A summarized experiment where each row corresponds to a feature and each column corresponds to an experimental sample. The layout of this data structure is based on Bioconductor's SummarizedExperiment class. This metadata document contains pointers to the various components of the summarized experiment, including the row data, column data and assays.
The schema to use.
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.
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.
An array of pointers to the assay data. Each entry corresponds to a single assay in the summarized experiment object.
Must contain a minimum of 1 items
Name of the assay. Each assay must have a non-empty name. Assay names should not be duplicated within assays.
Must be at least 1 characters long
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.
Pointer to the column data. This should be data frame (as defined by the data_frame schema) where each row corresponds to a column of the summarized experiment and each column contains some annotation for the experimental samples. Omitted if no sample-level annotation is present.
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.
Dimensions of a two-dimensional object.
Must contain a minimum of 2 items
Must contain a maximum of 2 items
Pointer to the additional metadata for this object, typically stored as a list (via the basic_list schema). Omitted if no additional metadata is present.
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.
Pointer to the row data. This should be data frame (as defined by the data_frame schema) where each row corresponds to a row of the summarized experiment and each column contains some annotation for the features. Omitted if no feature-level annotation is present.
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.
Pointer to the genomic coordinates corresponding to the rows. This should comply with the genomic_ranges or genomic_ranges_list schemas, where each range or group defines the genomic location of the feature corresponding to a row of the summarized experiment. Omitted if no genomic coordinates are present. This is based on Bioconductor's RangedSummarizedExperiment class.
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.
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