https://raw.githubusercontent.com/EbiEga/ega-metadata-schema/main/schemas/EGA.experiment.json#/properties/experimentTypeSpecifications/properties/arrayExperiment/properties/adfFiles/itemsObject containing the base metadata attributes of a file object in the EGA. These can inherited elsewhere with or without extending them.
| Abstract | Extensible | Status | Identifiable | Custom Properties | Additional Properties | Access Restrictions | Defined In |
|---|---|---|---|---|---|---|---|
| Can be instantiated | No | Unknown status | No | Forbidden | Forbidden | none | EGA.experiment.json* |
object (EGA File object)
all of
-
any of
-
any of
| Property | Type | Required | Nullable | Defined by |
|---|---|---|---|---|
| filename | string |
Required | cannot be null | EGA common metadata definitions |
| fileContent | array |
Optional | cannot be null | EGA common metadata definitions |
| filetype | string |
Required | cannot be null | EGA common metadata definitions |
| checksumMethod | string |
Required | cannot be null | EGA common metadata definitions |
| unencryptedChecksum | Merged | Required | cannot be null | EGA common metadata definitions |
| encryptedChecksum | Merged | Required | cannot be null | EGA common metadata definitions |
| sequenceQualityDetails | object |
Optional | cannot be null | EGA common metadata definitions |
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').
filename
-
is required
-
Type:
string(Filename) -
cannot be null
-
defined in: EGA common metadata definitions
string (Filename)
pattern: the string must match the following regular expression:
^[^<>:;,?"*|]+$"my-bam-file.bam.gpg"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.
fileContent
-
is optional
-
Type:
object[](File content item) -
cannot be null
-
defined in: EGA common metadata definitions
object[] (File content item)
minimum number of items: the minimum number of items for this array is: 1
unique items: all items in this array must be unique. Duplicates are not allowed.
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 proposing its addition.
filetype
-
is required
-
Type:
string(Filetype) -
cannot be null
-
defined in: EGA common metadata definitions
string (Filetype)
enum: the value of this property must be equal to one of the following values:
| Value | Explanation |
|---|---|
"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" |
[] |
"TXT" |
[format:2330] |
"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" |
[] |
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 proposing its addition.
checksumMethod
-
is required
-
Type:
string(Checksum method ID) -
cannot be null
-
defined in: EGA common metadata definitions
string (Checksum method ID)
enum: the value of this property must be equal to one of the following values:
| Value | Explanation |
|---|---|
"MD5" |
[NCIT:C171276] |
"SHA-256" |
[NCIT:C80226] |
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.
unencryptedChecksum
-
is required
-
Type:
string(Checksum [NCIT:C43522] of the unencrypted file) -
cannot be null
-
defined in: EGA common metadata definitions
string (Checksum [NCIT:C43522] of the unencrypted file)
one (and only one) of
"46798b5cfca45c46a84b7419f8b74735"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.
encryptedChecksum
-
is required
-
Type:
string(Checksum [NCIT:C43522] of the encrypted file) -
cannot be null
-
defined in: EGA common metadata definitions
string (Checksum [NCIT:C43522] of the encrypted file)
one (and only one) of
"bc527343c7ffc103111f3a694b004e2f"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.
sequenceQualityDetails
-
is optional
-
Type:
object(Sequence quality details) -
cannot be null
-
defined in: EGA common metadata definitions
object (Sequence quality details)