Bulk_ Rnaseq_Counts_File_Annotations
Files containing bulk RNA count matrix data [Source]
| Key | Key Description | Type | Valid Values | DependsOn | Required | Source | Module |
|---|---|---|---|---|---|---|---|
| assay | The technology used to generate the data in this file | STRING | rnaSeq,scrnaSeq | True | NGS | ||
| reference_set | A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data. | STRING | GRCh37,GRCm38,MMUL1.0,HRC,1000 Genomes phase 3,GRCh38,dmel_r6.06 | False | NGS | ||
| nucleic_acid_source | STRING | bulk cell,bulk nuclei,single cell,single nucleus | True | NGS | |||
| file_format | Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software | STRING | fastq,count matrix,bam,csv,xlsx,txt,pdf,tsv | False | File_Annotations | ||
| data_subtype | Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata. | STRING | raw,aligned,processed,normalized,aggregated | False | NGS | ||
| data_type | Types of input/output data in bioinformatics pipelines | STRING | genomicVariants,geneExpression | True | Sage Bionetworks | NGS | |
| resource_type | The type of resource being stored and annotated | STRING | analysis,curatedData,experimentalData,metadata,report,tool | True | File_Annotations | ||
| sample_type | rc2 sample type | STRING | pax_gene,pbmcs,biopsy,serum,whole_blood,dna,epithelial_organoid,bm_organoid,resected_tissue,plasma,unknown | True | Sage Bionetworks | Biospecimen | |
| site | site identifier (BCH = Boston, LMU = Munich, HSC = Toronto) | STRING | BCH,LMU,HSC | True | Sage Bionetworks | Clinical | |
| media | type of media | STRING | DMSO,FRZ,FORM,TCM,RNA,ORG | False | Biospecimen | ||
| filename | Name of a file | STRING | True | Other | |||
| individual_id | individual identifier | STRING | True | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.09d&code=C69256&ns=ncit | Clinical | ||
| sample_id | sample identifier | True | |||||
| Component | Category of metadata; provide the same one for all items/rows. | True | https://w3id.org/biolink/vocab/category |