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

InfoChem GmbH © 2016 Dr. Josef EiblmaierICIC 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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The Addition of Chemical Search Capabilities to PATENTSCOPE: Turning a Full-text Search System into a Chemistry Database

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