for 23 years. His current duties at FIZ Karlsruhe Inc. include sales, customer trainings, authoring workshop manuals and presentations, and representing FIZ at conferences and exhibits. At IFI, Jim started as a chemical patent indexer, and then moved on to chemical patent indexing training and chemical patent searching. He was also a special indexing project manager and technical representative while at IFI. Jim was on the PIUG Board of Directors from June 2010 to June 2012 in the position of secretary; from June 2012 to the present he has served on the PIUG Board of Directors as Vice-Chair.

Diane Webb, BizInt: 

Diane Webb is co-founder, President and CEO of BizInt Solutions, Inc.  Diane has over 20 years of experience managing the development of software tools for information analysis. Prior to joining TRW, Inc., Diane managed several US Government projects in which the core technology used in BizInt Smart Charts was developed. In 1993, she launched the TRW "defense conversion" project which created the initial Smart Charts concept and software. In 1996, Diane and John Willmore purchased the Smart Charts product and founded BizInt Solutions.  Diane has degrees in the history of science and physics from Harvard University and the University of Pennsylvania, and is actively involved with the Patent Information Users Group (PIUG) and the SLA Pharmaceutical and Health Technology Division.  She spends much of her time outside work training and competing with her longhaired dachshunds.

Alice Humel Denton, CAS

Alice is from a small rural community in Indiana - a town named Elwood, which is about 40 miles northeast of Indianapolis. She has a BS in Molecular Biology from Purdue, an MT from Methodist Hospital in Indianapolis, and an SBB in Immunohematology from OSU/ARC. Ms. Humel Denton has worked in the blood banks of all the major hospitals in Columbus, OH. For the last 11 years, she has been Sr. Help Desk Specialist for CAS specializing in sequence searching. Previously, she worked for CAS in EO as an analyst in Mammalian Pathological Biochemistry. Alice enjoys her job with CAS and enjoys speaking with STN customers every day. STN customers push the boundaries of STN with their amazing creativity. She looks forward to meeting all of you face-to-face and to finally put a face with the voice. Please introduce yourself.

Caroline Peel, Thomson Reuters

Caroline Peel completed her BSc Biological Sciences degree at the University of Leicester with a specialization in Genetics and went on to study for her PhD at the University of Sheffield in yeast cell cycle genetics focusing on replication and DNA damage checkpoint mutants. She joined Thomson Reuters in 2001 as part of the GENESEQ team responsible for the production of the patent sequence databases GENESEQ and GENESEQ FASTAlert, holding roles as an analyst, technology and policy expert and team leader. Caroline is currently the Content Specialist Manager for IPS, managing editorial teams delivering DWPI content and the SSR product Zoological Record.

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