The Addition of Chemical Search Capabilities to PATENTSCOPE: Turning a Full-text Search System into...

InfoChem GmbH © 2016 Dr. Josef Eiblmaier ICIC 2016 Heidelberg, October 16 – 18

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The Addition of Chemical Search Capabilities

to PATENTSCOPE: Turning a Full-text Search

System into a Chemistry Database

J. Eiblmaier1, C. Mazenc2, D. Geppert1, L. Isenko1, H. Saller1

1 InfoChem GmbH

2 World Intellectual Property Organization (WIPO)

ICIC 2016 Heidelberg, October 16 – 18


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» Introduction: WIPO & PATENTSCOPE

» Chemical structure search in PATENTSCOPE

» Technical approach

» Outlook

Outline

© cora / PIXELIO, www.pixelio.de


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World Intellectual Property Organization (WIPO)

» Founded 1967 to ‘encourage creative activity, to

promote the protection of intellectual property

throughout the world’

» A ‘Specialized Agency’ of the United Nations

» Currently 189 member states

» Headquartered in Geneva, Switzerland

By Metatron - Own work, CC BY-SA 3.0,

https://commons.wikimedia.org/w/index.php?curid=1644294

• Global Brand Database

• Global Design Database

• ROMARIN

• WIPO Lex patentscope.wipo.int


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Mission and Vision

» PATENTSCOPE is a global public good

promoting research and innovation

» It provides all stakeholders of innovation with

resources and tools for search and analysis of

trends and insights in business, technology and

academia

Stephanie Hofschlaeger / pixelio.de


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What is it?

» The world’s leading free public

resource of searchable patent full text

documents (descriptions and claims)

» The first site to view weekly PCT

publications

» Search and read all patent collections

in a familiar language and read in your

own language

» Global coverage Oliver Moosdorf / pixelio.de


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Coverage *

» 57,240,000 international and national

patent documents

» 2,926,619 (all) published PCT

applications

» 54,272,593 documents from 43

national & regional collections

» PCT national phase information from

47 countries

» User interface available in eight

languages

* as of September 30th 2016

Paul-Georg Meister / pixelio.de


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» Searchable full text in original

languages (even Chinese, Korean,

Japanese) with - when available -

embedded images

» Results ranking in search hit lists

(Tf/Idf Solr)

» Statistical overview for each result

list in tabular and graph formats

(using SOLR clustering capabilities)

» CLIR

» TAPTA

PATENTSCOPE Strengths



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PATENTSCOPE Key Features: Cross Lingual Information Retrieval

14 languages


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PATENTSCOPE Key Features: Cross Lingual Expansion


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TAPTA: Translation Assistant for Patent Titles and Abstracts


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2006 April: launch of

PATENTSCOPE

replacing the

paper and PDF

versions of the

PCT Gazette

2009 September:

addition of first

national/regional

collections

2010 June: CLIR in

production

2016 October: Chemical

structure search

2011 May: WIPO

Translate in

production

2012

2013

2014 addition of

regional/national

collections

2015 November: Over

50 million patent

documents

PATENTSCOPE Most Important Milestones

patentscope.wipo.int


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The Driving Force

» Chemical structure search

requested by end users

» Debate on the searchability of INNs

in WIPO's SCP (Standing

Committee on the Law of Patents) 1)

» The project can act as a proof of

concept.

» Good progress and availability of

related open source tools allowing us

to envisage a solution affordable by

WIPO (OPSIN, OSRA)

1) http://www.wipo.int/edocs/mdocs/scp/en/scp_21/scp_21_9.pdf



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The Project at a Glance: Addition of Chemical Search

Capabilities to the WIPO PATENTSCOPE Search System

» Project PTD/14/076, July 2015 – Feb. 2016

» Chemical annotation of PATENTSCOPE

full-text documents using InfoChem’s

ICANNOTATOR

» Recognition of graphical representations of

chemical compounds in PATENTSCOPE

documents using multiple I2S tools

» Solr/Lucene based exact structure search

» Workflow system KNIME

» Extension of the PATENTSCOPE GUI with

chemical structure search


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Pre-selection of Documents by IPC Code

» Aim: determination of patents and

applications which are chemically

relevant

» Saves time / reduces hardware

requirements

» Reduces false positive annotations

» 37 IPC codes were selected in an

iterative process using automatic

annotation and chemistry knowledge


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7 -chloro-1,3-dihydro-1-

methyl-5-phenyl-2H-1,4-

benzodiazepin-2-one

GUI: Structure Search


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GUI: Structure Display


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(…) At the moment the surgical procedure starts, benzodiazepin, e.g.

diazepam, is administered in a dose of no more than 5 mg. (…)

(…) At the moment the surgical procedure starts, benzodiazepin, e.g.

@AAOVKJBEBIDNHE-UHFFFAOYSA-N@, is administered in a dose of

no more than 5 mg. (…)

The Concept


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PATENTSCOPE Documents

Enriched PATENTSCOPE Documents

(…) At the moment the surgical

procedure starts, benzodiazepin, e.g.

diazepam, is administered in a dose of

no more than 5 mg. (…)

(…) At the moment the surgical procedure

starts, benzodiazepin, e.g.

@AAOVKJBEBIDNHE-UHFFFAOYSA-N@,

is administered in a dose of no more than 5

mg. (…)

AAOVKJBEBIDNH

E-UHFFFAOYSA-N


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Plausibility

Module

PATENTSCOPE Images (tiff)

ICImg2Struct

CT1

Imago CT2

OSRA

CT3

CT1/2/3

Enriched PATENTSCOPE Documents

(…) At the moment the surgical procedure

starts, benzodiazepin, e.g.

@AAOVKJBEBIDNHE-UHFFFAOYSA-N@,

is administered in a dose of no more than 5

mg. (…)


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Preliminary Results

USPTO

» 7.5 Million unique chemical structures

PCT

» 7.0 Million unique chemical structures


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duxschulz / pixelio.de

Let’s Compare …


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Quantitative Analysis


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Quantitative Analysis 1)

1) Mark Ede, John Endacott, Mark Harper, David Rees, Indexing chemical structures: Exemplified compound indexing in patents by the vendors

Thomson Reuters, Chemical Abstracts and Elsevier - A comparative study by the Patent Documentation Group (PDG), World. Pat. Inf. 44 (2016) 48 - 52

Case study - WO2010106249:

Database: CAplus/REGISTRY DWPI Reaxys

Compounds: 50 13 40

PATENTSCOPE

100

12 5

CAplus/REGISTRY Reaxys

DWPI

2

27

0 8

3 100

PATENTSCOPE


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Compounds: 50 13 40

57

PATENTSCOPE

100

CAPLUS/REGISTRY DWPI Reaxys

100

PATENTSCOPE


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Compounds: 50 13 40

51 (89%)

PATENTSCOPE

100

CAPLUS/REGISTRY DWPI Reaxys

PATENTSCOPE

6 49


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A Closer Look …

51

CAplus/REGISTRY DWPI + Reaxys

PATENTSCOPE

6 49 » ICANNOTATOR deficiency (2)

» One compound “falls out of

the scope of the invention”

» One extraction error

(‘TRIACETYL BORATE’)

» Extraction of additional salt

form from the text (2)

» List of pharmaceutically

acceptable acids such as ‘fumaric

acid’ or ‘camphoric acid’, …

» List of pharmaceutically

acceptable bases (‘potassium

hydroxide’, ‘t-butylamine’)

» Parts of the Pharmaceutical

Composition (‘lactose’,

‘magnesium stearate’)

» Receptors if not explicitly named

as ‘receptor’ e.g. AMPA α-amino-

3-hydroxy-5-methyl-4-isoxazole-

propionic acid (receptor)


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duxschulz / pixelio.de

Conclusion

» We are comparing manually created

databases with an automatically created one

and thus apples with pears!

» We used only one document for comparison,

so that’s not statistically significant

» Higher number of extracted compounds does

not mean ‘better database’

» But: the comparison provides a good

indication of where we stand!


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Outlook: What Comes Next?

» Annotation of Chinese, Japanese and Korean

national collections (collaboration with NextMove

software)

» Annotation of EPO collection (EN, DE, FR)

» Substructure / chemical similarity search © bbroianigo / PIXELIO, www.pixelio.de


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» WIPO

Christophe Mazenc

Paul Halfpenny

Iustin Diaconescu

» NextMove Software

Daniel Lowe

Roger Sayle

» PDG

» The InfoChem Team

Acknowledgements

© P. Storz / PIXELIO, www.pixelio.de


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