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The International Society for Patent Information Professionals

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PIUG 2022 Biotechnology Conference

Searching, Analytics, Reporting, and Client Engagement for the Biotechnology Searcher in the 21st Century

Tuesday, March 1, through Wednesday, March 2, 2022

Virtual Conference Only

Join us virtually through the Meeting App via web browser or Smartphone.

Twitter: #PIUG22BIO

Program

Wednesday, March 2, 2022

8:00 am Social Hour (optional start time to 30 mins before  program start)

Morning Session

9:00 am Welcoming Remarks
Greg Roland (Program Chair) Novartis
9:15 am IP Issues in AAV Gene Therapy (Keynote Speaker )
Adam Poulin-Kerstien Dyno Therapeutics, Inc
10:00 am

Vaccines and Vaccine Technologies: Search Strategies & Criteria
Luca Falciola Scibilis Consulting Services

10:30 am

Product Reviews and Questions
BizInt

10:45 am

Break

10:55 am Biotech Competitive Intelligence Using Patent Information
Ron Kaminecki Kaminecki IP LLC
11:25 am The Story of a Comprehensive siRNA Search
Anne Marie Clark and Matthew McBride CAS IP Services
11:55 am

Product Reviews and Questions: Aptean and Patsnap

12:15 am

Lunch

 

Afternoon Session

12:45 pm Convergence, Complexity & Connected Data: The Importance of Combining Human and AI-Driven Search Strategies
Sam Winders  PatSnap
1:15 pm Searching Patents for Biology-Related Information: Sequences, Biomarkers, Genes, Proteins, Peptides and Their Relationships and Applications Using Natural Language Processing (NLP)
Lutz Weber OntoChem GmbH
1:45 pm Powering Up Your Patent Search with Dimensions
Sofia Andreeva Digital Science
2:15 pm Break
2:25 pm Patent Searching Strategy
Julie Wu United States Patent and Trademark Office (USPTO)
2:55 pm The Future of Sequence Listing: WIPO ST.26
Wongel Tefera Zoetis
3:25 pm

Sequences Processing and Searching at the USPTO
Christopher Babic United States Patent and Trademark Office (USPTO)

3:55 pm Closing Remarks
4:00 pm Social Hour

Please note: This information is subject to change, due to circumstances beyond our control.

Meeting Abstracts

Top of Page
IP Issues in AAV Gene Therapy (Keynote Speaker )
Adam Poulin-Kerstien Dyno Therapeutics, Inc

Abstract

Adeno-associated virus (AAV)-based gene therapies have become one of the most prevalent forms of gene therapy in the last decade, and increasing numbers of AAV-based gene therapies. The intensifying interest in the field, coupled with the multicomponent nature of these products (e.g., capsid, vector backbone, promoter, genetic payload, etc.) makes navigating the IP landscape challenging. This talk will provide a brief overview of AAV-based gene therapy and address some of the issues facing patent and patent analytics practitioners when assessing internal patent filing opportunities and freedom-to-operate. Recent applications of machine learning and artificial intelligence to help address some of these challenges will also be discussed.

Biography

Adam is an experienced leader and intellectual property attorney with a scientific background in biology and chemistry, and is currently Vice President and Head of Intellectual Property at Dyno Therapeutics. Dyno is a pioneer in applying artificial intelligence/machine learning with quantitative high-throughput in vivo experimentation to design new gene therapies. Prior to joining Dyno, Adam worked for the Novartis Institutes for Biomedical Research where he led and coordinated IP support for Novartis’ respiratory disease and neuroscience research and development programs. Adam graduated from Amherst College with a BA in Chemistry before earning his PhD from Caltech and JD from UCLA School of Law.

Top of Page
Vaccines and Vaccine Technologies: Search Strategies & Criteria
Luca Falciola Scibilis Consulting Services

Abstract

The Covid-19 pandemic has highlighted the global, strategic importance of vaccine technologies that may be exploited for promptly establishing and supplying hundreds of millions of doses worldwide. Vaccines are based on quite similar and publicly available molecular information (immunogenic elements of a virus) but, in order to raise the desired protective response, they are produced and administered using a variety of structurally complex products (in the form of virus-like particles, inactivated viruses, liposomes, virus-based vectors, etc.). The search and analysis of patent information related to such diversified compositions is challenging, with relevant chemical or biological criteria applicable to the elements within vaccines to be attentively selected and combined according to the different manufacturing and administration platforms. The presentation will provide with some guidance for establishing search strategies and analyzing the patent situation for vaccines that are based on distinct technologies, using the patent production related to Covid-19 as case study.

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.

Top of Page
Biotech Competitive Intelligence Using Patent Information
Ron Kaminecki Kaminecki IP LLC

Abstract

Much has been written about competitive intelligence in various industries, but amongst the most competitive areas is the biotechnology market. Patents play a major role in determining who the players are, what is their expertise and possibly, what they are looking at for future development. With the long lead times that many biotech companies have with respect to creating new drugs, diagnostics, vaccines and treatments, and the speed at which they apply their expertise towards developing new products, it is important to look at how intellectual property information can help companies protect their investments, but also point out new products and the companies that develop what may be the next successful product. Patent research may show how the traditional competitors line up and what they focus on – or perhaps downplay – to focus on where the major players are going to be.

Biography

Ron has been involved with technical and patent information beginning with his work at IIT Research Institute and has continued at different information-intensive companies including Dialog, Knight Ridder Information, Thomson Reuters, ProQuest and Questel and was also Manager of Patent Information at Abbott Laboratories. He currently teaches patent searching at the University of New Hampshire Law School and DePaul Law School, both online and in-person. He is a patent attorney with a BS in Chemistry, an MS in Computer Science and a JD with a Certificate in Patent Law and is also a Qualified Patent Information Professional. He is an inventor, a co-author of a NISO standard for an online search language and has worked as an expert witness. He also serves on various boards and committees in the patent community, and on urban preservation and natural recreational concerns.

Top of Page
The Story of a Comprehensive siRNA Search
Anne Marie Clark and Matthew McBride CAS IP Services

Abstract

Searching siRNA comprehensively requires multiple strategies, search tools and techniques. A typical patent and/or literature search for a particular siRNA sequence against a specific target would begin with a sequence search using the RNA sequence, followed by a keyword search for the target of interest and siRNA keywords, followed by a chemical structure/term search for chemical modifications and ligands. The presentation will cover all aspects of a comprehensive (and well-told) RNA search, including analysis and visualization approaches - and prepare you to tell your own story.

Biographies

Anne Marie 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 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).

Top of Page
Convergence, Complexity & Connected Data: The Importance of Combining Human and AI-Driven Search Strategies
Sam Winders  PatSnap

Abstract

The rate of innovation is accelerating, and in no field more rapidly than the life sciences as the “biological century” gathers apace. In the same way as a comprehensive search must often draw upon both human curated and artificial intelligence (AI) indexed datasets, efficiently extracting the right results requires combining AI and manual search strategies. In this paper, we showcase how human and AI can work “hand in glove” to achieve the best results across life sciences fields that require accurate but fast search and extraction, such as Antibody Drug Conjugates, AI-driven drug discovery and digital health initiatives. We will show that, rather than a Terminator-esque scenario of a bitter contest between man and AI, we will instead see the modern patent information professional as the Ironman of IP, empowered by cutting-edge technology that augments and synergizes with their expertise.

Biography

Sam Winders is lead representative for PatSnap Life Sciences Europe and one of the company’s longest serving employees. Sam marries his interests in patent information and Artificial Intelligence with his previous experience in academia, where he focused on theory of knowledge and the structure of human language, culture and thought.

Top of Page
Searching Patents for Biology-Related Information: Sequences, Biomarkers, Genes, Proteins, Peptides and Their Relationships and Applications Using Natural Language Processing (NLP)
Lutz Weber OntoChem GmbH

Abstract

Semantic concept based search has become an interesting alternative to traditional searches using patent classes [1]. Thus, the full text of patents is annotated and indexed using very large gene, proteins and peptide ontologies containing about 950.000 different concepts with more than 2.5 million synonyms that are used by biologists to describe those entities of interest in text documents and in databases. OntoChem’s ontology is created by condensing information from MeSH, GO, PO ontologies as well as databases like Brenda, Swissprot, Entrez, Interpro, HUGO and Homologene. In a similar way, we integrated a novel Biomarker ontology resulting in 32 million searchable biomarker data points as well as therapeutic antibodies in development and on the market. Our OC|processor UIMA based NLP technology is then used to index the full text of about 70 million patents using these ontologies. Search engines using these semantic annotations are Google’s patent search, Digital Sciences Dimensions LC applications, as well as our customizable search platform SciWalker. Biological sequences such as oligonucleotide or protein and peptide sequences are extracted from USPTO CWU SEQ files. Also, extraction of nucleotide and amino acid sequences by OCR from images and full text has been tested and results will be presented for WIPO and EPO patent documents. Sequences and related patents can then be searched using a NIH Blast server in the background. Moreover, we extract relationships between those entities and their use as potential biomarkers for specific diseases. As a result, we may ask higher level semantic questions such as “What are hot target classes in most recent applications?”. “Which serine proteases are claimed as potential biomarkers for cancer?”. “Which targets and sequences are associated with interstitial pulmonary fibrosis?” Results may be exported on a large scale for further data analytics and processing. In the talk we will demonstrate sequence searching for Sars-Cov-2 Mpro related patents and other show cases. [1] L Weber, T Böhme, M Irmer, Ontology-based content analysis of US patent applications from 2001–2010, Pharmaceutical patent analyst 2013, (2), 30-54.

Biography

Dr. Weber has studied chemistry and pharmacy in Budapest, Hungary, and received its PhD and habilitation from the University of Leipzig, Germany. He has over 24 years of industrial research experience in pharmaceutical chemistry, chemoinformatics, drug discovery and development. Dr. Weber is a university lecturer, has held various scientific and managerial positions at Hoffman-La Roche in Basel Switzerland. Dr. Weber has been co-founder of biotech startups Morphochem AG, Alphaptose GmbH, OntoChem GmbH and MolGenie GmbH in Germany as well as NexusPharma Inc. in the U.S.A. He has been a recipient of two European Union research grants and several German government research grants. Dr. Weber is the author of over 100 scientific papers, book chapters and reviews. Dr. Weber’s experience includes the direction of several early drug discovery projects that led to the identification of new small molecules as drug candidates and moving four projects into clinical development.

Top of Page
Powering Up Your Patent Search with Dimensions
Sofia Andreeva Digital Science

Abstract

Research is being published at an unprecedented rate, and the translation of this research into practical solutions is booming. Capturing the most up to date patent and research information is more important than ever, but how do you keep on top of your search for and analysis of this wealth of knowledge to best inform your strategy when there are so many documents to wade through? At Dimensions Life Science & Chemistry we apply the latest semantic analysis tools and ontologies to over 120 million scientific publications, millions of patents, grants, and clinical trial documents, to create a unique tool for scientists that offers powerful discovery functionality on a game-changing new scale. You can quickly use Dimensions to develop your knowledge of a variety of possible applications and use-cases across life sciences and chemistry, from pharma drug development to materials chemistry. Thanks to the artificial intelligence powering our platform, we are making searching for research information quicker, easier and more comprehensive than ever before. We look forward to sharing some examples of this with you.

Biography

Sofia is an ex-scientist, who graduated with honours from Lomonosov Moscow State University where she got her Master of Science in Biochemical Physics. After her short career in a “wet lab” and a Russian pharmaceutical company, Sofia joined Thomson Reuters (now Clarivate) as a Science Research Analyst back in the start of 2012. In her role, Sofia was a part of the scientific database content team responsible for the creation and maintenance of molecular interactions and signalling pathways content from scientific literature. She also was involved in Discovery and Translational Science Service projects supporting Bioinformatician and Knowledge Curation teams with custom molecular signalling pathways & networks creation, OMICs data analysis, and disease mechanisms reconstruction. In 2017 Sofia moved to the Solutions Scientist team where her focus was on searching for solutions to address customers’ needs in early drug and biomarker discovery & preclinical research. Later she expanded her expertise into the commercial aspect of drug development. She joined Digital Science at the start of 2021 as a Product Solutions Manager and currently supports Digital Science’s customers to accelerate their drug development process and reach their goals faster through the integration of Digital Science’s content, technology and experts.

Top of Page
Patent Searching Strategy
Julie Wu United States Patent and Trademark Office (USPTO)

Abstract

Searching is an integral part of patent examination to ensure that issued patents are directed to claims that are clear, enabling, and free of prior art. Based on the broadest reasonable interpretation of the claims, Examiners design search strategies to search multiple non-patent and patent literature databases for prior art. Text and classification searches are routinely performed, and sequence and structure searches are also performed when needed. Examiners also use their scientific expertise to determine if every aspect of the claim is searched. The Information Disclosure Statement (IDS) is also thoroughly reviewed to learn about the state of the art for the claimed technology and to identify potential prior art. Overall, every application is thoroughly searched by examiners prior to allowance of an application.

Biography

Julie Wu received her BS in Pharmacology from SUNY Stony Brook in 1999, Ph.D. in Pharmacology from Yale University in 2004, and completed her postdoctoral training at the National Institutes of Health (NIH). She joined the USPTO in 2012 as a patent examiner, where she examined patent applications on immunotherapy for cancer, recombinant antibody, and CRISPR gene editing. In 2019, she was promoted to Supervisory Patent Examiner in the technology area of immunotherapy for cancer and recombinant antibody.

Top of Page
The Future of Sequence Listing: WIPO ST.26
Wongel Tefera Zoetis

Abstract

Currently genetic sequences are submitted to patent offices using WIPO Standard 25 (WIPO ST.25). In the near future sequences will be listed using ST.26 standard. The advancement in number and complexity of biological sequences disclosed in patents required a change in the way sequences are listed. The idea of a new standard has been contemplated for many years. Then a little over ten years ago, a Task Force was formed with EPO as a leader to work out the details. One of the goals of the task force was to develop a system that is universal and flexible to enable worldwide listing compliance. In this presentation, I will attempt to show the advantages of ST.26, some of the major differences between ST.25 and ST. 26 and possible implementation timeline of ST.26.

Biography

Wongel Tefera is a senior manager in the IP Department at Zoetis Inc. Wongel joined Zoetis when it was formed via a spin-off from Pfizer in 2013. Prior to Zoetis, Wongel worked at Pfizer and its legacy companies as a patent searcher as well as in research laboratory for over 15 years. In her current role Wongel, performs patent searches, assists in patent term extension filings, and competitor analysis. Wongel is a registered US patent agent. Wongel is a member of PIUG and volunteers in Member Relation Committee and Partnerships and Patent Offices Committee.

Top of Page
Sequences Processing and Searching at the USPTO
Christopher Babic United States Patent and Trademark Office (USPTO)

Abstract

In the ever evolving world of biotechnology, protection of proprietary biological sequences remains critically important to inventors. Strong patent protection for biological sequences depends on robust and accurate surveying of relevant prior art. With increasing complexity of sequence structure, and rapid growth of database volume, effective and efficient search strategies must be employed.   The United States Patent and Trademark Office (USPTO) provides its patent examiners and contractors with an array internal and external resources to perform extensive prior art searches of claims that recite specific biological sequences. These resources include a USPTO-maintained database that catalogues all sequence listings that accompany any filed utility application. Examiners and contractors use this database as a primary tool for their analysis. This database may be searched using a variety of parameters that can help the examiner make efficient use of their time. Turning claim language into effective search requests is a critical part of the examination process.

Biography

Chris joined the USPTO in 2005, and currently serves as a Supervisory Patent Examiner (SPE) within Technology Center 1600. He is a point of contact and subject matter expert for biological sequence matters. Before becoming a SPE, Chris was a primary patent examiner in the nucleic acid arts. He has a B.S. in Biochemistry and Molecular Biology, a M.S. in Biotechnology from the Pennsylvania State University, and J.D. from the George Mason Antonin Scalia Law School. 

 

 

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