"Preamble to Searching"
Elyse Turner, Merck & Co., Inc.
8:30-9:00am
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"
Bernard Piret, European Patent Office (EPO) 9:00-9:35am
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
Tel.+31(0)70340-1966
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 Sheppard
Scientific and Technical Information Center (STIC)
United States Patent and Trademark Office (USPT0)
9:35-10:00am
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
571-272-2529
paula.sheppard @ uspto.gov
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 Switzer
Merck & Co. Inc.
10:00-10:25am
Joan E.
Switzer
Assistant Counsel
Patent Department
Merck & Co., Inc. Merck & Co., Inc.
P.O. Box 2000
Rahway, NJ 07065 732-594-5616
joan_switzer @ merck.com
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”
Alison Taylor, Threshold Information, Inc
10:55-11:20am
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 @ threshinfo.com
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”
Kristine H. Atkinson, Boston Scientific Corporation
11:20-11:45am
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
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.
“Similarity Searching for Antibody Sequences”
Alice K. Goshorn, Amgen
11:45-12:10am
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
Amgen
1201 Amgen Court West
Seattle, WA 98119-3105
t 206-265-7311
f 206-217-4692
goshorna @ amgen.com
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"
Colin Williams, Thomson Scientific
1:20-1:45pm
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.com www.thomsonpharma.com http://scientific.thomson.com
Thomson Scientific
77 Hatton Garden
London EC1N 8JS
UK
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”
Ken Hoppe, ScienceIP
1:45-2:10pm
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 @ cas.org
Science IP
CAS
2540 Olentangy River Rd
Columbus OH 43202
www.scienceip.org
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”
Dr. Kamalakar Gulukota, Senior Director, Content Development, GenomeQuest Inc.
2:10-2:35pm
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 @ genomequest.com
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”
James A. Coburn, Harbor Consulting IP Services, Inc.
2:35-3:00pm
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 @ seqidno.com)
- Bridget Conroy - x 105 (bconroy @ seqidno.com)
Fax Number: 877-775-7756
www.seqidno.com
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”
Don Walter and Brian Larner, Thomson Scientific
3:30-3:55pm
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
don.walter @ thomson.com http://www.thomsonpharma.com
http://scientific.thomson.com
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”
Lora Burgess, Chemical Abstracts Service (CAS)
3:55-4:20pm
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
CAS
2540 Olentangy River Rd
Columbus OH 43202
1-800-848-6538 x 7034 (voice mail)
lburgess @ cas.org
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”
Rob Austin, FIZ Karlsruhe Inc.
4:20-4:45pm
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.
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”
Elyse Turner, Merck & Co., Inc.
4:45-5:00pm
