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ICIC 2014 New Product Introduction InfoChem
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InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
InfoChem Product Presentation
ICIC - International Conference for the Information Community
Heidelberg, October 13, 2014
Dr. Valentina Eigner-Pitto
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InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Business Areas
Outline
Software Services
Content Data Mining Projects
• ICFSE, ICCARTRIDGE, ICCHEMDESK
• ICMAP, CLASSIFY, ICNameRXN
• ICSYNTH, ICEDIT, ICTOOLS
• …
• Project development
• Consulting
• Database building
• SPRESIweb, SPRESImobile
• Patents / Structures
• Chemisches Zentralblatt
Structural Database
• Chemical entity recognition
• Name to structure conversion
• Image to structure conversion
• ChemDraw CDX work-up
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InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Manuscript submission
Publishing
Cost Explosion for Publishers
Manual Indexing
Database production
http://premium.wpmudev.org/blog/tutorial-
how-to-add-authors-images-to-your-
wordpress-blog/
Publishers Pain 3 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Manual Indexing
Publishing
Automatic Production of Chemical Content
Publishers Pain 4 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Automatic Abstraction of Chemical Content: One-Stop Solution
InfoChem Solution 5 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Full Text Annotation: ICANNOTATOR
Full text annotation 6 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Full Text Annotation Service
Full text annotation
• Buildup and maintainance of dictionaries and taxonomies for annotation
• Development of formats for annotation in and output
(standoff- and inline-annotation)
• Integration of annotation-modules in flexible workflows (e.g. KNIME)
• Development of workflows for real-time annotation of modified or new
documents
• Results evaluation with high quality, manually curated gold-standards
• Specific dictionaries in the fields of organic, inorganic, pharmaceutical and
biochemistry, diseases, medicine, biology
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InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Use Case: Wiley The Smart Article
*Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
Chemistry Enrichment Workflow*
Full text annotation 8 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Use Case: Springer Data Warehouse
Structures
Structures
Structures Reactions
Database Structures
-------- Full-text
Structures (annotated)
Full-text Structures (annotated)
Full-text Structures (annotated)
Full-text Structures (annotated)
Springer Chemistry
Data Warehouse
Full text annotation 9 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
CDX Scheme Processing Chemical structures (SD files)
ICSchemeProcessor
Reactions (RD files)
Source: Thieme Pharmaceutical Substances, Ticagrelor (in production)
Reagent Solvent Catalyst
SOCl2
LiOH H2O, THF Pd(OAc)2
Cl-Co2Et,
Et3N
Acetone,
H2O
Conditions (RD files)
CDX files work-up 10 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
ChemDraw CDX Files Work-up
CDX files work-up
• Hybrid algorithmic/templating approach (minimal manual support)
• Development of CDX templating guidelines for authors and typsetters:
o syntax definition for tables, R-groups, etc.
o syntax rules captions, fragments, etc.
o reaction arrangement, forked arrows
o rules for reaction conditions (reactants, catalysts, solvents, yields, etc.)
• Algorithmic detection of features:
o resolution of repeating groups
o enumeration of R-groups
o resolution of aliases/labels
o variable points of attachment
• Project/source specific solutions
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InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Use Case: Wiley The Smart Article
*Reinhard Neudert: Enhancing the User Experience for Wiley Chemistry Content, ICIC 2012 14. – 17. October, Berlin
Chemistry Enrichment Workflow*
CDX files work-up 12 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Use Case: Thieme Science of Synthesis
R4
O
R5
OH
+
H2N
HN H2O
H2
39
H2O
N
NH
R4
R5
N
O
R4
R5 NH3
40
NH
NHR5
HO
HO
R4
N
NR5
O
R4
• •
N
NHO
R5
R4
H2
R4
O
R5
OH
+
H2N
HN H2O
H2
39
H2O
N
NH
R4
R5
N
O
R4
R5 NH3
40
NH
NHR5
HO
HO
R4
N
NR5
O
R4
• •
N
NHO
R5
R4
H2
Correct /
extend process
ICSchemeProcessor
CDX-
Templating
Guidelines
(Reactions)
Scheme
error report R4
O
R5
OH
+
H2N
HN H2O
H2
39
H2O
N
NH
R4
R5
N
O
R4
R5 NH3
40
NH
NHR5
HO
HO
R4
N
NR5
O
R4
• •
N
NHO
R5
R4
H2
Manual data
entry
Scheme
correction not
possible
CDX files work-up 13 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
Use Case: Thieme Pharmaceutical Substances
CDX files work-up 14 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
News about ICSYNTH
• Evaluation packages for version 2.0 available
• Publication
o to be submitted by end 2014 to Organic Process Reasearch and Development
Route Design in the 21st Century –
Software-assisted Synthesis Planning Using ICSYNTH
Anders Bogevig, Hans-Jürgen Federsel, Fernando Huerta, Hans Kraut, Thomas Langer, Michael G.
Hutchings, Peter Löw, Christoph Oppawsky, Tobias Rein, and Heinz Saller
• Lecture about computer aided forward reaction prediction
o Fernando Huerta, Monday, October 13, 12:00
Knowledge-Based De Novo Molecular Design Using ICSYNTH FRP
ICSYNTH 15 / 16
InfoChem Copyright © 2014 Dr. Valentina Eigner Pitto Product Presentation ICIC 2014, Heidelberg, October 12-15
InfoChem GmbH: www.infochem.de, www.spresi.com, [email protected]
Visit us at the InfoChem booth!
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