KLIFS KNIME nodes

KNIME nodes for retrieving data from KLIFS (https://klifs.net/). KLIFS is a structural kinase-ligand interaction database. For more information regarding KLIFS see the website and the references at the bottom.

Installation

Requirements:

• KNIME, https://www.knime.org

Steps to get KLIFS nodes inside KNIME:

1. Goto Help > Install new software ... menu
2. Press add button
3. Fill text fields with https://3d-e-chem.github.io/knime-node-collection
4. Select --all sites-- in work with pulldown
5. Select KLIFS knime nodes
6. Install software & restart (for now an "Unsigned Content" warning can popup during the installation, you can safely ignore this)

Usage

See the example workflow in examples folder.

Build

mvn verify

Jar has been made in plugin/target folder. An Eclipse update site will be made in p2/target/repository repository.

Development

Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:

1. Install Java 17
2. Install Eclipse for RCP and RAP developers
3. Configure Java 17 inside Eclipse Window > Preferences > Java > Installed JREs
4. Import this repo as an Existing Maven project
5. Activate target platform by going to Window > Preferences > Plug-in Development > Target Platform and check the KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.sstea.targetplatform/KNIME-AP-5.1.target target definition.

During import the Tycho Eclipse providers must be installed.

New release

1. Update versions in pom files with mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT command.
2. Commit and push changes
3. Create package with mvn package, will create update site in p2/target/repository
4. Append new release to 3D-e-Chem update site
5. Make clone of https://github.com/3D-e-Chem/3D-e-Chem.github.io repo
6. Append release to 3D-e-Chem update site with mvn install -Dtarget.update.site=<3D-e-Chem repo/updates>
7. Commit and push changes in this repo and 3D-e-Chem.github.io repo
8. Make nodes available to 3D-e-Chem KNIME feature by following steps at https://github.com/3D-e-Chem/knime-node-collection#new-release
9. Create a GitHub release
10. Update DOI in CITATION.cff

Create KLIFS client

0. Generate client

wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/7.1.0/openapi-generator-cli-7.1.0.jar -O openapi-generator-cli.jar
java -jar openapi-generator-cli.jar generate -i https://klifs.net/swagger/swagger.json -o net.klifs.client -g java
# in knime-klifs/net.klifs.client/pom.xml change version of build-helper-maven-plugin to 3.4.0
mvn package

1. Compile client

cd net.klifs.client
mvn package

1. Make client jar and it's dependencies available in plugin

cp -r target/lib/* target/*jar ../nl.vu_compmedchem.klifs/lib/

1. Update plugin/META-INF/MANIFEST.MF, plugin/build.properties files to reflect contents of lib/

References

• Kooistra, A. J.; Kanev, G. K.; van Linden, O. P.; Leurs, R.; de Esch, I. J.; de Graaf, C. Klifs: A Structural Kinase-Ligand Interaction Database. Nucleic Acids Res. 2016, 44, D365-371. 10.1093/nar/gkv1082
• van Linden, O. P.; Kooistra, A. J.; Leurs, R.; de Esch, I. J.; de Graaf, C. Klifs: A Knowledge-Based Structural Database to Navigate Kinase–Ligand Interaction Space. J. Med. Chem. 2013, 57, 249-277. 10.1021/jm400378w