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bio-tools / biotoolsSchema

biotoolsSchema : Tool description data model for computational tools in life sciences
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SALAD version of biotools schema #10

Open tetron opened 8 years ago

tetron commented 8 years ago

It would be helpful for integration into linked data efforts such as Common Workflow Language if there were a Schema Salad (https://github.com/common-workflow-language/schema_salad) version of the biotools schema; this would provide schema support for expressing the biotools data model in YAML, JSON-LD and RDF.

joncison commented 8 years ago

That would be really great ... we are still working out details for biotoolsXSD 2.0 - to incorporate many suggestions we've had over the last year. Once it's out, we can look to Schema Salad - this also fits nicely with the plan to support multiple formats (for format interchange and validation)

mr-c commented 7 years ago

I just heard that @bgruening has a YAML version of biotoolsXSD 1.x?

redmitry commented 7 years ago

Not sure about the yaml, but I did biotoolsJSON Schema 2.0:

https://github.com/bio-tools/biotoolsSchema/tree/master/versions/biotools-2.0.0/json

technically I can provide YAML support for the elixibilitas proxy, but the idea is that bio.tool will expose the data in 2.0 version format soon (XML, JSON... YAML?).

http://elixir.bsc.es/elixibilitas/biotools/tools

On 2/22/2017 3:47 PM, Michael R. Crusoe wrote:

I just heard that @bgruening https://github.com/bgruening has a YAML version of biotoolsXSD 1.x?

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bgruening commented 7 years ago

First try was here: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/locarna/biotools.yaml Still waiting for the bio.tools to read these files automatically. @mr-c it was more a conversion from the official JSON file to yaml.

joncison commented 7 years ago

@ekry : can you please tweak the bio.tools API so I can get a YAML for https://bio.tools/api/tool/LocARNA/version/1.8.7

I assume here the framework supports YAML out of the box (for input and output) so this tweak is easy??

If we like the look of the format (which will be biotoolsSchema 2.0.0-compatible) and decide to use it, it would make slurping the files very easy