PIUG 2009 Boston Biotechnology Meeting

Sequence Searching and Beyond:
Build a Better Searcher, Build a Better Search

Program

Meeting Abstracts

Session I

"Please Come to Boston... for the Patent Searching?"
Elyse Turner, Merck & Co., Inc.
8:40-9:00am

For two years locals and not-so-locals have braved the cold of February to gather in Boston and discuss patent searching in the area of biotechnology. What have we learned from this? Haven’t we covered everything? What new challenges do the brave need to face?

Elyse D. Robinson Turner
Manager, Patent Information Legal Affairs
Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065
Ph: 732-594-6418
elyse_turner @ merck.com

Elyse Turner is a founding member of PIUG and one of the members who originated the local meeting in the northeast. She helped establish the Boston Biotechnology Meeting and has served as Chair of the Program Committee for all three years of its existence. She also serves as Chair of the Vendor and Producer Committee. She served as PIUG Secretary, Vice-Chair, Chair, and Past Chair. She chaired the Bylaws Committee, the Electronic Communications Committee, PIUG Webmaster and currently acts as Board Liaison to the Vendor/Producer Committee. She led the planning for the 2001, 2002 and 2003 PIUG NE and for the PIUG 2003 and 2004 Annual Conferences. Elyse served on the Questel-Orbit Advisory Council 1996-2004. She has been searching patents at Merck & Co., Inc since 1987. Before joining Merck, she was an intern at Bell Laboratories while completing her MLS at Rutgers University. She has been a member of SLA since 1985. She received her undergraduate degree in Biological Sciences from the University of Chicago.

"Sequence Searches – The Evalueserve Way"
Amit Kumar Goyal, Evalueserve
9:00-10:00am

A sequence search, like any other patent search, is affected a lot by the end analysis we wish to perform using its results. The presentation will walk through a typical search request received by Evalueserve, questions we ask our requesters to frame our searches, selection of databases, searching, combining results from multiple data sources, removing duplicates, and analysis of search results. We will conclude with the various methods used for the presentation of results to our clients.

Amit Kumar Goyal, Manager
Intellectual Property Research III
Evalueserve
CyberPark, 2nd Floor
Jharsa, Sector 39, Gurgaon – 122002

+91-124-462-2801 (Office)
+91-981-023-5592 (Mobile)
amit.goyal @ evalueserve.com

Amit is currently working as a Manager in the Lifesciences Intellectual Property Group of Evalueserve. He has been instrumental in expanding the sequence search capabilities by identifying new technologies and tools.

Evalueserve is a full service intellectual property firm, offering customized solutions to companies around the world. With a highly competent and large workforce of over 250 IP professionals, it can work across all industry verticals in multiple languages. Evalueserve IP associates have a vast experience in patent drafting, prior art searches, technical research, patent landscape analysis, overlap analysis and licensing and patent valuation. Evalueserve's IP group has conducted over 2,000 sequence search projects.

"Sequence Searching in Biotechnology"
Patrick Kools, European Patent Office
10:00-10:30am

Biotech specific sequence searches at the EPO A substantial part of Biotech applications claim protein and DNA sequences requiring computerized sequence searches. Additionally, specific uses of such sequences can be searched using the same tools. Hence, for an EPO Biotech examiner, good sequence searching tools are of major importance. Public domain sequence search engines are powerful and fast, however, the EPO uses different tools or access points to retrieve valuable information. In collaboration with EBI at Hinxton (UK) a suitable integrated system of search programs, databases and display of obtained results was created. The seminar will review the tools used for effectively searching DNA and protein sequences, or their (back-)translations and fragments. Evaluation of the obtained results in view of the wording of the claims will be the centre of the seminar. The formal aspects of a sequence listing and the effects of using sequence accession numbers will be discussed.

Patrick Kools
Examiner Directorate 1212 | Dir. 1.2.1.2
European Patent Office
Patentlaan 2 2288 EE
The Hague
The Netherlands

Tel. +31 (0)70 340 1964
pkools @ epo.org
http://www.epo.org

Patrick Kools joined the EPO in 2001 with a PhD in biomedical sciences from the University of Leuven and having worked as a PostDoc at the department for molecular biology (University of Ghent). At the EPO/The Hague he is considered as a specialist in DNA and protein sequence searches. He has given presentations on this subject in various national patent offices and during a Search matters session at the EPO. As a patent examiner he is involved in all aspects of the procedure, and in training colleagues.

"Search Strategies for Delivering Comprehensive Results from Your Antibody Searching"
Dr. Kamalakar Gulukota, GenomeQuest
11:00-11:25am

We will discuss the inherent challenges in Antibody patent searching and various strategies for delivering the most comprehensive results. Then, once the results are populated, demonstrate how you can quickly manipulate this information to answer questions about the competitive landscape, and make "fail early" decisions. Finally, generate a report on your findings, all using the GenomeQuest platform.

Dr. Kamalakar Gulukota, Senior Product Evangelist
GenomeQuest
508-616-0100
kamalakar.gulukota @ genomequest.com

Prior to joining GenomeQuest, Dr Gulukota built and directed the Clinical Research division at GVK Biosciences in India and prior to that directed the Bioinformatics Core Sciences group for Wyeth in Cambridge, MA. With rich experience in drug discovery and development as well as computational biology, Dr Gulukota brings a unique vision and direction for shaping GenomeQuest's content strategy for GenomeQuest.

“Exploring Patent Data at the EBI"
Jennifer McDowall, EMBL-EBI
11:25-11:55am

EBI (European Bioinformatics Institute) catalogues DNA and RNA sequence data in the EMBL database (>137 million entries), the main sources of which are submissions from individual researchers, genome sequencing projects and patent applications. The EMBL database contains sequence data from all four major patent offices: USPTO, EPO, JPO and KIPO. Patent offices submit sequences to their local INSDC node (EPO to EMBL, USPTO to GenBank and JPO/KIPO to DDBJ), however (all) nucleotide sequence data is then exchanged daily between EMBL, GenBank and DDBJ, so users are assured of accessing complete data sets regardless of where they perform their search. Protein sequence data from EPO is also loaded into the EMBL database; however patent protein data in GenBank/DDBJ go straight into SRS (Sequence Retrieval System) at EBI. The EMBL Version Sequence Archive catalogues all entries that have ever appeared in EMBL - a valuable resource for determining when a particular sequence became available in the public domain.

Patent sequence data generally has low quality annotation, but EBI does address some of the problems encountered. EBI helps correct EPO data by providing quality checks and fixing taxonomy. However, EBI can only inform GenBank or DDBJ when problems arise with USPTO, JPO or KIPO data. The information associated with a patent is accessible within an EMBL database entry, the DE line holding the patent number, and the reference block holding the patent number, sequence number, application details and the patent title. Links within the database provide direct access to the patent itself. Entries are rarely removed from EMBL; if there is an error, then the entry is replaced, not removed. However, there can be duplicate entries arising from changes in sequence numbers as the patent progresses through its various stages. Different sequences with the same sequence number can also occur.

The UniParc database (>17 million entries), the most comprehensive protein sequence database available, also archives data from USPTO, EPO, JPO and KIPO, in addition to protein sequences from (translated) EMBL, Ensembl, RefSeq, TROME, IPI, PIR-PSD, PDB and several model organism databases. UniParc provides a permanent, non-redundant record of every protein sequence. Each entry has a unique identifier (UPI), source database identifiers, source sequence identifiers, source database sequence versions, and a UniParc sequence version. UniParc entries are never deleted, even if the sequence itself becomes deleted from the source database(s). UniParc also provides direct links to original patent references. Several specialised EBI databases can provide valuable annotation for these sequences.

The sequence searches that EBI provides for EPO are also available to the public (e.g. SRS, FASTA, Patent Proteins, Patent DNA, etc.). However, the key to a good search often lies in knowing which database to search (smaller is better), using taxonomy exclusion to decrease database size, how to retrieve dates associated with sequences, which search engine to use when, and how to manipulate search parameters (such as filters, gap penalties and scores) to improve results

Jennifer McDowall
EMBL-EBI Wellcome Trust
Genome Campus
Hinxton, Cambridge, CB10 1SD
United Kingdom

jennifer @ ebi.ac.uk

Jennifer McDowall gained her PhD in Medical Genetics at UBC in Canada. She held a faculty position at Open University, as well as research positions in the pharmaceutical industry and academia, including working on the Human Genome Project. She currently works on the InterPro database at the EBI, which provides open-access bioinformatics databases and services to the scientific community.

Session II

"EPO Examiner Doing (its) BEST"
Wolfram Meyer, European Patent Office
1:00-1:25pm

The European Patent Office (EPO) has been in operation for over thirty years. In it's early days a search would be conducted by a search examiner for any prior art that was relevant to the application and the results were notified to the Applicant in a search report, indicating in what respect the documents cited were relevant (novelty, inventive step , background) and to what claims they were relevant. In a second stage, and on request by the Applicant, a substantive examination would be performed by a different person, the so-called substantive examiner. Examination is the process by which a patent office determines whether a patent application meets the requirements for granting a patent . This includes considering whether the invention is novel and inventive , whether the invention is in an excluded area and whether the application complies with the various formalities of the relevant patent law. Over the last ten years the EPO has implemented a procedure called BEST (Bringing Examination and Search Together), whereby the search examiners are is also the first substantive examiners in the examining division. For increased efficiency in the overall grant procedure, a BEST examiner prepares, already at the search stage, a written opinion about the patentability of the invention claimed. As a new service provided by the EPO, this written opinion is sent in parallel with the search report.

This change has a huge implication in the strategy of searching an application. Already in the beginning of the search the examiner will also include in his search strategy the legal framework of the application. The searcher can do a better a job if they understand how the examination will be carried out later.

Within the context of biotechnological applications this has major consequences for users of the system as the prior art needs to be fit not only for immediate consideration of novelty and inventive step but also for future consideration of other legal requirements (clarity, morality, excluded matter etc) during subsequent examination.
In this talk the presenter will briefly outline the historical journey of the EPOs former procedure towards the BEST procedure. He will emphasise the concrete consequences for users within the area of biotechnology.

Wolfram Meyer
EPO
Germany
Tel. 0049 89 2399 8187
wmeyer @ epo.org

Wolfram Meyer made his PhD at the Basel Institute for Immunology Hoffmann LaRoche and a PostDoc study at the Suisse Cancer Institute in Lausanne. The lecturer joined the EPO in 1998, he thereby went through several professional career steps, like e.g. patent examiner, with all its facet's (search, examination and opposition) coach, teacher and project leader of different projects for the European Patent Office. Wolfram is based in Munich.

“From Concept to Content: The Genesis of USGENE"
Martin Goffman, SequenceBase Corporation (presenter)
Robert Austin, FIZ Karlsruhe (co-author)
1:25-1:50pm

Information professionals are always in need of new tools and databases to help them do their jobs faster, better, and at less cost to their employer. As described in a recent edition of ONLINE magazine (PDF), USGENE was created to help meet this need for patent sequence searchers by providing a unified, timely and comprehensive USPTO patent sequence database.

This talk will focus on the genesis of the USGENE database from initial concept, launch on STN and subsequent evolution into an in-house subscription database. We will focus on origins of the idea as well as the “why” of creating a new genetic sequence database. We will then discuss the steps in making the decision to go ahead with the project. Details of the content and utility of USGENE will be explored as well as pointing out how USGENE compares to other data sources. Some examples of the unique retrieval of USGENE will be shown too.

Martin Goffman, Ph.D., President and CEO
SequenceBase Corporation
3 Dellview Drive
Edison, NJ 08820-2545
USA

Tel: +(732) 549-5433
mgoffman @ sequencebase.com
http://www.sequencebase.com

In 2006, Martin Goffman founded the SequenceBase Corporation (www.sequencebase.com), the organization that produces the USPTO Genetic Sequence Database, USGENE®. USGENE® is currently hosted on STN and is also available on a subscription basis. The database is the leader in providing patent sequence information to the biotechnology, legal, pharmaceutical, scientific, technical and academic bioinformatics communities.

Prior to founding SequenceBase, since 1985, Martin Goffman has been the owner and principal consultant of Martin Goffman Associates (www.goffman.com), a privately held research, development, and consulting organization. His company has a consulting base ranging from extremely large multinational corporations featured in the Fortune Magazine Top 10 to mid-sized corporations in the Fortune 500. His firm also consults with many of the top intellectual property firms in the country. The company has won research awards from the National Science Foundation, the Department of Defense, and the National Institutes of Health. Prior to starting his consulting practice Martin worked in industry. Martin has a BA, MA, and Ph.D. in Chemistry with a Physics Minor from Temple University.

He is also a co-founder and CEO of StockPricePredictor.com, LLC (www.patentvaluepredictor.com), a web based patent valuation service.

Robert Austin
FIZ Karlsruhe
Tel: +1 609 333 1466
Robert.Austin @ FIZ-K.com

Robert Austin has been the U.S. representative for FIZ Karlsruhe, the European partner of the Scientific and Technical Information Network (STN), since January 2001. In this role he specializes in technical training for STN patent databases throughout the United States, including the Derwent World Patents Index, USGENE, DGENE and INPADOCDB. Prior to working for FIZ Karlsruhe he worked for 9 years at Derwent Information Ltd (now Thomson Scientific) in the United Kingdom consecutively in three roles: Pharmaceutical Patent Indexer, European Customer Trainer, and Product Manager for Derwent World Patents Index on Dialog, Questel.Orbit and STN. He graduated from Huddersfield University (UK) with a bachelors degree in Applied Chemistry in 1991, and has been searching and teaching STN since 1996.

“Historical Changes in GENESEQ Indexing and Coverage of Emerging Nations"
Colin Williams, ThomsonReuters
1:50-2:15pm

In this presentation I will discuss the evolution of the GENESEQ file, how and when indexing and coverage policies changed and the potential implications for those searching the file. This presentation will also touch on coverage of patents from geographies where biosimilar development and manufacturing is growing.

Colin Williams
Thomson Reuters
77 Hatton Garden
London, UK EC1N 8JS
+44 (0)207 433 4843
colin.williams @ thomsonreuters.com

Colin Williams is the Product Manager for Biology and Bioinformatics. He has a degree in Biochemistry and PhD in X-ray Crystallography both from the University of Sheffield. After some brief post doctoral work he then moved to ASM Scientific, a start-up biotechnology company in Cambridge UK. Here, as part of a team of three, he developed a novel isothermal DNA amplification technology for use in point of care pathogen detection and contributed towards patent applications for the technology. Following this Colin joined Thomson Reuters as Editorial and Content Manager for GENESEQ in November 2005. He was responsible for optimizing production in terms of timeliness and quality, but also examining potential content changes and additions to the product. In June 2007 Colin moved into his current role where he is responsible for developing solutions for Biologists and those working with this information.

"Wikid Cool: Geneticists Working IT on the Interactive Internet"
Kristine H. Atkinson, Boston Scientific Corporation
2:15-2:30 pm

Interactive computer technology combined with modern electronic social networking has spawned novel ways to communicate and to publish data. The rise of wikis and shared public sites has unraveled the familiarity of indexed libraries and structured databases. We will explore special-interest genetics wikis that serve as platforms for education, expert information sharing, political action, IT problem-solving, data banking and genetic registries. Communal content administration and the ease of posting expert knowledge create a challenge for information professionals having a duty to be thorough and to uncover publicly available prior art.

Kristine H. Atkinson, Intellectual Property Researcher
Legal Department
Boston Scientific Corporation
One Boston Scientific Place
Natick, MA 01760
USA
508-652-5260
atkinsok @ bsci.com

Kris Atkinson’s doctoral thesis in genetics was a treatise on proteomic and karyotype speciation in a family cluster driven by continental drift and host/parasite coevolution. She also holds a master’s in cell biology, a bachelor’s in foreign languages, and has enjoyed incarnations as a protein chemistry laboratory director, electron microscopist, biomanufacturing trainer, research analyst, medical editor, biotech device and vaccine inventor, and discovery paralegal. She is a registered patent agent and specializes in patentability, freedom-to-operate and technology landscape searches. She has served on the Newsletter Committee of PIUG since 2005, and cochairs the Training Working Group of the PIUG Education and Training Task Force.

“Coverage of Asian authorities in Ppatent Sequence Databases"
Robert Austin FIZ Karlsruhe
3:00-3:25pm

Asian coverage is of great importance to many searchers of patent information, including those who wish to conduct comprehensive patent sequence searches. The author will provide a review of the coverage of Asian patent authorities in key patent sequence databases, including NCBI Genbank, Thomson Reuters GENESEQ and CAS REGISTRY. Differences and synergies between the resources will be demonstrated via the results of BLAST search examples.

Robert Austin
FIZ Karlsruhe
Tel: +1 609 333 1466
Robert.Austin @ FIZ-K.com

Robert Austin has been the U.S. representative for FIZ Karlsruhe, the European partner of the Scientific and Technical Information Network (STN), since January 2001. In this role he specializes in technical training for STN patent databases throughout the United States, including the Derwent World Patents Index, USGENE, DGENE and INPADOCDB. Prior to working for FIZ Karlsruhe he worked for 9 years at Derwent Information Ltd (now Thomson Scientific) in the United Kingdom consecutively in three roles: Pharmaceutical Patent Indexer, European Customer Trainer, and Product Manager for Derwent World Patents Index on Dialog, Questel.Orbit and STN. He graduated from Huddersfield University (UK) with a bachelors degree in Applied Chemistry in 1991, and has been searching and teaching STN since 1996.

"Biosimilars: Market, Patents, & Patent Search"
Sunny Wang, sanofi aventis"
3:25-3:50pm

The potential opportunity for Biosimilar drugs continues to attract huge interest and controversy. Lately, news has been reported not only on legislation, but also on more involvement in biosimilars from top pharmaceutical and generic drug companies. The successful company in this field will be those with the resources and preparation in order to position themselves well to gain in the future. So what are biosimilars? What are the legal and technological differences between biosimilars and small molecule generic drugs? Finally, what are the considerations for biosimilars in terms of patentability and patent searching? An example on biosimilar patent search is given here.

Sunny Wang, Patent Agent & Head
Patent Search Group
US Patent Department
sanofi-aventis
Phone: 908-231-3648
Fax: 908-231-4766
Email: sunny.wang @ sanofi-aventis.com

Sunny Wang, Head of Patent Search Group, US Patent, sanofi-aventis, is an information specialist and an US PTO registered patent agent (admitted in 2003). She has more than eight years experience in biotech search and analysis covering all aspects of patent information search, e.g., Freedom-to-Operate, Patentability, and other scientific or legal information searches. Prior to being an information specialist and patent agent, she was a highly productive molecular biology bench scientist with over fifteen peer-reviewed scientific papers and book chapters published as first author or co-author. Graduated from the University of North Carolina at Chapel Hill with a Master degree in Biological Chemistry, she had worked for Amgen for six years before joining the predecessor company of sanofi-aventis.

Concluding Remarks
Elyse Turner, Merck & Co., Inc.
3:50-4:00pm

Elyse D. Robinson Turner
Manager, Patent Information Legal Affairs
Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065
Ph: 732-594-6418
elyse_turner @ merck.com

Elyse Turner is a founding member of PIUG and one of the members who originated the local meeting in the northeast. She helped establish the Boston Biotechnology Meeting and has served as Chair of the Program Committee for all three years of its existence. She also serves as Chair of the Vendor and Producer Committee. She served as PIUG Secretary, Vice-Chair, Chair, and Past Chair. She chaired the Bylaws Committee, the Electronic Communications Committee, PIUG Webmaster and currently acts as Board Liaison to the Vendor/Producer Committee. She led the planning for the 2001, 2002 and 2003 PIUG NE and for the PIUG 2003 and 2004 Annual Conferences. Elyse served on the Questel-Orbit Advisory Council 1996-2004. She has been searching patents at Merck & Co., Inc since 1987. Before joining Merck, she was an intern at Bell Laboratories while completing her MLS at Rutgers University. She has been a member of SLA since 1985. She received her undergraduate degree in Biological Sciences from the University of Chicago.

Panel Discussion
4:00-4:30pm