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linked-data-hub-schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://github.com/biocompute-objects/linked-data-hub/blob/master/linked-data-hub-schema.json",
"title": "Linked Data Hub BioCompute Object",
"description": "Correct formatting for BioCompute Objects in the Linked Data Hub",
"type": "object",
"required": [
"ld",
"ldFor",
"entId",
"entIri",
"entType",
"ldhId",
"ldhIri",
"entAliases",
"entContent",
"entContentSrc",
"modifier",
"modified"
],
"properties": {
"entType": {
"type": "string",
"description": "Type of entity"
},
"entId": {
"type": "string",
"description": "Identifier of entity in the external data source"
},
"entIri": {
"type": "string",
"description": "IRI of entity in the external data source"
},
"ldhId": {
"type": "string",
"description": "LDH identifier"
},
"ldhIri": {
"type": "string",
"description": "LDH IRI"
},
"Id": {
"type": "array",
"description": "This entity is a linked data object for these entities",
"items": {
"type": "object",
"oneOf": [
{ "$ref": "#/definitions/AlleleFunctionalImpactStatement" },
{ "$ref": "#/definitions/AlleleMolecularConsequenceStatement" },
{ "$ref": "#/definitions/BrcaExchangeRecord" },
{ "$ref": "#/definitions/CivicEvidence" },
{ "$ref": "#/definitions/ClinVarSubmission" },
{ "$ref": "#/definitions/CommunityAnnotation" },
{ "$ref": "#/definitions/Gene" },
{ "$ref": "#/definitions/InSilicoPredictionScoreStatement" },
{ "$ref": "#/definitions/InSilicoPredictionScoreStatementEmbedded" },
{ "$ref": "#/definitions/MSeqDR" },
{ "$ref": "#/definitions/MaveDBMapping" },
{ "$ref": "#/definitions/PopulationAlleleFrequencySource" },
{ "$ref": "#/definitions/PopulationAlleleFrequencyStatement" },
{ "$ref": "#/definitions/PubMed" },
{ "$ref": "#/definitions/Variant" },
{ "$ref": "#/definitions/GnomADExomesV4.1" },
{ "$ref": "#/definitions/GnomADGenomesV4.1" },
{ "$ref": "#/definitions/RevelScore" }
]
}
},
"IdFor": {
"type": "array",
"description": "This entity is linked data FOR these other entities",
"items": {
"type": "object",
"oneOf": [
{ "$ref": "#/definitions/AlleleFunctionalImpactStatement" },
{ "$ref": "#/definitions/AlleleMolecularConsequenceStatement" },
{ "$ref": "#/definitions/BrcaExchangeRecord" },
{ "$ref": "#/definitions/CivicEvidence" },
{ "$ref": "#/definitions/ClinVarSubmission" },
{ "$ref": "#/definitions/CommunityAnnotation" },
{ "$ref": "#/definitions/Gene" },
{ "$ref": "#/definitions/InSilicoPredictionScoreStatement" },
{ "$ref": "#/definitions/InSilicoPredictionScoreStatementEmbedded" },
{ "$ref": "#/definitions/MSeqDR" },
{ "$ref": "#/definitions/MaveDBMapping" },
{ "$ref": "#/definitions/PopulationAlleleFrequencySource" },
{ "$ref": "#/definitions/PopulationAlleleFrequencyStatement" },
{ "$ref": "#/definitions/PubMed" },
{ "$ref": "#/definitions/Variant" },
{ "$ref": "#/definitions/GnomADExomesV4.1" },
{ "$ref": "#/definitions/GnomADGenomesV4.1" },
{ "$ref": "#/definitions/RevelScore" }
]
}
},
"entAliases": {
"type": "array",
"description": "List of aliases for the entity in other external data sources. ",
"items": {
"type": "string"
}
},
"entContentSrc": {
"type": "object",
"description": "BioCompute Object metadata."
},
"entContent": {
"type": "object",
"description": "BioCompute Object.",
"properties": {
"provenance_domain": {
"type": "object",
"description": "Structured field for tracking data through transformations, including contributors, reviewers, and versioning.",
"required": [
"name",
"version",
"created",
"modified",
"contributors",
"license"
],
"additionalProperties": false,
"properties": {
"name": {
"type": "string",
"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 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 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": [
"status",
"reviewer"
],
"additionalProperties": false,
"properties": {
"date": {
"type": "string",
"format": "date-time"
},
"reviewer": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/contributor",
"description": "Contributer that assigns IEEE-2791 review status."
},
"reviewer_comment": {
"type": "string",
"description": "Optional free text comment by reviewer",
"examples": [
"Approved by research institution staff. Waiting for approval from regulator"
]
},
"status": {
"type": "string",
"enum": [
"unreviewed",
"in-review",
"approved",
"rejected",
"suspended"
],
"description": "Current verification status of the IEEE-2791 Object",
"default": "unreviewed"
}
}
}
},
"derived_from": {
"description": "value of `ieee2791_id` field of another IEEE-2791 that this object is partially or fully derived from",
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/object_id"
},
"obsolete_after": {
"type": "string",
"description": "If the object has an expiration date, this optional field will specify that using the ‘datetime’ type described in ISO-8601 format, as clarified by W3C https://www.w3.org/TR/NOTE-datetime.",
"format": "date-time"
},
"embargo": {
"type": "object",
"description": "If the object has a period of time during which it shall not be made public, that range can be specified using these optional fields. Using the datetime type, a start and end time are specified for the embargo.",
"additionalProperties": false,
"properties": {
"start_time": {
"type": "string",
"description": "Beginning date of embargo period.",
"format": "date-time"
},
"end_time": {
"type": "string",
"description": "End date of embargo period.",
"format": "date-time"
}
}
},
"created": {
"type": "string",
"description": "Date and time of the IEEE-2791 Object creation",
"readOnly": true,
"format": "date-time"
},
"modified": {
"type": "string",
"description": "Date and time the IEEE-2791 Object was last modified",
"readOnly": true,
"format": "date-time"
},
"contributors": {
"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": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/contributor"
}
},
"license": {
"type": "string",
"description": "Creative Commons license or other license information (text) space. The default or recommended license can be Attribution 4.0 International as shown in example",
"examples": [
"https://spdx.org/licenses/CC-BY-4.0.html"
]
}
}
},
"description_domain": {
"type": "object",
"description": "Structured field for description of external references, the pipeline steps, and the relationship of I/O objects.",
"required": [
"keywords",
"pipeline_steps"
],
"properties": {
"keywords": {
"type": "array",
"description": "Keywords to aid in search-ability and description of the object.",
"items": {
"type": "string",
"description": "This field should take free text value using common biological research terminology.",
"examples": [
"HCV1a",
"Ledipasvir",
"antiviral resistance",
"SNP",
"amino acid substitutions"
]
}
},
"xref": {
"type": "array",
"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.",
"reference": "https://identifiers.org/",
"required": [
"namespace",
"name",
"ids",
"access_time"
],
"properties": {
"namespace": {
"type": "string",
"description": "External resource vendor prefix",
"examples": [
"pubchem.compound"
]
},
"name": {
"type": "string",
"description": "Name of external reference",
"examples": [
"PubChem-compound"
]
},
"ids": {
"type": "array",
"description": "List of reference identifiers",
"items": {
"type": "string",
"description": "Reference identifier",
"examples": [
"67505836"
]
}
},
"access_time": {
"type": "string",
"description": "Date and time the external reference was accessed",
"format": "date-time"
}
}
}
},
"platform": {
"type": "array",
"description": "reference to a particular deployment of an existing platform where this IEEE-2791 Object can be reproduced.",
"items": {
"type": "string",
"examples": [
"hive"
]
}
},
"pipeline_steps": {
"type": "array",
"description": "Each individual tool (or a well defined and reusable script) is represented as a step. Parallel processes are given the same step number.",
"items": {
"additionalProperties": false,
"type": "object",
"required": [
"step_number",
"name",
"description",
"input_list",
"output_list"
],
"properties": {
"step_number": {
"type": "integer",
"description": "Non-negative integer value representing the position of the tool in a one-dimensional representation of the pipeline."
},
"name": {
"type": "string",
"description": "This is a recognized name of the software tool",
"examples": [
"HIVE-hexagon"
]
},
"description": {
"type": "string",
"description": "Specific purpose of the tool.",
"examples": [
"Alignment of reads to a set of references"
]
},
"version": {
"type": "string",
"description": "Version assigned to the instance of the tool used corresponding to the upstream release.",
"examples": [
"1.3"
]
},
"prerequisite": {
"type": "array",
"description": "Reference or required prereqs",
"items": {
"type": "object",
"description": "Text value to indicate a package or prerequisite for running the tool used.",
"required": [
"name",
"uri"
],
"properties": {
"name": {
"type": "string",
"description": "Public searchable name for reference or prereq.",
"examples": [
"Hepatitis C virus genotype 1"
]
},
"uri": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
}
}
},
"input_list": {
"type": "array",
"description": "URIs (expressed as a URN or URL) of the input files for each tool.",
"items": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
},
"output_list": {
"type": "array",
"description": "URIs (expressed as a URN or URL) of the output files for each tool.",
"items": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
}
}
}
}
}
},
"error_domain": {
"type": "object",
"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",
"algorithmic_error"
],
"properties": {
"empirical_error": {
"type": "object",
"title": "Empirical Error",
"description": "empirically determined values such as limits of detectability, false positives, false negatives, statistical confidence of outcomes, etc. This can be measured by running the algorithm on multiple data samples of the usability domain or through the use of carefully designed in-silico data."
},
"algorithmic_error": {
"type": "object",
"title": "Algorithmic Error",
"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."
}
}
},
"execution_domain": {
"type": "object",
"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",
"software_prerequisites",
"external_data_endpoints",
"environment_variables"
],
"additionalProperties": false,
"properties": {
"script": {
"type": "array",
"description": "points to a script object or objects that was used to perform computations for this IEEE-2791 Object instance.",
"items": {
"additionalProperties": false,
"properties": {
"uri": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
}
}
},
"script_driver": {
"type": "string",
"description": "Indication of the kind of executable that can be launched in order to perform a sequence of commands described in the script in order to run the pipelin",
"examples": [
"hive",
"cwl-runner",
"shell"
]
},
"software_prerequisites": {
"type": "array",
"description": "Minimal necessary prerequisites, library, tool versions needed to successfully run the script to produce this IEEE-2791 Object.",
"items": {
"type": "object",
"description": "A necessary prerequisite, library, or tool version.",
"required": [
"name",
"version",
"uri"
],
"additionalProperties": false,
"properties": {
"name": {
"type": "string",
"description": "Names of software prerequisites",
"examples": [
"HIVE-hexagon"
]
},
"version": {
"type": "string",
"description": "Versions of the software prerequisites",
"examples": [
"babajanian.1"
]
},
"uri": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/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 this IEEE-2791 Object.",
"items": {
"type": "object",
"description": "Requirement for network protocol endpoints used by a pipeline’s scripts, or other software.",
"required": [
"name",
"url"
],
"additionalProperties": false,
"properties": {
"name": {
"type": "string",
"description": "Description of the service that is accessed",
"examples": [
"HIVE",
"access to e-utils"
]
},
"url": {
"type": "string",
"description": "The endpoint to be accessed.",
"examples": [
"https://hive.biochemistry.gwu.edu/dna.cgi?cmd=login"
]
}
}
}
},
"environment_variables": {
"type": "object",
"description": "Environmental parameters that are useful to configure the execution environment on the target platform.",
"additionalProperties": false,
"patternProperties": {
"^[a-zA-Z_]+[a-zA-Z0-9_]*$": {
"type": "string"
}
}
}
}
},
"io_domain": {
"type": "object",
"description": "The list of global input and output files created by the computational workflow, excluding the intermediate files. Custom to every specific IEEE-2791 Object implementation, these fields are pointers to objects that can reside in the system performing the computation or any other accessible system.",
"required": [
"input_subdomain",
"output_subdomain"
],
"properties": {
"input_subdomain": {
"type": "array",
"title": "input_domain",
"description": "A record of the references and input files for the entire pipeline. Each type of input file is listed under a key for that type.",
"items": {
"additionalProperties": false,
"type": "object",
"required": [
"uri"
],
"properties": {
"uri": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
}
}
},
"output_subdomain": {
"type": "array",
"title": "output_subdomain",
"description": "A record of the outputs for the entire pipeline.",
"items": {
"type": "object",
"title": "The Items Schema",
"required": [
"mediatype",
"uri"
],
"properties": {
"mediatype": {
"type": "string",
"title": "mediatype",
"description": "https://www.iana.org/assignments/media-types/",
"default": "application/octet-stream",
"examples": [
"text/csv"
],
"pattern": "^(.*)$"
},
"uri": {
"$ref": "https://w3id.org/ieee/ieee-2791-schema/2791object.json#/definitions/uri"
}
}
}
}
}
},
"parametric_domain": {
"type": "array",
"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",
"items": {
"required": [
"param",
"value",
"step"
],
"additionalProperties": false,
"properties": {
"param": {
"type": "string",
"title": "param",
"description": "Specific variables for the computational workflow",
"examples": [
"seed"
]
},
"value": {
"type": "string",
"description": "Specific (non-default) parameter values for the computational workflow",
"title": "value",
"examples": [
"14"
]
},
"step": {
"type": "string",
"title": "step",
"description": "Refers to the specific step of the workflow relevant to the parameters specified in 'param' and 'value'",
"examples": [
"1"
],
"pattern": "^(.*)$"
}
}
}
},
"usability_domain": {
"type": "array",
"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.",
"items": {
"type": "string",
"description": "Free text values that can be used to provide scientific reasoning and purpose for the experiment",
"examples": [
"Identify baseline single nucleotide polymorphisms SNPs [SO:0000694], insertions [so:SO:0000667], and deletions [so:SO:0000045] that correlate with reduced ledipasvir [pubchem.compound:67505836] antiviral drug efficacy in Hepatitis C virus subtype 1 [taxonomy:31646]",
"Identify treatment emergent amino acid substitutions [so:SO:0000048] that correlate with antiviral drug treatment failure",
"Determine whether the treatment emergent amino acid substitutions [so:SO:0000048] identified correlate with treatment failure involving other drugs against the same virus"
]
}
}
}
},
"modifier": {
"type": "string",
"description": "Person who added this entity to LDH"
},
"modified": {
"type": "string",
"description": "Modification timestamp value"
}
},
"definitions": {
"AlleleFunctionalImpactStatement": {
"type": "string"
},
"AlleleMolecularConsequenceStatement": {
"type": "string"
},
"BrcaExchangeRecord": {
"type": "string"
},
"CivicEvidence": {
"type": "string"
},
"ClinVarSubmission": {
"type": "string"
},
"CommunityAnnotation": {
"type": "string"
},
"Gene": {
"type": "string"
},
"InSilicoPredictionScoreStatement": {
"type": "string"
},
"InSilicoPredictionScoreStatementEmbedded": {
"type": "string"
},
"MSeqDR": {
"type": "string"
},
"MaveDBMapping": {
"type": "string"
},
"PopulationAlleleFrequencySource": {
"type": "string"
},
"PopulationAlleleFrequencyStatement": {
"type": "string"
},
"PubMed": {
"type": "string"
},
"Variant": {
"type": "string"
},
"GnomADExomesV4.1": {
"type": "string"
},
"GnomADGenomesV4.1": {
"type": "string"
},
"RevelScore": {
"type": "string"
}
}
}