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 |