Illustration Validator

What is the Reactome Illustration Validator

Reactome improves the graphical representation of higher-level pathways in the Reactome pathway browser with the idea of icon library and EHLD diagrams. This project validates the structure and value of each icon XML metadata file and the SVG structure of EHLD diagrams.

Icon XML Validation

The correct xml file should have the following structure:

<metadata>
    <categories>
        <category>{CATEGORY}</category>
    </categories>
    <person orcid="{ORCID}" role="curator">{CURATOR_NAME}</person>
    <person role="designer" url="{DESIGNER_URL}">{DESIGNER_NAME}</person>
    <name>{ICON_NAME}</name>
    <description>{DESCRIPTION}</description>
    <references>
        <reference>
            <db>{REFERENCE_NAME}</db>
            <id>{REFERENCE_ID}</id>
        </reference>
    </references>
    <synonyms>
        <synonym>{SYNONYM}</synonym>
    </synonyms>
</metadata>

• {CATEGORY} with one or more of the suggested categories: arrow, cell_element, cell_type, compound, human_tissue, protein, receptor and transporter.
• {REFERENCE_NAME} for the name of the resource you have used to find this component (e.g.: UNIPROT, GO, CHEBI … ).
• {SYNONYM} as any synonyms or alternative names your component might be known of.

EHLD SVG Validation

EHLD SVGs are validated for correct structure:

• Filename matches R-HSA-[numbers].svg
• BG group exists with a LOGO inside it
• At least one REGION-R-HSA-[numbers] group exists
• Each REGION has a matching OVERLAY-R-HSA-[numbers] inside it
• FG group is optional (warning if missing)

Installation & Usage

Requirements

1. Maven 3.X - [Installation Guide](http://maven.apache.org/install.html)

Git Clone

git clone https://github.com/reactome/illustration-validator.git
cd illustration-validator

Usage

To validate icon files and generate a validation log file, package and use the validator tool as follows:

mvn clean package

then start validating files by using the following line:

java -jar ./target/illustration-validator-jar-with-dependencies.jar
      -d path/to/icon/directory
      -s path/to/ehld/directory
      -r references.txt
      -c categories.txt

the expected result should be as below:

ERROR - Element "synonym" is missing value in R-ICO-013884.xml.
ERROR - The element type "description" must be terminated by the matching end-tag "</description>". File: R-ICO-013655.xml
ERROR - [proteoin] at the element "category" is not in the list CATEGORIES in the R-ICO-013736.xml.
ERROR - EHLD 'R-HSA-9735786.svg': missing 'LOGO' inside 'BG' group
...