Okubo Group • Gene-Expression Analysis Laboratory

Developing technologies to make BioMedicine comprehensible and tractable


Research Summary

A body of biomedical knowledge is developed in 2 steps: StepA: accumulating and exchanging situations captured in descriptions and data; and StepB: abstract situations into a coherent set of dogmatic or mathematical statements so that people can use in decision-making. The overwhelming output of A, mainly due to the technological assistance by diagnostic, laboratory and communication machines, is making a stressful situation called “information over-load” or “data deluge”. New technologies must be invented for B to make bigger return from investment in biomedicine.

Architecture of anatomical mapping service in Anatomography (A) and a use case (B). Service, still under development, is constructed and maintained in DBCLS. Similarly to Google Maps, custom anatomical maps can be exchanged as map URL with or without superimposed data. In (B), shown is body distribution of a bacterial species in meta-genome.jp.


Mitsuhashi, N., Fujieda, K., Tamura, T., Kawamoto, S., Takagi, T., and Okubo, K. (2009). BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Res 37 (Database issue), D782-785.

Ogasawara, O., Mashima, J., Kodama, Y., Kaminuma, E., Nakamura, Y., Okubo, K., and Takagi, T. (2013). DDBJ new system and service refactoring. Nucleic Acids Res 41 (Database issue), D25-29.

Okubo, K., and Tamura, T. (2011). System and computer software program for visibly processing an observed information’s relationship with knowledge accumulations. US patent 20050203889.

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