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EGA.common-definitions.json
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{
"$schema": "https://json-schema.org/draft/2019-09/schema",
"$id": "https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.common-definitions.json",
"type": "object",
"title": "EGA common metadata definitions",
"meta:version": "0.0.0",
"$async": true,
"description": "Metadata schema used by the European Genome-phenome Archive (EGA) to store common definitions for other metadata objects. Basically, we are defining here common properties (e.g. instances' aliases) that other metadata objects (e.g. sample) may use. The way we refer to them is by using this object's '$id' field, referencing it in other files (with '$ref' and the relative path of the property - e.g. '$ref': 'https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas/EGA.common-definitions.json#/$defs/objectCoreId'). See structuring documentation (https://json-schema.org/understanding-json-schema/structuring.html). Further details can be found in the EGA-metadata-schema GitHub repository (https://github.com/EbiEga/ega-metadata-schema/tree/main/schemas) and EGA-archive website (https://ega-archive.org/)",
"$defs": {
"objectCoreId": {
"type": "object",
"title": "Core identifiers of an object",
"description": "Base definition containing the properties (e.g. Sample's alias) of a minimal identification layer of an EGA object (e.g. Sample).",
"additionalProperties": false,
"properties": {
"alias": {
"type": "string",
"title": "Alias of an object",
"description": "Submitter designated name (e.g. 'my_sample_J13') for the object (e.g. Sample). The name must be unique within the submission account (e.g. 'ega-box-79'), since the aliases and submission accounts are concatenated within our database to obtain the unique alias (e.g. 'ega-box-79::my_sample_J13').",
"minLength": 1,
"examples": [ "my_sample_J13" ]
},
"centerName": {
"type": "string",
"title": "Center name of the submitter",
"description": "Center name (e.g. 'EBI-TEST') associated to the submitter. In other words, it is the acronym of the submitter's account (provided by the HelpDesk team).",
"minLength": 1,
"examples": [ "EBI-TEST" ]
},
"egaAccession": {
"type": "string",
"title": "EGA's accession of the object",
"description": "The object accession (i.e. unique identifier) assigned by the archive (EGA). Object accessions can be found in the 'Identifiers' section of the EGA-archive website (https://ega-archive.org/metadata/how-to-use-the-api) and commonly start with EGA, followed by the distinctive letter of the object and finally the numeric ID of the instance.",
"examples": [ "EGAN00003245489" ]
},
"externalAccessions": {
"type": "array",
"title": "External accessions array",
"description": "External accession node to reference objects in other archives (e.g. an already existing sample at BioSamples).",
"minItems": 1,
"additionalProperties": false,
"uniqueItems": true,
"items": {
"$ref": "./EGA.common-definitions.json#/$defs/objectExternalAccession"
}
}
},
"anyOf": [
{
"title": "Check core IDs: combination of Alias and Center name",
"required": ["alias", "centerName"]
},
{
"title": "Check core IDs: EGA accession ID",
"required": ["egaAccession"]
},
{
"title": "Check core IDs: external accessions",
"required": ["externalAccessions"]
}
]
},
"customAttribute": {
"type": "object",
"title": "Custom attribute of an object",
"description": "Reusable attributes to encode tag-value pairs (e.g. Tag being 'Age' and its Value '40') with optional units (e.g. 'years').",
"required": ["tag", "value"],
"additionalProperties": false,
"properties": {
"tag": {
"type": "string",
"title": "Tag of the custom attribute",
"description": "The name of the attribute (e.g. 'Age').",
"minLength": 1,
"examples": [ "age" ]
},
"value": {
"type": ["string", "number"],
"title": "Value of the custom attribute",
"description": "The value of the attribute (e.g. '40').",
"examples": [ "smoker", 40 ]
},
"units": {
"type": "string",
"title": "Units of the custom attribute",
"description": "The optional units of the attribute (e.g. 'years').",
"minLength": 1,
"examples": [ "years" ]
}
}
},
"fileObject": {
"type": "object",
"title": "EGA File object",
"description": "Object containing the base metadata attributes of a file object in the EGA. These can inherited elsewhere with or without extending them.",
"required": ["filename", "filetype", "checksumMethod", "unencryptedChecksum", "encryptedChecksum"],
"additionalProperties": false,
"properties": {
"filename": {
"type": "string",
"title": "Filename",
"meta:propertyCurie": "data:1050",
"description": "The full name of a file, including all of their file extensions (e.g. .gpg, .md5...), that identifies the file (e.g. 'my-bam-file.bam.gpg').",
"pattern": "^[^<>:;,?\"*|]+$",
"examples": [ "my-bam-file.bam.gpg" ]
},
"fileContent": {
"type": "array",
"title": "File content array",
"description": "Array of file content items. This array exists to clarify what the purpose of a file, regardless of its format, may be. For example, a TXT formatted file could contain multiple types of data, from gene annotations to READMEs. Therefore, select the items from the used ontology that best describe the content of your file.",
"additionalProperties": false,
"uniqueItems": true,
"minItems": 1,
"items": {
"type": "object",
"title": "File content item",
"description": "Item describing the type of data a file contains or represents.",
"meta:propertyCurie": "format:2350",
"allOf": [
{
"title": "Inherited ontologyTerm structure of termId and termLabel",
"$ref": "./EGA.common-definitions.json#/$defs/ontologyTerm"
}
],
"properties": {
"termId": {
"title": "Ontology constraints for this specific termId",
"description": "Property containing just the ontology constraints for the file content. Notice the 'direct' being 'true', which makes the constraint more stringent, and only allows for terms one step below [format:2350].",
"graphRestriction ": {
"ontologies" : ["obo:edam"],
"classes": ["format:2350"],
"relations": ["rdfs:subClassOf"],
"direct": true,
"include_self": false
},
"examples": [ "format:1919", "format:3326" ]
}
}
}
},
"filetype": {
"type": "string",
"title": "Filetype",
"meta:propertyCurie": "format:1915",
"description": "The main format in which data is structured and represented in an electronic file. It is normally defined by the file extension of the file (e.g. FASTQ for a '.fastq' file). The string corresponds to the ID or name (e.g. FASTA, TSV...), chosen from a list of controlled vocabulary (CV), associated with the given filetype. If you cannot find your term in the CV list, please create an issue at our [metadata GitHub repository](https://github.com/EbiEga/ega-metadata-schema/issues/new/choose) proposing its addition.",
"enum": ["CEL", "TSV", "FASTQ", "FASTA", "VCF", "SRA", "SRF", "SFF", "BAM", "CRAM", "XLSX", "CSV", "BED", "IDAT", "MAP", "PED", "BIM", "FAM", "TXT", "EXP", "GPR", "PY", "SH", "ADF", "SDRF", "IDF", "MD5", "HAP", "CSFASTA", "LOC", "HTML", "HIC", "MD", "MATLAB", "PERL", "TIF", "R", "SNP", "XML", "SVG", "PNG", "JPG", "GTC", "HDF5", "FAST5", "PAIR", "TXT", "BGI", "BGEN", "GEN", "PXF", "LOOM", "BAX.H5", "BAS.H5", "ASM", "CSI", "TBI", "BCF", "qual454", "qualsolid", "FASTQ-illumina", "FASTQ-helicos", "FASTQ-sanger", "FASTQ-solexa", "SAM", "CRAI", "BAI", "MTX", "MEX ", "GMX", "GMT", "GRP"],
"meta:enum": {
"CEL": "[format:1638]",
"TSV": "[format:3475]",
"FASTQ": "[format:1930]",
"FASTA": "[format:1929]",
"VCF": "[format:3016]",
"SRA": "[format:3698]",
"SRF": "[format:3698]",
"SFF": "[format:3284]",
"BAM": "[format:2572]",
"CRAM": "[format:3462]",
"XLSX": "[format:3620]",
"CSV": "[format:3752]",
"BED": "[format:3003]",
"IDAT": "[format:3578]",
"MAP": "[format:3285]",
"PED": "[format:3286]",
"BIM": "[]",
"FAM": "[]",
"EXP": "[format:1631]",
"GPR": "[format:3829]",
"PY": "[format:3996]",
"SH": "[]",
"ADF": "[NCIT:C172213]",
"SDRF": "[NCIT:C172211]",
"IDF": "[NCIT:C172212]",
"MD5": "[data:2190]",
"HAP": "[]",
"CSFASTA": "[]",
"LOC": "[]",
"HTML": "[format:2331]",
"HIC": "[]",
"MD": "[]",
"MATLAB": "[format:4007]",
"PERL": "[format:3998]",
"TIF": "[]",
"R": "[format:3999]",
"SNP": "[]",
"XML": "[format:2332]",
"SVG": "[format:3604]",
"PNG": "[format:3603]",
"JPG": "[format:3579]",
"GTC": "[]: An Illumina-specific file containing called genotypes in AA/AB/BB format",
"HDF5": "[format:3590]",
"FAST5": "[]",
"PAIR": "[]",
"TXT": "[format:2330]",
"BGI": "[]: Index file of a BGEN file",
"BGEN": "[]: Binary version of a GEN file",
"GEN": "[format:3812]",
"PXF": "[]: A phenopacket. An open standard for sharing disease and phenotype information represented as PXF (Phenotype Exchange Format) files, which may be encoded in JSON or YAML.",
"LOOM": "[format:3913]",
"BAX.H5": "[]",
"BAS.H5": "[]",
"ASM": "[]: The files in the ASM directory describe and annotate the genome assembly with respect to the reference genome.",
"CSI": "[]",
"TBI": "[format:3700]",
"BCF": "[format:3020]",
"qual454": "[format:3611]",
"qualsolid": "[format:3610]",
"FASTQ-illumina": "[format:1931]",
"FASTQ-helicos": "[]",
"FASTQ-sanger": "[format:1932]",
"FASTQ-solexa": "[format:1933]",
"SAM": "[format:2573]",
"CRAI": "[]: CRAM indexing format",
"BAI": "[format:3327]",
"MTX": "[format:3916]",
"MEX ": "[]: Market Exchange Format (MEX) for sparse matrices. It contains a matrix (MTX) file, and also gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively. Feature-barcode matrix",
"GMX": "[]",
"GMT": "[]",
"GRP": "[]"
}
},
"checksumMethod": {
"type": "string",
"title": "Checksum method ID",
"meta:propertyCurie": "REPR:ChecksumAlgorithm",
"description": "Node containing both the ID (MD5 or SHA-256), describing the method which yields the checksum from a data input for the purpose of detecting errors. Term chosen from a list of controlled vocabulary (CV). If you cannot find your term in the CV list, please create an issue at our [metadata GitHub repository](https://github.com/EbiEga/ega-metadata-schema/issues/new/choose) proposing its addition.",
"enum": ["MD5", "SHA-256"],
"meta:enum": {
"MD5": "[NCIT:C171276]",
"SHA-256": "[NCIT:C80226]"
}
},
"unencryptedChecksum": {
"type": "string",
"title": "Checksum [NCIT:C43522] of the unencrypted file",
"description": "A computed value which depends on the contents of a block of data and which is transmitted or stored along with the data in order to detect corruption of the data, computed from the unencrypted files.",
"examples": [ "46798b5cfca45c46a84b7419f8b74735" ],
"oneOf": [
{
"title": "Check of MD5 checksum pattern",
"$ref": "#/$defs/md5ChecksumPattern"
},
{
"title": "Check of SHA-256 checksum pattern",
"$ref": "#/$defs/SHA256ChecksumPattern"
}
]
},
"encryptedChecksum": {
"type": "string",
"title": "Checksum [NCIT:C43522] of the encrypted file",
"description": "A computed value which depends on the contents of a block of data and which is transmitted or stored along with the data in order to detect corruption of the data, computed from the encrypted files.",
"examples": [ "bc527343c7ffc103111f3a694b004e2f" ],
"oneOf": [
{
"title": "Check of MD5 checksum pattern",
"$ref": "#/$defs/md5ChecksumPattern"
},
{
"title": "Check of SHA-256 checksum pattern",
"$ref": "#/$defs/SHA256ChecksumPattern"
}
]
},
"sequenceQualityDetails": {
"type": "object",
"title": "Sequence quality details",
"description": "Sequencing quality scores measure the probability that a base is called (i.e. sequenced) incorrectly. New sequencing technologies assign a quality score to each of the bases in the sequence.",
"required": ["qualityScoringSystem"],
"additionalProperties": false,
"properties": {
"qualityScoringSystem": {
"type": "string",
"title": "Quality scoring system",
"description": "How the quality score was computed for the data.",
"enum": ["phred", "logOdds"],
"meta:enum": {
"phred": "The quality score is expressed as a probability of error in log form: -10 log(1/p) where p is the probability of error, with value range 0..63 (0 meaning no base call).",
"logOdds": "The quality score is expressed as the ratio of error to non-error in log form: -10 log(p/(1-p)) where p is the of error, with value range -40..40. The SRA will convert these into phred scale during loadtime."
}
},
"qualityEncoding": {
"type": "string",
"title": "Quality encoding format",
"description": "Encoding system used to represent the quality score.",
"enum": ["ascii", "decimal", "hexadecimal"],
"meta:enum": {
"ascii": "ASCII character based encoding.",
"decimal": "Single decimal value per quality score.",
"hexadecimal": "Single hexadecimal value per quality score."
}
},
"asciiOffset": {
"type": "string",
"title": "ASCII offset",
"description": "Character used in representing the minimum quality value. Helps specify how to decode text rendering of quality data.",
"enum": ["!", "@"],
"meta:enum": {
"!": "ASCII value 33. Typically used for range 0..63.",
"@": "ASCII value 64. Typically used for range 0..60."
}
}
}
}
},
"allOf": [
{
"title": "Inherited check of checksum patterns",
"$ref": "#/$defs/checksumPatternCheck"
},
{
"title": "Inherited check of filetype-filename patterns",
"$ref": "#/$defs/filenameFiletypePatternCheck"
}
]
},
"relationshipObject": {
"type": "object",
"title": "EGA Relationships object",
"description": "Object containing the base metadata attributes of a relationship object in the EGA. Comprises metadata (e.g. Source or Target) of a directional association between two entities. One of the entitis **needs** to be the current instance. For instance, a study JSON document should not contain relationships between a sample and an individual. Therefore, only one end of the relationship is given: if the source is present, the target is inferred to be the current instance; if the target is given, then it's the source the one inferred as the current instance. Examples of common relationships: (1) a sample being referenced in an experiment; (2) an study being the same as another study at a different archive (e.g. in BioStudies); (3) an individual being the parent of another individual; (4) hundreds of samples being grouped with each other for broad reasons.",
"required": ["rType"],
"additionalProperties": false,
"properties": {
"rType": {
"type": "string",
"title": "Relationship type",
"description": "ID (e.g. sameAs) of the type of the relationship. To be chosen from a controlled vocabulary (CV) list. If you cannot find your term in the CV list, please create an issue at our [metadata GitHub repository](https://github.com/EbiEga/ega-metadata-schema) proposing its addition.",
"enum": ["referencedBy", "developsFrom", "sameAs", "memberOf", "groupedWith", "familyRelationshipWith", "childOf", "isAfter", "publishedIn", "submittedBy", "contactOf", "mainContactOf"],
"meta:enum": {
"referencedBy": "[SIO:000252]",
"developsFrom": "[RO:0002202]",
"sameAs": "[NCIT:C64637]",
"memberOf": "[RO:0002350]",
"groupedWith": "",
"familyRelationshipWith": "[EFO:0004424]",
"childOf": "[GSSO:000728]",
"isAfter": "[SIO:000211]",
"publishedIn": "[EFO:0001796]",
"submittedBy": "[NCIT:C25695]",
"contactOf": "[NCIT:C25461]",
"mainContactOf": ""
},
"examples": [ "referencedBy" ]
},
"rSource": {
"type": "object",
"title": "Source of the relationship",
"description": "Object reference of the relationship's source. In other words, the starting point of the relationship: in 'sample_A developsFrom sample_B' the source is 'sample_A'.",
"allOf": [
{
"title": "Inherited oneRelationshipEnd object",
"$ref": "./EGA.common-definitions.json#/$defs/oneRelationshipEnd"
}
]
},
"rTarget": {
"type": "object",
"title": "Target of the relationship",
"description": "Object reference of the relationship's target. In other words, the ending point of the relationship: in 'sample_A developsFrom sample_B' the target is 'sample_B'.",
"allOf": [
{
"title": "Inherited oneRelationshipEnd object",
"$ref": "./EGA.common-definitions.json#/$defs/oneRelationshipEnd"
}
]
},
"rLabel": {
"type": "string",
"title": "Custom label of the relationship",
"description": "Custom free-form label of the relationship, used to add extra details of the relationship if needed.",
"minLength": 1,
"examples": [
"Source individual is the third child of the target individual",
"Grouped samples by colour of the medium",
"Both samples are the same because of an error in the submission at..."
]
}
},
"oneOf": [
{
"title": "The source is given (i.e. the target is inferred as the current instance)",
"required": ["rSource"]
},
{
"title": "The target is given (i.e. the source is inferred as the current instance)",
"required": ["rTarget"]
}
]
},
"arrayLabel": {
"type": "object",
"title": "Repeatable arrayLabel node",
"description": "Chemical conjugated to nucleic acid/proteins to label them before microarray hybridisation. This node defines one single label, and thus should be repeated as an array where inherited if multiple labels are intended to be described.",
"anyOf": [
{
"required": ["arrayLabelIdentifier"]
},
{
"required": ["arrayLabelDescription"]
}
],
"additionalProperties": false,
"properties": {
"arrayLabelIdentifier": {
"type": "object",
"title": "Array label identifier",
"description": "The chosen term (e.g. 'Cy3 dye' [CHEBI:37987]) needs to be a Chemical Entity from the CHEBI ontology, look for yours at: https://www.ebi.ac.uk/ols/search?q=&ontology=chebi",
"allOf": [
{
"title": "Inherited ontologyTerm structure of termId and termLabel",
"$ref": "./EGA.common-definitions.json#/$defs/ontologyTerm"
}
],
"properties": {
"termId": {
"title": "Ontology constraints for this specific termId",
"graphRestriction ": {
"ontologies" : ["obo:chebi"],
"classes": ["CHEBI:24431"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": false
},
"examples": [ "CHEBI:37987", "CHEBI:15956" ]
}
}
},
"arrayLabelDescription": {
"type": "string",
"title": "Array label description",
"description": "Additional description of the used array label, indicating further details: context, purpose of the label, description of the label in the absence of an ontologized term, etcetera.",
"minLength": 1,
"examples": [
"This label was used to dye the control samples",
"This newly discovered label (yet to be added to an ontology) consists of a compound of type X...",
"The label ID is unknown because we were given an already dyed kit..." ]
}
}
},
"objectIdAndObjectTypeCheck": {
"type": "object",
"title": "Check that the objectId's accession pattern and objectType match",
"description": "This object exists with the only purpose of being a reference as a pattern check of a given objectId and objectType. The constraint consists in asserting that, if the object identifier is an EGA accession, its pattern matches the object type (e.g. if objectType is 'sample', its EGA accession needs to match '^EGAN[0-9]{11}$')",
"anyOf": [
{
"title": "Alias and Centername: objectId and objectType check",
"description": "A check that ensures that the alias and centername are given as the objectType. Since the alias and centername cannot be checked for specific objectTypes (i.e. each can name their objects in different ways), this block exists here just so that this option is allowed.",
"properties": {
"objectId": {
"required": ["alias", "centerName"]
}
}
},
{
"title": "External accession: objectId and objectType check",
"description": "A check that ensures that, if 'externalAccession' is given as the objectType, the corresponding node exists within objectId",
"properties": {
"objectId": {
"required": ["externalAccessions"]
},
"objectType": {
"enum": ["externalAccession"]
}
}
},
{
"title": "Experiment: objectId and objectType check",
"description": "A check that ensures that, if 'experiment' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAExperimentIdPattern" }
}
},
"objectType": {
"enum": ["experiment"]
}
}
},
{
"title": "Study: objectId and objectType check",
"description": "A check that ensures that, if 'study' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAStudyIdPattern" }
}
},
"objectType": {
"enum": ["study"]
}
}
},
{
"title": "Sample: objectId and objectType check",
"description": "A check that ensures that, if 'sample' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGASampleIdPattern" }
}
},
"objectType": {
"enum": ["sample"]
}
}
},
{
"title": "Submission: objectId and objectType check",
"description": "A check that ensures that, if 'submission' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGASubmissionIdPattern" }
}
},
"objectType": {
"enum": ["submission"]
}
}
},
{
"title": "Assay: objectId and objectType check",
"description": "A check that ensures that, if 'assay' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAAssayIdPattern" }
}
},
"objectType": {
"enum": ["assay"]
}
}
},
{
"title": "Dataset: objectId and objectType check",
"description": "A check that ensures that, if 'dataset' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGADatasetIdPattern" }
}
},
"objectType": {
"enum": ["dataset"]
}
}
},
{
"title": "Analysis: objectId and objectType check",
"description": "A check that ensures that, if 'analysis' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAAnalysisIdPattern" }
}
},
"objectType": {
"enum": ["analysis"]
}
}
},
{
"title": "Policy: objectId and objectType check",
"description": "A check that ensures that, if 'policy' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAPolicyIdPattern" }
}
},
"objectType": {
"enum": ["policy"]
}
}
},
{
"title": "DAC: objectId and objectType check",
"description": "A check that ensures that, if 'DAC' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGADACIdPattern" }
}
},
"objectType": {
"enum": ["DAC"]
}
}
},
{
"title": "Individual: objectId and objectType check",
"description": "A check that ensures that, if 'individual' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAIndividualIdPattern" }
}
},
"objectType": {
"enum": ["individual"]
}
}
},
{
"title": "Protocol: objectId and objectType check",
"description": "A check that ensures that, if 'protocol' is given as the objectType and an EGA accession for it is given, it matches the corresponding EGA ID pattern.",
"properties": {
"objectId": {
"properties": {
"egaAccession": { "$ref": "#/$defs/EGAProtocolIdPattern" }
}
},
"objectType": {
"enum": ["protocol"]
}
}
}
]
},
"checksumPatternCheck": {
"type": "object",
"title": "Check: checksum checks based on its method",
"description": "This object exists with the only purpose of being a reference of pattern checks of the given checksum (e.g. 'c6779ec2960296ed9a04f08d67f64423') of a file based on its corresponding method (e.g. if the given checksum method is 'MD5' the checksum shall fit into MD5's format of '^[0-9a-z](?:-?[0-9a-z]){31}$')",
"anyOf": [
{
"title": "Checksum pattern check - MD5",
"description": "A check that ensures that, if MD5 is given as a checksumMethodId, the checksums per se (e.g. unencryptedChecksum) follow MD5 patterns (md5ChecksumPattern).",
"properties": {
"checksumMethod": {
"enum": ["MD5"]
},
"unencryptedChecksum": { "$ref": "#/$defs/md5ChecksumPattern" },
"encryptedChecksum": { "$ref": "#/$defs/md5ChecksumPattern" }
}
},
{
"title": "Checksum pattern check - SHA-256",
"description": "A check that ensures that, if SHA-256 is given as a checksumMethodId, the checksums per se (e.g. unencryptedChecksum) follow SHA-256 patterns (sha-256-checksum-pattern).",
"properties": {
"checksumMethod": {
"enum": ["SHA-256"]
},
"unencryptedChecksum": { "$ref": "#/$defs/SHA256ChecksumPattern" },
"encryptedChecksum": { "$ref": "#/$defs/SHA256ChecksumPattern" }
}
}
]
},
"md5ChecksumPattern": {
"type": "string",
"title": "Checksum pattern obtained by MD5",
"description": "This object exists to hold the pattern that a checksum would have if it was obtained using the algorithm MD5, for it to be referenced elsewhere within this (or other) JSON schema.",
"pattern": "^[0-9a-z](?:-?[0-9a-z]){31}$",
"examples": [ "bc527343c7ffc103111f3a694b004e2f" ]
},
"SHA256ChecksumPattern": {
"type": "string",
"title": "Checksum pattern obtained by SHA-256",
"description": "This object exists to hold the pattern that a checksum would have if it was obtained using the algorithm SHA-256, for it to be referenced elsewhere within this (or other) JSON schema.",
"pattern": "^[A-Fa-f0-9]{64}$",
"examples": [ "c01b39c7a35ccc3b081a3e83d2c71fa9a767ebfeb45c69f08e17dfe3ef375a7b" ]
},
"EGAExperimentIdPattern": {
"type": "string",
"title": "Pattern of an EGA experiment's ID (EGAX...)",
"pattern": "^EGAX[0-9]{11}$",
"examples": [ "EGAX00002189113" ]
},
"EGAStudyIdPattern": {
"type": "string",
"title": "Pattern of an EGA study's ID (EGAS...)",
"pattern": "^EGAS[0-9]{11}$",
"examples": [ "EGAS00001004508" ]
},
"EGASampleIdPattern": {
"type": "string",
"title": "Pattern of an EGA sample's ID (EGAN...)",
"pattern": "^EGAN[0-9]{11}$",
"examples": [ "EGAN00003245489" ]
},
"EGASubmissionIdPattern": {
"type": "string",
"title": "Pattern of an EGA submission's ID (EGAB...)",
"pattern": "^EGAB[0-9]{11}$",
"examples": [ "EGAB00001001831" ]
},
"EGAAssayIdPattern": {
"type": "string",
"title": "Pattern of an EGA assay's ID (EGAR...)",
"pattern": "^EGAR[0-9]{11}$",
"examples": [ "EGAR00001314547" ]
},
"EGADatasetIdPattern": {
"type": "string",
"title": "Pattern of an EGA dataset's ID (EGAD...)",
"pattern": "^EGAD[0-9]{11}$",
"examples": [ "EGAD00001004170" ]
},
"EGAAnalysisIdPattern": {
"type": "string",
"title": "Pattern of an EGA analysis's ID (EGAZ...)",
"pattern": "^EGAZ[0-9]{11}$",
"examples": [ "EGAZ00001004170" ]
},
"EGAPolicyIdPattern": {
"type": "string",
"title": "Pattern of an EGA policy's ID (EGAP...)",
"pattern": "^EGAP[0-9]{11}$",
"examples": [ "EGAP00001001831" ]
},
"EGADACIdPattern": {
"type": "string",
"title": "Pattern of an EGA DAC's ID (EGAC...)",
"pattern": "^EGAC[0-9]{11}$",
"examples": [ "EGAC00001000908" ]
},
"EGAIndividualIdPattern": {
"type": "string",
"title": "Pattern of an EGA Individual's ID (EGAI...)",
"pattern": "^EGAI[0-9]{11}$",
"examples": [ "EGAI00001159712" ]
},
"EGAProtocolIdPattern": {
"type": "string",
"title": "Pattern of an EGA protocol's ID (EGAO...)",
"pattern": "^EGAO[0-9]{11}$",
"examples": [ "EGAO00001159483" ]
},
"filenameFiletypePatternCheck": {
"type": "object",
"title": "Check: filetype checks based on its filename",
"description": "This object exists with the only purpose of being a reference of pattern checks of the given filetype of a file based on its corresponding filename (e.g. if the file is 'alignment.bam.gpg' its filetypeId shall be 'BAM' and not 'XLSX')",
"anyOf": [
{
"title": "CEL Filename patternCheck",
"properties": {
"filetype": {
"enum": ["CEL"]
},
"filename": { "$ref": "#/$defs/celFileFilenamePattern" }
}
},
{
"title": "TSV Filename patternCheck",
"properties": {
"filetype": {
"enum": ["TSV"]
},
"filename": { "$ref": "#/$defs/tsvFileFilenamePattern" }
}
},
{
"title": "ADF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["ADF"]
},
"filename": { "$ref": "#/$defs/adfFileFilenamePattern" }
}
},
{
"title": "FASTQ Filename patternCheck",
"properties": {
"filetype": {
"enum": ["FASTQ"]
},
"filename": { "$ref": "#/$defs/fastqFileFilenamePattern" }
}
},
{
"title": "FASTA Filename patternCheck",
"properties": {
"filetype": {
"enum": ["FASTA"]
},
"filename": { "$ref": "#/$defs/fastaFileFilenamePattern" }
}
},
{
"title": "SDRF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["SDRF"]
},
"filename": { "$ref": "#/$defs/sdrfFileFilenamePattern" }
}
},
{
"title": "IDF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["IDF"]
},
"filename": { "$ref": "#/$defs/idfFileFilenamePattern" }
}
},
{
"title": "VCF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["VCF"]
},
"filename": { "$ref": "#/$defs/vcfFileFilenamePattern" }
}
},
{
"title": "SRA Filename patternCheck",
"properties": {
"filetype": {
"enum": ["SRA"]
},
"filename": { "$ref": "#/$defs/sraFileFilenamePattern" }
}
},
{
"title": "SRF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["SRF"]
},
"filename": { "$ref": "#/$defs/srfFileFilenamePattern" }
}
},
{
"title": "SFF Filename patternCheck",
"properties": {
"filetype": {
"enum": ["SFF"]
},
"filename": { "$ref": "#/$defs/sffFileFilenamePattern" }
}
},
{
"title": "BAM Filename patternCheck",
"properties": {
"filetype": {
"enum": ["BAM"]
},
"filename": { "$ref": "#/$defs/bamFileFilenamePattern" }
}
},
{
"title": "CRAM Filename patternCheck",
"properties": {
"filetype": {
"enum": ["CRAM"]
},
"filename": { "$ref": "#/$defs/cramFileFilenamePattern" }
}
},
{
"title": "XLSX Filename patternCheck",
"properties": {
"filetype": {
"enum": ["XLSX"]
},
"filename": { "$ref": "#/$defs/xlsxFileFilenamePattern" }
}
},
{
"title": "CSV Filename patternCheck",
"properties": {
"filetype": {
"enum": ["CSV"]
},
"filename": { "$ref": "#/$defs/csvFileFilenamePattern" }
}
},
{
"title": "BED Filename patternCheck",
"properties": {
"filetype": {
"enum": ["BED"]
},
"filename": { "$ref": "#/$defs/bedFileFilenamePattern" }
}
},
{
"title": "IDAT Filename patternCheck",
"properties": {
"filetype": {
"enum": ["IDAT"]
},
"filename": { "$ref": "#/$defs/idatFileFilenamePattern" }
}
},
{
"title": "MAP Filename patternCheck",
"properties": {
"filetype": {
"enum": ["MAP"]
},
"filename": { "$ref": "#/$defs/mapFileFilenamePattern" }
}
},
{
"title": "PED Filename patternCheck",
"properties": {
"filetype": {
"enum": ["PED"]
},
"filename": { "$ref": "#/$defs/pedFileFilenamePattern" }
}
},
{
"title": "BIM Filename patternCheck",
"properties": {
"filetype": {
"enum": ["BIM"]
},
"filename": { "$ref": "#/$defs/bimFileFilenamePattern" }
}
},
{
"title": "FAM Filename patternCheck",
"properties": {
"filetype": {
"enum": ["FAM"]
},
"filename": { "$ref": "#/$defs/famFileFilenamePattern" }
}
},
{
"title": "TXT Filename patternCheck",
"properties": {
"filetype": {
"enum": ["TXT"]
},
"filename": { "$ref": "#/$defs/txtFileFilenamePattern" }
}
},
{
"title": "EXP Filename patternCheck",
"properties": {
"filetype": {
"enum": ["EXP"]
},
"filename": { "$ref": "#/$defs/expFileFilenamePattern" }
}
},
{
"title": "GPR Filename patternCheck",
"properties": {
"filetype": {
"enum": ["GPR"]
},
"filename": { "$ref": "#/$defs/gprFileFilenamePattern" }
}
},
{
"title": "PY Filename patternCheck",
"properties": {
"filetype": {
"enum": ["PY"]
},
"filename": { "$ref": "#/$defs/pyFileFilenamePattern" }
}
},
{
"title": "SH Filename patternCheck",
"properties": {
"filetype": {
"enum": ["SH"]
},
"filename": { "$ref": "#/$defs/shFileFilenamePattern" }
}
},
{
"title": "MD5 Filename patternCheck",
"properties": {
"filetype": {
"enum": ["MD5"]
},
"filename": { "$ref": "#/$defs/md5FileFilenamePattern" }
}
},
{
"title": "HAP Filename patternCheck",