A data frame stored in a CSV file. If the data_frame.row_names property is present and truthy, the first column of the CSV file contains the row names of the data frame as non-missing strings; this should be ignored when indexing entries of the data_frames.columns property. For complex columns, a placeholder column is created in the CSV and a pointer to the relevant resource is created in the corresponding entry of the data_frame.columns property. The CSV file may be compressed if the csv_data_frame.compression property is set to "gzip".
See here for specific details on the expected formatting of the CSV.
Derived from data_frame/v1.json: virtual data frame object stored in a yet-to-be-defined file format. Simple columns are stored directly in the file. For complex columns, their contents should be stored in other files, and a pointer to a resource is stored in the corresponding entry of columns (a placeholder column may be created in the file).
The schema to use.
Type of compression applied to the file.
Location of additional metadata for each column, stored as another data_frame. Omitted if there is no additional per-column metadata is provided.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Information about the columnar fields in the data frame. This follows the same order as the columns in the on-disk representation.
If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
Levels for the categorical factor. This is stored as a single-column data_frame. For ordered factors, the order is respected in the saved data frame.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"other" Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Name of the column. Each column must have a non-empty name. Column names should not be duplicated within columns.
Must be at least 1 characters long
What is the type of the column? Factors and ordered factors have an additional levels property specifying the levels. Dates are stored in YYYY-MM-DD format. Date-times should follow RFC 3339 Section 5.6. Columns listed as other are assumed to be non-atomic and should contain a resource property pointing towards the file containing the column's contents.
Dimensions of a two-dimensional object.
Must contain a minimum of 2 items
Must contain a maximum of 2 items
Location of additional metadata for this object, typically stored as a list (via the basic_list schema). Ommitted if no other metadata is provided.
Relative path of the resource from the root of the project directory.
Type of file. Local files should be present in the same project directory.
Whether the data frame has row names. If true, these are stored in the first column of the CSV.
Description of the resource.
UCSC, Ensembl or other genome builds involved in generating this resource.
Identifier for this genome build.
"mm10"
"NCBIm37"
Source of the genome build identifier.
Is this a child document, only to be interpreted in the context of the parent document from which it is linked? This may have implications for search and metadata requirements.
MD5 checksum for the file.
Origins of this resource.
If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"PubMed" ^[0-9]+$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"GEO" ^GSE[0-9]+$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"ArrayExpress" ^E-MTAB-[0-9]+$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"DOI" ^[0-9a-zA-Z\._-]+/[0-9a-zA-Z\._-]+$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"URI" ^(http|ftp|https|s3|sftp):// Identifier for the resource in the specified type.
Source database or repository.
Path to the file in the project directory.
NCBI taxonomy IDs of the species involved in this resource.
Terms from a controlled vocabulary, used to annotate this resource in a machine-readable manner.
If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"Experimental Factor Ontology" ^EFO:[0-9]{7}$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"Human Disease Ontology" ^DOID:[0-9]+$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"Cell Ontology" ^CL:[0-9]{7}$ If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
"UBERON" "^UBERON:[0-9]{7}$" Identifier for the term.
"EFO:0008913"
"DOID:13250"
"CL:0000097"
"UBERON:0005870"
Name of the vocabulary or ontology that is the source for this term.
Version of the vocabulary.
Title of the resource.
If the conditions in the "If" tab are respected, then the conditions in the "Then" tab should be respected. Otherwise, the conditions in the "Else" tab should be respected.
true