WorkflowHub makes use of, and contributes to, Bioschemas in a number of different ways.
ComputationalWorkflow Type and Profile
The WorkflowHub community initiated and produced the ComputationalWorkflow Type and associated Profile. The first stable release was made in March 2021 and is still being actively extended and improved. As part of this work, there was also a need to create the FormalParameter Type and associated Profile which is used to describe inputs and outputs and was released at the same time.
The WorkflowHub community has also been contributing to the ComputationalTool Profile, as they are related and work continues to keep them aligned.
Bioschemas Metadata in Page Markup
WorkflowHub makes use of Bioschemas to provide metadata about the page shown, by using a JSON-LD block within the page source. Markup is provided for Teams, Spaces, People, Workflows, Organizations, Events, Presentations, Data, Documents, Collections, Organisms and the WorkflowHub itself. Wherever possible and available, these are mapped and conform to a Bioschemas profile.
For example, the page source for CCS.BAM to FASTQ + QC (HiFi genome assembly stage 1) includes the JSON-LD:
<script type="application/ld+json">{
"@context": "https://schema.org",
"@type": [
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"@id": "https://workflowhub.eu/workflows/220?version=1",
"description": "Conversion of files from BAM to FASTQ, including FASTQC & CCS.BAM file quality control (QC) steps.\r\n\r\nInfrastructure_deployment_metadata: Galaxy Australia (Galaxy)",
"name": "CCS.BAM to FASTQ + QC (HiFi genome assembly stage 1)",
"url": "https://workflowhub.eu/workflows/220?version=1",
"keywords": "BAM, FASTQ, Conversion, QC",
"version": 1,
"license": "https://opensource.org/licenses/GPL-3.0",
"creator": [
{
"@type": "Person",
"@id": "https://workflowhub.eu/people/139",
"name": "Gareth Price"
}
],
"producer": [
{
"@type": [
"Project",
"Organization"
],
"@id": "https://workflowhub.eu/projects/30",
"name": "Australian BioCommons"
},
{
"@type": [
"Project",
"Organization"
],
"@id": "https://workflowhub.eu/projects/54",
"name": "Galaxy Australia"
}
],
"dateCreated": "2021-10-21T05:52:36Z",
"dateModified": "2022-04-11T09:27:55Z",
"isPartOf": [
],
"programmingLanguage": {
"@id": "#galaxy",
"@type": "ComputerLanguage",
"name": "Galaxy",
"identifier": {
"@id": "https://galaxyproject.org/"
},
"url": {
"@id": "https://galaxyproject.org/"
}
},
"input": [
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-inputs-Input BAM",
"name": "Input BAM",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-inputs-inputFile",
"name": "inputFile",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-inputs-adapters",
"name": "adapters",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-inputs-contaminants",
"name": "contaminants",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-inputs-limits",
"name": "limits",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
}
],
"output": [
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-fq_single",
"name": "fq_single",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-interleaved_fastq",
"name": "interleaved_fastq",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-fq1",
"name": "fq1",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-fq2",
"name": "fq2",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-fq_u",
"name": "fq_u",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-output1",
"name": "output1",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-html_file",
"name": "html_file",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
},
{
"@type": "FormalParameter",
"@id": "#ccs_bam_to_fastq___qc__hifi_genome_assembly_stage_1_-outputs-text_file",
"name": "text_file",
"dct:conformsTo": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
}
],
"sdPublisher": {
"@type": "Organization",
"@id": "https://about.workflowhub.eu/",
"name": "WorkflowHub",
"url": "https://about.workflowhub.eu/"
}
}</script>
Using Bioschemas in RO-Crate
WorkflowHub also reads and generates RO-Crate packages, which contain metadata described using Bioschemas, along with general schema.org.
In particular it makes use of the ComputationWorkflow type described above, as part of the Workflow-RO-Crate profile specification, the latest version being 1.0.1 released in November 2021.