Knime Analytics Platform For Data Scientists

[L1-LS] KNIME Analytics Platform
for Data Scientists (Life Science):

Basics
KNIME AG
1
Overview
KNIME Analytics Platform
What is KNIME Analytics Platform?
§ A tool for data analysis, manipulation, visualization, and reporting

§ Based on the graphical programming paradigm
§ Provides a diverse array of extensions:
§ Text Mining
§ Network Mining
§ Cheminformatics
§ Many integrations,
such as Java, R, Python,
Weka, Keras, Plotly, H2O, etc.
© 2021 KNIME AG. All rights reserved. 3

Visual KNIME Workflows
NODES perform tasks on data

Not Configured
Configured
Inputs Outputs Executed
Status Error
Nodes are combined to create

WORKFLOWS

4000+ Nodes for all Steps of End-To-End Data Science

Overview
§ Installing KNIME Analytics Platform

§ The KNIME Workspace
§ The KNIME File Extensions
§ The KNIME Workbench
§ Workflow editor
§ Explorer
§ Node Repository
§ Node Description
§ Installing new extensions

Install KNIME Analytics Platform
§ Select the KNIME version for

your computer:
§ Mac
§ Windows – 32 or 64 bit
§ Linux
§ Download archive and extract the
file, or download installer package
and run it

Start KNIME Analytics Platform
§ Use the shortcut created by the installer
§ Or go to the installation directory and launch KNIME via the knime.exe

The KNIME Workspace
§ The workspace is the folder/directory in which workflows (and potentially data

files) are stored for the current KNIME session.
§ Workspaces are portable (just like KNIME)

The KNIME Analytics Platform Workbench
KNIME Explorer
Node Description
Workflow Coach
Workflow Editor
KNIME Hub
Node Repository
Console & Node Monitor
Outline

KNIME Explorer
§ In LOCAL you can access your own

workflow projects.
§ Other mountpoints allow you to
connect to
§ EXAMPLE Server
§ KNIME Hub
§ KNIME Server
§ The Explorer toolbar on the top has a
search box and buttons to
§ select the workflow displayed in the active
editor
§ refresh the view
§ The KNIME Explorer can contain 4
types of content:
§ Workflows
§ Workflow groups
§ Data files
§ Shared Components

Creating New Workflows, Importing and Exporting
§ Right-click inside the KNIME Explorer to create a new workflow or a workflow

group, or to import a workflow
§ Right-click the workflow or workflow group to export

Node Repository
§ The Node Repository lists all

KNIME nodes
§ The search box has 2 modes
§ Standard Search – exact match of node
name
§ Fuzzy Search – finds the most similar node
name
§ Nodes can be added by drag and
drop from the Node Repository to
the Workflow Editor.

Description
§ The Description window gives

information about:
§ Node Functionality
§ Input & Output
§ Node Settings
§ Ports
§ References to literature

Workflow Description
§ When selecting the workflow, the

Description window gives
information about the workflow’s:
§ Title
§ Description
§ Associated Tags and Links
§ Creation Date
§ Author

Workflow Coach
§ Node recommendation engine

§ Gives hints about which node use next in the workflow
§ Based on KNIME communities' usage statistics
§ Based on own KNIME workflows

Node Monitor
§ By default the Node Monitor shows you the output table of the node selected in
the workflow editor
§ Click on the three dots on the upper right to show the flow variables,
configuration, etc.

Console and Other Views
§ Console view prints out error and

warning messages about what is
going on under the hood
§ Click on View and select Other…
to add different views
§ Node Monitor, Licenses, etc.

Inserting and Connecting Nodes
§ Insert nodes into workspace by dragging them from Node Repository or by

double-clicking in Node Repository
§ Connect nodes by left-clicking output port of Node A and dragging the cursor to
(matching) input port of Node B
§ Common port types:
Model
Flow Variable
Image
Database Database
Connection Query
Data

More on Nodes…
§ A node can have 4 states:
Not Configured:
The node is waiting for configuration or incoming data.
Configured:
The node has been configured correctly, and can be executed.
Executed:
The node has been successfully executed. Results
may be viewed and used in downstream nodes.
Error:
The node has encountered an error during execution.

Node Configuration
§ Most nodes require configuration

§ To access a node configuration
window:
§ Double-click the node
§ Right-click -> Configure

Node Execution
§ Right-click node
§ Select Execute in context menu
§ If execution is successful, status
shows green light
§ If execution encounters errors,
status shows red light

Tool Bar
The buttons in the toolbar can be used for the active workflow. The most important
buttons:
§ Execute selected and executable nodes (F7)
§ Execute all executable nodes
§ Execute selected nodes and open first view
§ Cancel all selected, running nodes (F9)
§ Cancel all running nodes

Node Views
§ Right-click node
§ Select Views in context menu
§ Select output port to inspect execution results
Plot View Data View

KNIME File Extensions
§ Dedicated file extensions for Workflows and Workflow groups associated with
KNIME Analytics Platform
§ *.knwf for KNIME Workflow Files
§ *.knar for KNIME Archive Files

Hot Keys (for Future Reference)
Task Hot key Description
Node Configuration F6 opens the configuration window of the selected node
F7 executes selected configured nodes
Shift + F7 executes all configured nodes
Node Execution Shift + F10 executes all configured nodes and opens all views
F9 cancels selected running nodes
Shift + F9 cancels all running nodes
Node Connections Ctrl + L connects selected nodes
Ctrl + Shift + L disconnects selected nodes
Ctrl + Shift + Arrow moves the selected node in the arrow direction
Move Nodes and Annotations moves the selected annotation in the front or in the back of all
Ctrl + Shift + PgUp/PgDown
overlapping annotations
F8 resets selected nodes
Ctrl + S saves the workflow
Workflow Operations Ctrl + Shift + S saves all open workflows
Ctrl + Shift + W closes all open workflows
Ctrl + F search workflow for nodes
Metanode Shift + F12 opens metanode wizard

Getting Started: KNIME Example Server
§ Connect via KNIME Explorer to a public repository with large selection of

example workflows for many, many applications
§ Workflows also available on KNIME Hub

KNIME Hub
A place to share knowledge

about Workflows and Nodes
https://hub.knime.com

The KNIME Hub

Searching Nodes and Workflows

Opening a Workflow from the Hub

Edit the Workflow
Drag & Drop

Sharing the Workflow on the Hub
1. Save your Edits
2. Connect to KNIME Hub

Log in the Hub
KNIME Forum
Account Credentials

Stay connected with KNIME
Blog: knime.com/blog
Follow us on social media:
Forum: forum.knime.com
KNIME Hub: hub.knime.com
KNIME E-Learning Course:

www.knime.com/e-learning-course
© 2021 KNIME AG. All rights reserved.

Exercise L1-LS:
§ Download the course material from the KNIME Hub

https://hub.knime.com/knime/spaces/Education/latest/Courses/

KNIME Extensions

Selected Extensions from the Life Science Community
Cheminformatics Bioinformatics Mass

Spectrometry
High Content
Screening

Selected Commercial Life Science Extensions
Further extensions including detailed descriptions can be found at https://hub.knime.com

Installing KNIME Extensions
There are different ways to install KNIME extensions:
Option 1: Via the menu bar in the KNIME Analytics Platform and select your
extension from the list (feasible if you know the name of the extension)

Option 2: Via the KNIME Hub (hub.knime.com): Drag-and-drop the required

extension (or node) to your workflow

Option 3: Opening a workflow that contains a node from an extension (KNIME

automatically detects the necessary extensions)

Installing Extensions Exercise
Open Exercise: 00. Installing Extensions
Activity I: Install the following Extensions

§ KNIME Base Chemistry Types & Nodes
§ KNIME JavaScript Views (Labs)
§ …

Importing Data
Data Source Nodes
Typically characterized by:

§ Orange color
§ By default no input ports, 1-2 output ports
§ New file handling with KNIME 4.3.
§ Consistent user experience across all nodes and file systems
§ Managing of various file systems within the same workflow
§ Performance improvements
Output port
Status
Node label

CSV Reader
Advanced settings
§ Reads either one or multiple
.csv and .txt files
File system
§ Further tabs to
§ limit the rows
File path
§ select encoding
Basic settings
Help button
Preview

Common Settings: Four Default File Systems
§ Local File System
§ Relative to …
§ Mountpoint
§ Custom URL

File Path Options Old File Handling
§ Local path New file handling
§ Absolute URL
§ Mountpoint-relative URL

Workflow-Relative File Paths
§ Best choice if workflows are to be

shared
§ Requires matching folder structure
within workflow group
§ Independent of environment outside of
workflow group
§ Example: Path to „Sentiment Analysis.table“
§ Local path:
§ C:\Users\rb\knime-workspace\KNIMEUserTraining\data\Sentiment Analysis.table
§ Workflow relative:
YouTube KNIME TV Channel:

https://youtu.be/U9sP4g4yGwY
Common Settings: Connecting to other File Systems
§ Add file system connection port to connect to another file system

§ Click on the three dots on the lower left to
add or remove a dynamic port.
§ Supported file systems

§ Microsoft Azure
§ Google
§ Amazon
§ Databricks
§ BigData file systems (hdfs, httpFS, …)
§ On-premise (e.g. ssh, ftp, …)

Common Settings: Read Single or Multiple Files
§ Single file
§ Files in a folder
§ Option to include subfolder

§ Option to define filter criterions

Common Settings: Transformation Tab
§ Supported operations
§ Column filtering
§ Column sorting
§ Column renaming
§ Column type mapping
§ Select between union or intersection of
columns (in case of reading many files)

Alternative Faster Way …
Drag & Drop

OR
Copy &
Paste

File Reader
Good option, if the CSV Reader node can't read your file
§ Reads all text-based files (e.g. csv, txt, etc.)
§ Many advanced features allow it to read most ‘weird’ files
§ Short lines, inline comments, headers and special encoding
YouTube KNIME TV Channel video:

https://youtu.be/flaHQw-Qhlg

File Reader
File path
Basic
Settings
Advanced
Settings
Preview
Help Button

Excel Reader (XLS)
§ Reads .xls and .xlsx file from Microsoft Excel

§ Supports reading from multiple sheets

Excel Reader
File path
File system
Sheet
specific
settings
Preview

Table Reader
§ Reads tables from the native KNIME Format

§ Maximum performance, minimum configuration
File path
YouTube KNIME TV channel video:

https://youtu.be/tid1qi2HAOo

SDF Reader
§ Reads chemical data from the .sdf file
Check the box to

extract all properties
File path
required Extension: KNIME Base Chemistry Types & Nodes

Table Creator

Other Useful Data Sources
§ KNIME Analytics Platform provides many more

options to access data:
§ PMML Reader – reads standard predictive models
§ XML Reader with XPATH support
§ Python/R Source nodes
§ Tika Parser – extracts textual data from 200+ file types
§ REST Web Services, and many more
§ Find out more in by downloading the free book

“Will they blend”
https://www.knime.com/knimepress/download-
will-they-blend
Our example data set
§ Malaria High-throughput Screening data

§ HTS hit list and compounds with confirmed IC50 data in malaria Plasmodium
falciparum whole cell assay
§ Content of the original dataset:
Column Name Description
SAMPLE sample identifier
Pf3D7_ps_green primary screen, measuring green fluorescence intensity
Pf3D7_ps_red primary screen, measuring red fluorescence intensity
standardized call on hits: ‘true’ if activity in red AND green 80% <= x < 250%; ‘false’ if activity in red
Pf3D7_ps_hit
AND green <20%; ‘ambiguous’ for all other compounds (20 – 80%, or >250%)
Pf3D7_pEC50 Reported pEC50 value (NA for compounds not submitted for dose-response confirmation)
Canonical_Smiles standardized structure information
http://www.tdtproject.org/challenge-1---malaria-hts.html#

Importing Data Exercise
Open exercise 01. Importing Data
Activity I: Importing Data

§ Read the following files:
§ malariahts_experiment_hits.csv
§ malariahts_experiment_no-hits.xlsx
§ malariahts_molecules.sdf
§ malariahts_molecules_feature.table
Hint: drag and drop the files from the KNIME Explorer
panel to get started
You can download the training workflows from the KNIME Hub:
https://hub.knime.com/knime/spaces/Education/latest/Courses/

Data Manipulation
Clean, Join, Aggregate
64
Data Manipulation Nodes
§ Yellow color with a variety of input and output ports

§ Apply a transformation to input data
§ Many, many nodes!

Missing Value
helps to handle missing values Define default values for all

columns of specific type
Define values for

every single column

Row Filter

Column Filter

Other Useful Nodes for Row and Column Handling

Concatenate
Combine rows from 2 or more tables with shared columns

§ Handles duplicate row keys gracefully
§ Take the union or intersection of columns

Dynamic Ports
Add and remove node ports based on your needs, e.g. in order to concatenate
three or more tables
Click on the three

dots in the bottom
left corner

Transpose

String Manipulation
Create and edit values in String columns

§ Clean up capitalization (e.g. Lowercase)
§ Replace strings
§ Modify existing strings or create new columns

More Nodes

Joining Columns of Data
Left Table Right Table
CustomerKey OrderDate OrderID CustomerKey DoB City Gender
22 2019-09-23 #23444 Join by CustomerKey 17 1974-02-23 Berlin F
24 2019-09-30 #23457 65 2001-05-25 Stuttgart F
15 2019-10-07 #28985 35 1988-08-05 Cologne M

Inner Join
10 2091-10-13 #29999 15 1983-07-20 Hamburg M
10 1993-01-13 Berlin M
CustomerKey OrderDate OrderID DoB City Gender
15 2019-10-07 #28985 1983-07-20 Hamburg M

Left Outer Join 10 2091-10-13 #29999 1993-01-13 Berlin M Right Outer Join
CustomerKey OrderDate OrderID DoB City Gender CustomerKey OrderDate OrderID DoB City Gender
22 2019-09-23 #23444 ? ? ? 17 ? ? 1974-02- Berlin F

23
24 2019-09-30 #23457 ? ? ?
65 ? ? 2001-05- Stuttgart F
15 2019-10-07 #28985 1983-07-20 Hamburg M 25
10 2091-10-13 #29999 1993-01-13 Berlin M 35 ? ? 1988-08- Cologne M
05
15 2019-10-07 #28985 1983-07- Hambur M
20 g
10 2091-10-13 #29999 1993-01- Berlin M
13
Joining Columns of Data
Left Table Right Table
CustomerKey OrderDate OrderID CustomerKey DoB City Gender
22 2019-09-23 #23444 Join by CustomerKey 17 1974-02-23 Berlin F
24 2019-09-30 #23457 65 2001-05-25 Stuttgart F
15 2019-10-07 #28985 35 1988-08-05 Cologne M

Full Outer Join
10 2091-10-13 #29999 15 1983-07-20 Hamburg M
10 1993-01-13 Berlin M
CustomerKey OrderDate OrderID DoB City Gender
17 ? ? 1974-02-23 Berlin F
Missing values in
the left table 65 ? ? 2001-05-25 Stuttgart F
35 ? ? 1988-08-05 Cologne M
15 2019-10-07 #28985 1983-07-20 Hamburg M

Missing values in
10 2091-10-13 #29999 1993-01-13 Berlin M the right table
22 2019-09-23 #23444 ? ? ?
24 2019-09-30 #23457 ? ? ?

Joiner
Combines columns from 2 different tables

§ Top port contains “Left” data table
§ Bottom port contains “Right” data table

Joiner Configuration – Linking Rows
Joiner mode
Values to join on.

Multiple joining columns
are allowed

Joiner Configuration – Column Selection
Columns from
left table to
output table
Columns from
right table to
output table

Data Aggregation (GroupBy)
Type Name Weigt
NSAID paracetamol 151.17
NSAID aspirin 180.16

Type Count(Name) Mean(Weight)
NSAID ibuprofen 206.29
NSAID 4 208.44
NSAID diclofenac 296.15
PPI 2 364.40
PPI omeprazole 345.42
SSRI 4 326.45
PPI pantoprazole 383.38
SSRI fluoxetine 309.33

Aggregated on Type (group) by
SSRI paroxetine 329.37
Count (aggregation method) and
SSRI citalopram 324.40 Mean (aggregation method)
SSRI sertraline 342.70

GroupBy
Aggregate to summarize data

§ First tab provides grouping options
Aggregation columns
§ Second tab provides control over aggregation details
Aggregation methods
YouTube KNIME TV video: https://youtu.be/bDwF-TOMtWw

Data Aggregation (Pivoting)
Type Name Safety
NSAIDs paracetamol irritant
NSAIDs aspirin irritant
NSAIDs ibuprofen health hazard
NSAID diclofenac acute toxic
PPIs omeprazole irritant Type Acute toxic Health hazard Irritant
PPIs pantoprazole irritant NSAIDs 1 1 2

SSRIs fluoxetine acute toxic PPIs ? ? 2
SSRIs paroxetine health hazard SSRIs 1 3 ?
SSRIs citalopram health hazard
SSRIs sertraline health hazard
Pivoting Node: Group - Pivot - Aggregate

Pivoting with Two Aggregation Methods
Pivoting Node: Group - Pivot - Aggregate

Pivoting
Performs pivoting on selected columns for grouping and pivoting

§ Values of group columns become unique rows
§ Values of the pivot columns become unique columns for each set of column
combination together with each aggregation
§ Many aggregation methods are provided (similar to GroupBy)

Pivoting
Groups ~ Rows
Pivots ~ Columns
Aggregation

Rule Engine

Math Formula
§ Row-wise calculations
§ Some column-wise statistics
§ Lots of mathematical functions
§ Double click on function,
then select column

Column Expression
§ Append or modify an arbitrary number of

columns using expressions
§ Many different functions are available
§ No restriction on number of lines per
expression allow to write complex
expressions
§ Part of the KNIME Labs extension

Table Manipulator
Allows for
§ Concatenation of multiple files/tables
§ Column filtering
§ Column sorting
§ Column renaming
§ Column type mapping

Data Manipulation Exercise
Open Exercise 02. Data Manipulation
Activity I: Filtering
§ Remove rows where column Pf3D7_pEC50 contains missing values
§ Filter rows with higher values than 150 in column Pf3D7_ps_red
§ Remove column Pf3D7_ps_green from the result

Data Manipulation Exercise
Still in Exercise: 02. Data Manipulation
Activity II: Data Manipulation & Aggregation

§ Concatenate, Join and Manipulate the data according to the instructions in the annotations
Activity III: Data Manipulation (Optional)

§ Use the Rule Engine node to add the following tags in a new column named REOS
(according to rules in the exercise)
§ Filter columns

Workflow Organization and
Documentation
92
Comments & Annotations
Double-click to write
Use the panel to
change properties
Double-click to write
Use the panel to
change properties
YouTube KNIME TV Channel:

https://youtu.be/AHURYB_O8sA

Workflow Organisation – Good Practices
§ Workflow annotations
§ Node labels
§ Metanodes
§ Right click -> Create Metanode...
§ Organize workflow by task
§ Hide complexity & improve readability

Workflow Organisation – Components
§ Component encapsulates a
reusable functionality as a KNIME
workflow
§ Components can be configured as
any KNIME nodes
§ Access and share components on
the KNIME Hub Drag and drop from the
KNIME Hub to your workflow

Data Visualization
Charts and Tables
96
Data Visualization
§ Large selection of easy to use

visualization nodes
§ Web-based and interactive
§ Dedicated nodes, no scripting required
§ Plotly nodes
§ Similar but integrated from an
external library
§ R and Python View nodes for
highly customizable graphics
§ Require scripting

Visualization

Table View

Data Explorer

Parallel Coordinates Plot

Color Manager
§ Color by nominal or continuous values

§ Sync colors between views using the color model port and Color Appender node
Color range
Discrete
for numerical
colors for
values
nominal
values

Selection & Filtering in JavaScript Views
Interactivity allows you to select data points in views

§ Selection is propagated to other views.
§ Highlight selected rows or filter them
§ Click “Apply” to add column to data that indicates selection (true/false)
for use in downstream nodes
Apply selection

Components – Combined Views
§ Multiple JavaScript View nodes Scatter Plot

can be combined in Components
§ Selections are transmitted to all
other views
§ Also for use on the KNIME
WebPortal
Table View

Interactivity across Charts: Selection and Filter Events


Subscribing to Selection and Filter

Publishing Selection

Configure Content and Views Layout
§ Click layout button when inside Component to assign views

to rows and columns
§ Add views and rows via drag&drop
§ Add columns using + buttons

Script-based View Nodes
§ R View nodes for greater customizability

§ Use your favorite libraries, e.g. ggplot2
§ If you prefer Python: Python View node
§ For JS developers: Generic JavaScript View

Legacy View Nodes: JFreeChart & KNIME Views
§ KNIME provides three types of

visualizations
§ JavaScript Views
§ JFreeChart Views
§ Local Views
§ Active development only for JavaScript JFreeChart Views

Views -> use those!
§ JFreeChart and Local Views still useful
when visualizing locally
Local Views

Visualization Exercise
Open Exercise: 03. Visualization

Activity: Visualization
§ Use the interactive view of the Data Explorer node to inspect the data.
§ Connect a Parallel Coordinates Plot node and adjust the configuration to display the REOS category
and other two numeric columns of interest.
§ Display the other columns of interest in a Table View node and add a title to the table
§ Count the number of molecules in each REOS category using a GroupBy node and display the result
in a second Table View node.
§ Create a component containing the newly added nodes (select desired nodes-> right click-> create
component)
§ Look into the component (Ctrl + doubleclick) and adjust the layout. Make sure that selection between
the views works (hint: enable hiliting in the GroupBy node)
§ Optional:
§ Add a Color Manager before the Table View node and Color the rows using the REOS category.
§ Add a Range Slider Filter Definition node before the Table View node and configure it to use FractionCSP3 column.

Image Processing
113
KNIME Image Processing
§ KNIME Image
Processing Extension
§ these nodes operate on multi-
dimensional image data (e.g.
videos, 3D images, multi-channel
images or even a combination of
them)
More infos:
https://www.knime.com/community/imag
e-processing
Video: Introduction to KNIME for Image

Processing

Gaussian Convolution
§ Applies a Gaussian blur to

reduce image noise and
reduce detail
§ Sigma: standard deviation used

for each dimension
§ Out of Bounds Strategy: defines

how to handle pixels which lie
outside of an image (for
convolutions)
§ Dimension Selection

Global Thresholder
§ The selected threshold algorithm

determines a threshold
§ any pixel above or below the threshold is
marked as “1” or “0”, respectively
§ Different Threshold methods are

available, e.g.
§ Otsu: threshold that minimizes the intra-
class variance, defined as a weighted sum
of variances of the two classes

Connected Component Analysis
§ Identifies connected components in an

image and assigns a label
§ FOUR_CONNECTED: These pixels are
neighbours to every pixel that touches one of
their edges. These pixels are
connected horizontally and vertically.
§ EIGHT_CONNECTED: These pixels are
neighbours to every pixel that touches one of
their edges or corners.

Waehlby Cell Clump Splitter
§ Waehlby Cell Clump Splitter

performs object split and
merge by shape on a labeling.
§ Distance Merge Threshold (Objects closer
than this distance threshold will be
considered candidates for merging)
§ Gauss Size (size of gaussian convolution

for pre-processing step of split and merge
method)
§ Size Merge Threshold (Objects which

contain less pixels than threshold will be
merged regardless of their shape)

Labeling Filter
§ Filters the segments of a

labeling according to some
filter criteria like
§ segment label,
§ segment area, or
§ whether the segment is touching

the labeling border

Image Segment Features
§ Calculate features of an
image under consideration
of a given labeling.
§ Tamura features: Granularity,
Maximal directionality, Skewness,…
§ Segment Geometry: size, perimeter,

centroid, convexity, ...
§ First order statistics: min, max, mean,

sum, …
§ Haralick: Statistical features based

on gray-level co-occurrence matrix

Image Processing Exercise
Open Exercise: 04. Image Processing

Activity: Image Processing of synthetic cells
§ Calculate the size of each cell using
§ Gaussian Convolution node to smooth your image and reduce noise
§ Global Thresholder node to determine foreground from background
§ Connected Component Analysis node to segment cells and apply labels
§ Waehlby Cell Clump Splitter node to segment cell clumps
§ Labeling Filter node to remove cells on image border
§ Image Segmentation Feature node to calculate the size of each cell
Broad Bioimage Benchmark Collection data set: https://bbbc.broadinstitute.org/bbbc/BBBC005

Database
Access, Read, Manipulate, Write
122
Database Extension
§ Visually assemble complex SQL statements (no SQL coding needed)

§ Connect to all JDBC-compliant databases
§ Harness the power of your database within KNIME
§ Complete rewrite in KNIME Analytics Platform 4.0

Database Port Types
DB Data Port
• Connection information
• SQL statement
DB Connection Port
Connection information

DB Table Selector
§ Takes connection information and constructs a query

§ Explore DB metadata
§ Outputs a SQL query

DB Reader
§ Executes incoming SQL Query on Database

§ Reads results into a KNIME data table
KNIME Data Table
DB Data Port

Database Connectors
§ Dedicated nodes to connect to specific Databases

§ Necessary JDBC driver included
§ Easy to use
§ Import DB specific behavior/capability
§ Hive, Impala connectors part of
the KNIME Big Data Connectors extension
§ General DB Connector
§ Can connect to any JDBC source
§ Register new JDBC driver via
File -> Preferences -> KNIME -> Databases

In-Database Processing
§ Database Manipulation node generates a SQL query on top of the input SQL
query (brown square port)

Query Nodes
§ Filter rows and columns

§ Join tables/queries
§ Extract samples
§ Bin numeric columns
§ Sort your data
§ Write your own query
§ Aggregate your data
§ Partition your data

DB GroupBy
Aggregate rows to summarize data

§ First tab provides grouping options
§ Second tab provides control over aggregation details
Returns number of rows per group

DB GroupBy – DB Specific Aggregation Methods
SQLite: 7 aggregation functions PostgreSQL: 25 aggregation functions

DB Joiner
§ Combines columns from 2 different tables

§ Top port contains “Left” data table
§ Bottom port contains the “Right” data table

DB Row Filter
§ Filters rows that do not match the filter criteria

§ Use the IS NULL or IS NOT NULL operator to filter missing values

Export Data
§ Writing data back into database

§ Exporting data into KNIME
§ SQL operations are executed on the database!

Database Writing Nodes
§ Create table as select

§ Insert/append/merge data
§ Update values in table
§ Delete rows from table

Databases Exercise
Open Exercise 05. Database

Activity I: Databases
§ Drag & drop the malariahts_DB.sqlite file into your workspace
§ Connect malariahts_DB.sqlite to the two DB Table Selector nodes to read the
"malariahts_experiment" and "malariahts_molecules_feature" table, respectively
§ Filter the Column called "Pf3D7_pEC50" in the "malariahts_experiment" table with the
Database Column Filter node
§ Join the two tables together with the DB Joiner node using "Sample" column
§ Read the data into KNIME using the DB Reader node.
§ Write the data into a csv file

Integrating External Tools
KNIME Labs
§ KNIME Labs enables you to preview new KNIME

features and plug-ins that are still under
development
§ The nodes provided in KNIME Labs are not (yet)

part of the official KNIME version because
functionality and/or API may not be finalized
§ You can get these plug-ins by installing the

extension from the KNIME Labs extensions
category

Scripting Integrations: R and Python
§ Run R or Python code in KNIME

Analytics Platform
§ Works with existing Python and R

installations
§ Syntax highlighting support
§ Different nodes for many tasks e.g

training a model using an algorithm
available in Python

R Integration
§ Run any R code from KNIME

§ Works with existing R installations
Train model
§ Nodes for many tasks Apply model
§ First run: install.packages(‘Rserve‘)
and install.packages(‘Cairo‘)*
*mac only
Run any R code
Pass one
workspace to
multiple nodes
Create plot

R Integration
Syntax highlighting
Create and
store
templates
R workspace
Show
results
Evaluate
script R
console
output

Python Integration
§ Run Python inside KNIME

§ Works with existing installations
§ UI modeled after R integration

Python Scripting UI

Java Snippet
§ Fastest running scripting node in KNIME
§ Syntax highlighting, auto completion,

error checking
§ Templates allow you to save scripts for

later re-use
§ Import custom libraries

RESTful Web Services
§ Use KNIME nodes to interact with RESTful web services

§ Send requests using standard HTTP methods
JSON Response:
XML Response:

RESTful Web Services
Provide authentication
Enter URL, or if necessary
use from column
Add delay between

individual requests
https://www.knime.com/blog/a-restful-way-to-find-and-retrieve-data
https://www.knime.com/blog/OSM-meets-CSV-file-and-Google-API

JSON Reader and JSON Path nodes
§ Use the JSON Reader (or GET

Request) node to get a JSON cell
§ Use the JSON Path node to query

the JSON file and extract parameters
§ Editor window simplifies construction

of JSON queries by auto-generating
them (click on properties)

XML Reader and XPath nodes
§ Use the XML Reader (or GET Resource)

nodes to get an XML cell
§ Use XPath nodes to query the XML and

extract certain parameters
§ Editor window simplifies construction of

XPath queries by auto-generating them
(click on XML elements)

External Tools Exercise
Open Exercise 06. Integrating External Tools

Activity: Use REST node to call an external Web Service
§ Configure the String Manipulation node so that it creates a new column called
resource_url with the following format.
https://www.ebi.ac.uk/chembl/api/data/molecule/<ChEMBL ID>.xml
§ Access the ChEMBL Rest API with the GET Request node
§ Use the XPath node to extract standard_inchi and standard_inchi_key
§ Use RDKit From InChI node to convert the standard_inchi column to RDKit molecules
type.
§ Use Renderer to Image node to convert the RDKit molecules into images.
§ Display the result in a table view
Optional:
§ Use the R Snippet to filter the standard_inchi and standard_inchi_key. Hint: You can use
the Regex column filter template in the snippet with the expression: standard.*

Exporting Data & Deployment
Exporting Data
After an analysis is completed, what next?

§ Write results to a file
§ Create/update a database
§ Upload results to a Cloud Storage
§ Generate a report
§ Send your data to Tableau, Spotfire, PowerBI to create a report
§ Deploy via KNIME WebPortal (KNIME Server required)
§ Deploy your model as RESTful web service (KNIME Server required)

Data Export Nodes
Typically characterized by:

§ Magenta color
§ 1 input port, no output ports
§ Create file on file system or
write to database

Write Files to a Remote File System
§ The new file handling framework makes it easy to upload data to remote file
systems
§ Write processed data directly with a writer node
§ Upload local files with the Transfer Files node
§ Supported file systems

§ Microsoft Azure
§ Google
§ Amazon
§ Databricks
§ BigData file systems (hdfs, httpFS, …)
§ On-premise (e.g. ssh, ftp, …)

Full Flexibility with the Transfer Files node
Same cloud environment
On-premise Cross cloud environments

Other Utility Nodes
Can be used local and with remote file systems

§ Create a folder
§ Delete files or folders
§ List all files is a folder
§ Further information about file handling

https://docs.knime.com/latest/analytics_platform_file_handling_guide/index.html

To Dashboard on WebPortal
Step 3
Step 1 Step 2 Step 4 Step 5
Customize
Upload File Select Columns Interactive View Download Image
Column Domains

Workflow on KNIME WebPortal
WebPortal Page
(Step 1)
Upload File
Available in WebPortal Page

(Step 4)
KNIME Server Interactive View

Components to Produce Dashboard on Web Page
File
Selection Column
Selection
Stacked
Area Chart
Filter by
Row Filter
Range

Demo: Deploy a Web App (KNIME Server required)
§ Deploy a workflow on KNIME Server and execute it on the KNIME Web Portal

KNIME Server as a REST Resource
https://www.knime.org/blog/giving-the-knime-server-a-rest

KNIME Server as a REST Resource
§ Use Swagger to explore the HTTP

requests and test them

Stay connected with KNIME
Blog: knime.com/blog
Follow us on social media:
Forum: forum.knime.com
KNIME Hub: hub.knime.com
KNIME E-Learning Course:

www.knime.com/e-learning-course

Thank You!
KNIME AG
164

Knime Analytics Platform For Data Scientists

Uploaded by

Knime Analytics Platform For Data Scientists

Uploaded by

[L1-LS] KNIME Analytics Platform

for Data Scientists (Life Science):

§ A tool for data analysis, manipulation, visualization, and reporting

© 2021 KNIME AG. All rights reserved. 3

NODES perform tasks on data

Nodes are combined to create

© 2021 KNIME AG. All rights reserved. 4

© 2021 KNIME AG. All rights reserved. 5

§ Installing KNIME Analytics Platform

© 2021 KNIME AG. All rights reserved. 6

§ Select the KNIME version for

© 2021 KNIME AG. All rights reserved. 7

§ Use the shortcut created by the installer

§ Or go to the installation directory and launch KNIME via the knime.exe

© 2021 KNIME AG. All rights reserved. 8

§ The workspace is the folder/directory in which workflows (and potentially data

§ Workspaces are portable (just like KNIME)

© 2021 KNIME AG. All rights reserved. 9

Console & Node Monitor

© 2021 KNIME AG. All rights reserved. 10

§ In LOCAL you can access your own

© 2021 KNIME AG. All rights reserved. 11

§ Right-click inside the KNIME Explorer to create a new workflow or a workflow

© 2021 KNIME AG. All rights reserved. 12

§ The Node Repository lists all

© 2021 KNIME AG. All rights reserved. 13

§ The Description window gives

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§ When selecting the workflow, the

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§ Node recommendation engine

© 2021 KNIME AG. All rights reserved. 16

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§ Console view prints out error and

© 2021 KNIME AG. All rights reserved. 18

§ Insert nodes into workspace by dragging them from Node Repository or by

© 2021 KNIME AG. All rights reserved. 19

§ A node can have 4 states:

© 2021 KNIME AG. All rights reserved. 20

§ Most nodes require configuration

© 2021 KNIME AG. All rights reserved. 21

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Plot View Data View

© 2021 KNIME AG. All rights reserved. 24

§ *.knwf for KNIME Workflow Files

§ *.knar for KNIME Archive Files

© 2021 KNIME AG. All rights reserved. 25

© 2021 KNIME AG. All rights reserved. 26

§ Connect via KNIME Explorer to a public repository with large selection of

© 2021 KNIME AG. All rights reserved. 27

A place to share knowledge

© 2021 KNIME AG. All rights reserved. 28

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Drag & Drop

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1. Save your Edits

2. Connect to KNIME Hub

© 2021 KNIME AG. All rights reserved. 33

© 2021 KNIME AG. All rights reserved. 34

Follow us on social media:

KNIME Hub: hub.knime.com

KNIME E-Learning Course:

© 2021 KNIME AG. All rights reserved.

§ Download the course material from the KNIME Hub

© 2021 KNIME AG. All rights reserved. 36

© 2021 KNIME AG. All rights reserved. 37

Cheminformatics Bioinformatics Mass

© 2021 KNIME AG. All rights reserved. 38

Further extensions including detailed descriptions can be found at https://hub.knime.com

© 2021 KNIME AG. All rights reserved. 39

There are different ways to install KNIME extensions:

© 2021 KNIME AG. All rights reserved.

There are different ways to install KNIME extensions: