ICIC 2014 New Product Introduction InfoChem

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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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

2 / 16


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

http://www.osi.lv/hgs/redangl.html


Manual Indexing

Publishing

Automatic Production of Chemical Content

Publishers Pain 4 / 16

http://www.osi.lv/hgs/redangl.html


Automatic Abstraction of Chemical Content: One-Stop Solution

InfoChem Solution 5 / 16


Full Text Annotation: ICANNOTATOR

Full text annotation 6 / 16

http://icons.iconarchive.com/icons/deleket/soft-scraps/96/Highlighter-Yellow-icon.png


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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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*



Use Case: Springer Data Warehouse

Structures

Structures

Structures Reactions

Database Structures

-------- Full-text

Structures (annotated)

Full-text Structures (annotated)



Springer Chemistry

Data Warehouse



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


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

11 / 16


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*



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



Use Case: Thieme Pharmaceutical Substances



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 GmbH: www.infochem.de, www.spresi.com, [email protected]

Visit us at the InfoChem booth!

16 / 16

http://www.infochem.de/

http://www.spresi.com/

mailto:[email protected]

ICIC 2014 New Product Introduction InfoChem

Internet

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cdx files workup12

text annotation8

wiley chemistry content

knime development of

user experience