STN Sequence Databases - FIZ Karlsruhe

Sequence Searching on STN ® 

Part I: STN Sequence Databases

Agenda 

• STN sequence searchable databases 

• Comparison to web-based resources 

• Results of a comparative search example 

• Summary and resources 

2 

2

STN sequence searchable databases 

• DGENE 

– Thomson Reuters GENESEQ TM 

– Value-added patent sequence data from around 

the globe 

• USGENE ® 

– The USPTO Genetic Sequence Database 

– A new and unique access point to USPTO 

sequence data 

3 

3

STN sequence searchable databases (cont.) 

• PCTGEN 

– WIPO/PCT Patent Application Biosequences 

– The complete collection of e-published 

sequences from WIPO 

• CAS REGISTRY SM 

– Chemical Abstracts Service (CAS) REGISTRY 

– Worldwide value-added patent and non-patent 

sequence data 

4 

4

Thomson Reuters GENESEQ (DGENE) 

• Largest value-added patent sequence database 

• Used routinely by all major patent offices* 

• Sequences from the basic patents of the 43 

authorities of the Derwent World Patents Index ® 

• Bibliography, enhanced title, abstract, indexing, 

and patent location provided for each sequence 

• Patent Family and Legal Status display 

• Updated every two weeks 

• 1981 – present 

* See page 11: www.trilateral.net/projects/biotechnology/guide2.pdf 

5 

5

Relationship between DWPI patent family 

and DGENE sequence database 

AN .... WPINDEX 

TI …. 

PA …. 

PI WO …. A1 

AB …. 

FR …. A1 

US …. A1 

US …. B2 

WPINDEX = Derwent World Patents Index (DWPI SM ) on STN 

DGENE = GENESEQ on STN 

AN .... Protein DGENE 

PI WO …. A1 

SEQ 1 …. 

AB …… AN .... DNA DGENE 

PI WO …. A1 

SEQ 2 …. 

AB …… AN .... Peptide DGENE 

PI WO …. A1 

SEQ n …. 

AB …… 

6 

6

What exactly is the “value-add” in DGENE? 

• DWPI patent title, concise sequence description, 

abstract, and keyword indexing per sequence 

– Context of each sequence illuminated within the 

invention 

– Superior text-based refinement of sequence searches 

– Efficient scanning and review of search results for 

relevance 

• Feature tables for sequence 

modifications/annotations 

– Extensive detailed annotations provided by indexers 

7 

7

What exactly is the “value-add” in DGENE? 

(cont.) 

• Patent sequence location (claim, example, 

etc.) 

– Assigned manually by Thomson Reuters 

indexers 

– Flexible filtering of searches to those described 

in the claims 

• Sequences intellectually derived by indexers 

– Unique sequence hits not disclosed in formal 

listings 

8 

8

Some editorial insights regarding 

WIPO/PCT sequences indexed in DGENE 

• On average 120 WIPO/PCT basic patents have 

sequences indexed into DGENE each week 

• Of these, about 15-20 may have electronic listings 

available – the rest are keyed manually 

– Sequences are independently double-keyed with a 

guaranteed accuracy of 99.995% (1 in 20,000) 

• About 15% of PCTs with electronic listings have 

extra sequences indexed from the specification 

• Typically 1 or 2 documents per week will also have 

intellectually derived sequences indexed, based 

upon the wording of the patent claims 

Source: Colin Williams, GENESEQ Editorial & Content Manager, Thomson Reuters (12/2006) 

9 

9

Derived sequences are intellectually 

created by indexers from wording in the 

patent text 

AN AEJ92622 protein DGENE 

TI Hydrolyzing/synthesizing carboxylic acid ester/amide from 

chiral/prochiral reactants for preparing e.g. pharmaceuticals, 

comprises contacting reactants with a polypeptide having hydrolytic 

activity. 

IN Svendsen A; Vind J; Brask J; De Maria L 

PA (NOVO) NOVOZYMES AS. 

PI WO 2006084470 A2 20060817 17 

In this example, the indexer has 

intellectually derived this sequence 

from the wild type lipolytic hydrolase. 

AI WO 2006-DK76 20060210 

PRAI EP 2005-388012 20050210 

PSL Claim 16 

DED 19 OCT 2006 (first entry) 

LA English 

OS 2006-560037 [57] 

DESC Variant fungal lipolytic hydrolase #2. 

KW hydrolysis; lipase; pharmaceutical; pesticide; enzyme; mutein. 

ORGN Thermomyces lanuginosus. Synthetic. 

AB The new invention relates to a enzymatic method of hydrolyzing or 

synthesizing carboxylic acid ester or amide from chiral or prochiral 

reactants, by providing reactants for hydrolysis or synthesis, and 

contacting the reactants with a polypeptide which has hydrolytic 

activity on ester or amide, and a sequence 50% homologous to 

Thermomyces lanuginosus lipase. Also described is a polypeptide, 

which has hydrolase activity on an ester or amide substrate, and has 

an amino acid sequence that has at least 80% identity to SEQ ID No: 

5 and compared to SEQ ID No: 5 comprises a substitution corresponding 

to I90Q, N92TD, F95Y, F113Y, I202M, V203GM, L269T and 270F. . . . . 

10 

10

Indexers explain exactly how they derived 

the sequence at the end of the abstract 

The polypeptide is at least 80% homologous to any of SEQ ID No: 1-6 

being amino acid sequences of lipolytic enzymes of fungus such as 

Rhizomucor miehei (SWISSPROT P19515), Rhizopus delemar, Fusarium 

oxysporum, Penicillium camemberti (SWISSPROT P25234), Thermomyces 

lanuginosus (SWISSPROT 059952) and Thermomyces ibadanensis . . . . . 

The method is useful in the preparation of pharmaceuticals or 

pesticides, where the synthesis includes synthesis of 2-butyl 

propionate. This sequence is a variant fungal lipolytic hydrolase 

(lipase), V203M T231R N233R. This sequence is not shown in the 

specification, but was created by the indexer using the information 

given in claim 16. 

SQL 269 

SEQ 1 evsqdlfnqf nlfaqysaaa ycgknndapa gtnitctgna cpevekadat 

51 flysfedsgv gdvtgflald ntnklivlsf rgsrsienwi gnlnfdlkei 

101 ndicsgcrgh dgftsswrsv adtlrqkved avrehpdyrv vftghslgga 

151 latvagadlr gngydidvfs ygaprvgnra faefltvqtg gtlyrithtn 

201 dimprlppre fgyshsspey wiksgtlvpv rrrdivkieg idatggnnqp 

251 nipdipahlw yfgligtcl 

FEATURE TABLE: 

Key |Location|Qualifier| 

=============+========+=========+========================== 

Modified-site|203 |note |"Wild type Val replaced by 

| | |Met" 

Modified-site|231 |note |"Wild type Thr replaced by 

| | |Arg" 

Modified-site|233 |note |"Wild type Asn replaced by 

| | |Arg" 

The indexer has added explanatory 

sentences to the abstract and 

annotations to the feature table. 

11 

11

Patent family and Legal Status information 

now displayable in DGENE 

• Patent family information from WPINDEX 

– FAM format provides all publication, application 

and priority numbers, and dates 

• Legal Status information from INPADOCDB 

– LS format is the standard legal status display for 

INPADOCDB 

– LS2 format contains same info as LS but also 

displays field headers 

12 

12

DGENE patent family display 

=> FILE DGENE 

=> S CA2325774/PN 

L1 17 CA 2325774/PN 

=> D FAM 

There are 17 sequence records 

in DGENE for CA2325774. 

The U.S. member of the family 

was granted on May 11, 2004. 

L1 ANSWER 1 OF 17 DGENE COPYRIGHT 2010 THOMSON REUTERS on STN 

PI CA 2325774 A1 20010610 (200144)* EN 79[1] 

US 20030115627 A1 20030619 (200341) EN 

US 6734344 B2 20040511 (200431) EN 

ADT CA 2325774 A1 CA 2000-2325774 20001208; US 6734344 B2 Provisional US 

1999-170168P 19991210; US 6734344 B2 US 2000-733643 20001208; US 

20030115627 A1 Provisional US 1999-170168P 19991210; US 20030115627 A1 

US 

2000-733643 20001208 

PRAI US 1999-170168P 19991210 

US 2000-733643 20001208 

13 

13

DGENE legal status display 

=> FILE DGENE 

=> S WO2002079175/PN 

L1 4 WO2002079175/PN 

=> D PI LS 

There are 4 sequence records in 

DGENE for WO2002079175. 


PI WO 2002079175 A1 20021010 67 

LEGAL STATUS INPADOCDB COPYRIGHT 2010 EPO / FIZ KARLSRUHE on STN 

AN ABP55034 DGENE 

20010330 GBA PRI Patent application 

GB 2001-8097 A 20010330 

20020318 WOW APP International application Number 

WO 2002-IB817 W 20020318 

. . . 

20040219 WOREG REFERENCE TO NATIONAL CODE 

DE8642 - DE: IMPACT ABOLISHED FOR DE - I.E. PCT APPL. NOT ENT. 

GERMAN PHASE 

NIF Lapses, Expiries, Withdrawals, Refusals 

20050608 WOWWG + WIPO INFORMATION: GRANT IN NATIONAL OFFICE 

EP 2002707045 

200824.................................20080612 

14 

14

SequenceBase USPTO Genetic Sequence 

Database (USGENE) 

• Sequences from all relevant USPTO 

published patent applications and granted 

(issued) patents 

• Original publication title, abstract, and 

claims 

• Publication, application, related application 

and priority numbers and dates; full 

assignee and inventor names 

15 

15

SequenceBase USPTO Genetic Sequence 

Database (USGENE) (cont.) 

• Organism name, Sequence Length, 

Molecule Type, SEQ ID NO, Feature 

Tables, and Patent Sequence Location 

• Calculated patent expiration date 

• Patent Family and Legal Status display 

• Updated weekly – within 3 days of 

publication 

• 1982 – present 

New in 2009 ! 

16 

16

USGENE consolidates unique USPTO 

sequence data from different sources 

• USPTO Publication Site for Issued and 

Published Sequences (PSIPS) 

– The official mega-publication download site, 

2001-date 

• International Nucleotide Sequence 

Database Collaboration (INSDC) 

(NCBI/EMBL/DDBJ, Genbank) 

– U.S. granted patent nucleotide sequences, 

1982-date 

17 

17

USGENE consolidates unique USPTO 

sequence data from different sources (cont.) 

• USPTO Protein Database (NCBI/EMBL) 

– U.S. granted patent protein/peptide sequences, 

1982-date 

• USPTO Published Applications and Patents 

Full-Text 

– Filling in omissions, coverage gaps, and to 

enhance timeliness 

The USGENE Sequence Source (/SSO) field indicates from which 

source any given USGENE sequence record was derived. 

18 

18

USGENE combines these sequences with 

bibliographic data and claims text 

INSDC 

USPTO nucleotide 

sequences 

NCBI/EMBL-EBI 

USPTO peptide 

sequences 

USPTO biblio, 

title, abstract, 

and claims text 

USPTO full-text 

sequences 

USPTO PSIPS 

sequences 

19 

19

Relationship between DWPI patent family 

and USGENE sequence databases 


TI …. 

PA …. 

PI WO …. A1 

AB …. 

FR …. A1 

US …. A1 

US …. B2 

WPINDEX = Derwent World Patents Index on STN 

USGENE = The USPTO Genetic Sequence Database 

AN .... Protein USGENE 

PI US …. A1 

SEQ 1 …. 

AN .... DNA USGENE 

PI US …. A1 

SEQ n …. 


PI US …. B2 

SEQ 1 …. 


PI US …. B2 

SEQ n …. 

20 

20

USGENE sequence records are available 

within 3 days of publication by the USPTO 

L2 ANSWER 1 OF 1 USGENE COPYRIGHT 2010 SEQUENCEBASE CORP on STN 

AN 20080256649.126 Protein USGENE 

TI Novel Acetylcholinesterase Gene Responsible for Insecticide Resistance 

and Applications Thereof (PublishedApplication) 

IN Weill Mylene (Montpellier, FR); Fort Philippe (Castelnau Le Lez, FR); 

Raymond Michel (Montpellier, FR); Pasteur Nicole (Montpellier, FR) 

PA CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE (PARIS CEDEX FR) 

PI US 20080256649 A1 20081016 

AI US 2003-518072 20030619 

RLI WO 2003-FR1876 20030619 

PRAI FR 2002-13799 20021105 

FR 2002-7622 20020620 

PSL Claim 4; SEQ ID NO 126 

DESC Anopheles gambiae Protein; sequence 126 of 129 

DT Patent 

AB The invention relates to a novel acetylcholinesterase gene (ace-1) 

responsible for resistance to organophosphorus and/or carbamates in 

. . . 

ECLM US20080256649 A1: 1. An insect acetylcholinesterase, characterized in 

that it comprises a central catalytic region which has an amino acid 

sequence selected from the group consisting of the sequence SEQ ID NO 1 

. . . 

SSO PROTEIN; USPTO; APPLICATION 

ORGN Anopheles gambiae 

SQL 737 

SEQ 

AN 20080256649.126 is SEQ ID 

NO: 126 from US20080069867. 

1 meirgllmgr lrlgrrmvpl gllgvtalll ilppsalvqg rhhelnngaa 

51 igshqlsaaa gvglssqsaq sgslasgvms svpaagasss ssssllsssa . . . . 

AN 20080256649.126 is 

displayed here in BRIEF format, 

which includes the Exemplary 

Claim (ECLM). 

21 

21

USGENE also has an extensive backfile 

This USPTO example is US5210028, 

which was issued on May 11, 1993. 

Published sequence data like this are 

identified, extracted, standardized, and 

loaded into USGENE on STN (compare 

this to the STN record on the next slide). 

22 

22

To facilitate precise searching, all USGENE 

sequences are in STN standardized format 


AN 5210028.1 protein USGENE 

TI Process for the production of unfused IGF-II protein in E. coli 

(Patent) 

IN Schmitz Albert (Basel, CH); Marki Walter (Mohlin, CH) 

PA Ciba Geigy Corporation (Ardsley NY) 

PI US 5210028 A 19930511 

AI US 1990-616470 19901121 

AB A process for the preparation of a recombinant IGF-II (rIGF-II) 

without a covalently attached foreign protein moiety and without Nterminal 

attached methionine or a derivative of methionine or of a 

salt of said IGF-II, rIGF-II produced by said method, . . . . 

ECLM US5210028 A: We claim:1. A process for the production of a 

recombinant IGF-II without a covalently attached foreign protein 

moiety and without N-terminal attached methionine or a derivative of 

methionine, said process comprising:a) transforming a suitable strain 

of E. coli, said strain being a lon.sup.- and htpR.sup.- double 

mutant, with a hybrid vector comprising an expression cassette 

consisting of the following elements in the 5' to 3' direction, said 

elements which are operably linked: an inducible promoter, a 

ribosomal binding site, and the codon for the amino acid methionine 

linked in proper reading frame to a DNA sequence encoding a human 

IGF-II having the amino acid sequence of SEQ ID NO. . . . 

SSO PROTEIN; USPTO; GRANTED 

ORGN Human IGF II 

SQL 67 

SEQ 

1 ayrpsetlcg gelvdtlqfv cgdrgfyfsr pasrvsrrsr giveeccfrs 

51 cdlalletyc atpakse 

AN 5210028.1 is SEQ ID NO: 1 

from US5210028. 

AN 5210028.1 is displayed here 

in BRIEF format, which includes 

the Exemplary Claim (ECLM). 

Compare the STN standardized 

USGENE record to the original 

data source on the previous 

slide. 

23 

23

USGENE is an essential tool for tackling 

business-critical searches 

• DGENE provides curated and indexed patent 

sequence data from the DWPI basic publication 

– 61% of basics are WIPO/PCT published applications 

– Updated biweekly, typically 65 days from publication 

• USGENE provides all available sequence data 

from the USPTO as a single merged resource 

– Both U.S. patents and U.S. published applications 

– Updated weekly, within 3 days of USPTO publication 

• Sequence listing variation often occurs between 

PCT and U.S. granted patent publication stages 

– Especially important, e.g., for freedom-to-operate 

24 

24

USGENE and DGENE capture sequence 

data from different patent family members 


PI US …. A1 

SEQ 1 …. 


PI US …. A1 

SEQ 2 …. 


PI US …. B2 

SEQ 1 …. 


PI US …. B2 

SEQ 2 …. 


PI WO ….. A1 

FR ….. A1 

EP ….. A1 

US ….. A1 

EP ….. B1 

US ….. B2 

AN .... Protein DGENE 

PI WO …. A1 

SEQ 1 …. 

AN .... DNA DGENE 

PI WO …. A1 

SEQ 2 …. 

DGENE sequences are 

indexed by Thomson 

Reuters from DWPI 

basic publications. 

WPINDEX = Derwent World Patents Index on STN 

DGENE = GENESEQ on STN 

USGENE = USPTO Genetic Sequence Database 

25 

25

Sequence listing variation often occurs 

between PCT and U.S. granted patent stage 

L1 ANSWER 1 OF 1 WPINDEX COPYRIGHT 2009 THOMSON REUTERS on STN 

AN 1994-358278 [44] WPINDEX 

TI New polynucleotide(s) specific for hepatitis C virus types 4, 5 and 6 - 

and related antigenic peptide(s) and antibodies, useful in vaccines, 

diagnosis, HCV typing and treatment 

DC B04; D16; S03 

IN PIKE I H; SIMMONDS P; YAP P L 

PA (COMM-N) COMMON SERVICES AGENCY; (MURE-N) MUREX DIAGNOSTICS INT INC; . . . 

PI WO 9425602 A1 19941110 (199444)* EN 70[5] 

AU 9465797 A 19941121 (199508) EN 

FI 9505224 A 19951220 (199611) FI 

EP 698101 A1 19960228 (199613) EN [0] 

JP 09500009 W 19970107 (199711) JA 52[0] 

AU 695259 B 19980813 (199844) EN 

EP 698101 B1 20041103 (200475) EN 

DE 69434116 E 20041209 (200481) DE 

US 20050032047 A1 20050210 (200512) EN 

US 6881821 B2 20050419 (200527) EN 

. . . . . 

ADT WO 9425602 A1 WO 1994-GB957 19940505 . . . . 

PRAI GB 1994-263 19940107 

GB 1993-9237 19930505 

In this example the patent 

family has: 

• 9 sequences from 

WO9425602 in DGENE 


US20050032047 in 

USGENE 


US6881821 in USGENE 

26 

26

USGENE enhancements 

• Patent family and Legal Status displays 

• Patent Sequence Location (/PSL) 

• Priority application info (/PRAI) 

• U.S. related application info (/RLI) 

• Calculated patent expiration date (/XPD) 

• Patent term adjustment info (/NTE, /PTA) 

• Concise, on-line Sequence Description 

(/DESC) 

Note: All fields available from June 5, 2007. 

27 

27


now displayable in USGENE 

• Patent family information from INPADOCDB 

– FAM format provides all publication, application 

and priority numbers, and dates in tabular 

format 

– CFAM format provides simple table of all 

publication numbers and dates 


– LS format is the standard legal status display for 

INPADOCDB 

– LS2 format contains the same info as LS but 

also displays field headers 

28 

28


available in USGENE 

=> FILE USGENE 

FILE 'USGENE' ENTERED AT 19:49:28 ON 12 JAN 2010 

COPYRIGHT (C) 2010 SEQUENCEBASE CORP 

FILE LAST UPDATED: 7 JAN 2010 

MOST RECENT PUBLICATION DATE: 7 JAN 2010 

FILE COVERS 1981 TO DATE 

>>> SIMULTANEOUS LEFT AND RIGHT TRUNCATION (SLART) IS AVAILABLE 

IN THE BASIC INDEX (/BI) AND FEATURE TABLE (/FEAT) FIELDS > DOWNLOAD THE USGENE WORKSHOP MANUAL: 

http://www.stn-international.com/USGENE_workshop_manual.html 

. . . 

=> S US2009004109/PN 

L1 103 US2009004109/PN 

(US20090004109/PN) 

29 

29


available in USGENE 

=> D BRIEF FAM LS 


AN 20090004109.103 Protein USGENE 

TI Antibodies and Molecules Derived Therefrom that Bind to Steap-1 Proteins 

(PublishedApplication) 

IN Jacobovits Aya (Beverly Hills, CA); Etessami Soudabeh (Tarzana, CA); 

Challita-Eid Pia M. (Encino, CA); Perez-Villar Juan J. (Los Angeles, CA); 

Morrison Karen J. (Santa Monica, CA); Jia Xiao-Chi (Los Angeles, CA); 

Faris Mary (Los Angeles, CA); Gudas Jean (Pacific Palisades, CA); Raitano 

Arthur B. (Los Angeles, CA) 

PA AGENSYS INC (Santa Monica CA) 

PI US 20090004109 A1 20090101 

AI US 2004-587197 20040422 

RLI WO 2004-US12625 20040422 

PRAI US 2004-587197 20040422 

PSL SEQ ID NO 103 

DESC Homo Sapiens Protein; sequence 103 of 103 

DT Patent 

AB Antibodies and molecules derived there from that bind to novel STEAP-1 

… 

STEAP-1 can be used in active or passive immunization. 

ECLM US20090004109 A1: 1. An antibody or fragment thereof comprising an 

antigen binding site that binds specifically to STEAP-1 protein . . . 

SSO PROTEIN; USPTO; APPLICATION 

ORGN Homo Sapiens 

SQL 29 

SEQ 1 dkwmltrkqf gllslffavl haiyslsyp 

20090004109.103 is displayed 

here in BRIEF format. 

30 

30

Patent family information available in 

USGENE 

PATENT FAMILY INFORMATION INPADOCDB COPYRIGHT 2010 EPO / FIZ KARLSRUHE on STN 

AN 20090004109.103 USGENE 

+-------------PRAI-------------+ +--------------AI--------------+ 

WO 2004-US12625 W 20040422 AU 2004-319915 A 20040422 

BR 2004-18766 A 20040422 

CA 2004-2563735 A 20040422 

EA 2006-1946 A 20040422 

EP 2004-750565 A 20040422 

JP 2007-509439 T 20040422 

MX 2006-12187 A 20061020 

NO 2006-5366 A 20061121 

US 2004-587197 A 20040422 

WO 2004-US12625 W 20040422 

+--------------AI--------------+ +--------------PI--------------+ 

AU 2004-319915 A 20040422 AU 2004319915 A1 20051201 

BR 2004-18766 A 20040422 BR 2004018766 A 20071009 

CA 2004-2563735 A 20040422 CA 2563735 A1 20051201 

EA 2006-1946 A 20040422 EA 2006001946 A2 20070629 

EA 2006001946 A3 20070831 

EP 2004-750565 A 20040422 EP 1742966 A2 20070117 

EP 1742966 A4 20080402 

JP 2007-509439 T 20040422 JP 2008509880 T 20080403 

MX 2006-12187 A 20061020 MX 2006012187 A 20070328 

NO 2006-5366 A 20061121 NO 2006005366 A 20070119 

US 2004-587197 A 20040422 US 20090004109 A1 20090101 

WO 2004-US12625 W 20040422 WO 2005113601 A2 20051201 

WO 2005113601 A8 20070628 

1 priority, 10 applications, 13 publications 

20090004109.103 is displayed 

here in FAM format, which 

includes the patent family 

information from INPADOCDB. 

31 

31

Legal Status information available in 

USGENE 


AN 20090004109.103 USGENE 

20040422 WOWA PRI PCT application claimed from national procedure 

WO 2004-US12625 WA 20040422 

.......................................20090115 

20040422 USA APP Patent application 

US 2004-587197 A 20040422 

.......................................20090115 

20090101 USA1 PUB FIRST PUBLISHED PATENT 20090004109.103 APPLICATION [FROM is 2001 displayed ONWARDS] 

US 20090004109 A1 20090101 

here in LS format, which 

200903.................................20090115 

20090701 USAS ASSIGNMENT includes the Legal Status 

20090521 

AGENSYS, INC., CALIFORNIA 


ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:JAKOBOVITS, 

AYA;ESTESSAMI, SOUDABEH;CHALLITA-EID, PIA M.;AND 

OTHERS;REEL/FRAME:022905/0519;SIGNING DATES FROM 

TO 20090528 

CHG Change of Owner, Inventor, Applicant 

200942.................................20091015 

32 

32

USGENE now provides Patent Sequence 

Location (/PSL) 

• /PSL includes 

– Sequence identity number 

– If claimed, the corresponding claim number 

• Easily identify claimed sequences 

• Available from publication date of June 5, 

2007 

33 

33

USGENE now provides Patent Sequence 

Location (/PSL) 


AN 7482426.2 protein USGENE 

TI C23 Polypeptides (Patent) 

IN Franz-Bacon Karin (San Diego, CA); Gorman Daniel M. (Newark, CA); 

McClanahan Terrill K. (Sunnyvale, CA) 

PA Schering Corporation (Kenilworth NJ) 

PI US 7482426 B2 20090127 

US 20030092123 A1 20030515 

AI US 2002-246983 20020918 

RLI US 1998-99898 19980618 

PRAI US 1997-50156P 19970619 

XPD 20180618 (calculated) 

NTE Subject to any Disclaimer, the term of this patent is extended or 

adjusted under 35 USC 154(b) by 548 days. 

PSL Claim 1; SEQ ID NO 2 

DESC Protein; sequence 2 of 4 

DT Patent 

AB Nucleic acids encoding a new family of small cysteine rich soluble 

7482426.2 is displayed here in 

BRIEF format, which includes 

the Patent Sequence Location 

(/PSL). 

. . . 

ECLM US7482426 B2: 1. An isolated polypeptide comprising the sequence of 

residues 1 to 90 of SEQ ID NO: 2. 

SSO PROTEIN; USPTO; GRANTED 

ORGN Not provided 

SQL 108 

SEQ 1 mkalcllllp vlgllvsskt lcsmeeaine riqevagsli fraissigle 

51 cqsvtsrgdl atcprgfavt gctcgsacgs wdvraettch cqcagmdwtg 

101 arccrvqp 

34 

34

PCTGEN is the World Patent Application 

Biosequences database on STN 

• Produced by FIZ Karlsruhe and WIPO 

• Sequences submitted & published electronically 

as a formal part of PCT patent applications 

• Publication number and date, patent applicant 

name(s) and the original publication title are 

provided for each sequence 

• Sequence length, SEQ ID, organism name, and 

molecule type are included for each sequence 

• Updated weekly – within 24 hours of publication 

• August 2001 – present 

35 

35

Relationship between PCTFULL and 

PCTGEN databases 

AN … PCTFULL 

TI .... 

PA .... 

PI WO …. A1 

AB …. 

DETD .... 

CLM .... 

PCTFULL = WIPO/PCT patent applications full-text 

PCTGEN = WIPO/PCT patent application biosequences 

AN .... Protein PCTGEN 

PI WO …. A1 

SEQ 1 …. 

AN .... DNA PCTGEN 

PI WO …. A1 

SEQ 2 …. 

AN .... Peptide PCTGEN 

PI WO …. A1 

SEQ n …. 

36 

36

Each PCTGEN sequence record includes 

publication title and bibliography 

L1 ANSWER 1 OF 1 PCTGEN COPYRIGHT 2010 WIPO on STN 

AN 2006069200.16112 PRT PCTGEN 

TI Group B Streptococcus 

PA Tettelin, Herve 

Masignani, Vega 

PI WO 2006069200 20060629 

RLI US 2004-638943P 20041222; US 2004-640438P 20041230 

ED 20060630 

DT Patent 

ORGN Streptococcus agalactiae 

SQL 302 

SEQ 

1 mflmplasll gnltvwhhlk heiikipfsr ldilihlrpt lmlflpqitm 

51 qiylslnksm lgamdsvvsa gyfdqsdkii rilftivsai ggvflprlss 

. . . . 

251 atlsgavlyy intqmsvslv nyviqslvav tiyvgivfit kapviqllXX 

301 Xn 


Key |Location | 

==========+=============+======================= 

VARIANT |299, 300, 301|Xaa = Any Amino Acid 

AN 2006069200.16112 is 

SEQ ID NO: 16112 from 

WO2006069200. 

Sequences are typically 

added to PCTGEN within 24 

hours of publication by WIPO. 

37 

37


now displayable in PCTGEN 

• Patent family information from INPADOCDB 

– FAM format provides all publication, application and 

priority numbers, and dates in tabular format 

– CFAM format provides table of all publication numbers 

and dates 


– LS format is the standard Legal Status display for 

INPADOCDB 

– LS2 format contains the same info as LS but also 

displays field headers 

38 

38


available in PCTGEN 

=> FILE PCTGEN 

FILE 'PCTGEN' ENTERED AT 20:01:02 ON 12 JAN 2010 

COPYRIGHT (C) 2010 WIPO 

FILE LAST UPDATED: 8 JAN 2010 

MOST RECENT PCT PUB DATE: 7 JAN 2010 

PCTGEN CURRENTLY CONTAINS 7,004,444 BIOSEQUENCES 

>>> DOWNLOAD COMPLETE PCTGEN HELP AS PDF: 

http://www.stn-international.com/pctgen_help.html 

. . . 

>>> Percent identity sorting is now available


available in PCTGEN 

=> D ALL FAM LS 


AN 2009010296.16 PRT PCTGEN 

TI Antibodies against 4-(methylnitrosamino)-1-(3-pyridy1)-1-butanone 

andmetabolites thereof [File created by using OCR software] 

PA Centre de Recherche Publique Sante 

PI WO 2009010296 20090122 

RLI EP 2007-7 20070718 

ED 20090128 

DT Patent 

ORGN artificial sequence 

SQL 11 

SEQ 

1 qqwrshppal t 


Key |Location| 

==========+========+============================== 

source | |Description 

| |of artificial sequence:CDR3 of 

| |VL of antibody produced 

WO2009010296.16 is displayed 

here in ALL format. 

40 

40

Patent family information available 

in PCTGEN 

PATENT FAMILY INFORMATION INPADOCDB COPYRIGHT 2010 EPO / FIZ KARLSRUHE on 

STN 

AN 2009010296.16 PCTGEN 

+-------------PRAI-------------+ +--------------AI--------------+ 

EP 2007-14089 A 20070718 EP 2007-14089 A 20070718 

WO 2008-EP5876 W 20080717 

+--------------AI--------------+ +--------------PI--------------+ 

EP 2007-14089 A 20070718 EP 2016954 A1 20090121 

WO 2008-EP5876 W 20080717 WO 2009010296 A2 20090122 

WO 2009010296 A3 20090618 

1 priority, 2 applications, 3 publications 

WO2009010296.16 is displayed here in FAM 

format, which includes the patent family 


41 

41

Legal Status information available 

in PCTGEN 


AN 2009010296.16 PCTGEN 

20070718 EPA PRI Patent application 

EP 2007-14089 A 20070718 

.......................................20090129 

20080717 WOW APP International application Number 

WO 2008-EP5876 W 20080717 

.......................................20090129 

20090122 WOA2 PUB INTERNATIONAL APPLICATION PUBLISHED WITHOUT 

INTERNATIONAL SEARCH REPORT or INTERNATIONAL 

APPLICATION PUBLISHED WITH 

DECLARATION UNDER ARTICLE 17 (2) (A) 

WO 2009010296 A2 20090122 

200905.................................20090129 

20090318 WO121 EP: THE EPO HAS BEEN INFORMED BY WIPO THAT EP WAS 

DESIGNATED IN THIS APPLICATION 

EP 08784856 A2 

WO2009010296.16 is displayed 

here in LS format, which includes 

the Legal Status information from 

INPADOCDB. 

200912.................................20090320 

20090618 WOA3 PUB LATER PUBLICATION OF ISR WITH REVISED FRONT PAGE 

WO 2009010296 A3 20090618 

200926.................................20090625 

42 

42

CAS REGISTRY 

• Produced by CAS 

• Sequences from >3,000 life science journals 

and the basic patents of the 60 patent 

authorities in CAplus SM on STN 

• Patent number, location, and standardized 

nomenclature provided for each sequence 

• >61.5 million sequence records 

• Updated daily 

• Comprehensively from 1957 - present 

43 

43

Relationship between CAplus patent family 

and CAS REGISTRY databases 

AN .... CAPLUS 

TI …. 

PA …. 

PI WO …. A1 

AB …. 

FR …. A1 

US …. A1 

US …. B2 

IT RN .... 

RN .... Protein REGISTRY 

PI WO …. A1 

SEQ 1 …. 

RN .... DNA REGISTRY 

PI WO …. A1 

SEQ 2 …. 

RN .... Peptide REGISTRY 

PI WO …. A1 

SEQ 3 …. 

44 

44

A typical REGISTRY sequence record for a 

patent sequence 

L1 ANSWER 1 OF 1 REGISTRY COPYRIGHT 2009 ACS on STN 

ED Entered STN: 16 Jan 2007 

RN 917531-59-0 REGISTRY 

CN 20: PN: WO2006137596 SEQID: 21 unclaimed protein (CA INDEX NAME) 

FS PROTEIN SEQUENCE 

SQL 128 

PATENT ANNOTATIONS (PNTE): 

Sequence |Patent 

Source |Reference 

=========+============ 

Not Given|WO2006137596 

|unclaimed 

|SEQID 21 

WIPO and other patent sequences typically 

enter REGISTRY within 27 days of publication 

– in this example only 20 days. 

SEQ 1 KCDLALDPDL ARIMAHSRDY DEQLHVWLAW RDAIGPQIRD KYIQYVQMAN 

51 HAARLNGFHD AGQQQREAYE DSDINSQLTE LWATLAPLYR ELHAYVRRHL 

101 VQRYGPERVR PDGPMPAHLL GNMWSRAN 

MF Unspecified 

CI MAN 

SR CA 

LC STN Files: CA, CAPLUS 

DT.CA CAplus document type: Patent 

RL.P Roles from patents: PRP (Properties) 

Since October 1999, CAS REGISTRY patent sequence 

records include the publication number, SEQ ID number, and 

an intellectually assigned claimed/unclaimed notation. 

45 

45

The corresponding basic patent record is 

in CAplus on STN 

CAS provides value added 

abstracting and indexing for the 

L1 ANSWER 1 OF 1 CAPLUS COPYRIGHT 2009 ACS on STN 

AN 2006:1357195 CAPLUS 

DN 146:95066 

TI Screening for effectors of insect dipeptidyl CAplus carboxypeptidase basic publication. A as 

insecticides 

IN Shimokawatoko, Yasutaka; Craen, Marc Van De; Nooren, Irene; Turconi, 

Sandra; Naudet, Yann; Nys, Guy; Debaveye, Jurgen 

PA Sumitomo Chemical Company, Limited, Japan 

FAN.CNT 1 

PATENT NO. KIND DATE APPLICATION NO. DATE 

--------------- ---- -------- -------------------- -------- 

PI WO 2006137596 A2 20061228 WO 2006-JP313039 20060623 

JP 2007000060 A 20070111 JP 2005-183031 20050623 

PRAI JP 2005-183031 A 20050623 

The sequence is linked to the 

AB Methods of screening for effector of the dipeptidyl carboxypeptidase A 

(I) of insects for use as insecticides is described. . . . . 

IC ICM A01N 

CC 5-4 (Agrochemical Bioregulators) 

Section cross-reference(s): 3, 7, 12 

. . . . 

IT 917531-51-2 917531-53-4 917531-55-6 917531-57-8 917531-59-0 

RL: PRP (Properties) 

(unclaimed protein sequence; screening for effectors of insect 

dipeptidyl carboxypeptidase A as insecticides) 

CAplus patent family record by its 

CAS Registry Number ® . 

46 

46

Sequences are indexed from patents 

• 60 patent authorities from around the world 

– Including WIPO, EPO, USPTO, JP, DE, GB, 

FR, RU, and CA 

• For the major patent authorities listed 

above, timeliness is top notch 

– Bibliographic information is available in CAplus 

within 2 days of patent issuance 

– Sequences are available in REGISTRY within 1 

month 

47 

47

REGISTRY sequences also come from 

>3,000 life science journals 

• Biochemistry 

• Cell 

• EMBO Journal 

• Gene 

• Journal of Biological Chemistry 

• Journal of Cell Biology 

• Journal of Molecular Biology 

• Nature 

• Nucleic Acid Research 

• Nature Genetics 

• Proceedings of the National Academy of Sciences 

• Science 

48 

48

Unique sequence types are indexed 

in CAS REGISTRY 

• Naturally occurring proteins and nucleotides 

• Chemically modified peptides and proteins 

• Sequences deduced from gene translations 

• GenBank sequences and translations 

• Multichain proteins 

• Cyclic peptides 

• Fusion proteins 

• Peptide-metal complexes 

• Sequences containing uncommon amino acids 

• Protein-nucleotide sequences (PNA sequences) 

49 

49

Sequence searching in CAS REGISTRY 

has many advantages 

• Links to CAplus and other databases for 

references 

– Add date restrictions 

– Add keywords for relevance 

• Links to electronic full text of journal articles 

and patents 

• Current awareness alerts based on similarity 

search results 

50 

50

Agenda 





51 

51

There are three main web resources that 

provide searchable patent sequence data 

• National Center for Biotechnology Information 

(NCBI) of the U.S. National Library of Medicine 

– www.ncbi.nlm.nih.gov 

• European Bioinformatics Institute* (EBI) 

– www.ebi.ac.uk 

• DNA DataBank of Japan (DDBJ) 

– www.ddbj.nig.ac.jp 

• The USPTO, EPO, and JPO rely on the NCBI, 

EBI, and DDBJ, respectively, to provide an 

interface for searching patent sequence data 

(* The EBI is the U.K. based outstation of the European Molecular Biology Laboratory – EMBL) 

52 

52

Why does STN have more patent 

sequences than NCBI? 

1. NCBI has a substantially incomplete collection of 

WIPO/PCT sequence data 

2. NCBI does not cover any USPTO Published 

Application sequence data 

3. DGENE and REGISTRY cover many more patent 

authorities than NCBI 

4. DGENE, USGENE, PCTGEN, and REGISTRY 

are typically much more timely than NCBI 

5. NCBI does not cover all of the USPTO granted 

patent sequence data available in USGENE 

53 

53

In addition, NCBI/EMBL/DDBJ patent 

records have only minimal bibliographic 

and text data 

Reminder: NCBI/EMBL/DDBJ cover 

sequences from U.S. granted 

patents – sequences from U.S. 

published applications are not 

covered (see previous slide). 

54 

54

Agenda 





55 

55

A simple BLAST ® example shows the 

importance of using STN databases 

Search Question 

Find all patent references to Breast Cancer 1, early 

onset isoform 1 (NCBI: NP_009225), or other very 

similar proteins (i.e. >80% match). 

(Search conducted on June 12, 2008) 

56 

56

Homo sapiens Breast Cancer 1, early onset 

isoform 1 protein (NCBI: NP_009225) 

57 

57

The best answer from DGENE 

=> D BIB AB PSL ORGN SCORE ALIGN 

114 sequence hits were 

found in DGENE. 


AN AFU71404 protein DGENE 

TI Diagnosing breast cancer or a susceptibility to breast cancer 

comprises detecting BRCA2 999del5 and BARD1 Cys557Ser. 

IN Stacey S N; Sulem P; Thorsteinsdottir U; Kong A 

PA (STAC-I) STACEY S N. . . . . 

PI US 2007092900 A1 20070426 65 

AI US 2006-515368 20060831 

PRAI US 2005-730703P 20051026 

OS 2007-556498 [54] 

CR N-PSDB: AFU71403 

DESC Human breast cancer 1 (BRCA1) protein. 

PSL Disclosure; SEQ ID NO 2 

AB The present invention relates to a methods for diagnosing and 

characterizing breast cancer or a susceptibility to breast cancer in 

an individual comprising detecting breast cancer 2 (BRCA2) 999del5 

and BRCA1 associated RING domain 1 (BARD1) Cys557Ser. . . . . 

ORGN Homo sapiens. 

SCORE 3722 100% of query self score 3722 

BLASTALIGN 

Query = 1863 letters 

Length = 1863 

Score = 3722 bits (9652), Expect = 0.0 

Identities = 1863/1863 (100%), Positives = 1863/1863 (100%) 

Query: 1 MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ 

MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ 

Sbjct: 1 MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ 

DGENE records feature 

extensive Thomson Reuters 

value-added content. 

58 

58

The best answer from USGENE 

=> D BIB AB ECLM ORGN SCORE ALIGN 


found in USGENE. 


AN 20070083334.873670 Protein USGENE 

TI Methods and systems for annotating biomolecular sequences 

(PublishedApplication) 

IN Mintz Liat (Kendall-Park, NJ); Xie Hanqing (Plainsboro, NJ); . . . . 

PA Compugen Ltd 

PI US 20070083334 A1 20070412 

AI US 2006-443428 20060531 

DT Patent 

AB A method of annotating biomolecular sequences. The method comprises 

(a) computationally clustering the biomolecular sequences according 

to a progressive homology range, to thereby generate a plurality of 

clusters each being of a predetermined homology . . . . 

ECLM US20070083334 A1: 1-98. (canceled) 99. An isolated protein, having a 

sequence according to the amino acid sequence of SEQ ID NO: 836875. 

ORGN Homo Sapiens 


BLASTALIGN 


Length = 1863 






Note that this best answer differs 

from that found in DGENE. 

59 

59

The best answer from PCTGEN 

=> D BIB ORGN SCORE ALIGN 


AN 2007047796.8180 PRT PCTGEN 

TI TISSUE- AND SERUM-DERIVED GLYCOPROTEINSAND METHODS OF THEIR USE 

PA Institute for Systems Biology 

Zhang, Hui 

Aebersold, Rudolf H. 

PI WO 2007047796 20070426 

RLI US 2005-728044P 20051017 

ED 20070427 

DT Patent 

ORGN Homo sapiens 


found in PCTGEN. 

Note that this is a different 

best answer from those found 

in DGENE and USGENE 

(previous slides). 


BLASTALIGN 


Length = 1863 






60 

60

The best patent answer from REGISTRY 

Note that this is the same 

best answer found in 

DGENE. 

53 sequence hits were found 

in REGISTRY. 

61 

61

The best patent answer from NCBI 


found at NCBI. 

Note that these patents are not the same 

best answers seen in DGENE, USGENE, 

PCTGEN, or REGISTRY. 

Reminder: NCBI provides only protein 

patent sequence coverage from U.S. issued 

patents. U.S. and WIPO/PCT (WO) 

published application protein sequences 

cannot be retrieved from NCBI. 

62 

62

Summary of results for Breast Cancer 1, 

early onset isoform 1 protein (NCBI: 

NP_009225) 

SEQs 

> 80% 

PNs 

PATENT 

FAMILIES 

DGENE 114 36 26 

USGENE 70 38 22 

PCTGEN 7 4 4 

REGISTRY 52 30 23 

NCBI* 32 21 9 

Total Unique - - 34 

(* All of the NCBI patent hits were for U.S. patents, and none of them were unique compared to USGENE.) 

63 

63

Agenda 





64 

64

Comparing databases 

• DGENE 

– The most comprehensive global patent 

sequence database 

– Implemented in-house at major patent offices* 

• USGENE 

– Sequences from equivalent USPTO 

applications and patents 

– Incorporates all U.S. patent sequence data 

available at NCBI 

* See page 11: www.trilateral.net/projects/biotechnology/guide2.pdf 

65 

65

Comparing databases (cont.) 

• PCTGEN 

– Sequences from equivalent WIPO/PCT 

publications 

– The complete collection of e-published 

sequences from WIPO 

• REGISTRY 

– Complementary value-added indexing to 

DGENE 

– Unique non-patent literature coverage 

66 

66

Database timeliness is an important factor 

in understanding comprehensiveness 

Update 

Frequency 

Typical 

Timeliness 

PCTGEN Weekly 24 hours 

USGENE Weekly 3 days 

REGISTRY Daily 27 days 

DGENE Biweekly 65 days 

NCBI/EMBL Daily 1-6 months 

Value 

added 

67 

67

Resources for sequence searching on STN 

• Sequence Searching on STN modular workshop 

www.fiz-k.com/bostonsequenceworkshop 

– Sequence Code Match (SCM) searching 

– DGENE, USGENE, PCTGEN content and searching 

– CAS REGISTRY and REGISTRY BLAST 

– Multifile searching and post-processing 

• USGENE resources, reference materials and FAQ 

www.sequencebase.com 

• CAS REGISTRY sequence coverage and 

resources 

www.cas.org/support/stngen/stndoc/sequences.html 

68 

68

For more information … 

CAS 

• E-mail: help@cas.org 

• Training and Support: 

www.cas.org/support/ 

FIZ Karlsruhe 

• E-mail: helpdesk@fiz-karlsruhe.de 

• Training and Support: 

www.stn-international.de 

Feb. 2010

STN Sequence Databases - FIZ Karlsruhe

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