Background: In this review, an outline of the development of omics studies in recent years was envisaged. The bottom-up and top-down approaches on system biology were discussed and some of the recent tools that integrate multiomics data on system biology studies were examined. The improvements in omics applications from genomics to metabolomics were inspected in the light of breast cancer biomarker discovery. Results: It is known that genome or proteome analysis alone is not sufficient to elucidate the molecular mechanism of any disease, but instead, a holistic evaluation, including metabolomics studies, is rational and gives definite results. Breast cancer markers approved at the beginning of the millennium encouraged researchers to search for diagnostic and prognostic biomarkers with the improvements of advanced analytical strategies. Obviously, the recent developments on omics techniques and tools to process multiomics data are capable of presenting valuable scientific information better than ever before. Conclusion: Clinical researches using omics techniques might be supported with the integration of multiomics data to validate the results and to understand the molecular interactions in the biological system.