Dense array, saved in a HDF5 file as an N-dimensional dataset for positive N.
The dimensions reported in array.dimensions are be ordered from fastest-changing to slowest, i.e., the first entry of the array.dimensions property corresponds to the fastest-changing dimension. In the context of matrices, this implies a column-major layout where the first (faster) dimension corresponds to the rows and the second (slower) dimension corresponds to the columns. Note that this ordering is reversed in the dimensions of the HDF5 dataset, as the HDF5 library lists the dimensions from slowest-changing to fastest.
The file may also contain the dimnames of the array, stored in a separate HDF5 group. If present, the name of the group should be listed in the hdf5_dense_array.dimnames property.
For a signed integer dataset, missing values are represented by -2147483648.
A string dataset may contain a missing attribute. This should be a scalar string dataset that contains the string used to represent missing values. If no attribute exists, it is assumed that all strings are non-missing.
Derived from array/v1.json: some kind of multi-dimensional array, where we store metadata about the dimensions and type of data. The exact implementation of the array is left to concrete subclasses.
The schema to use.
Dimensions of an n-dimensional array.
Must contain a minimum of 1 items
Type of data stored in this array.
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.
Name of the dataset inside the HDF5 file that contains the array.
Name of the HDF5 group containing the dimnames. This group should contain zero or one string datasets for each dimension. Each string dataset is numbered after a dimension of the dense array (ordered from fastest- to slowest-changing) and should have length equal to the extent of that dimension, i.e., the dataset named "0" should have length equal to the first entry of array.dimensions. If this property is not provided, it can be assumed that no dimnames are available. Each dataset should not contain any missing values, so each string can be interpreted as-is.
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