ontoloviz 1.7.4

OntoloViz drug- and phenotype-ontology visualization GUI

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OntoloViz is a user-friendly interface that enables the creation of interactive sunburst plots for biomedical ontologies. It allows you to conveniently visualize your data for reports or share the generated plots with collaborators. Check out the examples section to download interactive .html examples and to gain a better understanding of the package's capabilities.

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Quickstart

The GUI can be run by downloading the latest release or by installing the package via PyPi (OS independent, requires Python 3.8+):

pip install ontoloviz

After the installation you can run the GUI from the command line with the following command:

ontoloviz

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Usage

The application allows importing .tsv and .xlsx files, but the use of .tsv and tab as a separator is recommended. The GUI can create two types of sunburst diagrams to represent either phenotype or drug ontologies, which is determined by the structure of the loaded files. Any numbers entered in the input file will be converted to integers and decimal points will be rounded.

GUI Options

Load File: load an .tsv or .xlsx file containing ontology data based below defined file formats

Load from Web: load an .obo ontology from a pre-defined list, or define a URL to any ontology

General options

• Set Color Scale: define a custom color scale for the sunburst color scaling when color propagation is active
• Set Border: configures the border properties drawn around sunburst wedges
• Drop empty nodes (phenotype sunburst only): drops nodes who have no further children and 0 counts
• Wedge Width (drug sunburst only): switch from full outer circle (total) to count-based wedge widths (remainder)
• Display Labels: controls display of labels inside sunburst wedges, available options:
  • all
  • propagation
  • drugs (drug sunburst only)
  • none
• Legend: displays a weighted color bar (disabled for summary plots with specific color propagation enabled)

Propagation options

• Enable: enables count- and color propagation from child to parent nodes
• Color: controls color propagation by the options:
  • off: color scale is based on 'Color' column from imported file
  • specific: color scale is based on the maximum values of the corresponding subtree
  • global: color scale is based on the maximum values of the entire tree ontology
  • phenotype (phenotype sunburst only): Only the most outer phenotype in a branch is colored
• Counts: controls count propagation by the options:
  • off: no counts are propagated, counts equal imported values
  • level: counts are propagated up to defined level, values above threshold remain unchanged
  • all: counts are propagated up to central node, imported values are corrected and overwritten
• Level: controls color- and count-propagation from outer to inner levels up to defined level
  • affects color propagation when Color is set to specific or global
  • affects count propagation when Counts is set to level
  • drug sunburst: 1 corresponds to the central node, 5 to the outermost node (=drug)
  • phenotype sunburst: 0 corresponds to the central node, 13 to the outermost node

Summary options

• Enable: displays all available subtrees in a single view (resource intensive, set Labels to none for faster loading)
• Columns: defines the amount of columns when summary plot is enabled

Save and Plot options

• Save: when enabled, an interactive .html file containing the plot as well as a .tsv file containing the ontology data based on the current settings is generated for later use
• Plot: Process and generate plot, opens in a Browser window

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MeSH Ontology

This separator-based ontology follows the principles of the MeSH tree.

• A Tree ID is defined by a combination of three numbers or letters, for example C01.
• Levels are separated by a dot ., for example C01.001.
• Ontologies up to thirteen hierarchical levels are supported.
• A single phenotype end-node can be assigned to multiple parent-nodes by specifying the parents tree ids as a pipe separated string in the column Tree ID, for example C01.001.001|C02.001.001.
• If a child element is defined without a valid parent node existing, the GUI generates all parent elements with the default color and value 0. For example, the node 123.001 is automatically generated if only the child node 123.001.001 was defined. This works only if at least the most central node 123 was defined manually.
• Counts entered in the file will be converted to integers. If a node should be displayed without counts, use 0.
• The loaded file must contain 7 columns and follow the below structure to be correctly recognized:

Column Index	Header Text	Description
0	MeSH ID	Required primary identifier of a node in format C01.001
1	Tree ID	Required | pipe delimited list of Tree IDs of a node (allows 1:N mappings)
2	Name	Optional label to be displayed inside the sunburst wedges
3	Description	Optional description displayed in the sunburst wedge tooltip
4	Comment	Optional comment displayed in the sunburst wedge tooltip
5	Counts [Name]	Required count for wedge weights, Name will be used as figure title
6	Color	Optional color for the sunburst wedges, must be hex-string in format #FFFFFF

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ATC Ontology

This kind of sunbursts have a fixed hierarchy of 5 levels and are based on the ATC tree.

• ATC codes are divided into five levels, which must follow the following naming conventions:
  • 1st level: letter
  • 2nd level: two numbers
  • 3rd level: letter
  • 4th level: letter
  • 5th level: two numbers
• Example ATC code: A10BA02
• The hierarchy does only allow 1:1 child-parent relationships, contrary to the other ontologies. For example, if the drug deltatonin should be assigned to the parent nodes A01AA and B01BB, it must be defined twice with the ids A01AA01 and B01BB01.
• The loaded file must contain 6 columns and follow the below structure to be correctly recognized as a ATC ontology:

Column Index	Header Text	Description
0	ATC code	Required primary identifier of a node in format A10BA02
1	Level	Optional level as number, not used for building tree
2	Label	Optional label to be displayed inside the sunburst wedges
3	Comment	Optional comment displayed in the sunburst wedge tooltip
4	Counts [Name]	Required count for wedge weights, Name will be used as figure title
5	Color	Optional color for the sunburst wedges, must be hex-string in format #FFFFFF

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Custom Separator-based Ontologies

OntoloViz supports loading of custom ontologies - if no known format is detected, a prompt will ask whether the loaded file is a separator-based ontology or if it does contain identifiers with child- and parent-ids. For separator-based ontologies, the following separators are supported: . (dot), , (colon), _ (underscore), / (slash). To generate such an ontology, the following 5-column layout is required:

Column Index	Header Text	Description
0	ID	Required node identifier of a node in format A.1 - multiple IDs can be separated with | (pipe)
1	Label	Optional label to be displayed inside the sunburst wedges
2	Comment	Optional comment displayed in the sunburst wedge tooltip
3	Count	Optional count for wedge weights
4	Color	Optional color for the sunburst wedges, must be hex-string in format #FFFFFF

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Custom Parent-based Ontologies

For loading any ontology with arbitrary IDs that do not follow a structured schema, the definition of a child-parent relationship using a 6-column layout is required:

Column Index	Header Text	Description
0	ID	Required node identifier in any format - multiple IDs can be separated with | (pipe)
1	Parent	Required parent identifier in any format - if parent ID does not exist, node will be removed
2	Label	Optional label to be displayed inside the sunburst wedges
3	Comment	Optional comment displayed in the sunburst wedge tooltip
4	Count	Optional count for wedge weights
5	Color	Optional color for the sunburst wedges, must be hex-string in format #FFFFFF

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Templates and Examples

Filename	Description
atc_example_covid_drugs_experimental.tsv	ATC-based example with data from the DrugBank indicating experimental drugs related to COVID-19.
atc_example_covid_drugs_trial_summary.tsv	ATC-based example with data from publicly available clinical trial data indicating drugs tested in clinical studies, one count represents usage in one study.
atc_template.tsv	ATC-based empty template of the ATC tree based on the manually curated chemical database of bioactive molecules ChEMBL v29.
custom_template_parent_based.tsv	Template for creating your own ontology based on any child and parent terms.
custom_template_separator_based.tsv	Template to create your own ontology based on a separator-based tree structure - for this template the underscore character _ has been used.
mesh_example_pubmed_mapped.tsv	MeSH-based example with data from the publicly available PubMed database of publications (title + abstract), where disease-related MeSH terms were extracted and mapped to the MeSH-tree.
mesh_template.tsv	MeSH-based empty template of the MeSH tree C and F03. Terms are unique and mapped to all related parent nodes.
atc_example.html	ATC-based sample plot generated with the provided covid_drugs_trial_summary.tsv file.
mesh_example.html	MeSH-based sample plot generated with the provided covid_drugs_trial_summary.tsv file.

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Screenshots and Demos

Demo 1: Minimal example for creating a phenotype based ontology

Demo 2: Showcase of some of the features available in OntoloViz (used template: test_tree.zip)

Screenshot 1: Drug sunburst plot with enabled labels, counts propagated up to level 3

Screenshot 2: Summary phenotype sunburst plot with tooltip, counts propagated up to the central node, color coded

Screenshot 3 & 4: Left: define automatic color scales based on defined counts with thresholds and hex color codes, Right: define border properties (width, opacity, colors) or disable them entirely

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Special Thanks to

• Paul Perco, who had the initial idea for this package and provided support throughout the entire process
• Andreas Heinzel, for inspiration regarding architectural- and software-related topics
• The Delta4 GmbH team for providing helpful inputs

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Reference

Matthias Ley, Andreas Heinzel, Lucas Fillinger, Klaus Kratochwill, Paul Perco, OntoloViz: a GUI for interactive visualization of ranked disease or drug lists using the MeSH and ATC ontologies, Bioinformatics Advances, 2023; vbad113, https://doi.org/10.1093/bioadv/vbad113