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Patent Information Users Group, Inc.

The International Society for Patent Information Professionals

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Patent Information Users Group, Inc.  The International Society for Patent Information Professionals


Tuesday, February 23, 2016

7:00 AM Vendor Set-up and Breakfast

Registration, Exhibits open
8:15 AM Welcome Remarks and Meeting Logistics
Jeannette Fiala, PIUG 2016 Biotechnology Conference Co-Chair
Greg Roland, PIUG 2016 Biotechnology Program Co-Chair

Morning Session

8:30 AM Validity of Antibody Patents in View of Recent Changes to US Case Law
Forrester Liddle, J.D. Novartis
9:15 AM CDR Identification and Searching
Seth Mendelson Eisai
9:45 AM Product Reviews (Linguamatics, BizInt, EBSCO GQ life Sciences)
10:05 AM Break & Vendor Exhibits
10:35 AM CRISPR/Cas9 Gene Editing Tool: The Future of the Biotechnology
DeeptiTayal Ingenious ebrain Solutions
11:05 AM Developments in the Microbiome Space: Tracking Innovation Trends
Larry Mulcahy Thomson Reuters
11:35 AM
CAR Shopping: Finding the Right Chimeric Antigen Receptors for You
Barbara Miller Novartis Institutes for Biomedical Research
12:05 PM Product Reviews (STN, Minesoft)
12:15 PM Lunch & Vendor Exhibits

Afternoon Session

1:45 PM It’s All About Your Colleagues: How Patent Searchers Can Support Each Other to Raise Their Level of Expertise
Doris Roth Danish Patent and Trademark Office
2:15 PM Patent Searchers Mini-Poll: Training / Search Skills Upkeep
Moderated by: Alison Taylor & Greg Roland, PIUG Program Co-Chairs
2:30 PM Computer-assisted Solutions to Understand the Competitive Landscape and Own Patent Creation: Introducing the Chemaxon Biomolecule Toolkit
Arpad Figyelmesi, Chemaxon
3:00 PM Break & Vendor Exhibits
3:45 PM Applying Text Mining Technologies to Patent Analyses
Matthew Crawford Pfizer
4:15 PM Mining Information from Tables within Patents
David Milward Linguamatics
4:45 PM Closing Remarks
Elliott Linder, PIUG Chair
Alison Taylor, PIUG 2016 Program Co-Chair
6:30 PM Networking Dinner (registration required)

Meeting Abstracts

Validity of Antibody Patents in View of Recent Changes to US Case LawTop of Page
Forrester Liddle, JD, Novartis


Many factors must be considered when conducting freedom to operate and validity searches related to antibodies. The complexity arises from a diverse set of claiming strategies employed to cover antibodies and their uses. Based on a single discovery, an Applicant can potentially attempt to file, and obtain, claims that cover any antibody that binds a particular target, any antibody that binds a particular epitope, any antibody that competes for binding with structurally defined antibody, any antibody that binds an epitope or target with a certain affinity, as well as claims directed to structural features of the antibody itself. Recent changes in U.S. case law appear to cast some doubt on the validity of antibody claims that lack antibody structural limitations. These changes in case law potentially create new opportunities for contesting the validity of issued U.S. antibody patents. This talk will explore some of these changes to U.S. case law, and their implications for freedom to operate and validity searches.


Forrester Liddle has been working in the field of patent law for 11 years. While a graduate student, Forrester worked part time with Global Prior Art, Inc., as a contract searcher. He obtained a Ph.D. in Cell Biology from Harvard University in 2005 and immediately thereafter began work as a Technology Specialist at Clark and Elbing, LLP, a boutique law firm specializing in biotechnology patent law. There, Forrester specialized in the design and execution of freedom to operate and validity searches for investment due diligence. Forrester obtained a J.D. from Suffolk law in 2011 and joined Novartis as a Patent Attorney in 2014. Now at Novartis, Forrester represents business units focused on ophthalmic and immunotherapies. Forrester's doctoral research employed biochemical, genetic, and molecular biological techniques to study signaling pathways involved in cancer. His research has been published in Biochemistry, Molecular Carcinogenesis, and Carcinogenesis.

CDR Identification and SearchingTop of Page
Seth Mendelson, Eisai


Sequence searching of antibodies has become more and more prevalent. Specifically, identifying CDRs (Complementarity Determining Regions) has become the focus of antibody searching. As patent analysts, we rely on attorneys to guide us in setting search parameters, such as "anything greater than one amino acid difference in two CDRs will be 'different enough.'" We also rely on our scientist to clearly identify the sequence of the antibody, and the CDR regions. In order for us to be savvy analysts, we should endeavor to understand HOW the scientists arrived at the sequences and WHY the variations matter.

I will discuss some of the most widely used and accepted methods for identifying CDR regions, highlighting the differences. I will then discuss several methods of searching for CDRs, allowing us to find sequences presented in a variety of forms. Finally, I will weave together the concepts of CDR identification and searching in an effort to help you provide relevant information to your attorney.


Seth Mendelson is a Senior Patent Information Scientist at Eisai. 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 Eisai since 2014.

CRISPR-Cas9 Gene Editing Tool: The Future of Biotechnology IndustryTop of Page
Deepti Tayal, PhD Ingenious e-Brain Solutions


Over the past two years, the site specificity gene editing via CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeats (CRISPR)–CRISPR-associated protein) technology has shown a stunning progress, triggering a revolution in the genome wide studies. Keeping the technical details aside, CRISPR/Cas9 makes it very simple, economical and quick to move around any genes, in any living system ranging from simple bacteria to human. Therefore, CRISPR-Cas9 technology will be expected to have wide market applicability over various industrial sectors, including therapeutics, agriculture, food technology, biofuel, veterinary and other industries involving biological system. This growth and applicability will require careful consideration of intellectual property rights and protections for new and exciting CRISPR/Cas9 endeavors.

This paper will provide an overview of CRISPR/Cas9 technology by presenting details of patents, products, white spaces, key companies, key research institutes and trend analysis around this technology. If armed with right information of IP, biotechnology companies shall be able to seize the vast opportunity presented by the CRISPR/Cas9 gene editing tool. This presentation will also provide inventors and investors with the resources to navigate through this period of exponential growth and opportunity in genome engineering, further exploring the approaches for collaboration and best practices in IP Industry.


Deepti Tayal is the Director at Ingenious e-Brain Solutions. She also heads the Life Science Department at Ingenious e-Brain Solutions with a big team of PhDs in Life Sciences. She has more than fifteen years of experience in Biotechnology IP and Research industry. After obtaining her PhD degree in Biotechnology, she worked as a post-doctoral fellow at the International Centre for Genetic Engineering and Biotechnology. She started her professional career as a research scientist with TCGA group. She then became fascinated in and stimulated by the growing IP industry and developed professional expertise in patents and non-patent literature for IP protection, specializing in Cancer Biology, Genomics, Virology, Immunology and next generation Biotechnology.

Developments in the Microbiome Space: Tracking Innovation TrendsTop of Page
Larry Mulcahy, Thomson Reuters


How do you stay on top of a new and rapidly moving technology space? I will explore the emerging area of human gut microbiome therapeutics. Scientists have been studying what lives in our digestive tracts for years (decades really), but only recently have the cost and accessibility of genomic tools allowed us to make rational manipulation of our microbial hitchhikers possible. Some of the first companies in this space have products in advanced clinical trials and have even gone from stealth start up to serious IPO in a few short years. I will go through examples of discovering the who (inventors, authors, institutions), the what (terminology and classifications), and the where using both Thomson Innovation and Thomson Data Analyzer.


Larry Mulcahy is a Solution Consultant at Thomson Reuters where his primary responsibility is to train and consult with users on Thomson Reuters' databases and solutions, specializing in research and analytics of patent and non-patent literature.  With his background in education, Larry has conducted patent search and patent landscaping courses as part of two master’s programs.  Larry has experience in several life sciences fields as a graduate student, postdoctoral fellow, and applications scientist.  Larry received his Ph.D. from Brown University in Molecular & Cellular Biology and Biochemistry.  He lives with his family in the suburbs of Boston, MA. 

CAR Shopping: Finding the Right Chimeric Antigen Receptors for YouTop of Page
Barbara Miller, Novartis Institutes for Biomedical Research


As an expert biopatent searcher, you understand how to best utilize the latest search tools and techniques in order to meet your client’s information needs. However, those needs are constantly changing, and if you want to continue to meet their needs, you need to have a general understanding of recent advances in the field. It’s rather like buying a car- you need to have a general understanding of what’s available in order to make an informed decision. Yet how can you, a busy information professional, quickly and easily keep tabs on all of the new scientific technologies? We will explore one way to stay informed by examining CARs- chimeric antigen receptors- as our model. CARs are receptors engineered to be expressed primarily in T cells, and these T cells are used to target specific cancers. Because questions around CAR therapy can be complex and involve numerous parts, we will discuss how to break down the search into the different questions by analyzing the structure, function, and methodology of CAR T cell therapy. By the end of the discussion, you will have a better understanding of this exciting new technology, and you will have developed new approaches to better meeting the complex and ever-changing information needs of your clients.


Barbara Miller is currently a Patent and Scientific Analyst at the Novartis Institutes for Biomedical Research (NIBR) in Cambridge, MA. Prior to joining Novartis in August of 2009, she was an Information Scientist at Pfizer in Groton, CT, where she supported a variety of research and development teams by providing literature, patent, regulatory, and competitive information. Barbara began her searching career at the Pfizer facility in Ann Arbor, MI, in 2001 as a biopatent searcher after completing a postdoctoral fellowship at the University of Michigan. She has a PhD in Biological Sciences from Emory University in Atlanta, GA, a MS in Regulatory Affairs and Quality Assurance from Temple University, and a BS in Chemistry from Rhodes College in Memphis, TN.

It’s All about Your Colleagues: How Patent Searchers Can Support Each Other to Raise Their Level of ExpertiseTop of Page
Doris Roth, Danish Patent and Trademark Office


Experts work differently, but they can overcome these differences, when they work together and share knowledge. How can such collaboration be facilitated and put into practice? A corporate culture that prioritizes supporting colleagues over individual tasks can create an atmosphere, in which search experts do not compete against each other but focus their ambition on raising the competence level of their colleagues. This results in an increase of the average quality of the search results produced by their department. A particularly beneficial team work can be created in a work force that unites patent searchers with diverse backgrounds. For example, search experts with many years of experience in patent information can create synergies with colleagues having recently joined from R&D who bring with them cutting edge technical knowledge. This presentation will provide specific examples of how search experts can support and improve each other on a daily basis. The talk will also illustrate how cooperating in-house leads to a higher average skill level, more enthusiasm about work and, most importantly, more valuable outcomes for our customers.


Doris was trained as a biochemist at ETH Zurich, from where she also received her PhD. She did her postdoctoral work in biotechnology in Denmark. In 2014, she started working at the Nordic Patent Institute and the Danish Patent and Trademark Office, where she provides patent search services as well as search and examination reports for PCT and national patent applications (Denmark, Iceland, Turkey, Brunei and Singapore). Furthermore, she has been involved in coaching trainees and advising independent inventors. She enjoys working together with her colleagues in Denmark and Norway and competes in mountain bike and track cycling.

Patent Searchers Mini-Poll: Training / Search Skills Upkeep
Moderated by: Alison Taylor & Greg Roland  PIUG Program Co-Chairs

The following questions will be posed to the audience and a quick hand-count taken of responses.  We hope the results will help us gain insight into current biotech IP searcher practices, where future development needs may lie and help us plan for future PIUG Biotech meetings.

  1. Do you consider personal development training on new tools and searching skills important for your job?
  2. Does your company have a training and/or growth development plan?
  3. Would you like to see more PIUG-sponsored training opportunities on various biotech-related databases, topics or skills?

Computer assisted Solutions to Understand Competitive Landscape and Own Patent CreationTop of Page
Arpad Figyelmesi, Chemaxon


Understanding competitive landscape is essential in drug discovery projects, including early phase idea generation, lead candidates prioritization and creating your own patents. However, extraction and formalized representation of chemical and biochemical information in prior art documents is a complex and time consuming task. Both manual and automated data extraction, analysis and Markush creation methods have their own benefits. Using real-life examples in the biotechnology research field, I will demonstrate how ChemAxon’s Biomolecule toolkit and other techniques can assist you in reaching the best solution for high quality data extraction and analysis in reasonable time.


Árpád Figyelmesi graduated from the Budapest University of Technology and Economics as MSc Chemical Engineer in 2008. After several years of industrial experience, he joined the Hungarian Intellectual Property Office as a patent examiner and later as a business analyst. Árpád has been with ChemAxon since 2013 leading the development of ChemCurator and Markush technologies.

Applying Text Mining Technologies to Patent AnalysesTop of Page
Matthew Crawford, Pfizer


Text mining has been a proven technology for extracting facts and concepts from peer-reviewed literature, particularly when applied to the short, well-formatted text found in Medline abstracts. While it has been applied with some success to patent literature, most of the focus has been on improving document retrieval--that is, finding a small set of documents for further review. Compared to the relatively consistent nature of peer-reviewed literature abstracts, patents present several challenges with their complex internal structure, multi-document, multi-language family structure, and frustratingly vague writing style. Facing these challenges with text-mining can, however, assist in several other complementary tasks, such as concept extraction and relevance ranking. While reliance on human-curated databases can work well for some applications, it has some potential drawbacks including cost, completeness, and timeliness. At Pfizer, the Medicinal Chemistry group has commissioned an investigation into using comprehensive gene, indication, and organization dictionaries to ferret out much of the same information found in curated databases. The benefits of this approach include a more comprehensive view of the patent literature, a statistical framework for evaluating the confidence of text mining predictions, and a high degree of flexibility when interpreting results. In several instances, the complex nature of patent filings improves the robustness of the statistical predictions.


Matthew Crawford currently works in the Molecular Informatics group at Pfizer.  In addition to supervising the incorporation of public and proprietary structured data sources, his work has focused on text mining applications of in-house clinical study reports,  project work based on large-scale analysis of therapeutic opportunities, and fine-tuning target-selection processes.  Current interests include supervised machine learning approaches to assist in combining vocabularies used for text-mining and for gene function prediction.  He developed his passion for high-throughput applications of literature as the director of curation technology at Proteome, Inc., and his appreciation of machine learning algorithms as a software developer at the Broad Institute.  He received his PhD in Molecular Biology at the University of New Mexico in 1999.

Mining Information from Tables within PatentsTop of Page
David Milward, Linguamatics


Information in patent publications provides a wealth of opportunities for identifying prior art, technology landscapes, and white space. However, valuable intelligence is often split between free text and tables. We will discuss some of the challenges of extracting information from tables, and show recent advances in reconstructing information split across table cells. We will also show how the information from within the tables can be linked to information within the free text.


David Milward is chief technology officer (CTO) at Linguamatics. He is a pioneer of interactive text mining, and a founder of Linguamatics. He has over 20 years experience of product development, consultancy and research in natural language processing (NLP). After receiving a PhD from the University of Cambridge, he was a researcher and lecturer at the University of Edinburgh. He has published in the areas of information extraction, spoken dialogue, parsing, syntax and semantics.

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