PIUG 2021 - Thursday (Biotech)

Patent Information Users Group, Inc.

Contents Fighting Coronavirus with Patent Information 2 Early Disclosures of Biosequences Related to SARS-Cov-2 Biology and Covid-19 Medical Management in Patent Literature 4 Chimeric Antigen Receptor Immunotherapy – Beyond T-cell 6 Preparing Reports for Off-Patent Legal Analysis: an Example with CDRs 8 Identifying the Key Patents in Cancer Immunotherapy with Unique Patent Search Strategy 10 Using KNIME for Mining and Combining Scientific and Patent Data for Insights: RNA Examples 12 USPTO’s Efforts Related to ST.26 14 Panel Discussion: The Challenges and Opportunities of Working Remotely 16 Plenary Sessions: THURSDAY (BIOTECH)

Unconventional Times Require Unconventional Search and Analysis Techniques

Monday, May 24 – Friday, May 28  Virtual Meeting 2021 ANNUAL CONFERENCE

Meeting Book prepared by BizInt Solutions Inc., a proud sponsor of the 2021 PIUG Annual Conference

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y M O R N I N G 8 : 0 0 A M – 12 : 1 0 P M

Fighting Coronavirus with Patent Information Geert Boedt (European Patent Office) 9:30 – 10:05 am

 ABSTRACT The European Patent Office has responded to the COVID-19 pandemic in many ways. With its extensive patent databases and freely available patent search tools, the EPO created curated dynamic datasets of patents on the “Fighting coronavirus” platform covering technologies directed at combating COVID 19. The data is specifically directed to researchers, clinicians, and other professionals working in the front line. The platform allows easy user access to dynamically updated patent searches in the EPO’s Espacenet database, and to pre-calculated patent statistics in selected technical fields. Users can also download raw data sets to analyse for themselves. Examples of searches, patent statistics and downloads will be presented.  BIOGRAPHY Geert Boedt has a Bachelor of Science in Applied Informatics. After many years working in IT for international organisations he joined the EPO in 2004 in the Espacenet customer support area and subsequently gained experience in all of the EPO’s public patent information tools. He moved to become business application manager for the PATSTAT database; and is an expert on statistical analysis of patent datasets. He advises researchers and policy makers worldwide on correct interpretation of patent data and value indicators and has many years’ experience of presenting on patent analytics topics.

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PIUG 2021  THURSDAY  Virtual Meeting

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Fighting Coronavirus with Patent Information  Geert Boedt (European Patent Office)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y M O R N I N G 8 : 0 0 A M – 12 : 1 0 P M

Early Disclosures of Biosequences Related to SARS-Cov-2 Biology and Covid-19 Medical Management in Patent Literature Luca Falciola (Scibilis Consulting Services SRL) 10:05 – 10:40 am  ABSTRACT Since early 2020, the global impact of Covid-19 emergency is affecting patent-related activities, from prosecution and filing policies to be adapted to lockdown conditions to short-term but possibly also more long-term effects over objectives and resources for innovation. As of spring 2021, it is still too early to have a complete view about if and how the newly established technologies adapted to this “new normal” situation have been also disclosed and claimed in patent literature, in particular for biotech products with longer clinical and manufacturing development time. It is anyway expected that, at least some applicants, given the financial and strategic interest to obtain a patent granted as early as possible, may have accelerated not only the filing but also the examination and publication of patent applications in their own country or other countries. The presentation, starting from a study of the earliest published patent documents related to SARS-Cov-2/Covid-19 (published as preprint in SSRN, https://ssrn.com/abstract=3771756), provides some guidance, data, and examples about how combining different approaches (text-mining, patent classification, sequence comparison) for searching and analyzing relevant DNA and protein sequences relating to detection, prophylaxis, or therapy (such as antibodies, vaccines, antigens, or biomarkers) that were disclosed in patent literature published by main authorities worldwide between March 2020 and April 2021.  BIOGRAPHY Luca Falciola is manager at Scibilis SRL consultancy (Bruxelles, Belgium). He previously held positions as IP Manager in bio-pharmaceutical companies in Belgium, France and Switzerland. Luca holds a PhD in Applied Genetics in Italy and has pursued post-doc molecular biology research activities in Switzerland. He is Member of AIDB (Italian Association of Patent Searchers), wherein he acts as editor of monthly “AIDB Newsletter”. He has published articles and provided courses, webinars, and presentations about searching, analyzing and using information in patent and scientific databases, in particular for pharma and life sciences.

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PIUG 2021  THURSDAY  Virtual Meeting

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Early Disclosures of Biosequences Related to SARS-Cov-2 Biology and Covid-19 Medical Management in Patent Literature  Luca Falciola (Scibilis Consulting Services SRL)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y M O R N I N G 8 : 0 0 A M – 12 : 1 0 P M

Chimeric Antigen Receptor Immunotherapy – Beyond T-cell Dominique Manu (European Patent Office), Björn Jürgens (Innovation and Development Agency of Andalusia) and Nigel Clarke (Independent Consultant) 11:00 – 11:35 am  ABSTRACT In 2017 the European Patent Office completed a patent landscape study into the emerging technology of chimeric antigen receptor – genetically engineered T-cell - immunotherapy. The study revealed the growth of patent activity in autologous immunotherapies directed mainly against human haematological malignancies. In the few intervening years the field has not only expanded in terms of volume of activity but also in terms of the scientific and technical scope. Our latest research completed in 2020 has identified developments in non-oncological therapies, the use of NK and NKT cells, and allogeneic transplants.  BIOGRAPHIES Björn Jürgens is senior analyst at the patent information centre CITPIA of the Innovation and Development Agency of Andalusia, a major Spanish public institution dedicated to innovation and R&D fostering of SMEs. He has worked for 15 years in the field of patent analytics and competitive intelligence and has extensive practical experience in patent searching and patent databases. Björn is actively involved in the PATLIB project from the European Patent Office and the Enterprise Europe Network for technology transfer from the European Commission. Furthermore he works as IPR ambassador from the EU IP Helpdesk network since 2016. He regularly speaks in international conferences and has published articles in peer reviewed journals about patent databases and patent landscaping. Björn has an academic background in Information and Knowledge Management at the University of Applied Sciences Darmstadt (Germany), a Master’s degree in Information Science and a PhD in the field of bibliometric patent analysis, both from the University of Granada (Spain). Dominique Manu joined the EPO in 2005. He is a patent examiner specialized in the field of cellular immunotherapy; a field which is now dominated by applications on chimeric antigen receptors. Before joining the EPO, Dominique did his PhD on the function of oestrogen receptors in osteoblasts at the European Molecular Biology Laboratory in Heidelberg Germany. Nigel Clarke is recently retired from the EPO and an independent consultant. Until recently he managed patent knowledge research projects focussing on future and emerging technologies, such as Blockchain, graphene, quantum, and cancer immunotherapy. Research results have been published in leading peer reviewed journals and on the EPO’s “Patent insight reports” web pages. He joined the EPO as patent examiner in electron and ion optics and subsequently became IT manager. For many years he was department head responsible for Espacenet and the European Patent Register. Leaving academia, Nigel started work in the UK Scientific Civil Service, mainly on focused energy beams for microanalysis. He published numerous scientific papers. Nigel studied physical chemistry at Exeter University and holds a PhD in neutron science. He carried out post-doctoral research on carbon fibres at Surrey University. He holds memberships of the Royal Society of Chemistry, Institute of Physics and is a Chartered Scientist, UK Science Council.

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PIUG 2021  THURSDAY  Virtual Meeting

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Chimeric Antigen Receptor Immunotherapy – Beyond T-cell  Dominique Manu (European Patent Office), Björn Jürgens (Innovation and Development Agency of Andalusia) and Nigel Clarke (Independent Consultant)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y M O R N I N G 8 : 0 0 A M – 12 : 1 0 P M

Preparing Reports for Off-Patent Legal Analysis: an Example with CDRs Steve Allen (Aptean GenomeQuest) 11:35 – 11:55 am

 ABSTRACT Frequently IP Sequence Searchers are asked to identify the earliest IP for a sequence or group of sequences. For example, there may be interest in assessing the current status of an antibody, and whether or not it may go off patent. The evaluation of the status and future status is a legal decision made by an attorney. Preparing a report so that the attorney can easily review the information can be challenging, particularly for older IP that can return 100’s of thousands of hits. The GenomeQuest Discover browser can aid in preparing and reporting this data through filtering, annotation of key items, and specific sorts that present the data in an organized fashion. I will review some of the techniques and interfaces to prepare a report from a search of six antibody CDR sequences.  BIOGRAPHY Steve Allen joined Aptean GenomeQuest in September of 2017, he is the Solutions Consultant for GenomeQuest & LifeQuest. Steve previously worked at Dupont and his background includes work in a patent group and work as a computational biologist in an agricultural discovery group. Steve has been working with sequence data of one form or another for over 30 years.

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› Workshop: Discover Analysis - Prioritization and Annotation Strategies Monday, May 24, 11:30 - 1 2 :30

› Breakout Session: Preparing Reports for Off-Patent Legal Analysis: an Example with CDRs Thursday, May 27, 11:35 - 11:55

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y A F T E R N O O N 12 : 3 0 P M – 3 : 5 5 P M

Identifying the Key Patents in Cancer Immunotherapy with Unique Patent Search Strategy Dr. Sarbani Chattopadhyay (Consultant, LexisNexis PatentSight) 1:00 – 1:35 pm  ABSTRACT The technique to deploy the body’s own immune system to identify and address genetic and cellular alterations due to cancer led to the field of Onco-immunology. The therapies that have emerged and are being developed in this field are expected to lead to oncolytic vaccines and other remedies to treat a range of human cancers, beyond melanoma. This rapidly developing field has very active ongoing patenting activity and it is crucial to have a through monitoring of the patent literature to ascertain the direction of development in the field of cancer immunotherapy. A unique strategy to generate the search syntax to define this field is to address each stage of the cell immunity cycle so that patents related to each of the stages can be retrieved. Such details bring to the forefront not only established players in this field but also emerging key players in the field that have path breaking invention worthy of being protected by patents.  BIOGRAPHY Dr. Sarbani Chattopadhyay PhD, LL.M., is a computational biologist with a PhD in Biochemistry from the University of Calcutta in Calcutta, India, and a LL.M. in European IP and IT Law from the University of Göttingen in Göttingen, Germany. As a Consultant at PatentSight GmbH, a LexisNexis company, in Bonn, Germany, she works with clients all across the globe in different technology fields in searching and analyzing patents, patent landscape and technologies from a patent perspective, where she utilizes her knowledge and expertise in combination with the PatentSight Business Intelligence Analytics Software to gain insights about patent portfolios and technologies.

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PIUG 2021  THURSDAY  Virtual Meeting

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Identifying the Key Patents in Cancer Immunotherapy with Unique Patent Search Strategy  Dr. Sarbani Chattopadhyay (Consultant, LexisNexis PatentSight)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y A F T E R N O O N 12 : 3 0 P M – 3 : 5 5 P M

Using KNIME for Mining and Combining Scientific and Patent Data for Insights: RNA Examples Anne Marie Clark (CAS IP Services) andMatthewMcBride (CAS) 1:35 – 2:10 pm  ABSTRACT Therapeutic use of RNA is increasing as shown by the recently approved mRNA vaccines and siRNA drugs. Due to the fragility of RNA, these substances are either chemically modified or encapsulated in lipids to protect them. This presentation will demonstrate techniques using CAS® information and KNIME® to analyze siRNA chemical modification patterns, and will demonstrate combining CAS information with DrugBank and FDA data in KNIME for insights into mRNA delivery.  BIOGRAPHIES Anne Marie Clark is a Senior Searcher on the CAS IP Services team. Her particular subject expertise is small molecules, sequences and formulations. She is skilled in patent search, analysis and landscaping. Anne Marie holds a Doctorate in biophysical chemistry from the University of Louisville. Prior to joining CAS, she was a Principal at Long Eaton LLC, where she searched and analyzed patents related to biotechnology and pharmaceuticals. Anne Marie was also an Intellectual Property Manager and Principal Scientist at Bausch & Lomb, and an Information Scientist and Associate Director in Information Management at Pfizer. Anne Marie is a member of the Patent Information Users Group (PIUG®), Licensing Executive Society (LES), Women in Bio, Association for Research in Vision and Ophthalmology (ARVO®), and the American Chemical Society (ACS). Matt McBride is Director IP Search at CAS, where he manages all aspects of IP service development and sales, and works regularly with CAS customers to develop effective strategies for delivering high-quality IP and scientific information. He became a member of the IP Services team in 2010, after spending six years as a Senior Application Specialist providing technical training for the STN and SciFinder software platforms to CAS customers. He holds a Master of Science degree in plant pathology from the University of Minnesota and a Bachelor of Science degree in molecular biology from Purdue University. In addition to his research experience at CAS, Matt was an information consultant with Thomson Reuters and a biologist at Rohm and Haas. Matt is a member of the Patent Information Users Group (PIUG®) and the American Chemical Society (ACS).

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PIUG 2021  THURSDAY  Virtual Meeting

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Using KNIME for Mining and Combining Scientific and Patent Data for Insights: RNA Examples  Anne Marie Clark (CAS IP Services) andMatthewMcBride (CAS)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y A F T E R N O O N 12 : 3 0 P M – 3 : 5 5 P M

USPTO’s Efforts Related to ST.26 Stefanos Karmis and Kathleen Kalafus (United States Patent and Trademark Office) 2:25 – 2:55 pm  ABSTRACT The goal of this presentation is to familiarize patent practitioners with the basics of WIPO ST.26 – the new sequence listing rules that will go into effect worldwide on January 1, 2022. Topics covered will include the benefits of ST.26, differences between ST.25 and ST.26, XML basics, the anatomy of an ST.26 XML sequence listing, and an introduction to the WIPO Sequence authoring tool.  BIOGRAPHIES Stefanos Karmis is the Director of the Office of Patent Quality Assurance (OPQA) where he is responsible for providing reliable and meaningful indicators of patent examination quality to identify quality trends and develop data-driven improvement strategies. Prior to this role, Stefanos served as a Senior Advisor in the Office of the Deputy Commissioner for Patent Quality and the Office of the Deputy Commissioner for Patent Examination Policy. In this role he led several initiatives to improve patent quality and further agency priorities and also engaged with external stakeholders and international offices. Stefanos began his career at the USPTO as a patent examiner in business methods and later became a supervisory patent examiner, managing patent examiners in various mechanical engineering technologies. Stefanos holds a J.D. from The Catholic University of America Columbus School of Law and a B.S. in Industrial and Systems Engineering from Virginia Tech. Kathleen Kalafus is a member of the Scientific and Technical Information Center (STIC) where she provides subject matter expertise in the development of policies and IT systems for the processing and dissemination of biological sequence data. Kathleen has been a member of the USPTO ST.26 Task Force since 2014. In this role, she has worked closely with international partners to develop policies that will benefit IP Offices worldwide, as well as the scientific community. Kathleen began her career as a patent agent in a boutique IP law firm, drafting and prosecuting patent applications for a wide variety of biotech clients, with a particular emphasis on biologics and genetic engineering. Kathleen holds a PhD in Genetics and Molecular Biology from Baylor College of Medicine and a B.S. in Biology from Cornell University.

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PIUG 2021  THURSDAY  Virtual Meeting

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USPTO’s Efforts Related to ST.26  Stefanos Karmis and Kathleen Kalafus (United States Patent and Trademark Office)

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PIUG 2021  BIOTECH DAY  Virtual Meeting

 T H U R S D A Y A F T E R N O O N 12 : 3 0 P M – 3 : 5 5 P M

Panel Discussion: The Challenges and Opportunities of Working Remotely Andrea Davis (Bodkin IP), Rosanna Lindquist (The Hershey Company) and Greg Roland (Novartis) 2:55 – 3:45 pm  BIOGRAPHIES Andrea Davis is an accomplished intellectual property (IP) professional with expertise in medical devices and the mechanical sector. She is a Qualified Patent Information Professional QPIP and a registered patent agent with a M.Sc. degree in Engineering Physics. Andrea’s extensive patent research experience in both in-house, at outside firms and running her own patent search firm has shaped an understanding of patent process requirements and the importance of quality in patent research. She is passionate about the science of patent searching and is participating in efforts to create a global certification for patent information professionals. Andrea is actively involved in Patent Information Users Group (PIUG) and is a co-founder of the international patent searching competition, the Patent Olympiad. Her expertise is also sought by database providers to develop the next generation of tools and analytics with an eye towards accuracy. Rosanna Lindquist is an Information Research Scientist in R&D for the Hershey Company, a global confectionery and snacking company, where she is part of the Technical Intelligence team. Rosanna specializes in technical and patent research with a focus on packaging and design. She is also passionate about business intelligence and enjoys using IP as one of many resources in her arsenal. Rosanna is co-chair of the Patent Office and Partnerships Committee of the Patent Information Users Group (PIUG). She is also an active member of the Special Library Association’s Competitive Intelligence Division. Rosanna holds a Masters in Library & Information Science from Clarion University of Pennsylvania and a BA in Creative Writing from Randolph-Macon Woman’s College. Since November 2014, Greg Roland has been the Global Head of Search and Analytics within the Research and Development IP group at the Novartis Institutes of BioMedical Research leading a team of chemistry and biology information professionals. Greg has 32 years of experience in the pharmaceutical industry spending the last 22 years providing information support to IP and BD&L. Greg started his pharma career in 1990 as a bench scientist at Parke-Davis in Ann Arbor, Michigan as a member of the anti-infective group. After Pfizer acquired Parke-Davis in 2000, Greg managed a team of biomedical, chemistry and CI professionals. In 2005, Greg transitioned to Pfizer’s Patent department as part of the Global Legal Information Science Teammanaging teams at four sites. In August of 2009, he joined Merck’s Knowledge Discovery Knowledge Management group in World Wide Licensing as a Director in Boston. Greg has a B.S and M.S from Eastern Michigan University in Biology.

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PIUG 2021  THURSDAY  Virtual Meeting

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Panel Discussion: The Challenges and Opportunities of Working Remotely  Andrea Davis (Bodkin IP), Rosanna Lindquist (The Hershey Company) and Greg Roland (Novartis)