Merge branch 'bco_to_2791_rename' into 'ballot-crg-r1'

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

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

biocomputeobject.json → 2791object.json

-{
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/biocomputeobject.json",
+    "$id": "https://w3id.org/2791/schemas/2791object.json",
     "type": "object",
-    "title": "Base type for all BioCompute Objects",
-    "description": "All BioCompute object types must adhear to this type in order to be compliant with BioCompute framework",
+    "title": "Base type for all IEEE-2791 Objects",
+    "description": "All IEEE-2791 object types must adhear to this type in order to be compliant with IEEE-2791 standard",
     "required": [
-        "bco_id",
-        "bco_spec_version",
+        "ieee2791_id",
+        "ieee2791_spec_version",
         "etag",
         "provenance_domain",
         "usability_domain",
@@ -15,11 +14,11 @@
         "io_domain"
     ],
     "definitions": {
-        "bco_id": {
+        "ieee2791_id": {
             "type": "string",
-            "description": "A unique identifier that should be applied to each BCO instance, generated and assigned by a BCO database engine. IDs should never be reused",
+            "description": "A unique identifier that should be applied to each IEEE-2791 Object instance, generated and assigned by a IEEE-2791 database engine. IDs should never be reused",
             "examples": [
-                "https://w3id.org/biocompute/examples/HCV1a.json"
+                "https://w3id.org/2791/examples/HCV1a.json"
             ]
         },
         "uri": {
@@ -115,15 +114,15 @@
     },
     "additionalProperties": false,
     "properties": {
-        "bco_id": {
-            "$ref": "#/definitions/bco_id",
+        "ieee2791_id": {
+            "$ref": "#/definitions/ieee2791_id",
             "readOnly": true
         },
-        "bco_spec_version": {
+        "ieee2791_spec_version": {
             "type": "string",
-            "description": "Version of the BCO specification used to define this document",
+            "description": "Version of the IEEE-2791 specification used to define this document",
             "examples": [
-                "https://w3id.org/biocompute/spec/v1.2"
+                "https://w3id.org/2791/v1.2"
             ],
             "readOnly": true,
             "format": "uri"
@@ -145,7 +144,7 @@
         },
         "extension_domain": {
             "type": "array",
-            "description": "points to internal or external references to a script object that was used to perform computations for this BCO instance.",
+            "description": "points to internal or external references to a script object that was used to perform computations for this IEEE-2791 Object instance.",
             "items":{
                 "required":[
                     "extension_schema"
@@ -177,4 +176,4 @@
             "$ref": "error_domain.json"
         }
     }
-}
\ No newline at end of file
+}

AUTHORS

-# This is the list of BioCompute Object Schema authors for copyright purposes.
+# This is the list of IEEE-2791 Object Schema authors for copyright purposes.
 #
 # This does not necessarily list everyone who has contributed code,
 # since in some cases, their employer may be the copyright holder.

CONTRIBUTORS

-# This is the list of BioCompute Object Schema contributors
+# This is the list of IEEE-2791 Object Schema contributors
 #
 # This does not necessarily list the copyright holders, since in some
 # cases, an employer may be the copyright holder. To see the full

LICENSE

-Copyright 2019 The BioCompute Object Schema Authors
+Copyright 2019 The IEEE-2791 Object Schema Authors
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
@@ -27,4 +27,4 @@ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-SPDX-License-Identifier: BSD-3-Clause
\ No newline at end of file
+SPDX-License-Identifier: BSD-3-Clause

README.md

-# BioCompute Object Schema
+# IEEE-2791 Object Schema
 
-BioCompute Object Schema is a project of the IEEE P2791 BioCompute
-Working Group intended for use as part of IEEE P2791 (Standard for
-Bioinformatics Computations and Analyses Generated by High-Throughput
-Sequencing (HTS) to Facilitate Communication).
+IEEE-2791 (previously known as "BioCompute") Object Schema is a project of the
+IEEE P2791 BioCompute Working Group intended for use as part of IEEE P2791
+(Standard for Bioinformatics Computations and Analyses Generated by
+High-Throughput Sequencing (HTS) to Facilitate Communication).
 
 ## License
 
 All source files (.json files) in this repository are subject to the
 following copyright and licensing terms.
 
-Copyright 2019 The BioCompute Object Schema Authors. 
+Copyright 2019 The IEEE-2791 Schema Authors. 
 
 See the LICENSE file distributed with this work for copyright and
 licensing information, the AUTHORS file for a list of copyright

description_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/description_domain.json",
+    "$id": "https://w3id.org/2791/schemas/description_domain.json",
     "type": "object",
     "title": "Description Domain",
     "description": "Structured field for description of external references, the pipeline steps, and the relationship of I/O objects.",
@@ -26,7 +26,7 @@
         },
         "xref": {
             "type": "array",
-            "description": "List of the databases or ontology IDs that are cross-referenced in the BCO.",
+            "description": "List of the databases or ontology IDs that are cross-referenced in the IEEE-2791 Object.",
             "items": {
                 "type": "object",
                 "description": "External references are stored in the form of prefixed identifiers (CURIEs). These CURIEs map directly to the URIs maintained by Identifiers.org.",
@@ -73,7 +73,7 @@
         },
         "platform": {
             "type": "array",
-            "description": "reference to a particular deployment of an existing platform where this BCO can be reproduced.",
+            "description": "reference to a particular deployment of an existing platform where this IEEE-2791 Object can be reproduced.",
             "items": {
                 "type": "string",
                 "examples": [
@@ -139,7 +139,7 @@
                                     ]
                                 },
                                 "uri": {
-                                    "$ref": "biocomputeobject.json#/definitions/uri"
+                                    "$ref": "2791object.json#/definitions/uri"
                                 }
                             }
                         }
@@ -148,14 +148,14 @@
                         "type": "array",
                         "description": "URIs (expressed as a URN or URL) of the input files for each tool.",
                         "items": {
-                            "$ref": "biocomputeobject.json#/definitions/uri"
+                            "$ref": "2791object.json#/definitions/uri"
                         }
                     },
                     "output_list": {
                         "type": "array",
                         "description": "URIs (expressed as a URN or URL) of the output files for each tool.",
                         "items": {
-                            "$ref": "biocomputeobject.json#/definitions/uri"
+                            "$ref": "2791object.json#/definitions/uri"
                         }
                     }
                 }

error_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/error_domain.json",
+    "$id": "https://w3id.org/2791/schemas/error_domain.json",
     "type": "object",
     "title": "Error Domain",
-    "description": "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",
+    "description": "Fields in the Error Domain are open-ended and not restricted nor defined by the IEEE-2791 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",
     "additionalProperties": false,
     "required": [
         "empirical_error",
@@ -21,4 +21,4 @@
             "description": "descriptive of errors that originate by fuzziness of the algorithms, driven by stochastic processes, in dynamically parallelized multi-threaded executions, or in machine learning methodologies where the state of the machine can affect the outcome."
         }
     }
-}
\ No newline at end of file
+}

execution_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/execution_domain.json",
+    "$id": "https://w3id.org/2791/schemas/execution_domain.json",
     "type": "object",
     "title": "Execution Domain",
-    "description": "The fields required for execution of the BCO are herein encapsulated together in order to clearly separate information needed for deployment, software configuration, and running applications in a dependent environment",
+    "description": "The fields required for execution of the IEEE-2791 Object are herein encapsulated together in order to clearly separate information needed for deployment, software configuration, and running applications in a dependent environment",
     "required": [
         "script",
         "script_driver",
@@ -15,12 +15,12 @@
     "properties": {
         "script": {
             "type": "array",
-            "description": "points to internal or external references to a script object that was used to perform computations for this BCO instance.",
+            "description": "points to internal or external references to a script object that was used to perform computations for this IEEE-2791 Object instance.",
             "items": {
                 "additionalProperties": false,
                 "properties": {
                     "uri": {
-                        "$ref": "biocomputeobject.json#/definitions/uri"
+                        "$ref": "2791object.json#/definitions/uri"
                     }
                 }
 			}
@@ -36,7 +36,7 @@
         },
         "software_prerequisites": {
             "type": "array",
-            "description": "Minimal necessary prerequisites, library, tool versions needed to successfully run the script to produce BCO.",
+            "description": "Minimal necessary prerequisites, library, tool versions needed to successfully run the script to produce this IEEE-2791 Object.",
             "items": {
                 "type": "object",
                 "description": "A necessary prerequisite, library, or tool version.",
@@ -62,14 +62,14 @@
                         ]
                     },
                     "uri": {
-                        "$ref": "biocomputeobject.json#/definitions/uri"
+                        "$ref": "2791object.json#/definitions/uri"
                     }
                 }
             }
         },
         "external_data_endpoints": {
             "type": "array",
-            "description": "Minimal necessary domain-specific external data source access in order to successfully run the script to produce BCO.",
+            "description": "Minimal necessary domain-specific external data source access in order to successfully run the script to produce this IEEE-2791 Object.",
             "items": {
                 "type": "object",
                 "description": "Requirement for network protocol endpoints used by a pipeline’s scripts, or other software.",

io_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/io_domain.json",
+    "$id": "https://w3id.org/2791/schemas/io_domain.json",
     "type": "object",
     "title": "Input and Output Domain",
-    "description": "The list of global input and output files created by the computational workflow, excluding the intermediate files. Custom to every specific BCO implementation, these fields are pointers to objects that can reside in the system performing the computation or any other accessible system.",
+    "description": "The list of global input and output files created by the computational workflow, excluding the intermediate files. Custom to every specific IEEE-2791 Object implementation, these fields are pointers to objects that can reside in the system performing the computation or any other accessible system.",
     "required": [
         "input_subdomain",
         "output_subdomain"
@@ -21,7 +21,7 @@
                 ],
                 "properties": {
                     "uri": {
-                        "$ref": "biocomputeobject.json#/definitions/uri"
+                        "$ref": "2791object.json#/definitions/uri"
                     }
                 }
             }
@@ -48,7 +48,7 @@
                         "pattern": "^(.*)$"
                     },
                     "uri": {
-                        "$ref": "biocomputeobject.json#/definitions/uri"
+                        "$ref": "2791object.json#/definitions/uri"
                     }
                 }
             }

parametric_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/parametric_domain",
+    "$id": "https://w3id.org/schemas/parametric_domain",
     "type": "array",
     "title": "Parametric Domain",
     "description": "This represents the list of NON-default parameters customizing the computational flow which can affect the output of the calculations. These fields can be custom to each kind of analysis and are tied to a particular pipeline implementation",
@@ -41,4 +41,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}

provenance_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/provenance_domain.json",
+    "$id": "https://w3id.org/2791/schemas/provenance_domain.json",
     "type": "object",
     "title": "Provenance Domain",
     "description": "Structured field for tracking data through transformations, including contributors, reviewers, and versioning.",
@@ -16,22 +16,22 @@
     "properties": {
         "name": {
             "type": "string",
-            "description": "Public searchable name for BioCompute Object. This public field should take free text value using common biological research terminology supporting the terminology used in the usability_domain, external references (xref), and keywords sections.",
+            "description": "Public searchable name for IEEE-2791 Object. This public field should take free text value using common biological research terminology supporting the terminology used in the usability_domain, external references (xref), and keywords sections.",
             "examples": [
                 "HCV1a ledipasvir resistance SNP detection"
             ]
         },
         "version": {
             "type": "string",
-            "description": "Records the versioning of this BCO instance object. BioCompute Object Version should adhere to semantic versioning as recommended by Semantic Versioning 2.0.0.",
-		    "reference": "https://semver.org/",
+            "description": "Records the versioning of this IEEE-2791 Object instance. IEEE-2791 Object Version should adhere to semantic versioning as recommended by Semantic Versioning 2.0.0.",
+            "reference": "https://semver.org/spec/v2.0.0.html",
             "examples": [
                 "2.9"
             ]
         },
         "review": {
             "type": "array",
-            "description": "Description of the current verification status of an object in the review process. The unreviewed flag indicates that the object has been submitted, but no further evaluation or verification has occurred. The in-review flag indicates that verification is underway. The approved flag indicates that the BCO has been verified and reviewed. The suspended flag indicates an object that was once valid is no longer considered valid. The rejected flag indicates that an error or inconsistency was detected in the BCO, and it has been removed or rejected. The fields from the contributor object (described in section 2.1.10) is inherited to populate the reviewer section.",
+            "description": "Description of the current verification status of an object in the review process. The unreviewed flag indicates that the object has been submitted, but no further evaluation or verification has occurred. The in-review flag indicates that verification is underway. The approved flag indicates that the IEEE-2791 Object has been verified and reviewed. The suspended flag indicates an object that was once valid is no longer considered valid. The rejected flag indicates that an error or inconsistency was detected in the IEEE-2791 Object, and it has been removed or rejected. The fields from the contributor object (described in section 2.1.10) is inherited to populate the reviewer section.",
             "items": {
                 "type": "object",
                 "required": [
@@ -45,8 +45,8 @@
                         "format": "date-time"
                     },
                     "reviewer": {
-                        "$ref": "biocomputeobject.json#/definitions/contributor",
-                        "description": "Contributer that assigns BCO review status."
+                        "$ref": "2791object.json#/definitions/contributor",
+                        "description": "Contributer that assigns IEEE-2791 review status."
                     },
                     "reviewer_comment": {
                         "type": "string",
@@ -64,15 +64,15 @@
                             "rejected",
                             "suspended"
                         ],
-                        "description": "Current verification status of the BioCompute Object",
+                        "description": "Current verification status of the IEEE-2791 Object",
                         "default": "unreviewed"
                     }
                 }
             }
         },
         "derived_from": {
-            "description": "value of `bco_id` field of another BioCompute object",
-            "$ref": "biocomputeobject.json#/definitions/bco_id"
+            "description": "value of `ieee2791_id` field of another IEEE-2791 Object",
+            "$ref": "2791object.json#/definitions/ieee2791_id"
         },
         "obsolete_after": {
             "type": "string",
@@ -98,13 +98,13 @@
         },
         "created": {
             "type": "string",
-            "description": "Date and time of the BioCompute Object creation",
+            "description": "Date and time of the IEEE-2791 Object creation",
             "readOnly": true,
             "format": "date-time"
         },
         "modified": {
             "type": "string",
-            "description": "Date and time the BioCompute Object was last modified",
+            "description": "Date and time the IEEE-2791 Object was last modified",
             "readOnly": true,
             "format": "date-time"
         },
@@ -112,7 +112,7 @@
             "type": "array",
             "description": "This is a list to hold contributor identifiers and a description of their type of contribution, including a field for ORCIDs to record author information, as they allow for the author to curate their information after submission. The contribution type is a choice taken from PAV ontology: provenance, authoring and versioning, which also maps to the PROV-O.",
             "items": {
-                "$ref": "biocomputeobject.json#/definitions/contributor"
+                "$ref": "2791object.json#/definitions/contributor"
             }
         },
         "license": {

usability_domain.json

 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "http://biocomputeobject.org/schemas/usability_domain.json",
+    "$id": "https://w3id.org/2791/schemas/usability_domain.json",
     "type": "array",
     "title": "Usability Domain",
-    "description": "Author-defined usability domain of the BCO. This field is to aid in search-ability and provide a specific description of the function of the object. It is recommended that a novel use of the BCO could result in the creation of a new entry with a new usability domain",
+    "description": "Author-defined usability domain of the IEEE-2791 Object. This field is to aid in search-ability and provide a specific description of the function of the object. It is recommended that a novel use of the IEEE-2791 Object could result in the creation of a new entry with a new usability domain",
     "items": {
         "type": "string",
         "description": "Free text values that can accept template language to indicate values from the external_references",
@@ -14,4 +14,4 @@
             "GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20"
         ]
     }
-}
\ No newline at end of file
+}