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. 2022 Sep 30;9:592. doi: 10.1038/s41597-022-01707-6

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Difference in representation of the MIAME checklist in two public repositories: GEO and ArrayExpress. (A) GEO (10.25504/FAIRsharing.5hc8vt) and ArrayExpress (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 (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 (10.25504/FAIRsharing.3gxr9) and MINiML (10.25504/FAIRsharing.gaegy8) for GEO; MAGE-ML (10.25504/FAIRsharing.x964fb) that is now deprecated and superseded by MAGE-TAB (10.25504/FAIRsharing.ak8p5g) for the ArrayExpress, which also uses the EFO terminology (10.25504/FAIRsharing.1gr4tz) to annotate the metadata.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.