ArrayExpress, a public repository of gene expression data developed at the European Bioinformatics Institute, had its official debut at the most recent meeting of the Microarray Gene Expression Database group in Boston, February 13-16.
The database currently offers human, baker’s yeast, and fission yeast data, but the availability of this information isn’t the big story, according to Alvis Brazma, team leader of the microarray informatics group at EBI. “The main news is we are able to accept submissions by our new web-based submission tool as well as MAGE-ML format files,” he said. The tool, called MIAMExpress after the MIAME (minimum information about a microarray experiment) standard, walks users through all the requirements to ensure that gene expression submissions are compliant with the MIAME standard.
MIAMExpress is still in beta testing, but the EBI is encouraging users to practice using the tool. Noting that it’s “not perfect yet,” Brazma said “the very first submissions probably will be a bit cumbersome and will require some patience from the labs and also our curators, but once it’s done the second time should be easier for everyone.”
Brazma said the EBI is also working on other ways to ease the submission process. It has already established a pipeline with the Sanger Center so that data can be submitted to ArrayExpress “just by one click.” EBI is developing a similar pipeline for the Institute for Genomic Research. While data coming from these sources isn’t required to be MIAME-compliant, Brazma said that EBI curators would flag those data sets that do comply with the standard.
Building a User Base
ArrayExpress (www.ebi.uk/micro- array/ArrayExpress) accepts three kinds of submissions — hybridization data sets, laboratory and data processing protocols, and array design. On the third point, users of the database will gain from Affymetrix’s new Open Access Initiative, which will make all of the company’s array designs publicly available through ArrayExpress. Users will just have to reference the array accession number once the design is placed in the database, Brazma said.
Affy’s Open Access Initiative also covers the company’s release of its probe sequences and annotations on its own NetAffx website; a collaboration with the University of California, Santa Cruz, to provide its target sequences with the Golden Path assembly; and an effort to provide more support to third-party software developers by writing openly available application program interfaces into its data system.
Paul Dansky, senior director of marketing of informatics at Affymetrix, said that gene expression repository efforts such as ArrayExpress and the NCBI’s Gene Expression Omnibus were a key factor in the company’s decision to open up a bit. “We see the Open Access Initiative as being critical to the next stage of genome study, where gene expression databases are being generated and shared worldwide by scientists,” said Dansky. “The key to that is having data that can be broadly accessible by the web and then experiments that can be comparable and verified from researcher to researcher.”
But critical to making this data available to researchers is getting it in the repositories in the first place, a challenge Brazma and his colleagues are tackling now. With MIAMExpress still not 100 percent user-friendly, it may take some time before a reasonable body of data is available through the resource. However, Brazma predicted, as more freely available and commercial software packages support MIAME-type annotation and MAGE-ML format export “within six months,” submissions will be easier and, hopefully, more frequent.
While some journals have approached Brazma about the possibility of requiring submission in ArrayExpress upon publication of gene expression experiments, Brazma said it’s still too early to require such submissions, although he would like to see it encouraged. MGED is currently preparing a checklist of recommendations for authors and reviewers of microarray experiments based on MIAME, Brazma said, which will be submitted to “all the major journals” in about a month.
Finally, in order to support these mounting efforts, Brazma said that MGED is looking into becoming a formal scientific society. The move, which will involve incorporating as a non-profit entity, will allow the group to organize its annual meetings a bit easier and to provide travel grants to some active participants without travel budgets.
Brazma said he hopes to see MGED become a formal society by the group’s next meeting in Tokyo in September.