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File

Attribute: File Level

Valid Value Description Ontology
Level 1 Raw or minimally processed data NCIT:C142663
Level 2 Data that has undergone a basic or initial processing step, like quality control, alignment, or stitching. Typically derived from Level 1 files. Not available
Level 3 Files that contain summary counts, coverage files, or other processed representations of the data. Typically derived from Level 2 files. Not available
Level 4 "Files that are processed through multiple steps or contain descriptors of the data. Typically derived from Level 2, Level 3, and/or auxiliary files."Not available
Auxiliary Additional files that contain information or experimental details, but do not contain data or processed derivatives Not available
Not ApplicableFiles that fall outside of the level structure or are uploaded as a package. NCIT:C48660
Metadata Files that are or will be stored and shared as metadata. NCIT:C52095

Attribute: File Format

Valid Value Description Ontology
ADF Array Design Format. NCIT:C172213
AVI AVI Format file format. NCIT:C190162
BAI BAI File file format. NCIT:C190163
BAM Binary Alignment Map file format. NCIT:C153249
BAS BAM statistics file format. Not available
BCR Biotab BCR Biotab file format. NCIT:C190164
BED BED Format file format. EDAM:format_3003
bedgraph Bedgraph Format file format. NCIT:C190165
BEDPE Format BEDPE paired-end feature file format. NCIT:C184749
bigBed BigBed file format. NCIT:C190166
bigWig BigWig Format file format. NCIT:C190167
Binary Format The Binary Format file format. EDAM:format_2333
BIOM Biological Observation Matrix (BIOM) file format. NCIT:C190169
cdf A file that provides information about the probes contained within an Affymetrix expression microarray probe set. NCIT:C209894
CEL Affymetrix CEL Format file format. NCIT:C191737
CNS Cytoscape input file format. NCIT:C209889
CRAI CRAM index file format. NCIT:C192224
CRAM CRAM sequence alignment file format. NCIT:C190170
CSV Comma Separated Values Format file format. NCIT:C182456
DICOM A comprehensive set of standards for communications between medical imaging devices, including a file format definition.NCIT:C49059
DICT HET group dictionary entry file format. NCIT:C209890
DOC Microsoft Word legacy document file format. NCIT:C210442
DOCX DOCX Format file format. NCIT:C190171
DSV DSV Format file format. EDAM:format_3751
EMF Enhanced Metafile image file format. NCIT:C224003
FASTA FASTA Format file format. EDAM:format_1929
FASTQ Investigation Description Format file format. EFO:0004155
GCT/Res Format GCT/RES Format file format. EDAM:format_3709
GenBank Format GenBank sequence file format. NCIT:C190174
GFF3 General Feature Format Version 3 file format. NCIT:C190175
GIF Graphics Interchange Format file format. EDAM:format_3467
GPR GenePix Results file format. NCIT:C190176
GTF GTF Format file format. NCIT:C190177
gVCF Genomic Variant Call Format, an extension of VCF that records genotype information for all positions. NCIT:C204352
GZIP Format Gzip File Format file format. NCIT:C80220
HDF5 Hierarchical Data Format 5 file format. NCIT:C184763
HIC HIC contact matrix file format. NCIT:C203672
HTML Hypertext Markup Language file format. EDAM:format_2331
HTSeq Count HTSeq-count tool output file format. NCIT:C205749
IDAT IDAT Format file format. NCIT:C184762
IDF Investigation Description Format. NCIT:C172212
idpDB IDPicker file format. NCIT:C209893
im3 Vectra multispectral image file format. Not available
JPEG Joint Photographic Experts Group (JPEG) image file format. NCIT:C48230
JPEG 2000 JPEG 2000 image file format. NCIT:C184768
JSON JSON Format file format. NCIT:C184769
MAF Mutation Annotation Format file format. NCIT:C172215
MAGE-TAB The MAGE-TAB file format. EDAM:format_3162
MAT MAT Format file format. NCIT:C190178
MATLAB Script MATLAB Script File file format. EDAM:format_4007
MCD Fluidigm Hyperion mass cytometry data file format. NCIT:C224107
MEX Market Exchange (MEX) sparse matrix file format. NCIT:C184778
MPEG-4 MP4 multimedia file format. NCIT:C190180
mtx The mtx file format. NCIT:C201789
mzIdentML The mzIdentML file format. EDAM:format_3247
mzML Mass Spectrometry Markup Language file format. EDAM:format_3244
mzXML Mass Spectrometry Extensible Markup Language file format. EDAM:format_3654
NIFTI Format NIfTI Format file format. EDAM:format_3549
ODS OpenDocument spreadsheet file format. NCIT:C224004
ODT OpenDocument text file format. NCIT:C224005
OME-TIFF Open Microscopy Environment Tagged Image File Format file format. EDAM:format_3727
Parquet Apache Parquet columnar storage file format. NCIT:C223247
PDF Portable Document Format file format. NCIT:C63805
PDT Pro Tools session file legacy format. NCIT:C224007
PED Pedigree file format. NCIT:C209891
Plain Text Data FormatA file format consisting of unformatted plain text. NCIT:C85873
PNG Portable Network Graphics file format. NCIT:C85437
PRISM GraphPad Prism project file format. NCIT:C224010
Python Script Format Python script file format. NCIT:C190184
PZFX GraphPad Prism XML File Format file format. NCIT:C224011
QPTIFF QPTIFF tagged image file format used for multispectral imaging. NCIT:C222390
R File Format R Format file format. NCIT:C190186
R Markdown R Markdown document file format. NCIT:C190187
rdata R data file format. NCIT:C224809
rds R Data Serialization file format. NCIT:C209895
RTF Rich Text Format file format. NCIT:C209896
SAS Statistical Analysis System (SAS) file format. NCIT:C219045
SAS binary SAS binary file format. NCIT:C219048
SDRF Sample and Data Relationship Format. NCIT:C172211
SEG Segmented Data Format. NCIT:C209892
Sequence Record FormatThe Sequence Record Format file format. EDAM:format_1919
SPSS SPSS statistical software file format. NCIT:C219046
STATA STATA statistical software file format. NCIT:C219047
SVG Scalable Vector Graphics file format. EDAM:format_3604
SVS Spectral View Settings Format file format. NCIT:C162692
TAR TAR archive file format. NCIT:C190189
TBI Tabix index file format. NCIT:C184806
Thermo RAW Thermo Fisher mass spectrometry RAW file format. NCIT:C190190
TIFF The TIFF file format. EDAM:format_3591
TSV Tab-Separated Value Format file format. NCIT:C164049
TXT Plain Text Data Format file format. NCIT:C85873
VCF Variant Call File Format file format. NCIT:C172216
XLS XLS Format file format. NCIT:C190191
XLSX Excel Open XML Format file format. NCIT:C164050
XML Extensible Markup Language file format. EDAM:format_2332
YAML YAML Language file format. EDAM:format_3750
ZIP ZIP Format file format. NCIT:C190192