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PIUG 2008 Boston Biotechnology Meeting

Overview | Program | Conference Materials (members only) | Accommodations | Dining | Travel | Workshops

Thursday, February 14, 2008
8:00 AM - 5:00 PM

Genzyme Corporation
500 Kendall Street
Cambridge, MA 02142
+1 (617) 252-7500

Final Program

Presentations (Members Only)
8:00 am
Breakfast & Registration

Session I: Searchers in the Field
Chair: Elyse Turner

8:30 am
Preamble to Searching, Elyse Turner, Merck & Co., Inc.
9:00 am
Sequence Searching at the European Patent Office, Bernard Piret, European Patent Office (EPO)
9:35 am
(The Automated Biotech Sequence Search System, ABSS, System Reviewed) Paula Sheppard, Scientific and Technical Information Center (STIC), United States Patent and Trademark Office (USPT0)
10:00 am
10:25 am
10:55 am
11:20 am
Searching Biotech Devices: The Proficient Trapping of Boojums, Kristine H. Atkinson, Boston Scientific Corporation
11:45 am
12:10 pm

Session II: Details on Databases and Strategies for Searching
Chair: Rick Williams

1:20 pm
GENESEQ - Status and New Content Update, Colin Williams, Thomson Scientific
1:45 pm
2:10 pm
Ensuring a Thorough Sequence Patent Search, Dr. Kamalakar Gulukota, GenomeQuest Inc.
2:35 pm

The Good, The Bad and The Ugly - The Truth about Sequence Listing Submissions and Consequences for Comprehensive IP Searching, James A. Coburn, Harbor Consulting IP Services, Inc.

3:00 pm
3:30 pm

The SECOND Most Obvious Places to Search Sequences, Don Walter and Brian Larner , Thomson Scientific

3:55 pm

Structure Searching for Small Sequences in the CAS REGISTRYSM File, Lora Burgess, Chemical Abstracts Service (CAS)

4:25 pm

Synergies and Surprises - USGENE and DGENE Multifile Patent Sequence Searching on STN, Rob Austin, FIZ Karlsruhe Inc.

4:45 pm
Putting It All Together, Elyse Turner, Merck & Co., Inc.
5:00 pm

Meeting Abstracts

Session I: Searchers in the Field

"Preamble to Searching"top of page
Elyse Turner, Merck & Co., Inc.

On a cold day in February 2007, a crowd of 50 gathered at Amgen to discuss sequence searching. Why have this meeting? How to approach the content? What is the meeting going to include? The discussion will continue with a crowd double the size and expand into other areas of biotechnology and biopharma.

Elyse D. Robinson Turner
Manager, Patent Information Patent Department
Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065 732-594-6418

Elyse Turner is a founding member of PIUG and one of the members who originated the local meeting in the northeast. She wrote the original constitution and bylaws for PIUG and chaired the Bylaws Committee. She served as PIUG Secretary 1994-1996, PIUG Vice-Chair 2002-2004, PIUG Chair 2004-2006 and currently serves as PIUG Past Chair 2006-2008. The Electronic Communications committee was established by Elyse. She initiated and maintained the PIUG/PATMG DIALMAIL Bulletin Board then worked with Sandra Unger and Derwent to migrate and maintain communications on an internet discussion list sponsored by Derwent. She also worked with Sharon Peterson to create the PIUG web pages and with Tommy Ebe for CAS to provide the server for the web pages. In 1999, she became the PIUG webmaster. In 2000, she received an Award of Appreciation for 12 years of championing and facilitating electronic communications within PIUG. She took on the planning for the 2001 PIUG NE Workshop and continued with planning for the 2002 and 2003. She spearheaded planning for the PIUG 2003 and 2004 Annual Conferences. She currently acts as Board Liaison to the Vendor/Producer Committee.

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 in 1983.

"Sequence Searching at the European Patent Office"top of page
Bernard Piret, European Patent Office (EPO)

Search is the cornerstone of patent examination and granting. Some of the main challenges faced by EPO examiners include (but are not limited to) 1) how to decide what to search. This may be more complicated than it seems, e.g. when the claims are not clear or when the patent application seems to relate to several inventions; 2) how to search, i.e. how to translate any sequence-related claim into a sensible sequence search strategy. This can cause special problems, for instance when a claim relates to e.g. polymorphic sequences, fragments, antibodies, splice variants, etc. and often requires the use of more sophisticated tools than the "classical" FASTA-based search engine, such as STN®/RegistrySM and GenomeQuest™; 3) to be able to find quickly the most relevant documents when the sequence search returns a large number of potentially relevant hits. This step of filtering/selection (called "post-processing" by EPO examiners) also requires specially adapted software tools (some of them developed in-house).

Bernard Piret
European Patent Office
Patentlaan 2
P.O. Box 5818
2280 HV Rijswijk
The Netherlands

Bernard Piret is of Belgian nationality and has worked at the European Patent Office (The Hague branch) for about 6 years, as an examiner in the Joint Cluster Biotechnology. Before that, he worked as a post-doctoral research scientist at the Institute of Toxicology and Genetics in Karlsruhe, Germany. He has a PhD in Biochemistry from the University of Liège, Belgium. Bernard Piret is a BEST examiner, i.e. he handles both search and substantive examination (as well as oppositions) at the EPO.

Paula Sheppardtop of page
Scientific and Technical Information Center (STIC)
United States Patent and Trademark Office (USPT0)

Since 1989, an automated search system has been the key factor in the business function of performing prior-art searching of polynucleotide and polypeptide sequences claimed in patent applications examined by Technology Center 1600 (Biotechnology). The Automated Biotech Sequence Search System (ABSS) System is designed to accept and store electronic sequence listing data submitted by applicants, and support searching of polynucleotide sequences using data stored from both applicant submissions and public and commercial databases of published sequence information. The ABSS system includes many search features as, full implementation of the highly sensitive Smith-Waterman sequence searching algorithm, automated batch submission of multiple searches against multiple databases using a graphical user interface, and ability to support a variety of matrices. The system provides reports that include such things as alignments, statistical and bibliographic information for top scores. The ABSS system supports publication and dissemination of sequence information. This presentation will provide review of the ABSS system.

Paula Sheppard
Scientific and Technical Information Center (STIC)
United States Patent and Trademark Office (USPTO)
P.O. Box 1450
Alexandria, Virginia 22313-1450
paula.sheppard @

Paula Sheppard is a Technical Information Specialist with the U.S. Patent and Trademark Office’s Scientific and Technical Information Center. She has been at the U.S. Patent and Trademark Office for eighteen years and has provided informational services to examiners in Technology Center 1600 (Biotechnology). She has a B.A. in Biology and a M.S. in Genetics.

"Getting to Yes: What Patent Attorneys Want to Learn from a Sequence Search"
Joan Switzertop of page
Merck & Co. Inc.

Joan E. Switzer
Assistant Counsel
Patent Department
Merck & Co., Inc.
Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065
joan_switzer @

Joan E. Switzer is an Assistant Counsel in the Neuroscience and Opthalmics Group of Merck & Co., Inc.’s Patent Department. Her areas of responsibility include patent prosecution, non-infringement and validity opinions and due diligence for research collaborations, joint ventures and license agreements relating to Alzheimer’s disease and other neurological disorders.

 “Use of Patent Classification and Manual Codes to Assist with Retrieval of Antibody Patents: Patents and Sequences Related to Therapeutic Antibodies Directed Against Multiple Myeloma Antigens”top of page
Alison Taylor, Threshold Information, Inc

A patent search case study will be presented covering the construction and use of comprehensive and efficient search techniques aimed at methods to determine patentability and FTO around therapeutic antibody technologies. Particular emphasis will be on the use (or not) of patent classification coding systems, including US, IPC and Derwent manual codes. Specific sequence search parameters will be discussed, related to current rules at the USPTO and EPO.

Alison Taylor, PhD
Threshold Information, Inc.
1601 Sherman Ave., Suite 500
Evanston, IL 60201
847 433 8306
ataylor @

Alison Taylor is currently Director of the Science team and scientific information analyst at Threshold Information, Inc., a private information consulting company based in the Chicago area. She has a PhD in biochemistry and molecular biology from Kings’ College London and a BSc in biochemistry from the University of Surrey. Her first job upon graduation and moving to Chicago was as a bench scientist with Abbott Laboratories, Abbott Park, IL, in the Molecular Biology Dept. of PPD. Prior to joining Threshold in 2003, Alison was Manager of the Scientific and Patent Information Searchers for Pharmacia Corp (previously Monsanto, Pharma division; G.D. Searle) in Skokie, IL. She specializes in scientific and patent information searches in the biotech and life sciences areas and has almost 20 years experience working in the pharmaceutical and food science industries.

“Searching Biotech Devices: The Proficient Trapping of Boojums”top of page
Kristine H. Atkinson, Boston Scientific Corporation

Biotech devices comprise high-value, innovation-driven commercial applications that may be invented before a recognizable idiom matures to describe them. The nuances of language, search database idiosyncrasies, patent office protocols, and evolving patent prosecution rules coalesce to create a challenging brainteaser where combination device search can involve as much art as science. We will explore cautionary examples of original inventors who lost major patent rights to their miracle compounds, and the dissonance of rational language with descriptions that work.

Kristine H. Atkinson
Intellectual Property Researcher Legal Department
Boston Scientific Corporation
One Boston Scientific Place
Natick, MA 01760
atkinsok @

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.

“Similarity Searching for Antibody Sequences”top of page
Alice K. Goshorn, Amgen

Therapeutic antibodies comprise an increasing number of biotechnology patents. There are nineteen therapeutic monoclonal antibodies approved in the US. Hundreds more are in development using a variety of drug design technologies. Favorable pharmacological properties, design and optimization methods, and availability of bioprocess technologies for production have made antibodies an expanding drug class.

Similarity searching of the patent and scientific literature using antibody sequences requires some basic knowledge of the structure and molecular biology of antibodies. The searcher must identify the specific sequences that make up the unique target-binding sites and distinguish these from portions of the molecule that perform other functions. The similarity search algorithms (BLAST, GenePast, Motif search) and subsequent analyses must be performed on the appropriate sequences in order to assess the level of similarity between one molecule and another. Small molecular changes of just a few amino acid residues often result in significant changes in function or binding affinity.

Beginning with an amino acid sequence of a therapeutic antibody, what are the necessary steps and recommended resources you will need to run a similarity search for patentability or FTO analysis? A basic, step-wise “how-to” approach for someone who is unfamiliar with antibody engineering technology will be outlined.

Alice K. Goshorn, Ph.D
Scientific Editor
1201 Amgen Court West
Seattle, WA 98119-3105
t  206-265-7311
f  206-217-4692
goshorna @

Alice Goshorn has a PhD in Microbiology from the University of Minnesota and a BS in Biochemistry from Rutgers University. She spent six years as a Molecular Biology Scientist at several Seattle biotech companies including some antibody work using ribosome display. She joined Immunex as an Information Scientist in 1999, specializing in scientific searching and biosequence searching of patent and scientific databases. She is currently a Scientific Editor at Amgen, Research & Development Informatics working on ontology and data integration projects.

Session II: Details on Databases and Strategies for Searching

"GENESEQ - Status and New Content Update"top of page
Colin Williams, Thomson Scientific

The effective, and accurate, retrieval of biological sequence information is crucial to users of patent databases. GENESEQ, provided by Thomson Scientific, is one such database covering nucleotide and amino acid sequences disclosed in patents from 41 patent issuing authorities with coverage back to 1981. This presentation will give an update on the file status, including how the many patents with high sequence numbers are being dealt with. Also covered will be the enhancements made to the file in mid 2007, the guidelines for the enhancements and how users can make the most of these.

Colin Williams PhD
Product Manager – Biology & Bioinformatics
Pharmaceutical & Chemical Markets
Tel +44 (0)207 433 4843
Fax +44 (0)207 433 4301
colin.williams @
Thomson Scientific
77 Hatton Garden
London EC1N 8JS

Colin Williams is the Product Manager for Biology and Bioinformatics at Thomson Scientific. He studied Biochemistry at the University of Sheffield before completing a PhD in protein X-ray crystallography. Following post doctoral work he 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. Subsequent to this he joined Thomson Scientific as GENESEQ Editorial and Content manager in November 2005. Here 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 he moved into his current role where amongst other things he is responsible for development of the GENESEQ file.

“Where is My Sequence?: Feature/Notes Table, Uncommon Amino Acids, and Wildcards”top of page
Ken Hoppe, ScienceIP

STN Express has numerous means to refine a peptide sequence search in the sequence databases: exact match, conserved substitution, exact length, subsequence, uncommon amino acids, modified amino acids, or cyclic peptides. These search tools can be used to refine your answer set. As with any sharp instrument, if you do not know how to use it, you may cut off something you want to keep. This is especially important in intellectual property searching where you need to find as much as you can. The talk will cover issues to watch out for, better understanding of how sequences may appear in databases and ways to help find what you are looking for and still keep all you fingers – findings. This becomes very evident when you take as your query a modified sequence from the published patent claims and end up cutting it out of the answer set by using too many limiters or too simple a search strategy.

Kenneth L. Hoppe
Senior Searcher
1-512-219-0442 (Direct)
khoppe @
  Science IP
2540 Olentangy River Rd
Columbus OH 43202
1-866-360-0814 (toll-free in U.S.)
1-614-447-3787 (phone)
1-614-447-5443 (fax)

Ken Hoppe has a BS and MS in Biology. He has ten years laboratory experience in molecular biology working at the University of Connecticut Medical Center’s Department of Biochemistry, Harvard Medical School at Beth Israel and Children’s Hospitals in Boston, and in Pfizer’s Groton Connecticut research laboratories working in the area of atherosclerosis. Ken has worked for six years in the biotechnology patent searching field in Pfizer’s Information Management and Patent Departments. In this role, Ken helped manage the development of an in-house software application that helps post-process results from in-house biosequence patent databases. Currently, Ken is a Senior Searcher with Science IP® - The CAS Search Service.

“Ensuring a Thorough Sequence Patent Search”top of page
Dr. Kamalakar Gulukota, Senior Director, Content Development, GenomeQuest Inc.

Sequence patent information comes in many forms and from many sources. Conducting a thorough search can be costly, if not done right, and time consuming. GenomeQuest's philosophy toward biological patent searching encourages searching of diverse databases (patent and non-patent) and also searching patents from various patent offices, simultaneously. With a focus on our US patent efforts, we will discuss our proprietary semi-manual, QC process to make sequences and all annotations searchable and browsable in GQ-PAT (the largest annotated sequence patent database). We will also cover the recent enhancements we have made to our patent archive. Finally, we will touch upon other non-patent public data redistributed through GenomeQuest and why this data is integral to any patent search process.

Dr. Kamalakar Gulukota ("Gulu")
Senior Director, Content Development
GenomeQuest, Inc.
1700 West Park Drive, Suite 260
Westborough, MA 01581
Tel: (508) 616-0100 ext 404
Fax: (508) 616-0110
E-mail: kamalakar.gulukota @

Dr. Gulukota has more than 12 years of experience in drug discovery in the big pharma, academic, and contract research settings.  Throughout his career, he has been applying in-silico methods to improve the productivity of drug discovery.  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.

“The Good, The Bad and The Ugly - The Truth about Sequence Listing Submissions and Consequences for Comprehensive IP Searching”top of page
James A. Coburn, Harbor Consulting IP Services, Inc.

Statistics from the U.S. Patent and Trademark Office (USPTO) reflect close to a 50% error rate for all submissions of DNA and amino acid Sequence Listings under 37 C.F.R. §§1.821-825, and one could surmise that there is a similar error rate for all submission in other authoring countries under WIPO Standard ST.25. In addition, the USPTO is using a new, overly sensitive CRF check program (CRFValidator ver. 1.0.3), which often produces false positive rejections. To compound things, certain USPTO reviewers/examiners are issuing subjective Sequence Listing rejections on such issues as variable length sequences/positions, listing file extensions, organism designation, and the necessity to include sequences with D-amino acids, all of which eat up valuable patent term to address.

That said, erroneous and incorrect Sequence Listings in granted patents/published applications directly affect a larger IP issue, namely portfolio assessment for patentability, validity, freedom to operate, and due diligence purposes, costing biopharma businesses perhaps tens of millions of dollars in search and opinion fees that may be otherwise unnecessary. In the same vein, sequence searching has its own set of ambiguities/difficulties such as detailed use of public and private databases, including GenBank, EMBLE, SWISSPROT, and STN, database crossing to eliminate duplicate records, manual fragment searching, variable residue/base searching, etc. Thus, the preparation of Sequence Listings for examination purposes and the exercise of sequence searching are inherently intertwined, and incomplete/erroneous listings can negatively affect the ever so important end product, the opinion.

Harbor Consulting IP Services, Inc.
DNA & Amino Acid Sequence Listing and Search Service
1500A Lafayette Rd. #262
Portsmouth, New Hampshire 03801
Phone Number: 800-318-3021
-  James Coburn - x101 (jcoburn @
-  Bridget Conroy - x 105 (bconroy @
Fax Number: 877-775-7756

James Coburn is President of Harbor Consulting IP Services, Inc., the leading outsource provider to law firm, in-house and sole practitioner patent attorneys & agents for meeting the U.S. and foreign Sequence Listing requirements under 37 C.F.R. §§1.821-825 and WIPO Standard ST.25, as well as providing technical online sequence and text searching using the STN database platform. Prior to forming Harbor Consulting in the fall of 1995, Mr. Coburn worked as a technical assistant in the biotech and pharmaceutical practice group of the Washington, D.C. law firm of Foley & Lardner. Mr. Coburn holds a liberal arts degree from the University of Southern Maine, with a concentration in biology, supplemented with numerous patent oriented seminars and coursework.

Bridget Conroy is the technical group leader at Harbor Consulting IP Services, Inc., and is in charge of all project related procedural and quality aspects of day to day operations at the company. Ms. Conroy supervises staff, sets and manages company processes and procedures, and interacts with our client base regarding substantive case and search issues. Ms. Conroy holds a BS in Biochemistry from the University of New Hampshire.

“The SECOND Most Obvious Places to Search Sequences”top of page
Don Walter and Brian Larner, Thomson Scientific

Certain peptides have been searchable in the Derwent World Patents Index® (DWPISM) since the beginning. As the capabilities for indexing and searching peptides has grown, from fragmentation codes to the Merged Markush Service to the Derwent Chemistry Resource, so have the capabilities for finding new and unique information in these traditional indexes. This talk will focus on how to find that information, and possibly more.

Donald Walter, Ph.D.
Training Executive Pharmaceutical & Chemical Markets
Thomson Scientific
Tel +1 703 706 4220 extension 4820
Fax +1 703 519 5838 @

Donald Walter joined Thomson Scientific, which was then called Derwent Information, in 1992, where his primary job is to train users on Thomson Scientific and Thomson Healthcare databases, specializing in chemical and patent information. He also conducts searches and analyses for legal and industrial clients of the Thomson Scientific Search Service, with a special emphasis on pharmaceutical and chemical subjects. He learned his craft at Exxon Research and Engineering Co., conducting patent and scientific literature searching for clients in the legal and technical departments. Don’s Ph.D. from Yale is in Chemistry. He lives just outside Washington DC.

Brian Larner is a customer trainer for Thomson Scientific, where he is responsible for training Thomson Scientific’s European customers how to search the DWPI and other Thomson Scientific products. He joined Thomson Scientific, then called Derwent Information, in 1988, initially as a chemical and pharmaceutical indexer based in London responsible for applying manual codes, fragmentation codes and MMS indexing to Chemical Patent documents. He was promoted to technical trainer, where he was responsible for training internal staff how to do the chemical and pharmaceutical indexing. He also acted as an adviser on indexing update and development projects within Thomson. Brian studied pure chemistry at the University of Newcastle upon Tyne where he gained a first class honors degree. He was born in Sheffield, England.

“Structure Searching for Small Sequences in the CAS REGISTRYSM File”top of page
Lora Burgess, Chemical Abstracts Service (CAS)

The CAS REGISTRYSM file contains information about biological sequences gathered since the 1950's. Several approaches can be used to search for this information, including nomenclature, sequence searching algorithms, and also structure searches for small sequences. This presentation will focus on the unique information that can be retrieved using structure searches in the REGISTRY file.

Lora Burgess
Senior Applications Specialist
2540 Olentangy River Rd
Columbus OH 43202
1-800-848-6538 x 7034 (voice mail)
lburgess @

Lora Burgess has been working as an STN trainer at Chemical Abstracts Service since December 2000. She supports training for major customers in pharmaceutical, biotech, chemical and legal areas in the eastern US. Prior to her work at CAS, she spent 4 years as an Information Technology Resource Provider at the US Patent and Trademark Office, training patent examiners on commercial search systems, PTO in-house systems, and chemical structure searching. She has been searching on STN since 1991, when she began using STN for her graduate studies in chemistry. She holds a Master's degree in Chemistry from John's Hopkins University.

“Synergies and Surprises - USGENE and DGENE Multifile Patent Sequence Searching on STN”top of page
Rob Austin, FIZ Karlsruhe Inc.

Abstract: The launch of The USPTO Genetic Sequence Database, USGENE, on STN by the SequenceBase Corporation and FIZ Karlsruhe in July 2007 provided a unique and powerful additional resource for STN patent sequence searchers. This talk will focus on the importance and practicalities of comprehensive multifile searching for US patent sequence data using both USGENE and DGENE on STN.

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

Biography: 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.

“Putting It All Together”top of page
Elyse Turner, Merck & Co., Inc.

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