Tool annotation for Galaxy tools

[bgruening]

Hi all!

I would like to add BioSchemas support for our Galaxy instances, or more concrete for the tools include in our Galaxy instances.

This is how a tool looks like and I'm wondering if it would be enough to include the schema somewhere on this page:

https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjbrowse%2Fjbrowse%2F0.7.0.3&version=0.7.0.3&__identifer=bg95609u5oq

If so, would the following schema be enough to get started?

{
    "@context": "http://schema.org/",
    "@type": "SoftwareApplication",
    "@type": "SIO:000097",
    "name": "Validata",
    "citation": ["10.1101/gr.094607.109"],
    "description": "JBrowse genome browser",
    "url": "https://jbrowse.org",
    "featureList": "http://edamontology.org/operation_3208"
}

[AlasdairGray]

You would need to wrap your JSON in some script tags, so it would be something like

<script type="application/ld+json">
{
    "@context": "http://schema.org/",
    "@type": "SoftwareApplication",
    "@type": "http://semanticscience.org/resource/SIO_000097",
    "name": "JBrowse Genome Browser",
    "citation": ["10.1101/gr.094607.109"],
    "description": "JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5.

The JBrowse-in-Galaxy (JiG) tool was written to help build complex JBrowse installations straight from Galaxy, taking advantage of the latest Galaxy features such as dataset collections, sections, and colour pickers. It allows you to build up a JBrowse instance without worrying about how to run the command line tools to format your data, and which options need to be supplied and where. Additionally it comes with many javascript functions to handle colouring of features which would be nearly impossible to write without the assistance of this tool.",
    "url": "https://jbrowse.org",
    "featureList": "http://edamontology.org/operation_3208"
}
</script>

Note that I've updated the name of your tool, expanded the SIO namespace as it is not defined in the context, and I've extended the description of the tool. However, this still does not meet the minimum requirements for Bioschemas. You would need to add details of the software version and the URL. See the Tools Specification for details.

[bgruening]

Cool, thanks. The version would not be a problem, the URL could be - this is not always available. Is a link to a pkg, lets say Debian pkg, or pypi link be enough?

These description I would like to add it automatically determined, so I have no chance to enhance the description and so on. I can only take what lives inside the Galaxy tool. Would you still think this is ok?

[AlasdairGray]

Cool, thanks. The version would not be a problem, the URL could be - this is not always available. Is a link to a pkg, lets say Debian pkg, or pypi link be enough?

The URL of the page that you are embedding the markup on would probably suffice, e.g. https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fjbrowse%2Fjbrowse%2F0.7.0.3&version=0.7.0.3&__identifer=bg95609u5oq for JBrowse

These description I would like to add it automatically determined, so I have no chance to enhance the description and so on. I can only take what lives inside the Galaxy tool. Would you still think this is ok?

Yes, whatever you can get automatically. I just grabbed the first paragraph from your page to try and show that the description should be more than a few words.

[bgruening]

Perfect, can the URL be the URL to the Galaxy ToolShed of this Tool? The Galaxy Appstore were tools are installed from?

[AlasdairGray]

I would think so