Stanford Microarray Database

http://genome-www.stanford.edu/microarray

Gollub, G.¹, Ball, C.A.¹, Binkley, G.², Demeter, J.¹, Finkelstein, D.B.³, Hebert, J.M.⁴, Hernandez-Boussard, T.¹, Jin, H.¹, Kaloper, M.², Matese, J.C.¹, Schroeder, M.², Brown, P.O.⁵, Botstein, D.², Sherlock, G.¹

¹Department of Genetics, Center For Clinical Sciences Research, 269, Campus Drive, Room 2255 Stanford University, Stanford, CA 94305-5136, USA
²Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305-5120, USA
³Affymetrix, Inc., 6550 Vallejo St., Suite 100, Emeryville, CA 94608, USA
⁴Stanford Functional Genomics Facility, Center For Clinical Sciences Research, 269 Campus Drive, Room 4256 Stanford University, CA 94305-5163, USA
⁵Howard Hughes Medical Institute, Dept. of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA

Contact sherlock@genome.stanford.edu

Database Description

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code, and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3000 microarrays, including data from 70 publications, and this total is increasing rapidly. SMD makes use of many public sources of biological annotation, which are used to connect the entities on the microarrays with their most current biological information. This is of paramount importance, as expression data in the absence of biological context are meaningless.

Recent Developments

SMD has had two source code releases, the most recent being in January of 2002, and has been installed a a dozen institutes worldwide. SMD currently makes available more public data than any other microarray database, totalling more than 3000 arrays and over 70 publications. In addition SMD is committed to adopting the MIAME guidelines for annotating microarray experiments, and to the MAGE-ML data exchange format.