JChem Extensions for KNIME

Attila Szabó Takahiro Ohshima

February 2012, Zürich

5th KNIME User Group Meeting

About ChemAxon

• Cheminformatics software – since ’98

• Pharma, biotech, agrochem, academia

• Global sales – USA, Europe, Japan, RoW

Product Overview

Support Forum

Thank you for your attention!

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

INFOCOM

IT Business company of Teijin Group

Offering wide varieties of IT services & solutions

Head office: Tokyo, JAPAN

Capital: 1.59 billion yen (ca. $15M)

No. of employees:

676 (stand-alone) / 1,193 (consolidated) , as of Sep 30, 2011

Chem & Bio Informatics Department

for life science market in Japan

for more than 25 years

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

Our Business (Life science area)

Genome Proteome

Data Mining

ADMET/PK

Pre-Clinical Drug Design / ChemoInformatics

Clinical

Infocom

Chem & Bio Informatics

Development & SI, Service

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

JChem Extensions

Extensions of ChemAxon’s tool for

KNIME workflow

Infocom implement it with the

support of ChemAxon

Contains over 90% of ChemAxon's

cheminformatics functionality

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

Marvin Family Nodes and Marvin are FREELY

available in KNIME

What are “Marvin Family Nodes” ?

Marvin Sketch node

Marvin View node

Marvin Space node

Converter nodes

Available on KNIME Update Site (Standard Chemistry Tool in KNIME)

Free of charge for ALL customers!!

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

Document to Structure

Extracts names from text

documents (Text, PDF and HTML)

Structure images are also

converted

Automatic text OCR

Also import smiles, InChI and CAS

number

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

Markush structures

Markush enumeration

Markush search

Markush structure generation

Markush Viewer (It’s new!)

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

JChem for Excel

JC4XL Reader

Reads Excel file created with

JChem For Excel.

JC4XL Writer

Writes JChem For Excel

compatible xlsx file.

© 2012 INFOCOM CORPORATION All right reserved. 5th KNIME Users Group Meeting and Workshop

Let’s try

JChem Extensions:

http://www.infocom.co.jp/bio/develop/jchemextension_en.html

http://www.infocom.co.jp/bio/develop/jchemextension_update_en.html

Download and Install via the update site

Update Site : https://www.infocom.co.jp/bio/knime/update/2.5

KNIME:

http://www.knime.org/

http://tech.knime.org/

E-MAIL:

info-science@infocom.co.jp