scVDJSeq Processed Data Annotation Template
A data contributor template outlining metadata to be collected as file annotations for scVDJ-seq (i.e., immune repertoire profiling) processed data files (i.e., anything not a fastq file)
Instructions
This template collects file-level metadata and curates your file with this critical information thereby enabling discoverability, SQL queries, and overall organization and metrics calculations of your data files.
| Attribute | Description | Required | Valid Values |
|---|---|---|---|
| RObjectClass | Rds files store R objects, one per file. This label details the class of the R object saved to the Rds file or other similar file types. | FALSE | ROCR prediction.object, Seurat object, SummarizedExperiment, Symphony reference, data.frame, list, matrix, sparse matrix, vector |
| biospecimenID | A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list. | TRUE | |
| dataLevel | Level of data processing applied to file. Levels refer to pre-defined standards of processing for the given assay. | TRUE | 1, 2, 3, 4, 5, Not Applicable, unknown |
| fileFormat | Standard file format name or file extension | TRUE | csv, tsv, txt, xlsx, xls, fam, bim, bed, bam, h5, mtx, bai, rds, tgz, zip, h5ad, html |
| individualID | Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list. | TRUE | |
| metadataType | A label further classifying the content of metadata resource. | TRUE | single-cell metadata |
| processedDataType | A label used for file annotations to provide a brief description of the processed data file. Multiple selections can be provided in a comma-delimited list. | FALSE | barcode counts, differential expression results, epigenomic peaks, gene counts |
| resourceType | High-level classification of the file content | TRUE | experimental data, metadata |
| specimenModality | Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens | TRUE | multispecimen, single specimen, unknown |