Fig. 1
Difference in representation of the MIAME checklist in two public repositories: GEO and ArrayExpress. (A) GEO (https://doi.org/10.25504/FAIRsharing.5hc8vt) and ArrayExpress (https://doi.org/10.25504/FAIRsharing.6k0kwd) are two databases highly recommended by journals and funders data policies, and both implement the community-defined MIAME reporting guideline to describe microarray experiment (https://doi.org/10.25504/FAIRsharing.32b10v), among others. The implementation of MIAME is done via several formats (used to upload and download datasets from these two databases), which include SOFT (https://doi.org/10.25504/FAIRsharing.3gxr9) and MINiML (https://doi.org/10.25504/FAIRsharing.gaegy8) for GEO; MAGE-ML (https://doi.org/10.25504/FAIRsharing.x964fb) that is now deprecated and superseded by MAGE-TAB (10.25504/FAIRsharing.ak8p5g) for the ArrayExpress, which also uses the EFO terminology (10.25504/FAIRsharing.1gr4tz) to annotate the metadata. (B) Using a few metadata requirements from MIAME as example (namely: study, study title, study description) we illustrate how the metadata labels, along with their level of requirement (must, should, may), varies across the formats used by the two databases.
