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. 2023 Oct 5;21:4895–4913. doi: 10.1016/j.csbj.2023.10.006

Table 3.

Summary of the FAIR Cookbook suggestions for recommended metadata (modified after chapter “11.5.1 Metadata profile for transcriptomics” of the current FAIR Cookbook (September 2023) [37].

Metadata field Definition Comment Metadata type
sample collection technique The technique used to collect the specimen, e.g., blood draw or surgical resection ontology field - e.g. EFO or OBI Common metadata
age Age of the organism from which the sample was collected Common metadata
age unit Unit of the value of the age field ontology field - e.g. UO Common metadata
ancestry/ethnicity Ancestry or ethnic group of the individual from which the sample was collected ontology field - e.g. HANCESTRO Common metadata
BMI Body mass index of the individual from which the sample was collected Only applies to human samples Common metadata
strain Strain of the species from which the sample was collected, if applicable ontology field - e.g. NCBITaxonomy Common metadata
cell type The cell type(s) known or selected to be present in the sample ontology field - e.g. CL Common metadata
cell location The cell location from which genetic material was collected (usually either nucleus or mitochondria) ontology field - e.g. GO Common metadata
treatment category Treatments that the sample might have undergone after collection ontology field - e.g. OBI, NCIt or OGMS Common metadata
growth conditions Features relating to the growth and/or maintenance of the sample Common metadata
genetic variation Any relevant genetic differences from the specimen or sample to the expected genomic information for this species, e.g., abnormal chromosome counts, major translocations or indels Common metadata
phenotype Any relevant (usually abnormal) phenotypes of the specimen or sample ontology field - e.g. HP or MP; species dependent
cell cycle The cell cycle phase of the sample (for synchronized growing cells or a single-cell sample), if known ontology field - e.g. GO Common metadata
cell quality Information about the quality of a single cell such as morphology or percent viability standardised field or ontology Assay metadata
cell barcode Information about the cell identifier barcode used to tag individual cells in single cell sequencing Assay metadata
UMI barcode Information about the Unique Molecular Identifier barcodes used to tag DNA fragments Assay metadata
assay start time The exact time at which the assay was started Assay metadata
assay end time The exact time at which the assay was completed Assay metadata
assay duration The duration, in a relevant time unit (e.g., minutes or hours), of the assay from start to finish Assay metadata
array quality The overall quality of the array Assay metadata
chemical compound Any relevant chemical compounds used in the assay ontology field - e.g. ChEBI Assay metadata
labeling molecule used The type of labeling molecule used in an array-based experiment ontology field - e.g. ChEBI Assay metadata
spike-in kit used Information about the spike-in kit used during sequencing library preparation Assay metadata
cDNA primer Type of primer used for cDNA synthesis from RNA, e.g., polyA or random standardised field or ontology Assay metadata
library strandedness The strandedness of the cDNA library standardised field or ontology Assay metadata
analysis date The date on which the analysis was performed Analysis metadata
read index The sequencing read a specific file represents, e.g., read1 or index1 Analysis metadata
read length The length of a sequenced read in this file, in nucleotides. Analysis metadata
assembly type The assembly type of the genome reference file, e.g., primary, complete or patch assembly. standardised field or ontology Analysis metadata
reference genome version The genome version of the reference file. Analysis metadata
software package The software package used for data analysis Analysis metadata
software version The exact version number of the software package Analysis metadata
external accessions Accession numbers from any external resources to which the sample was submitted or to which assay or protocol information was submitted e.g. Biosamples, Biostudies
e.g. protocols.io, AE
Common metadata, Assay metadata