GitLab

Rename all BCO →  IEEE-2791 Object (and similar)

See merge request IEEE-SA/BioCompute/crg/bco-schema!1

Transformations made:

http://biocomputeobject.org/schemas/ → https://w3id.org/2791/schemas/
BioCompute Object →  IEEE-2791 Object
BioCompute framework →  IEEE-2791 standard
bco_id →  ieee2791_id
bco_spec_version → ieee2791_spec_version
BCO instance →  IEEE-2791 Object instance
BCO →  IEEE-2791 Object
biocomputobject.json →  2791object.json

Comment ID: 26446300023
Page: 3
Line: 21
Comment: ".. should be included in the generation of the hash"  - Hashsum calculation of JSON object trees are non-trivial and must be clearly defined. Out of scope for BioCompute?
Must Be Satisfied: Yes
Proposed Change: Reference a formal specification of JSON object hashing, or remove 'hash'. (alternative: rename to 'etag' and have looser definition)

RE: Comment #: i-56, are the bundled domain extensions part of P2791 or not?

Issue #57

The `extension_domain` folder has been removed.

Page: 3

Line: 21

Remove: "Two Extension Domain example files exist... FHIR...SCM"

Replace with: "The Extension Domain is for the inclusion of any additional structured information. A valid JSON schema for each extension used in this domain has to be specified. The schema should be name spaced, and it is RECOMMENDED that resolving the namespaced URI will provide the extension's JSON Schema. The URL should be provided in the **required** `"extension_schema"` field."

RE: Comment #: i-59, empirical_error and algorithmic_error definition?

Issue #60

Comment ID: 26446700023
Page: 3
Line:37
Replace: "Fields in the Error Domain..."
With: "Fields in the Error Domain are open-ended and not restricted nor defined by the current BioCompute standard. It is RECOMMENDED that the keys directly under empirical_error and algorithmic_error use a full URI. Resolving the URI SHOULD give a JSON Schema or textual definition of the field. Other keys are not allowed error_domain"

issues #60

I think for this version we should not allow additional keys in the error_domain. Any other additions can be put in the extension_domain
'It's RECOMMEND that the keys directly under empirical_error and algorithmic_error use a full URI for their "$ref": value. Resolving the URI SHOULD give a JSON Schema or textual definition of the field. At this time it is RECOMMENDED that no other keys be used in this domain"

issue #53
Change: "The error_domain.json is an optional domain that further describes a bioinformatics workflow"

To: "The error_domain.json is an optional domain to further describe empirical and algorithmic sources and measures of error for a bioinformatics workflow"

- error_domain is no longer **required** in biocompute.json.

Signed-off-by: Joshua Gay <j.gay@ieee.org>

Signed-off-by: Joshua Gay <j.gay@ieee.org>