A biomarker is a measurable indicator of a disease or abnormal state of a body that plays an important role in disease diagnosis, prognosis, and treatment. The biomarker has become a significant topic due to its versatile usage in the medical field and in rapid detection of the presence or severity of some diseases. The volume of biomarker data is rapidly increasing and the identified data is scattered. To provide comprehensive information, the explosively growing data needs to be recorded in a single platform. There is no open-source freely available comprehensive online biomarker database. To fulfill this purpose, we have developed a human biomarker database as part of the KNApSAcK family of databases which contain a vast quantity of information on the relationships between biomarkers and diseases. We have classified the diseases into 18 disease classes, mostly according to NCBI definitions. Apart from this database development, we also have performed disease classification by separately using protein and metabolite biomarkers based on the network clustering algorithm DPClusO and hierarchical clustering. Finally, we reached a conclusion about the relationships among the disease classes. The human biomarker database can be accessed online and the inter-disease relationships may be helpful in understanding the molecular mechanisms of diseases. To our knowledge, this is the first approach to classify diseases based on biomarkers.