Schemas
JSON Schemas
JSON Schema is a vocabulary that allows you to annotate and validate JSON documents.
Tools JSON Schemas
Every tool has its own JSON Schema with the next structure for the Template tool:
https://github.com/bioexcel/biobb_template/blob/master/biobb_template/json_schemas/template.json
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://bioexcel.eu/biobb_template/json_schemas/1.0/template",
"name": "biobb_template Template",
"title": "Short description for the template module in Restructured Text (reST) syntax. Mandatory.",
"description": "Long description for the template module in Restructured Text (reST) syntax. Optional.",
"type": "object",
"info": {
"wrapped_software": {
"name": "Zip",
"version": ">=3.0",
"license": "BSD 3-Clause"
},
"ontology": {
"name": "EDAM",
"schema": "http://edamontology.org/EDAM.owl"
}
},
"required": [
"input_file_path1",
"output_file_path"
],
"properties": {
"input_file_path1": {
"type": "string",
"description": "Description for the first input file path",
"filetype": "input",
"sample": "https://urlto.sample",
"enum": [
".*\\.top$"
],
"file_formats": [
{
"extension": ".*\\.top$",
"description": "Description for the first input file path",
"edam": "format_3881"
}
]
},
"input_file_path2": {
"type": "string",
"description": "Description for the second input file path (optional)",
"filetype": "input",
"sample": "https://urlto.sample",
"enum": [
".*\\.dcd$"
],
"file_formats": [
{
"extension": ".*\\.dcd$",
"description": "Description for the second input file path (optional)",
"edam": "format_3878"
}
]
},
"output_file_path": {
"type": "string",
"description": "Description for the output file path",
"filetype": "output",
"sample": "https://urlto.sample",
"enum": [
".*\\.zip$"
],
"file_formats": [
{
"extension": ".*\\.zip$",
"description": "Description for the output file path",
"edam": "format_3987"
}
]
},
"properties": {
"type": "object",
"properties": {
"boolean_property": {
"type": "boolean",
"default": true,
"wf_prop": false,
"description": "Example of boolean property."
},
"binary_path": {
"type": "string",
"default": "zip",
"wf_prop": false,
"description": "Example of executable binary property."
},
"remove_tmp": {
"type": "boolean",
"default": true,
"wf_prop": true,
"description": "Remove temporal files."
},
"restart": {
"type": "boolean",
"default": false,
"wf_prop": true,
"description": "Do not execute if output files exist."
}
}
}
},
"additionalProperties": false
}
JSON Schema Generator
Although it’s not difficult to create a JSON Schema by your own, we provide a tool for generating them automatically:
https://github.com/bioexcel/utils_biobb/tree/master/utils_biobb/json
Following the instructions of this json_generator tool, especially those referred to the files structure and to the docs specifications, the tool will generate these JSON Schema files for you.
Additionally, in the utils_biobb package there is another script also generates the configuration files from the data taken from the biobb_template/biobb_template/test/conf.yml file:
https://github.com/bioexcel/utils_biobb/tree/master/utils_biobb/configs
The script will generate two config files (jSON and YAML formats) for each module with properties defined in its parameters. More information about these configuration files in the Execution section.
JSON Schema Validator
In order to validate the JSON Schema generated with the JSON Generator Tool, a JSON Validator Tool can be found in the same json module of the utils_biobb package. Click here to follow the execution instructions of this tool.
This is the schema generated for the validation of the BioBB JSON Schemas:
https://github.com/bioexcel/utils_biobb/blob/master/utils_biobb/json/schema/master_schema.json
Package JSON
Additionally, in the same json_schemas folder, there is a JSON file with information related with the BioBB package.
This information is used for automate the maintenance of the Source & Docs table in the BioBB official website.
As you can see below, you need to provide a general description, the addresses to repositories and containers, tools’ descriptions, dependencies and some descriptive keywords of the package:
{
"_id": "biobb_template",
"desc": "Description for biobb_template package",
"github": "https://github.com/bioexcel/biobb_template",
"readthedocs": "https://biobb-template.readthedocs.io/en/latest/",
"conda": "",
"docker": "",
"singularity": "",
"version": "4.1.0",
"tools" : [
{
"block" : "Template",
"tool" : "zip",
"desc" : "Short description for the template module.",
"exec" : "template",
"docs": "https://biobb-template.readthedocs.io/en/latest/template.html#module-template.template"
},
{
"block" : "TemplateContainer",
"tool" : "zip",
"desc" : "Short description for the template_container module.",
"exec" : "template_container",
"docs": "https://biobb-template.readthedocs.io/en/latest/template.html#module-template.template_container"
}
],
"dep_pypi" : [
"install_requires=['biobb_common==4.1.0']",
"python_requires='>=3.8'"
],
"dep_conda" : [
"python >=3.8",
"biobb_common ==4.1.0"
],
"keywords" : [
"template",
"keywords"
]
}
Bioschemas
Bioschemas aims to improve the Findability of data in the life sciences. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed data.
Bioschemas is making two main contributions:
Proposing new types and properties to Schema.org to allow for the description of life science resources.
Profiles over the Schema.org types that identify the essential properties to use in describing a resource.
Bioschemas started as a community effort in November 2015. It operates as an open community initiative with representatives from a wide variety of institutions. You are welcome to join the community.
Schema.org
Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond.
Schema.org vocabulary can be used with many different encodings, including RDFa, Microdata and JSON-LD. These vocabularies cover entities, relationships between entities and actions, and can easily be extended through a well-documented extension model. Over 10 million sites use Schema.org to markup their web pages and email messages. Many applications from Google, Microsoft, Pinterest, Yandex and others already use these vocabularies to power rich, extensible experiences.
Founded by Google, Microsoft, Yahoo and Yandex, Schema.org vocabularies are developed by an open community process, using the public-schemaorg@w3.org mailing list and through GitHub.
BioBB schema
https://github.com/bioexcel/biobb_template/blob/master/biobb_template/docs/source/schema.html
The BioBB HTML schema is in the docs/source/ folder. The basic code is the next one:
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "SoftwareApplication",
"description": "Biobb_template is the Biobb module collection to perform molecular dynamics simulations.",
"name": "BioBB Template",
"url": "https://github.com/bioexcel/biobb_template",
"additionalType": "Library",
"applicationCategory": "Computational Biology tool",
"applicationSubCategory": "http://www.edamontology.org/topic_3892",
"citation": "https://www.nature.com/articles/s41597-019-0177-4",
"license": "https://www.apache.org/licenses/LICENSE-2.0",
"softwareVersion": "4.1.0",
"applicationSuite": "BioBB BioExcel Building Blocks",
"codeRepository": "https://github.com/bioexcel/biobb_template",
"isAccessibleForFree": "True",
"image": "http://mmb.irbbarcelona.org/biobb/public/assets/layouts/layout3/img/logo.png",
"operatingSystem": ["Linux", "MacOS"],
"offers": {
"@type": "Offer",
"price": "0",
"priceCurrency":"EUR"
}
}
</script>