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PIUG 2015 Biotechnology Conference

Maximizing Value in Biotechnology Searching with New Technologies and Trends

Monday, February 16, through Friday, February 20

Genentech
611 Gateway Blvd
South San Francisco, California 94080
+1 (650) 225-1000

Program
Tuesday, February 17

Building 83, Conference Room 1A

7:30 AM Breakfast, Registration and Vendor Exhibits
8:15 AM Welcome Remarks
Ruben Diaz, PIUG 2015 Biotechnology Program Co-Chair
8:30 AM FTO and Patentability Searches: Meeting Business Goals
Michelle Lewis, Genentech
9:05 AM Updates and initiatives from the US
John Cabeca, USPTO
9:40 AM Product Reviews
GenomeQuest, Linguamatics, EBSCO
9:55 AM Break
10:25 AM Panel Session - Maintaining Biotech Search Team Excellence / ROI
Doreen Alberts, Ruben Diaz, Greg Roland and Steve Mitchell
11:45 AM Product Reviews
STN, BIZINT
12:00 PM Lunch
1:40 PM Integrating Sequence Results with Multiple Patent Sources to Provide Better Reports and Visualizations
Monica Weiss-Nolen, Sanofi, and John Willmore, BIZINT
2:10 PM Do biotech patent landscapes reflect global innovation indices? A cross-platform analysis?
Heinz Mueller, Swiss Federal Institute of Intellectual Property
2:40 PM Integrated Keyword and Biological Sequence Searching in the Life Sciences
Henk Heus, GenomeQuest
3:10 PM Break
3:40 PM Product Reviews
Search Technology, Minesoft, Intellixir
3:55 PM Patent searching for predictive biomarkers for use in cancer treatment
Leah Sandvoss, Pfizer
4:25 PM Text-mining Patents for Antibody Drug Conjugates
Julia Heinrich, Bristol Myers Squibb
4:55 PM Closing Remarks and Thanks
Alison Taylor, PIUG 2015 Biotechnology Program Co-Chair
Doreen Alberts, PIUG 2015 Biotechnology Conference Chair
7:00 PM Networking Dinner (registration required)

The Program and Planning Committees would appreciate your conference-related feedback. Our survey addresses plenary sessions, workshops, and vendor interactions. Hyperlinks to the survey have been sent to all conference registrants.

Feel free to submit your feedback during or after the conference (you will have the opportunity to save and return where you left off). We appreciate your completing the survey prior to March 6, 2015. Your feedback helps us make the conference ever better going forward.

 

Meeting Abstracts

FTO and Patentability Searches: Meeting Business Goals Top of Page
Michelle Lewis, Genentech
Abstract

Freedom to operate (FTO) and patentability search results are both mainstays in the arsenal of necessary information for patent professionals to do their job effectively and comprehensively. This talk will contrast and compare these two types of searches, particularly from an in-house counsel's point of view. The talk will go on to discuss possible approaches to ensure that the search results requested not only meet the expressed goals from the professional, but also the ultimate business goals that these searches are meant to perform. By comparing and contrasting the ultimate use of the results, and providing possible question paths to reveal and better understand these potential uses, the aim of the presentation is to provide concrete approaches that can improve search strategy targeting, appropriately narrow results, and ultimately, provide the business with the informational support it needs.

Biography

Michelle began her patent career as a Patent Examiner and then worked as a patent agent and attorney for several law firms. She then moved in house and has had the pleasure of working for small start ups (Molecular Templates), mid-sized companies (ZymoGenetics), and large companies (Bristol-Myers Squibb). She joined the patent department at Genentech about a year ago and works on a variety of projects in the oncology area as well as supporting specific groups in Global Technical Development. She has requested and received innumerable results of patent searches over the years and enjoys collaborating on the retrieval and review of the legal information necessary to perform her responsibilities.

Integrating Sequence Results with Multiple Patent Sources to Provide Better Reports and Visualizations
Monica Weiss-Nolen, Sanofi Pasteur, and John Willmore, BizInt Solutions Top of Page
Abstract

In this case study we examine techniques for integrating data from different patent and sequence databases in order to create more comprehensive reports and visualizations.  We can, for example, combine sequence results from GenomeQuest, legal status information from Orbit, and standardized company/assignee information from WPI in Cortellis to leverage the strengths of each database.  Data normalization, filtering and visualization tools will be used to help analyze and present key features of the patent landscape.

Biographies

Monica Weiss-Nolen has been an Information Scientist in the Scientific Intelligence group at Sanofi Pasteur for almost 10 years. She supports North American R&D, Corporate Development and Intellectual Property attorneys with customized scientific, competitive and patent information search reports. Before joining Sanofi, she served as a Senior Analyst for the Business Intelligence group at Ortho Biotech, a Johnson & Johnson company. Prior to that, she was an information scientist at DuPont Pharmaceuticals for 10 years, conducting patent and scientific searches for R&D. She started her information science career at BIOSIS. Monica holds a BS in Biochemistry from Millersville University of PA and an MSIS from Drexel University, and has been a member of the PIUG for over 10 years. She has also been a potter for over 20 years, showing her ceramics work at local art shows in the Lehigh Valley PA.

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 over 20 years of experience in processing, analyzing and integrating drug pipeline, patent and clinical trial information, and has worked closely with information publishers over that period. He was the head of the TRW Smart Charts team at TRW, Inc. and along with Diane Webb, founded BizInt Solutions in 1996. John has a B.S. in Electrical Engineering from Rice University and over 20 years experience in software development. He plays recreational ice hockey and competes with his dachshunds in agility and field events.

Do biotech patent landscapes reflect global innovation indices? A cross-platform analysis
Heinz Mueller, Swiss Federal Institute of Intellectual Property Top of Page
Abstract:

Patent landscape analyses using different software tools and data sources were performed to evaluate the inventive power of various countries including the US and some selected European countries with a strong high-tech economy, among them Switzerland as the global innovation leader. The analyses were based on patent class searches to generate the baseline numbers of documents used to perform statistical analysis, data and text mining. The results of these patent literature investigations were then compared with different global innovation indices. Since inventions are an important prerequisite for innovations in highly technical fields such as biotechnology and all innovation indices use the number of patent applications per capita as an important parameter, one could expect that the innovative power is indeed reflected in the patent landscape. Indeed, the biotech patent landscape reflects to a certain degree these general global innovation indices. This might have to do with the fact that countries with a strong high-tech industry, of which the biotech industry is certainly an important part, are usually in the top countries on these competitiveness lists. Furthermore, today a large number of sophisticated software-tools are available to present patent search data in many different formats and everyone can easily use these tools to generate complex graphs. Thus, quality of patent intelligence does not depend on the use of such tools per se, but on the retrieval of the correct data set and the selection of the respective graphs to meet the customer’s needs. For this, an experienced and well trained patent information specialist is needed more than ever.

Biography

Heinz Mueller was educated as a biochemist at the ETH Zurich, where he also received his PhD. In 1985, he moved to the US to work for several years at different research institutions in San Diego (Scripps Research Institute) and Chicago (Northwestern University). He returned to Switzerland to work as a principal investigator in breast cancer research at the University of Basel. From this university, he received his Venia legendi and the title of a professor. In 2002, he started working as a patent expert in the patent department of the Swiss Federal Institute of Intellectual Property while remaining a regular lecturer in biochemistry at the medical faculty of the University of Basel. He also teaches intellectual property law at different Swiss universities, in particular for life science students, and has written extensively on a number of pertinent topics.

Swiss Federal Institute of Intellectual Property
Stauffacherstrasse 65
3003 Bern
SWITZERLAND
Tel: ++41 31 377 7368
Fax: ++41 31 377 7793
e-mail: heinz.mueller@ipi.ch

Integrated Keyword and Biological Sequence Searching in the Life Sciences Top of Page
Henk Heus, GenomeQuest
Abstract

Biotech patent searchers are masters in the art of knowing which tools to use and when to use them to accomplish a wide range of research tasks. In order to complete comprehensive searches, analysts must perform biological sequence searching in one application, full text searching in another, and report production in yet a third. Furthermore, searching text in the life sciences is fraught with challenges such as the overloaded use of words to name biological concepts (for example, the slingshot gene), and the complexity of biological concepts which forces biotech searchers to build and manage large lists of synonyms. We present here case examples using a unified framework for the comprehensive searching of both life science text and biological sequences in a single environment. The framework utilizes life science ontologies to aid the user in developing conceptual queries that avoid the typical challenges in biotech patent text searching combined with a mouse-free interaction to aid in rapidly examining merged results from text and sequence searches.

Biography

With GenomeQuest since 2001, Dr. Heus leads the team responsible for all Product Management and Professional Services. He also leads the entire GQ-Pat build efforts and all content production. Dr. Heus holds a PhD in human genetics from the Erasmus Medical Center, Department of Clinical Genetics. With over 15 years experience in genomics, including at NV Organon/Akzo Nobel, he brings expertise and invention from all fields critical to the company's products and customers. 

Patent searching for predictive biomarkers for use in cancer treatment Top of Page
Leah Sandvoss, Pfizer
Abstract

Predictive biomarkers are becoming increasingly important in cancer therapy as personalized medicine treatments evolve. A biomarker is defined as a naturally occurring molecule, gene or characteristic that can be objectively measured and evaluated as an indicator of either normal biological or pathogenic processes, or pharmacological response to a disease treatment. They are particularly useful in prognosing cancer patients, where an early, specific diagnosis and timely intervention can lead to a more successful treatment outcome. Understanding patent language in this area to devise effective search strategies can be challenging. This presentation will provide an overview defining predictive biomarkers, why they are critical to cancer treatments, and address how they are used as approved companion diagnostics for marketed products. Hypothetical patent claim examples will be shown, along with suggested approaches for designing search strategies to uncover relevant patents and applications.

Biography

Leah has worked as a biotechnology patent analyst in the Patent Searching & Information group within the Legal Department at Pfizer La Jolla since 2008. In this role, Leah supports intellectual property attorneys by providing in-depth patent searching and analysis on key assets in the company portfolio. She originally joined Pfizer in 2004 as an information scientist supporting researchers on drug development project teams by providing pertinent literature and competitive intelligence information. She holds a Master of Science in Chemical Informatics from Indiana University, a Master of Science in Medicinal Chemistry from the University of Michigan, and a Bachelor of Science degree in Chemistry from Kent State University.

Text-mining Patents for Antibody Drug Conjugates Top of Page
Julia N. Heinrich, Bristol-Myers Squibb
Abstract

There is considerable interest in the patent community to identify technologies that will both streamline the process by which patent information is searched as well as retrieve results in formats that are ready for making business decisions. Extracting information from patents is a challenging process because patents fall into the category of semi-structured data, which means the meta-data, i.e., title, assignee, priority date etc., may be easily parsed in relationship columns but the bulk of information, i.e., claims, specifications is not. The Linguamatics-I2E platform uses Natural Language Processing (NLP) technology that integrates a variety of tools (linguistic patterns, taxonomies, source fields) in the information retrieval process in order to parse “unstructured data” into meaningful output columns. This approach is dubbed “text-mining” as compared to the traditional “searching”.

Some of the key features of I2E text-mining, unlike traditional command-line searching, include: 1) queries are run as a single (Multi)Query rather than sequentially; 2) results are displayed as an Excel table and/or bar chart rather than as a list of documents; 3) the resulting Excel table might be immediately compatible with a number of visualization applications, i.e., Spotfire, while in traditional command-line searching, documents need to be first read and their content excised for subsequent visualization; and 4) the I2E (Multi)Query might be enabled as a SmartQuery and searched at will on your favorite parameter, i.e., antibody-drug conjugate (ADC) drug name such as T-DM1, also known as ado-trastuzumab emtansine or Kadcyla.

This presentation will cover the use of Linguamatics-I2E in text-mining patents on the topic of ADC to illustrate a simple scenario of the 4 points listed above.

Biography

J.N. Heinrich is a Senior Patent Analyst, Biotechnology at Bristol-Myers Squibb, Hopewell, NJ. She is a member of the Scientific Information & Patent Analysis group that is within Information & Analytics Sciences and part of Research IT & Automation. Julia entered the field of patent information in March, 2010 as a consultant for iConma under contract by Sanofi, Bridgewater, NJ and was first introduced to the awesome power of text-mining on the Linguamatics-I2E technology. Her engagement in the field was generously recognized the following year by PIUG when she was awarded their annual Brian Stockdale Memorial Award. In support of PIUG programs, Julia has volunteered at and attended PIUG Biotechnology and Northeast Conferences. Previously, Julia has spent fourteen years in various roles across Research and Development, Drug Discovery ranging from designing, developing and implementing high-throughput screens based in yeast for multiple therapeutic areas to leading exploratory programs in the Neuroscience Department, at Wyeth, Princeton, NJ.

Julia earned her B.A. in the Department of Biology from Brown University, Providence, RI; her Ph.D. in the Department of Molecular Biology and Virology at Memorial Sloan Kettering division of Cornell University, NYC, NY; and did her Postdoctoral Fellowship at the Pharmaceutical Research Institute, Bristol-Myers Squibb, Princeton, NJ.

Updates and initiatives from the USPTOTop of Page
John Cabeca, USPTO

Silicon Valley USPTO Director John Cabeca will speak about USPTO initiatives and pilot programs that are designed to offer patent applicants an array of prosecution options.  Director Cabeca will highlight Agency developments to improve user access to patent-related information, including the newly released patent assignment tool as well as classification reform efforts to implement a multinational Cooperative Patent Classification system.  He will also speak about the role of the Silicon Valley Office and his efforts to engage with and tailor programs for innovation communities across the region.

Biography

A 25-year veteran of the U.S. Patent and Trademark Office, John Cabeca is the Director of the Silicon Valley USPTO.  In this role, John carries out the strategic direction of the Under Secretary of Commerce for Intellectual Property and Director of the USPTO, and is responsible for establishing and leading the Silicon Valley satellite office. Focusing on the region and actively engaging with the community, Mr. Cabeca ensures the USPTO’s initiatives and programs are tailored to the Silicon Valley's unique ecosystem of industries and stakeholders.

Panel Session - Maintaining Biotech Search Team Excellence / ROI
Doreen Alberts, Ruben Diaz, Greg Roland and Steve Mitchell

Panelists will introduce themselves, and then all will participate in a question-and-answer session. Topics to be covered by the panelists include:

  • Factors leading to a successful search service
  • Experiences and lessons learned during times of growth or cutbacks
  • Prioritization of work to focus on high impact work

We encourage members of the audience to participate in the Q&A session.

Doreen Alberts, Theravance

Doreen Alberts is the Associate Director of the Knowledge Management Department at Theravance Biopharma US, Inc. (TBPH) , a pharmaceutical company focused on the discovery, development and commercialization of small molecule medicines across a number of therapeutic areas including respiratory disease, bacterial infections, central nervous system (CNS)/pain and gastrointestinal (GI) motility dysfunction.  As the department head, Doreen is responsible for managing the following functions at TBPH: Patent and Literature searching, Library Services, Document Delivery, Competitive Intelligence, Medical Information and Enduser education and training.

Doreen has a BA in Chemistry, minor in Economics from the University of California, San Diego. Prior to working for TBPH, Doreen worked for SmithKline Beecham (now Glaxo SmithKline) as a medicinal chemist for 11 years, and as an information analyst for 2 years.

Doreen was one of the recipients of the 2007 PIUG Service Awards in recognition of her service to PIUG as the Annual Conference Sponsorship Committee Chair for 2005-2006 and the Strategic Planning Committee Chair for 2006-2007. She co-chaired the Program Committee of the 2008 PIUG Annual Conference, and was a Strategic Planning Committee Member 2012-2013. Doreen is currently the Planning Committee Chairperson of the 2015 PIUG Biotechnology Conference having held the same position in 2011 and 2012.

Ruben Diaz, Genentech

Ruben Diaz has a BA in Biology from Pomona College and an MLIS from UC Berkeley. Ruben began at Genentech in 1991. He provides patent, scientific and business search support to the Genentech Legal Department.

Greg Roland, Novartis

Greg is currently the Global Head of Novartis Institutes of BioMedical Research (NIBR) located in Cambridge, MA.  Greg has 25 years of experience in the pharmaceutical industry and searching the biotechnology patent literature, including BLAST searching, for over 15 years. He started his career as a bench scientist at Parke-Davis in Ann Arbor MI in the antiinfective group in 1990 doing in vivo and in vitro evaluation of novel anti-bacterial mechanism. In 1999 he transitioned to the Research Library at Parke-Davis taking on the role of supporting FTO requests for research tools.  After Pfizer acquired Parke-Davis in 2000, Greg moved to a senior manager role continuing to act as an individual contributor in the patent space and leading a team of biomedical, chemistry and CI professionals.  In 2005 Greg transitioned to the Patent department at Pfizer as part of the management team where he stayed until the end of 2008.  In August of 2009 he joined the Merck’s Knowledge Discovery Knowledge Management group in World Wide Licensing as a Director where he was responsible for the pre-clinical competitive intelligence for Oncology, Inflammation and Biologics as well as lead editor of the pre-clinical in house competitor compound database.

Steve Mitchell, Technology and Patent Research International (TPRI)

Steve Chappell Mitchell has 18 years of professional experience in patents and non-patent literature for Intellectual Property protection, specializing in Cancer Biology, Genomics, Virology and Immunology. Steve developed expertise with specialized leadership experience at top companies including Abbott and Technology & Patent Research International, where he is Director of Biotechnology and Genomic Services. His intellectual property protection involves Freedom to Operate, Validity, Patentability, and Litigation support. He holds fifty (50) granted United States patents, through his 20-year career in scientific discovery and development at Harvard, UCLA, Agensys (Astellas) and Caltech. Steve’s clients include most all big pharmaceutical companies, and a large group of biotechnology companies and law firms worldwide.

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