Public Galaxy Server and Tool Metadata

Had a conversation with @matuskalas at 2 consecutive Galaxy CoFests about improving the search functionality of the Galaxy Platform Directory. In between those two conversations I had a conversation with my bosses about increasing the amount of information related to Galaxy in Bio.Tools and GalaxyCat.

It became obvious while talking with Matúš at this year’s CoFest that these goals complement each other nicely.

This issue could be created in many places:

• Bio.Tools, any number or repos (Picked Content
• GalaxyCat
• GalaxyProject, any number of repos (including galaxy, galaxy-hub,...)

Eventually there may be pull requests in many of those places (including ToolDog).

Goals

Increase presence of public Galaxy servers and their tools in Bio.Tools and GalaxyCat.
Increase Awareness of Bio.Tools and GalaxyCat in the Galaxy Community.
Simultaneously, make the Galaxy Platform Directory contain more useful and searchable information about those platforms.

How?

That’s what this issue is here to discuss. One item seems uncontroversial to me:

• We should use ontology terms to do this. EDAM and a Taxa ontology seem most useful, but others also have obvious applications. For example, RepeatExplorer is all about repetitive elements, and that suggests the sequence ontology

And a starting smattering of open questions:

• Which ontologies? Any ontology that is available in a lookup service, or only a core set of ontologies?
• How do we add new ontologies, either to our limited list, or that aren’t in our selected lookup service? For example the Climate Workbench server may use ontologies that aren’t in biology-centric lookup services.
• Where and how do we store and access server ontology information? On the server itself, seems like a good idea, but adding this to metadata in the hub might be a good fallback.
• A fair amount of work (I think) has gone into supporting EDAM annotation of individual tools. How can we encourage tool wrappers to actually use this functionality?
• How do we make the Galaxy, and larger bioinformatics communities aware of these resources, once they are updated?

Start by reviewing the linked Bio.Tools Content, GalaxyCat, Galaxy, galaxy-hub, and ToolDog repositories, then compare how the Galaxy Platform Directory stores searchable platform information. The issue leaves the ontology set, metadata location, participating repositories, and implementation scope open. Done would require an agreed cross-project plan for exposing public Galaxy servers and tool metadata.