1. Design and development of a
novel Patent Alerting System
2014-04-14
Dr. Wolfgang Thielemann

2. Slide No. 2 • 2014-04-14 Wolfgang Thielemann2 • Dr. Ortrud Steinführ • 23-JUN-2011
Agenda/
Content
Introduction
Workflow
Using the platform to Search, Browse and Filter
Email push service
Summary

3. Slide No. 3 • 2014-04-14 Wolfgang Thielemann
Introduction:
What does this novel service do
and why did we need it?
1

4. Slide No. 4 • 2014-04-14 Wolfgang Thielemann
Patent Alerting System
What does it do?

5. Slide No. 5 • 2014-04-14 Wolfgang Thielemann
Patent alerting options existing at the start of project:
• End-Users browse results of commercial alerting services like “Current
Patents Gazette”
• End-Users set up alerts in databases (e.g. Scifinder) themselves
• Information professionals create alerts in various added-value databases
and/or patent full-text databases
Challenges for a novel, proprietary alerting service:
• The number of newly published healthcare & chemistry patents is huge
(2000-5000/week)
• The bandwidth of topics to be tracked and the corresponding terminology is
huge too
A powerful, precise and focused alerting system is needed
Patent alerting options

6. Slide No. 6 • 2014-04-14 Wolfgang Thielemann6
Using advanced text mining workflows, new patents have to be categorized
into clearly defined, project specific folders
Criteria for categorization should include:
• Drug action / molecular target (PDE 5 inhibitors)
• Specific medical condition (e.g. pulmonary hypertension)
• Specific technology (e.g. positron emission tomography)
• Compound class (e.g. antibodies)
A
The platform must be easy to use and end-user searchableC
Minimal costs for creation, maintenance, uploads, license fees and hardwareD
What did we expect from our new
patent alerting system?
The platform has to provide chemical structures which are representative for
novel chemical space covered in medicinal chemistry patents
B

7. Slide No. 7 • 2014-04-14 Wolfgang Thielemann
Workflow
2

8. Slide No. 8 • 2014-04-14 Wolfgang Thielemann
1. Download of patent full-text
2. Filtering and categorization
3. Adding key content
Overall workflow of novel patent
alerting service
Email
push-
service;
RSS
feeds
Searching or
Browsing
APIs
other prop.
platforms
Enrichment with chemical structures
Patent full-text source
Orbit
Broad healthcare & chemistry
related search for all alerts in:
Chemical structure DBs
CAS /
Registry
WPIX / DCR
SureChem
patent numbers of
substructure hits for
selected alerts
Patent alerting
platform
Tabular patent sheets enriched &
categorized with:
• Project name
• Indication
• Molecular targets
• Chemical structures
• Technologies
• …

9. Slide No. 9 • 2014-04-14 Wolfgang Thielemann
The engine within the novel service
1. Download of patent full-text
2. Filtering and categorization
3. Adding key content
1. Download of patent full-text
2. Filtering and categorization
3. Adding key content

10. Slide No. 10 • 2014-04-14 Wolfgang Thielemann
It’s not a commercial
black box!
We have full control over:
• The process
• The vocabulary
• The rules
… and can adjust it to the needs of
our organization!
The engine within the novel service

11. Slide No. 11 • 2014-04-14 Wolfgang Thielemann
2000-5000 newly published healthcare and chemistry related
patent applications per week (first published member of a patent family +
first US or EP application)
Details of proprietary categorization,
filtering, indexing steps
+ + +
In-depth text mining analysis of the patent full-text to
extract, standardize and add key terms (targets,
indications, technologies etc.)
Adding key content
typically 0 - 5 patents per alert / week
In-depth text mining analysis of the patent full-text for
identification of relevant patents
Filtering & Categorization

12. Slide No. 12 • 2014-04-14 Wolfgang Thielemann
Added key content
• Alert relevant keywords (e.g. drug action)
• Indication
• Molecular target (official NCBI Gene name + Gene ID)
• Formulation (Route of Admin + Dosage forms)
• Species
• Technologies (e.g. prodrug, freeze drying, pegylation etc.; can be
augmented to the needs of the organization)
• Molecule type (small molecules, biologicals, natural products)
• Patent type (compound, formulation, method general, diagnosis,
preparation method, combination etc.)
Keywords relating to the following topics are
extracted, standardized and added:
+
+
+
+
+
+
+
+

13. Slide No. 13 • 2014-04-14 Wolfgang Thielemann
Details of enrichment with chemical
structures
identifies chemical compounds:
• from names (incl. IUPAC, brand names, generic names, trivial names) within
24 h after publication of a patent (WO, US, EP)
• from drawn structures (only high quality structures without variables) within
2-3 days after publication of a patent (WO, US, EP)
We add these structures to the new patents within the patent alerting workflow
*
*will soon become SureChEMBL

14. Slide No. 14 • 2014-04-14 Wolfgang Thielemann
Tuesday Wednesday Thursday Friday Saturday Sunday Monday
New
WO
New
US
New
EP
Name2str Name2str Name2str
Conversion chem drawings
Conversion chem drawings
Conversion chem drawings
Generation chemical structures
Timelines:
Providing alerts as fast as possible
• Download
• Categorization
• Text Mining
• Upload
Alert
…+ documents from other patent offices

15. Slide No. 15 • 2014-04-14 Wolfgang Thielemann
Inclusion / Exclusion criteria
The keywords are mentioned:
• 1x in core fields (e.g. title)
• Multiple times in other fields (e.g.
description)
The keywords are mentioned:
• a few times in a non-core field
Documents & keywords Chemical structures
• Novel compounds (incl.
intermediates) with a global
frequency of <= 10 in all patents*
which also pass our chemical
purging filter
• Common reagents, catalysts, or
drugs which are often mentioned in
“washing lists”
* General WO, US, EP patent database
Selection criteria for novel patents

16. Slide No. 16 • 2014-04-14 Wolfgang Thielemann
Using the platform to
Search, Browse and Filter
3

17. Slide No. 17 • 2014-04-14 Wolfgang Thielemann
Alerting System Main Navigation:
Subscriptions & Search
Shows alerts you have subscribed to
All other available alerts
Google like search (keywords or chemical structures)
with facetted filter options
Administration of alerts (only for information professionals)

18. Slide No. 18 • 2014-04-14 Wolfgang Thielemann
Alerting System Main Navigation:
Entry page: “My Subscriptions”
Information about scope of the alert Stop subscribing to the alert
Show list of all documents collected for this alert so far

19. Slide No. 19 • 2014-04-14 Wolfgang Thielemann
Alerting System Main Navigation:
Other available alerts
Information about scope of the alert Subscribe to the alert
Show list of all documents collected for this alert so far

20. Slide No. 20 • 2014-04-14 Wolfgang Thielemann
Document List view
All documents related to Endometriosis alert:

21. Slide No. 21 • 2014-04-14 Wolfgang Thielemann
Links in Document List View
Link to corresponding
enhanced alerting system
record with:
• Key content
• Chemical structures
Original full-text
Link to corresponding patent record from
Thomson World Patent Index
Original PDF
Patent DB

22. Slide No. 22 • 2014-04-14 Wolfgang Thielemann
Document view
added key content

23. Slide No. 23 • 2014-04-14 Wolfgang Thielemann
browse records
+ chemical structures
Document view
+ chemical structures

24. Slide No. 24 • 2014-04-14 Wolfgang Thielemann
Alerting System Main Navigation:
Search

25. Slide No. 25 • 2014-04-14 Wolfgang Thielemann
Search result list with filter options
Search for: “endometriosis”

26. Slide No. 26 • 2014-04-14 Wolfgang Thielemann
Logic “OR” within on topic and “AND” between topics
OR AND
Text mining generated, standardized added value terms allow easy filtering:
Faceted Filter Options

27. Slide No. 27 • 2014-04-14 Wolfgang Thielemann
Faceted Filter Options

28. Slide No. 28 • 2014-04-14 Wolfgang Thielemann
Email push service
4

29. Slide No. 29 • 2014-04-14 Wolfgang Thielemann
Email push service

30. Slide No. 30 • 2014-04-14 Wolfgang Thielemann
Summary
5

31. Slide No. 31 • 2014-04-14 Wolfgang Thielemann
Advantages of proprietary
Patent Alerting System
• Grouping of patents into project specific folders (full flexibility in defining project
relevant parameters like indication, target, technology etc.). Faster evaluation by
project team members due to high relevance of hits
• Use of already existing, proprietary terminology for search and analysis of
patents
• Systems maintained by patent information professionals who are experts in
the field of patent specific sources, challenges, pitfalls as well as scientific text
mining analysis
• System open to link and exchange information to other internal platforms via
automated protocols / APIs
• Fast provision of representative chemical structures allow quick evaluation of
novel chemical space as well as easy download & processing of real chemical
structures

32. Thank you!
Acknowledgements:
Selected images were licensed from: 123RF©