icic 2016: new product introduction infochem

InfoChem Copyright © 2016 Dr. Valentina Eigner Pitto Product Presentation ICIC 2016, Heidelberg, Germany, October 17

InfoChem Product Presentation

ICIC - International Conference for the Information Community

Heidelberg, Germany, October 17, 2016

Dr. Valentina Eigner-Pitto

1 / 14


InfoChem at a Glance

People

• 21 full time employees

(Munich office)

• 1 consultants in UK

• 60 freelance abstractors

(residing offshore)

Company

• specialized in chemoinformatics

• founded in 1989

• based in Munich, Germany

• owned by Springer Nature

Business Areas

• Software products

• Projects

• Text/Data mining

• Database building

Customers

• Pharmaceutical industry

• Chemical industry

• Scientific publishers

• Academia

• IP Professionals

Company overview 2 / 14


Data Mining Projects

Services

• Project development

• Consulting


• Chemical entity recognition

• Name to structure conversion

• Image to structure conversion

• ChemDraw CDX files work-up

Software

• ICFSE, ICCARTRIDGE, ICCHEMDESK

• ICMAP, CLASSIFY, ICNameRXN

• ICSYNTH, ICFRP, ICEDIT, ICTOOLS

• Markush…

Business Areas

Company overview

Content

• SPRESIweb, SPRESImobile

• Patents / Structures

• Chemisches Zentralblatt

Structural Database

3 / 14


Services

Content Data Mining Projects

• Project development

• Consulting


• SPRESIweb, SPRESImobile

• Patents / Structures

• Chemisches Zentralblatt

Structural Database

• Chemical entity recognition

• Name to structure conversion

• Image to structure conversion

• ChemDraw CDX files work-up

Software

• ICFSE, ICCARTRIDGE, ICCHEMDESK

• ICMAP, CLASSIFY, ICNameRXN

• ICSYNTH, ICFRP, ICEDIT, ICTOOLS

• Markush…

Business Areas

Company overview

MARKUSH

4 / 14


InfoChem Fast Search Engine: ICFSE

• High performance chemistry search engine

• Retrieval of data from millions of records in seconds

• Easy integration in any desktop or web application with

multiple platform support

• Supports typical query features and search types for

structures and reactions

o atom query: any atom, heteroatom, list/not list...

o bond query: bond type, topology...

o reacting center query: change, make/break...

o search types: exact, substructure, tautomer, isomer,

flexmatch, similarity, all-in-one...

Search engine for Markush 5 / 14


Deployment in New STN

Lecture ICIC 2015 Fiz-

Karlsruhe, Thomson Reuters

The Driving Force

First milestone

• Definition of specific data

format for Markush structures

• First prototype for storage

and retrieval

Search engine for Markush

2008 - 2010 2015 2012 …

MARKUSH

Cooperation goal:

• Integrate in New STN

o generic searches

o Markush searches of

DWPIM

Future developments:

• Search functionalties

o Nested R-groups

o Markush query

• Performance

• …

6 / 14


Structure Searchable Representation of Markush

• Generation of a specific structure representation to

enable structure searches in the ICFSE index

o normalisation of text to atom properties

o evaluation and enumeration of variations (s, p, f, h) s-variation: R1 = methyl or ethyl

p-variation: R3 = amino

f-variation: n= 1 – 3

h-variation: R2 = alkyl [Size(3-9);TB(>0)]

MARKUSH Search engine for Markush 7 / 14


A Novel Concept for the Search and Retrieval of the Derwent Markush

Resource Database Andreas Barth,*,† Thomas Stengel,† Edwin Litterst,† Hans Kraut,‡ Henry Matuszczyk,‡ Franz Ailer,‡ and Steve Hajkowski§ †FIZ Karlsruhe − Leibniz Institute for Information Infrastructure, D-76344 Eggenstein-Leopoldshafen, Germany

‡InfoChem GmbH, D-81241 Munich, Germany

§Thomson Reuters, London EC1N 8JS, United Kingdom

Product Match Levels

STN match level concept:

• ATOM retrieves only specific nodes (standard for ring nodes):

o Specific atoms in the query match only specific atoms in the file

o Generic groups in the query match only specific atoms/groups in

the file

• CLASS retrieves both specific and generic nodes (standard for

chain nodes):

o Specific atoms/generic groups in the query match to specific or

generic atoms/groups in the file

• ANY retrieves specific and generic nodes plus the R (XX) node

MARKUSH

Mechanism to control the searching level in Markush structures (Marpat, Questel)



Hit Visualization

MARKUSH

S

O

Query:



Hit Visualization: Highlighting

MARKUSH

S

O


Query:

10 / 14


Hit Visualization: Assembled Hit

MARKUSH

S

O


Query:

11 / 14


Support of Superatoms

MARKUSH

Acyclic Cyclic

Ak (Chain) Cy (Ring)

Cb (Carbcycle)

Hy (Heterocycle)

CHK (Alkyl, Alkylene)

CHE (Alkenyl, Alkenylene)

CHY (Alkynyl, Alkynyline)

CYC (Cycloaliphatic)

HEA (Monocyclic heteroaryl)

HEF (Fused heterocyclic)

HET (Monocyclic nonaromatic)

ARY (Aryl)



New @ InfoChem

Reaction prediction tools

• Further development and optimisation of the algorithm

• Design of a collaborative platform enabling user team work

Other news from InfoChem

Data mining

• ICANNOTATOR extended to further languages:

o French

o Chinese, Japanese, Korean (in cooperation with

NextMove Software)

13 / 14


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

Visit us at the InfoChem booth!

14 / 14

http://www.infochem.de/

http://www.spresi.com/

mailto:[email protected]

icic 2016: new product introduction infochem

Internet