bco-domains.md

This document is part of the BioCompute Object User Guide

BCO domains

A BCO JSON object is split into different parts, or domains, detailed below.

Condensed example:

{
    "bco_spec_version" : "https://w3id.org/biocompute/1.3.0/",
    "bco_id": "https://example.com/bco/9487ae7e-c1aa-4a3c-b18f-3d3695b33ace",
    "type": "antiviral_resistance_detection", 
    "checksum": "584C7FE128717E1712426AB19CAAEA8BC1E27365B54285BBEA1221284C7D3A48",
    "provenance_domain": {
    },
    "usability_domain": [
    ],
    "extension_domain":{
        "fhir_extension": [
        ],
        "scm_extension": {
        }
    },
    "description_domain": {
    },
    "execution_domain": {
    }, 
    "parametric_domain": {
    }, 
    "io_domain": {
    }, 
    "error_domain": {
    }
}

2.0 Top Level Fields

The top level JSON object of a BCO include attributes to define the BCO itself.

Definition:

• Top level fields

The remaining top level fields details different domains of the BCO, as listed below.

2.1 Provenance Domain "provenance_domain"

The provenance_domain defines the history, version and status of this BCO as part of the review process.

Definition:

• Provenance domain

2.2 Usability Domain "usability_domain"

The usability_domain is meant to improve searchability by allowing free-text description of the BCO.

Definition:

• Usability domain

2.3 Extension Domain "extension_domain"

The extension_domain is a space for a user to add additional structured information that is not defined in the BioCompute shcema. The extension_domain section is not evaluated by checks for BCO validity or computational correctness and as such is the place to add ANY type of additional structured information. We provide two examples that are neither exclusive nor exhaustive.

Definitions:

• fhir extension
• scm extension

2.4 Description Domain "description_domain"

The description_domain contain structured field for description of external references, the pipeline steps, and the relationship of I/O objects.

Definition:

• Description domain

2.5 Execution Domain "execution_domain"

The execution_domain contains fields for execution of the BCO.

Definition:

• Execution domain

2.6 Parametric Domain "parametric_domain"

The parametric_domain represents the list of parameters customizing the computational flow which can affect the output of the calculations.

Definition:

• Parametric domain

2.7 Input and Output Domain "io_domain"

The io_domain represents the list of global input and output files created by the computational workflow.

Definition:

• Input and Output domain

2.8 Error Domain, acceptable range of variability "error_domain"

The error_domain defines the empirical and algorithmic limits an d error sources of the BCO.

Definition:

• Error domain