Sample and Data Relationship Format

The Sample and Data Relationship Format (SDRF) is a tab-delimited file describing the relationships between samples and data in fields such as genomics and proteomcs. The format originated as part of the MAGE-TAB standard for communicating the results of microarray investigations, including all information required for MIAME compliance.^[1] It was later extended to, and is currently primarily used for, next generation sequencing and proteomics.^[2]

For simple experimental designs, constructing the SDRF file is straightforward, and even complex loop designs can be expressed in this format. In practise, tools such as lesSDRF ^[3] are often used to annotate experimental metadata in SDRF.

References

↑ Dziuda, Darius M. (2010-07-16). Data Mining for Genomics and Proteomics: Analysis of Gene and Protein Expression Data. ISBN 9780470593400.
↑ Dai, C., Füllgrabe, A., Pfeuffer, J., Solovyeva, E. M., Deng, J., Moreno, P., Kamatchinathan, S., Kundu, D. J., George, N., Fexova, S., Grüning, B., Föll, M. C., Griss, J., Vaudel, M., Audain, E., Locard-Paulet, M., Turewicz, M., Eisenacher, M., Uszkoreit, J., Van Den Bossche, T., Schwämmle, V., Webel, H., Schulze, S., Bouyssié, D., Jayaram, S., Duggineni, V. K., Samaras, P., Wilhelm, M., Choi, M., Wang, M., Kohlbacher, O., Brazma, A., Papatheodorou, I., Bandeira, N., Deutsch, E. W., Vizcaíno, J. A., Bai, M., Sachsenberg, T., Levitsky, L. I., Perez-Riverol, Y. (6 October 2021). "A proteomics sample metadata representation for multiomics integration and big data analysis". Nature Communications. 12 (1). Springer Science and Business Media LLC. doi:10.1038/s41467-021-26111-3. PMC 8494749.
↑ Claeys, T., Van Den Bossche, T., Perez-Riverol, Y., Gevaert, K., Vizcaíno, J. A., Martens, L. (24 October 2023). "lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation". Nature Communications. 14 (1). Springer Science and Business Media LLC. doi:10.1038/s41467-023-42543-5. hdl:1854/LU-01HDKJ5JGC19K1HGT55Q2V07D9.

External links

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[1] Dziuda, Darius M. (2010-07-16). Data Mining for Genomics and Proteomics: Analysis of Gene and Protein Expression Data. ISBN 9780470593400.

[2] Dai, C., Füllgrabe, A., Pfeuffer, J., Solovyeva, E. M., Deng, J., Moreno, P., Kamatchinathan, S., Kundu, D. J., George, N., Fexova, S., Grüning, B., Föll, M. C., Griss, J., Vaudel, M., Audain, E., Locard-Paulet, M., Turewicz, M., Eisenacher, M., Uszkoreit, J., Van Den Bossche, T., Schwämmle, V., Webel, H., Schulze, S., Bouyssié, D., Jayaram, S., Duggineni, V. K., Samaras, P., Wilhelm, M., Choi, M., Wang, M., Kohlbacher, O., Brazma, A., Papatheodorou, I., Bandeira, N., Deutsch, E. W., Vizcaíno, J. A., Bai, M., Sachsenberg, T., Levitsky, L. I., Perez-Riverol, Y. (6 October 2021). "A proteomics sample metadata representation for multiomics integration and big data analysis". Nature Communications. 12 (1). Springer Science and Business Media LLC. doi:10.1038/s41467-021-26111-3. PMC 8494749.

[3] Claeys, T., Van Den Bossche, T., Perez-Riverol, Y., Gevaert, K., Vizcaíno, J. A., Martens, L. (24 October 2023). "lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation". Nature Communications. 14 (1). Springer Science and Business Media LLC. doi:10.1038/s41467-023-42543-5. hdl:1854/LU-01HDKJ5JGC19K1HGT55Q2V07D9.

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References

External links