Structure searching Derwent World Patents ... - STN International

STRUCTURE SEARCHING DERWENT WORLD 

PATENTS INDEX ® (DWPI SM ) USING STN 

EXPRESS ® : Part I 

INTELLECTUAL PROPERTY SOLUTIONS 

DONALD WALTER 

AUGUST 16, 2011

AGENDA 

•Part I 

– THE PROBLEM; WHY IS IT DIFFICULT TO SEARCH 

CHEMICAL STRUCTURES IN PATENTS? 

– SOLUTION; DWPI STRUCTURAL REPRESENTATIONS 

– DWPI PATENT COVERAGE 

– COMPOUND COVERAGE – WHICH COMPOUNDS ARE 

COVERED? 

– COMPOUND COVERAGE – WHAT INFORMATION ABOUT 

THE COMPOUNDS IS COVERED? 

– STRUCTURE OF A DCR RECORD 

• Part II 

– CHEMICAL STRUCTURE SEARCH EXAMPLE 

– CHEMICAL FRAGMENTATION CODE SEARCH EXAMPLE 

– MULTIFILE STRUCTURE SEARCH EXAMPLE 

2

THE PROBLEM; WHY IS IT DIFFICULT TO SEARCH 


• Although patents 

are easily word 

searchable, 

chemical 

structures are 

often not 

represented by 

words 

• For example, US 

7,956,219 … 

3

AGENDA 

•Part I 






COVERED? 




• Part II 




4

SOLUTION; DWPI STRUCTURAL 

REPRESENTATIONS 

AN 2004-061945 [200406] WPIX 

ED 20050528 

DNC C2004-025265 [200406] 

TI New AB amino WO 2003095421 acid analogues A1 UPAB: are L-arginine 20090205 transport modulators useful in the treatment 

of conditions NOVELTY - associated Amino acid with analogues underactivity (I) that of are nitric able oxide to modulate synthetic L-arginine pathway transport e.g. 

diabetes into and cells hypertension 

are new. 

DC B05 

IN EDE N CMC J; HUNTER UPB DETAILED 

A 20060121 DESCRIPTION - Amino acid analogues of formula (I) that are able to 

modulate N; KAYE D M; TRAINOR R W; EDE N; HUNTER A; KAYE D; TRAINOR R 

PA (BAKE-N) BAKER M2 

L-arginine transport into cells are new. 

A 

*01* 

= IDI optionally HEART&DIABETES G015 G016 

CH2; 

G030 INST G112 HOLDINGS; G543 H5 (BAKE-N) H541 H6 H685 BAKER H689 MEDICAL H8 J0 RES J011 INST; J3 J331 K0 L2 

(EDEN-I) EDE G N = J; optionally (HUNT-I) L250 M280 

O; HUNTER M311 A M323 N; (KAYE-I) M342 M344 KAYE M353 D M; M373 (MIMO-N) M392 M414 MIMOTOPES M510 M520 PTY M532 M541 M 

LTD; (TRAI-I) R1 TRAINOR = H, thio, 

P450 R W; NH2 

P520 (BAKE-N) or 

P522 

optionally 

P526 BAKER P528 IDI substituted HEART&DIABETES P814 P816 Specific lower 

M905 INST alkyl, 

M904 compound 

lower alkylamino, 

CYC 102 arylamino, aralkylamino, DCN: RACNZ5-N aryloxy, RACNZ5-T heteroaryloxy, cycloalkyloxy, cycloheteroalkyloxy, 

PI WO 2003095421 aralkyloxy, A1 heteroaralkyloxy, 20031120 DCR: 825134-N (200406)* ,... 825134-T EN 127[4] numbers - role 

AU 2003221636 M2 R2, *02* R3, A1 20031111 R4 G015 = H, G016 optionally (200442) G030 G112 EN substituted G543 H5 H541 lower H6 alkyl, H602 H608 aryl, H642 aralkyl, H8 J0 ... J011 J3 J331 K 

An INDEPENDENT L2 L250 CLAIM M280 is M311 also . M322 . included . M342 for M373 a M392 combinational M414 M510 library M520 M532 of M541 M710 P45 

ADT WO 2003095421 compounds. A1 WO 2003-AU551 P520 P522 P526 20030508; P528 US P814 20060094902 P816 M905 A1 M904 Provisional US . . . 

FDT DE 60325959 ACTIVITY E Based on DCN: - Vasotropic; EP RACNZ6-N 1501791 A; Antiatherosclerotic; RACNZ6-T AU 2003221636 A1 Based Antidiabetic; on WO 2003095421 Hypotensive; A; ... 

PRAI US 2002-379556P Cardiant; Cardiovascular-Gen. 

DCR: 20020509 825135-N 825135-T 

US 2002-379305P MECHANISM 20020509 OF ACTION - L-arginine transport . . . modulator. Generic (I) (Markush) 

were tested for the 

US 2005-513768 modulation M2 *21* of arginine F010 20050831 F019 entry F020 into F029 the G003 cells G010 by using G014 G015 HeLa G019 cells. G020 3- G021 G029 G030 G039 G 

IC ICM C07C279-16 

cyclobutylmethoxy-4-(N'-3,5-trifluoromethyl-benzyl-... 

G050 G100 G111 G112 G113 G221 G299 G553 G563 H100 H102 H161 H401 H441 H 

ICS A61K031-166; USE - A61K031-341; (I) H541 is useful H8 J011 A61K031-351; in J197 the treatment J221 A61K031-36; J241 of J261 conditions J271 compound A61K031-44; J290 associated J321 A61P003-10; J341 numbers 

with J361 J371 J471 J58 

A61P009-04; underactivity A61P009-08; (preferred) K0 K820 A61P009-10; K850 or hyperactivity L2 L250 A61P009-12; M116 M119 of the M121 C07D213-74; nitric M122 oxide M123 C07D307-52; synthetic M124 M125 C07D309- pathway, M126 M129 M135 

06; abnormal C07D407-12 transport M137 of M139 L-arginine M141 M210 and M211 beneficial M212 M213 vasodilatation... 

IPCI A61K0031-155 ADVANTAGE [I,A]; A61K0031-155 - (I) have the [I,A]; potential A61K0031-155 to retard [I,C]; -role M214 M215 M216 M220 M221 M222 M223 M 

M225 M226 M231 M232 M233 M240 M262 the M271 A61K0031-155 progression M272 M273 M280 of [I,C]; vascular M281 M282 M283 M 

A61K0031-155 disease in conditions [I,C]; M312 A61K0031-166 M313 such M314 as hypertension, M315 [I,A]; M316 A61K0031-166 M320 heart M321 failure M322 [I,C]; M323 and A61K0031-341 diabetes.... 

M331 M332 M333 [I,A]; M340 M342 M 

TECH A61K0031-341 ORGANIC CHEMISTRY [I,A]; M372 - A61K0031-341 Preparation: M373 M381 M391 [I,C]; (I) M392 can A61K0031-341 be M393 synthesized M413 M414 [I,C]; by M510 using A61K0031-341 M520 techniques M521 M522 [I,C]; and M523 M531 M 

A61K0031-351 materials according [I,A]; M533 A61K0031-351 to M540 Carey M541 and M542 [I,A]; Sundberg M543 A61K0031-351 M630 1989 and M640 Greene M650 [I,C]; M710 and A61K0031-351 Wuts P450 1991.... P520 P522 [I,C]; P526 P528 P 

ABEX A61K0031-351 DEFINITIONS - [I,C]; Preferred P816 A61K0031-357 M905 Definition: M904 [I,C]; - R1 A61K0031-36 = 4-6C cycloalkyl [I,A]; (preferably A61K0031-44 cyclobutyl [I,A]; or 

... cyclohexyl); - R2 MCN: = (optional) 0117-09801-N 1-3C 0117-09801-T 

trihaloalkyl; - R3 = optionally halo; and - R4 = 

IPCR A61K0031-155 halo or M2 1-3C [I,A]; *22* trihaloalkyl A61K0031-155 F010 F019 (chlorine F020 [I,C]; F029 A61K0031-166 or... G003 G010 G014 [I,A]; Chemical 

G015 A61K0031-166 G019 G020 G021 [I,C]; G029 G030 G039 G 

A61K0031-341 ADMINISTRATION [I,A]; G050 - (I) A61K0031-341 G100 can be G111 administered G112 [I,C]; G113 A61K0031-351 G221 by oral, G299 intravenous, G553 [I,A]; G563 A61K0031-351 H100 intraarterial, 

H102 H161 [I,C]; H401 H441 H 

A61K0031-357 buccal, sub-lingual [I,C]; A61K0031-36 or intranasal [I,A]; routes. A61K0031-44 [I,A]; A61K0031-44 [I,C];... 

EPC A61K0031-155; SPECIFIC A61K0031-341; COMPOUNDS 

H541 

- 

H8 

20 

J011 

A61K0031-351; compounds 

J193 J221 

(I) A61K0031-44; are 

J231 

specifically 

J290 J321 fragmentation J331 

C07C0279-18; claimed 

J431 

e.g. 

J581 K0 codes 

K820 K850 L2 L2 

C07D0213-75; ... 

ICO M07C0101:04; 3-cyclobutylmethoxy-4-(N'-3,5-trifluoromethyl-benzyl-guanidino)benzamide. 

M116 M119 M121 M122 M123 M124 M125 M126 M129 M135 M136 M137 M139 M141 M 

M07C0101:14; M07D0407:12 

NCL NCLM 564/147.000 

EXAMPLE - Thioalkyl M211 derivative M212 M213 M214 of 2-methyleneoxy M215 M216 M220 cyclobutyl-4-amino 

M221 M222 M223 M224 M225 M226 M231 M 

FCL A61K0031-166; substituted A61K0031-341; benzamide M233 M240 was A61K0031-351; added M262 M271 to 3,5-bis(trifluoromethyl) M272 M273 M280 M281 M282 

A61K0031-36; A61K0031-44; benzylamine M283 M311 

A61P0003-10; in M312 M313 M314 M 

... 5 

FTRM 4C037; dimethyl 4C055; sulfoxide M316 

4C062; 4C063; and M320 kept M321 

4C086; at 4C201; 75degreesC M322 M323 M331 

4C206; for 4H006; 8.5 M332 hours. M333 

4H777; Finally, M340 M342 

4C055/AA01; the M349 M372 M373 M381 M 

4C063/AA01; amine solution 4C086/AA01; was M392 worked M393 

4C206/AA01; up M413 to M414 

4H006/AA01; give M510 3,5-bis(trifluoromethyl) M520 M521 M522 M523 

4C086/AA02; 4C206/AA02; benzylamine 

M531 M532 M533 M540 M541 M

AGENDA 

•Part I 






COVERED? 




• Part II 




6

DWPI PATENT COVERAGE 

• Pharmaceutical 

– Patents stated to be of pharmaceutical or 

veterinary interest, as well as those that refer 

to compounds used as intermediates in the 

manufacture of pharmaceutical or veterinary 

products. 

– Patents on compositions used for diagnosis 

or analysis in the pharmaceutical and/or 

veterinary fields (e.g. stains for bacterial 

pathogens). 

– Patents on artificial sweeteners, chemical 

warfare agents, and plaque-disclosing 

compositions. 

– Patents dealing with the production of 

formulations, e.g. tablets, pills, capsules, 

suppositories, aerosols, etc. Also patents on 

devices specifically designed for dispensing 

pharmaceuticals, e.g. syringes, child-proof 

closures, calendar pill boxes, aerosol 

devices, etc. 7


• Agricultural and veterinary 

– Pest control agents such as insecticides, 

miticides, rodenticides, molluscicides, 

slugicides, vermicides (nematocides, 

anthelmintics, etc.), pest repellents and 

attractants, and soil fumigants. Also biological 

control using microorganisms, predators, or 

natural products. 

– Chemical warfare agents 

– Plant growth control agents such as 

herbicides, weedicides, defoliants, desiccants, 

fruit drop and set controllers, rooting 

compounds, sprouting inhibitors, growth 

stimulants and retardants, moss and lichen 

controllers. Also plant genetics. 

– Plant disease control agents such as 

fungicides, viricides, timber preservatives, and 

bactericides. 

– Soil improvement agents such as fertilisers, 

trace metal additives, bacterial action control 

stimulants, and soil consolidation agents (if 

used for agricultural purposes). 

– Veterinary products such as disease control 

agents, nutritional agents, and veterinary 

vaccines. 

8


• Other chemical compounds (non-polymeric), as well 

as the apparatus and novel catalysts for producing 

them. For example, compounds used in cosmetics, 

fuels, dyes and more). 

• Includes their production, purification, use, detection, 

removal, and phase changes 

• Exceptions 

– Monomers taking part in a polymerisation reaction unless the 

patent is concerned with the production or purification of the 

monomer 

– Starting materials for a chemical reaction unless the patent is 

concerned with the production or purification of the starting 

material. 

– Polymerisation catalysts are not normally classified in 

Section E unless the novelty of the invention is the catalyst. 

– Mixtures of compounds described as a cut (i.e. hydrocarbon 

feedstock) in a petrochemical process (usually) 

– Highly complex, non-stoichiometric compounds, e.g. those 

used as fluorescent materials, might not bem but simpler 

compounds normally are. 

– Solvents and very common reagents, e.g. water 

9

AGENDA 

•Part I 






COVERED? 




• Part II 




10

COMPOUND COVERAGE – WHICH 

COMPOUNDS ARE COVERED? 

The following specific and Markush structures are indexed with BCE 

Chemical Fragmentation Codes and the Merged Markush Service; 

• All compounds and reaction intermediates stated to be novel 

• Products of new processes 

• New uses of known materials 

• Materials detected and detecting agents 

• Detection media 

• Materials recovered or purified in new ways 

• Materials removed and removing agents (only since 1977, unless they 

were the only chemicals in the invention that could be indexed) 

• Components of compositions that are essential to the invention 

• Novel catalysts (1970+) 

• Activities, properties, and uses 

• Chemical formulations and apparatus 

11



The following specific structures are also indexed with 

Derwent Registry numbers 

• It is on the list of ~2100 compounds in the DRN 

• Significant compounds or significant non-metallic 

elements mentioned in the claims or examples 

– An example of an insignificant compound is a solvent 

mentioned in a process in which any solvent may be used. 

More details are in “CPI Chemical Indexing Guidelines Indexing 

of Chemical and Pharmaceutical Patents”, 

http://science.thomsonreuters.com/scientific/m/pdfs/mgr/che 

mical_index_guidelines.pdf 

12



The following specific structures are also indexed with the Derwent 

Chemistry Resource 

• All claimed compounds up to a maximum of ~99. This number is 

reduced if a Markush is also needed. (Max no. of DCR + Markush 

records =99.). 

• At least 1 example, which should be the best example illustrating the 

invention (usually the one in the abstract). If the abstract (best) example 

is also claimed, then another should be selected. 

• Further examples input at analysts discretion, but more should be 

selected if there are examples which are structurally dissimilar from 

those claimed, but still representative of the Markush. 

• Selected examples should be "real" not prophetic; i.e. should have 

supporting data such as preparative data, activity data etc. 

• Compounds from the disclosure can be indexed at the Analysts 

discretion. Usually these would be if there are no (or few) claimed or 

exemplified compounds, or if there are novel disclosed compounds that 

are not claimed. 

13



Indexing year Patent says 

, for example where R 1 =H, 

R 2 R O 

=H [i.e. Penicillin G] 

(a Markush) (a specific example of the 

Markush) 

1 

CH 

3 

CO H 

2 

A specific which is not part of a 

Markush 

1963 BCE BCE 

1981 BCE DRN 1 

BCE, DRN 1 

1987 BCE, MMS DRN 1 

BCE, MMS, DRN 1 

1999 BCE, MMS DRN 1 , DCR BCE, MMS, DRN 1 , DCR 

Note 1; DRNs are applied if there is a number representing the compound 

R 2 

O 

NH 

N 

S 

CH 3 

CO 2 H 

O 

C 

O 

14

AGENDA 

•Part I 






COVERED? 




• Part II 




15

COMPOUND COVERAGE – WHAT INFORMATION 

ABOUT THE COMPOUNDS IS COVERED*? 

* Besides the structure itself 

• USES of novel and known materials 

• Synthesis 

• Chemical formulations and apparatus 

• Materials detected and detecting agents 

• Detection media 

• Materials recovered or purified in new ways 

• Materials removed and removing agents (only since 1977, unless they 

were the only chemicals in the invention that could be indexed) 

• Components that are essential to the inventive formulation 

• Novel catalysts (1970+) 

• Activities, properties, and uses 

16

AGENDA 

•Part I 






COVERED? 




• Part II 




17

STRUCTURE OF A DCR RECORD 

DCR number (used to find the biblio AN.S DCR-90406 

record covering this cpd) 

DCSE 90406-0-0-0 

Preferred chemical name CN.P CEPHALOSPORIN-C 

Systematic chemical name CN.S 3-Acetoxymethyl-7-(5-amino-5-carboxypentanoylamino)-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic 

acid 

Synonyms SY CEPHALOSPORIN C; CEPHALOSPORIN-C; 

VIFAZOLIN 

Molecular formula MF C16 H21 N3 O8 S 

Segment molecular formulae SMF C16 H21 N3 O8 S *1; TOTAL *1; TYPE *1 

Molecular weight MW 415.4251 

Structure Derwent Compound Number SDCN R00220 

Structure Derwent Registry Number SDRN 0220 

Class of compound CC BETA LACTAMS 

18

AGENDA 

•Part I 






COVERED? 




• Part II 




19

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20

Structure Searching Derwent World Patents 

Index ® (DWPI SM ) using STN Express ® : Part II 

Robert Austin – FIZ Karlsruhe

Agenda 

• Chemical structure search example 

– The DWPI Chemistry Resource (DCR) 

• Chemical fragmentation code search example 

– Generating and searching queries using STN Express 

• Multifile structure search example 

– Searching in combination with REGISTRY/CAplus SM 

2

Chemical structure search example 

Search Question: 

Search for DWPI patent references to specific 

carbapenem derivatives of substructure (I) 

(I) 

Learn more about the basics of structure searching: 

http://www.cas.org/support/stngen/stndoc/structure.html. 

3

Chemical structure search options 

• Exact search (EXA) 

– Retrieves specific compounds and isotopes 

• Family search (FAM) 

– Retrieves specific compounds, isotopes, salts and mixtures 

• Closed Substructure Search (CSS) 

– Allows for substitution at defined positions 

• Substructure Search (SSS) 

– Allows for substitution at any position 

• Sample search (SAM) 

– Free-of-charge pre-search 

• Subset search (SUBSET) 

– Structure search on a database subset 

• Batch search (BATCH) 

– For broad structure queries which may reach system limits 

4

How to run a structure search in DWPI 

1. Draw & save the structure query in standard 

format with STN Express (or STN on the Web) 

2. Upload the structure query to DWPI on STN 

3. Run the structure search, e.g.: 

a. Sample search => S L1 SSS SAM 

b. Full search => S L1 SSS FULL 

4. Retrieve DWPI patent records 

E.g.: => S L2/DCR 

5. Display DWPI patent records with DCR hit 

structures (HITSTR) in-context 

E.g.: => D L3 1- FULLG HITSTR 

5

Draw & save the structure query in standard 

format with STN Express 

6

Upload the structure query to DWPI on STN 

Upload the query with the ‘Q’ button. 

7

=> 

Uploading C:\. . . .\My Documents\STN Express 8.4\Queries\CARBAPENEM.str 

L1 STRUCTURE UPLOADED 

=> D 

L1 HAS NO ANSWERS 

L1 STR 

Structure attributes must be viewed using STN Express query preparation. 

=> S L1 SSS SAM 

Run a sample structure search 

SAMPLE SEARCH INITIATED 15:58:51 FILE 'WPIX' 

SAMPLE SCREEN SEARCH COMPLETED - 157 TO ITERATE 

100.0% PROCESSED 157 ITERATIONS 50 ANSWER 

. . . . 

L2 50 SEA SSS SAM L1 

The uploaded structure query (L1). 

Option: display the query (L1), to 

verify that the Upload was successful. 

Run a substructure (SSS) sample 

(SAM) search using the query (L1). 

50 compounds are retrieved (L2). 

8

=> D SCAN 

Review some answers using D SCAN 

L2 50 ANSWERS WPIX COPYRIGHT 2011 THOMSON REUTERS on STN 

CN.S 3-{5-[2-(7-Fluoro-2,3-dihydro-benzo[1,4]dioxin-6-yl)-ethylcarbamoyl]pyrrolidin-3-ylsulfanyl}-6-(1-hydroxy-ethyl)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic 

acid 

MF C25 H30 F N3 O7 S 

HOW MANY MORE ANSWERS DO YOU WISH TO SCAN? (1):3 

The effectiveness of 

the query (L1) may be 

assessed by reviewing 

some records (L2), e.g. 

using the free-ofcharge 

SCAN format. 

L2 50 ANSWERS WPIX COPYRIGHT 2011 THOMSON REUTERS on STN 

CN.S 3-{5-[2-(7-Fluoro-2,3-dihydro-benzo[1,4]dioxin-6-yl)-ethylcarbamoyl]pyrrolidin-3-ylsulfanyl}-6-(1-hydroxy-ethyl)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic 

acid 

MF C25 H30 F N3 O7 S 

. . . . 

9

=> S L1 SSS FUL 

Run a substructure (SSS) full-file 

FULL SEARCH INITIATED 15:59:53 FILE (FUL) 'WPIX' search using the query (L1). 

FULL SCREEN SEARCH COMPLETED - 1444 TO ITERATE 

100.0% PROCESSED 1444 ITERATIONS 

1210 ANSWERS 

. . . 

L3 1210 SEA SSS FUL L1 

=> S L3/DCR 

L4 678 L3/DCR 

Run a full structure search 


678 DWPI patent records are retrieved (L4). 

10

Retrieve and display DWPI patent records 

=> D BIB HITSTR 

L4 ANSWER 1 OF 678 WPIX COPYRIGHT 2011 THOMSON REUTERS on STN 

AN 2011-J51474 [201150] WPIX 

TI Producing biosensor for identifying anti-infective substances by 

selecting clones with anti-infective-responsive reporter expression 

and identifying clones exhibiting different anti-infective-responsive 

reporter expression as biosensors 

DC B04; D16; S03 

IN BUMANN D; HAHN C; MECKLENBRAEUKER I; RUBNER Y; SCHLEBERGER C 

PA (UYFR-N) UNIV FREIBURG ALBERT-LUDWIGS 

CYC 125 

PIA EP 2348127 A1 20110727 (201150)* EN 29[6] 

WO 2011089260 A1 20110728 (201150) EN 

ADT EP 2348127 A1 EP 2010-732 20100125; WO 2011089260 A1 WO 2011-EP50959 

20110125 

PRAI EP 2010-732 20100125 

AN.S DCR-97728 

CN.P IMIPENEM 

CN.S 3-(2-Formimidoylamino-ethylsulfanyl)-6-(1-hydroxy-ethyl)-7-oxo-1-azabicyclo[3.2 

.0]hept-2-ene-2-carboxylic acid 

SDCN R15097 

Display the DWPI patent 

records with in-context hit 

structures (HITSTR). 

11

Searches may be refined using roles 

• “Roles” in DWPI describe the function of a 

compound in the patent, e.g. 

– Compound is prepared, purified or part of a mixture 

– Compound is claimed or from the examples 

• DCR compounds can have two types of roles 

assigned in DWPI 

– 2-3-letter codes in the IT-display (DCR Roles) 

– Single-letter codes in the CMC display (DCN Roles) 

• Roles can be linked to DCR numbers in the DCR 

search field using the (T)-proximity operator 

12

Example: DCR role searching for preparations 

=> S L3/DCR (T) (PRD OR P OR NEW OR N)/DCR 

L5 290 L3/DCR (T) (PRD OR P OR NEW OR N)/DCR 

=> D TRIAL HIT 2 

L3 = carbapenem 

structure search. 

Use (T)-operator to link DCR 


AN 2011-G80386 [201143] WPIX 

numbers to their roles (/DCR). 

TI Preparing carbapenem derivatives, useful as antibacterial agent, 

comprises contacting or incubating a carbapenem substrate with ThnQ 

enzyme 

DC B02; D16 

IPCI A61K0031-407 [I,A]; A61P0031-00 [I,A]; C07D0477-20 [I,A]; . . . . 

MC CPI: B02-P; B06-D04; B11-A02A3; B14-A01; D05-A02A; D05-C 

IT UPIT 20110708 

108756-CL 108756-PRD; 2512871-CL 2512871-PRD; 2512872-CL 

2512872-PRD; 2512870-CL 2512870-PRD; 1109-67201-CL . . . . 

CMC UPB 20110708 

M2 *01* C108 C810 D011 D013 D016 PRD, D019 P – preparation D030 D690 H1 roles. H100 H181 H4 H401 

H481 H5 H592 H8 H9 J0 J011 J1 J111 J5 J521 L9 L941 M280 M312 

M322 M331 M332 M340 M342 NEW, M373 N – M383 new compound M391 M412 M511 roles. 

M520 M530 

M540 M720 M800 N134 N224 N342 N511 N512 N513 P220 Q233 M905 

M904 

RIN: 41252 

DCN: R04390-K R04390-P 

DCR: 108756-K 108756-P 

DCR-108756: Thienamycin. 

. . . . 

13

DCR searches may also be refined using 

chemical fragmentation codes (CMC) 

=> S L3/DCR (P) (Q262 OR Q263 OR P94!)/M0,M2,M3 

L6 57 L3/DCR (P) (Q262 OR Q263 OR P94!)/M0,M2,M3 

=> D AN TI HIT 


structure search. 

WPIDS/WPIX-users can link DCR 

numbers with fragmentation codes 


AN 2011-B76492 [201118] WPIX via the (P)-proximity operator. 

TI Anti-infective composition, e.g. used for coating medical device 

comprises antimicrobial compound, fatty acid, and glyceride, the fatty 

acid and glyceride being crosslinked 

CMC UPB 20110315 

M2 *17* C101 C108 C550 C800 C801 C802 C804 C805 C807 D013 D019 D690 

H4 H401 H481 H5 H592 H8 H9 J0 J011 J1 J111 J5 J521 K0 L3 

L340 L9 L941 M280 M312 M322 M331 M332 M340 M342 M373 M383 

M391 M412 M431 M511 M520 M530 M540 M782 P210 P220 P942 Q261 

(P) 

Q262 R022 R043 R052 M905 M904 

RIN: 41252 

DCN: R15097-K R15097-M 

DCR-97728: Imipenem. 

DCR: 97728-K 97728-M 

Example: Q263 = sunscreen agent. Q262 = skin protection (except Q263). P94+ = burn, wound and skin treatments. 

14

Chemical fragmentation code search example 


Search for DWPI patent references to all 

carbapenem derivatives of substructure (I) 

(I) 

15

How to run a fragmentation code search 

1. Draw & save the structure query in WPI format 

2. Select Query and Generate WPI strategy from 

the main STN Express window 

3. Select the fields to be searched, e.g. /M0,M2, 

and the strategy is generated and saved 

4. Logon to STN, access WPIDS or WPIX, then 

select Query and Run Command File 

5. Select the command file – this runs line-by-line 

automatically – and review the results 

16

Open, Draw and save the query structure in 

“WPI” format 

Draw and 

save the WPI 

structure. 

Note: By convention, unlike an STN 

structure search, all unsubstituted 

positions are assumed to be H. 

Open a new WPI format 

drawing window. 

17

Alternatively a standard format structure can 

be converted to a WPI format structure 

A standard STN structure 

query can usually be 

converted to WPI format, 

for generating a 

fragmentation code query. 

18

Use STN Express to generate the 

fragmentation code script 

19

Select the search fields (subheadings) and 

generate the fragmentation codes 

STN Express search field options: 

/M0 Pre-1970 Pharma/agrochem 

/M2 1970-date Pharma/agrochem 

/M3 1970-date Other chemicals (excl. M4) 

/M4 1970-date Dyes & pigments 

Other fragmentation code fields 

/M1 1970-date Natural products 

/M5 1963-1999 Steroids 

/M6 1976-date Galenicals/formulations 

20

DWPI fragmentation code strategy is 

generated in Command File format 

Tip: Check that any manual edits 

you make are valid codes, with 

Utilities, Check Command File. 

21

Use Run Command File to execute the 

fragmentation code search online 

22

The command file code query runs 

automatically line-by-line 

=> S (D690(P)H401(P)H481(P)J111(P)J521(P)M331(P)M412)/M0,M2 

L7 2230 (D690(P)H401(P)H481(P)J111(P)J521(P)M331(P)M412)/M0,M2 

=> S L7(P)(M511(P)M520(P)M530(P)M540)/M2 

L8 1274 L7(P)(M511(P)M520(P)M530(P)M540)/M2 

=> S L8(P)(M280(P)M312(P)M321(P)M340(P)M342(P)M391(P). . . .)/M2 

L9 771 L8(P)(M280(P)M312(P)M321(P)M340(P)M342(P)M391(P). . . .)/M2 

=> S L9(P)41252/RIN 

L10 234 L9(P)41252/RIN 

=> S L10(P)(D011(P)D013(P)J011(P)"L941")/M2 

L11 146 L10(P)(D011(P)D013(P)J011(P)"L941")/M2 

=> S (L7(P)M900/M0) OR (L8(P)M901/M2) OR (L10(P)M902/M2) OR L11 

L12 154 (L7(P)M900/M0) OR (L8(P)M901/M2) OR (L10(P)M902/M2) OR L11 

. . . . 

=> S L15(NOTP)("L8" OR M1)/M2 

L16 94 L15(NOTP)("L8" OR M1)/M2 

The Command File runs 

automatically line-by-line. 

STN Express links and groups codes 

together into correctly formatted queries. 

Note: A relatively small answer 

set (L16) is retrieved because this 

is not a substructure search. 

23

Fragmentation code searches may also be 

refined with role codes 

=> S L16 (P) (M720 OR M710)/M2 

L17 78 L16 (P) (M710 OR M720)/M2 

=> D AN TI HITCMC 


code search. 

M720 – preparation role code. 


AN 2009-F45171 [200966] WPIX 

TI New 4-alkyl-7-oxo-1-azabicyclo- (3,2,0)-hept-2-ene-2-carboxylic acid 

derivative for use in preparing medicine for treating and/or 

preventing infectious diseases 

CMC UPB 20091015 

M2 *05* B614 B711 B720 B731 B743 The B744 HITCMC B760 format B791 B793 is often B794 helpful B831 B832 for 

C316 D011 D013 D014 D019 displaying D021 D022 hit fragmentation D601 D690 E720 paragraphs. 

. . . . 

H323 H341 H401 H402 H404 H405 H421 H423 H441 H481 H482 H484 

H521 H522 H523 H541 H592 H600 H608 H609 H621 H622 H623 H641 

H685 H689 H721 H722 J011 J012 J013 J014 J111 J112 J113 J131 

J171 J172 J173 J211 J271 J272 J311 J312 J331 J371 J372 J373 

J521 J522 J523 J581 J582 K353 K399 K620 K640 K699 K810 L142 

L143 L199 L250 L410 L431 L463 L543 L640 L650 L660 L699 L721 

L910 L941 L943 L999 M121 M126 M132 M142 M143 M150 . . . . 

M650 M710 M771 P210 P220 M905 M904 

RIN: 00904 41252 

MCN: 1058-36001-N This hit is a Markush compound. 

M710 – new compound role code. 

24

Option: Edit the fragmentation code query, 

to run a full substructure search…. 

Manually edit, check and save 

a broader, substructure query. 

25

Run the edited fragmentation code query 

=> S (D690(P)J11!(P)J52!(P)(M412 OR M411))/M0,M2 

L18 3236 (D690(P)J11!(P)J52!(P)(M412 OR M411))/M0,M2 

=> S L18(P)(M511 OR M512 OR M513)/M2 

L19 3218 L18(P)(M511 OR M512 OR M513)/M2 

=> S L19(P)(M321 OR M322 OR M323)/M2 

L20 3100 L19(P)(M321 OR M322 OR M323)/M2 

=> S L20(P)41252/RIN 

L21 1275 L20(P)41252/RIN 

=> S L21(P)(D013(P)(D011 OR D019 OR D014)(P)"L941")/M2 

L22 1267 L21(P)(D013(P)(D011 OR D019 OR D014)(P)"L941")/M2 

=> S (L18(P)M900/M0) OR (L19(P)M901/M2) OR (L21(P)M902/M2) OR L22 

L23 1285 (L18(P)M900/M0) OR (L19(P)M901/M2) OR (L21(P)M902/M2) OR L22 

=> S L23(NOTP)"L1"/M2 

L24 1283 L23(NOTP)"L1"/M2 

The Command File runs 

automatically line-by-line. 

Note: This is a substructure search (L24). 

26

Review fragmentation code answers 

=> D AN TI HITCMC FRAGHITSTR 

The fragmentation code hit 

structure (FRAGHITSTR) format 


AN 2011-J51474 [201150] WPIX 

displays the DCR structure for any 

TI Producing biosensor for identifying anti-infective substances by 

selecting clones with anti-infective-responsive specific compounds reporter retrieved. 

expression 

and identifying clones exhibiting different anti-infective-responsive 

reporter expression as biosensors 

CMC UPB 20110805 

M2 *06* C101 C108 C550 C800 C801 C802 C804 C805 C807 D013 D019 D690 

H4 H401 H481 H5 H592 H8 H9 J0 J011 J1 J111 J5 J521 K0 L3 

L340 L9 L941 M280 M312 M322 M331 M332 M340 M342 M373 M383 

M391 M412 M431 M511 M520 M530 M540 M782 M800 Q233 M905 M904 

RIN: 41252 

DCN: R15097-K R15097-M 

DCR: 97728-K 97728-M 

AN.S DCR-97728 

CN.P IMIPENEM 

CN.S 3-(2-Formimidoylamino-ethylsulfanyl)-6-(1-hydroxy-ethyl)-7-oxo-1-azabicyclo[3.2 

.0]hept-2-ene-2-carboxylic acid 

SDCN R15097 

. . . . 

27

Option: Use the (NOTP) operator to exclude hits 

already found via the DCR structure search 

=> S L24 (NOTP) L4 

L25 819 L24 (NOTP) L4 

=> D AN TI HITCMC 

L24 = carbapenem code search. 

L4 = carbapenem structure search. 


AN 2011-H38000 [201146] WPIX 

TI New carbapenem derivatives useful for treatment of infection by 

bacteria e.g. methicillin-resistant staphylococcus aureus 

CMC UPB 20110720 

M2 *17* C316 D013 D014 D690 F011 F012 F014 F423 G010 G011 . . . . 

H682 H683 H684 H685 H686 H689 H8 H9 J0 J012 J013 J014 J111 

J131 J132 J133 J171 J172 J173 J211 J241 J242 J3 J311 J331 

J332 J341 J342 J371 J372 J373 J5 J521 J581 J582 J583 K353 

K399 K442 K499 L143 L145 L199 L640 L650 L660 L699 L9 L941 M1 

M126 M142 M210 M211 M212 M213 M214 M215 M216 M231 M232 M233 

M240 M262 M271 M272 M273 M281 M282 M283 M311 M312 M313 M314 

M315 M321 M322 M323 M331 M332 M333 M340 M342 M349 M353 M362 

M372 M373 M381 M382 M383 M391 M392 M393 M412 M511 M521 M531 

M540 M630 M640 M650 M710 P210 P220 P241 P420 P714 M905 M904 

RIN: 41252 

This hit is a Markush compound. 

MCN: 1111-00001-N 

28

=> D IFULLG 

If we explore this answer further… 


ACCESSION NUMBER: 2011-H38000 [201146] WPIX Full-text 

TITLE: New carbapenem derivatives useful for treatment of 

infection by bacteria e.g. methicillin-resistant 

staphylococcus aureus 

DERWENT CLASS: B02 

INVENTOR: DONG Y; HUANG Z 

PATENT ASSIGNEE: (DONG-I) DONG Y; (HUAN-I) HUANG Z 

COUNTRY COUNT: 1 

PATENT INFORMATION: 

PATENT NO KIND DATE WEEK LA PG MAIN IPC 

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

US 20110160177 A1 20110630 (201146)* EN 17[0] 

APPLICATION DETAILS: 

Use the IFULLG format to 

see patent family, abstract, 

and selected drawing image. 

PATENT NO KIND APPLICATION DATE 

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

US 20110160177 A1 US 2009-650742 20091231 

PRIORITY APPLN. INFO: US 2009-650742 20091231 

INT. PATENT CLASSIF.: 

IPC ORIGINAL: A61K0031-397 [I,A]; A61P0031-00 [I,A]; A61P0031-12 

[I,A]; 

C07D0487-04 [I,A] 

USCLASS NCLM: 514/210.130 

NCLS: 540/350.000 

. . . . 

29

Display formats for reviewing chemical 

fragmentation codes in DWPI 

D CODE All codes, indexing and classes 

D CMC All chemical codes, M0-M6 

D M2, etc Pharma/Agrochem only, etc 

D RIN Ring Index Numbers only 

D HITCMC The hit fragmentation code 

paragraph(s) found in a 

fragmentation code search 

D FRAGHITSTR The DCR structure for any 

specific compounds retrieved in 

a fragmentation code search 

30

Multifile structure search example 


Search for all patent references of cetirizine, 

including salts and mixtures 

31

Multifile structure searching using 

DCR/DWPI and REGISTRY/CAplus 

1. Prepare a suitable standard structure query for 

REGISTRY/CAplus and DCR/DWPI 

2. Run the structure search in REGISTRY/CAplus 

3. Display CAplus records of interest 

4. Run the structure search in DCR/DWPI, and 

remove duplicates between CAplus and DWPI 

5. Display any additional DWPI records 

Note: A comprehensive STN search would also include 

CAS MARPAT and DWPI Chemical Fragmentation Codes. 

32

=> FILE REGISTRY 

Run a sample structure search 

=> 

Uploading C:\. . . .\My Documents\STN Express 8.4\Queries\cetirizine.str 

L1 STRUCTURE UPLOADED 

=> D 

L1 HAS NO ANSWERS 

L1 STR 

Structure attributes must be viewed using STN Express query preparation. 

=> S L1 FAM SAM 

SAMPLE SEARCH INITIATED 18:58:00 FILE 'REGISTRY' 

SAMPLE SCREEN SEARCH COMPLETED - 14 TO ITERATE 

. . . . 

L2 3 SEA FAM SAM L1 

The uploaded structure query (L1). 

Option: display the query (L1), to 

verify that the Upload was successful. 

Run a family (FAM) sample (SAM) 

search using the query (L1). 


33

=> D SCAN 

Review some answers using D SCAN 

L2 3 ANSWERS REGISTRY COPYRIGHT 2011 ACS on STN 

IN Acetic acid, 2-[2-[4-[(R)-(4-chlorophenyl)phenylmethyl]-1piperazinyl]ethoxy]-, 

sodium salt (1:1) 

MF C21 H25 Cl N2 O3 . Na 

Absolute stereochemistry. 

HOW MANY MORE ANSWERS DO YOU WISH TO SCAN? (1):2 

L2 3 ANSWERS REGISTRY COPYRIGHT 2011 ACS on STN 

IN Acetic acid, 2-[2-[4-[(4-chlorophenyl)phenylmethyl]-1piperazinyl]ethoxy]-, 

4-methylbenzenesulfonate (1:1) 

MF C21 H25 Cl N2 O3 . C7 H8 O3 S 

. . . . 

The effectiveness of 

the query (L1) may be 

assessed by reviewing 

some records (L2), e.g. 

using the free-ofcharge 

SCAN format. 

34

=> S L1 FAM FUL 

Run a family (FAM) full-file (FUL) 

FULL SEARCH INITIATED 18:58:25 FILE 'REGISTRY' search using the query (L1). 


100.0% PROCESSED 380 ITERATIONS 85 ANSWERS 

SEARCH TIME: 00.00.01 

L3 85 SEA FAM FUL L1 

=> FILE HCAPLUS 

=> S L3 AND P/DT 

L4 761 L3 AND P/DT 

Run a full structure search 

The full file structure search retrieves 

85 REGISTRY records (L3). 

The full file structure search (L3) retrieves 

761 patent records (P/DT) in CAplus (L4). 

35

Example: CAplus answer retrieved 

=> D BIB HITSTR 

L4 ANSWER 1 OF 761 HCAPLUS COPYRIGHT 2011 ACS on STN 

AN 2011:967083 HCAPLUS Full-text 

TI Oral complex composition comprising pseudoephedrine and levocetirizine 

IN Woo, Jong Soo; Park, Jae Hyun; Kim, Yong Il; Na, Young Jun; . . . . 

PA Hanmi Holdings Co., Ltd., S. Korea 

SO PCT Int. Appl., 29pp. 

CODEN: PIXXD2 

DT Patent 

LA English 

FAN.CNT 1 

PATENT NO. KIND DATE APPLICATION NO. DATE 

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

PI WO 2011093612 A2 20110804 WO 2011-KR367 20110118 

. . . . 

IT 130018-77-8 

RL: PKT (Pharmacokinetics); THU (Therapeutic use); BIOL (Biological 

study); USES (Uses) 

(oral complex composition comprising pseudoephedrine and 

levocetirizine) 

RN 130018-77-8 HCAPLUS 

CN Acetic acid, 2-[2-[4-[(R)-(4-chlorophenyl)phenylmethyl]-1piperazinyl]ethoxy]- 

(CA INDEX NAME) 

Display CAplus patent 

records with in-context 

hit structures (HITSTR). 

36

Repeat the structure search in DCR 

=> FILE WPIX 

=> S L1 FAM FUL 

FULL SEARCH INITIATED 18:59:24 FILE 'WPIX' 


100.0% PROCESSED 49 ITERATIONS 

44 ANSWERS 

SEARCH TIME: 00.00.02 

L5 44 SEA FAM FUL L1 

=> S L5/DCR 

L6 611 L5/DCR 

Access the Derwent World Patents Index 

(DWPI) (files WPINDEX, WPIDS or WPIX). 

Repeat the structure search 

using the same query (L1). 

The full file family search 

retrieves 44 DCR records (L5). 

The 44 DCR records (L5) retrieve 

611 patent records (L6). 

37

Retrieve the unique DWPI records 

=> TRANSFER L4 1- PNK 

Use TRANSFER PNK to 

L7 TRANSFER L4 1- PNK : 4752 crossover TERMSthe 

CAplus 

L8 885 L7 

results (L4) to DWPI (L8). 

=> S L6 NOT L8 

L9 117 L6 NOT L8 

The DCR/DWPI search (L6) adds 

117 unique inventions (L9) to the 

REGISTRY/CAplus results (L4). 

PNK = The patent number/kind code field. This is the most precise field 

to use when crossing over results between STN patent databases. 

38

=> D AN TI 1-50 

Review the unique DWPI records 


AN 2011-J36917 [201149] WPIX 

TI Interleukin-containing composition, comprises interleukin-1 and a 

cyclooxygenase inhibitor, which is diclofenac 

. . . . 


AN 2010-K89255 [201064] WPIX 

TI Oil in water emulsion aerosol foam, useful for treating a skin disease 

e.g. acne and psoriasis, composition comprises active agent, water, 

oil, oil miscible organic solvent, surfactant component and propellant 

. . . . 


AN 2010-F66310 [201037] WPIX 

TI Making levocetirizine involves resolving pair of diastereomer of 

piperazine compound into single diastereomer, and converting single 

diastereomer of piperazine compound with 

1-((4-chloro-phenyl)-phenyl-methyl)-piperazine into levocetirizine 

. . . . 


AN 2009-J67366 [200936] WPIX 

TI Orally disintegrating tablet useful for delivering main ingredient 

e.g. cetirizine hydrochloride for treating allergy, comprises main 

ingredient having specified water solubility and does not contain 

binder 

. . . . 

39

Example: DWPI answer retrieved 

=> D BIB HITSTR 13 


AN 2010-F66310 [201037] WPIX 

TI Making levocetirizine involves resolving pair of diastereomer of 

piperazine compound into single diastereomer, and converting single 

diastereomer of piperazine compound with 

1-((4-chloro-phenyl)-phenyl-methyl)-piperazine into levocetirizine 

DC B03; B05 

IN FIRET J J; ZHU J 

PA (SYNT-N) SYNTHON BV 

CYC 122 

PIA WO 2010057515 A1 20100527 (201037)* EN 35[0] 

NL 1037485 C 20100727 (201140) NL 

ADT WO 2010057515 A1 WO 2008-EP9977 20081121; NL 1037485 C NL 2009-1037485 

20091120 

PRAI WO 2008-EP9977 20081121 

AN.S DCR-174423 

CN.P LEVOCETIRIZINE 

CN.S (2-{4-[(4-Chloro-phenyl)-phenyl-methyl]-piperazin-1-yl}-ethoxy)-acetic 

acid 

SDCN RA0WVA 

. . . . 

40

Summary 

• Chemical structure search example 

– The DWPI Chemistry Resource (DCR) 

• Chemical fragmentation code search example 

– Generating and searching queries using STN Express 

• Multifile structure search example 

– Searching in combination with REGISTRY/CAplus 

41

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