Although this potentially leaves the databases susceptible to accusations of poor coding quality, 24 25 the HES data submissions are regularly cleaned and monitored for data quality and consistency.
We gratefully acknowledge contributions from Patrick Plettner for SRA data submissions, Armelle Troussard for project management, Martin Krzywinski for guidance in figure design, and GSC's LIMS, systems, engineering, library, sequencing, and bioinformatics teams.
The term "mock submissions" is used in this report as opposed to "voluntary submissions" discussed in the FDA pharmacogenomics data submissions guidance (FDA 2005b), which are to be reviewed by the FDA Interdisciplinary Pharmacogenomics Review Group (CDER 2005a, 2005b).
Data submissions may include HPO Human Phenotype Ontologyy) terms, other trait descriptions, NGS technology information and the identity of the submitter.
As a member of the International Nucleotide Sequence Database Collaboration, the ENA exchanges data submissions each day with both the DNA Data Bank of Japan and GenBank.
In addition to the guidance on pharmacogenomics data submissions (FDA 2003), the FDA is embarking on a new guidance initiative for the co-development of pharmacogenomics-based drugs and biologic products and the diagnostic tests necessary for therapeutic decision making.
Data submissions undergo internal evaluations to look for inconsistency in the data format and any missing or unreliable information, before getting uploaded to the database.
The FDA has recently issued a draft, "Guidance for Industry: Pharmacogenomic Data Submissions" (FDA 2003), and has held workshops to discuss issues related to pharmacogenomics data submissions (Salerno and Lesko 2004a, 2004b; Leighton et al. 2004; Ruaño et al. 2004; Trepicchio et al. 2004).
Data submissions are accepted from individual researchers, groups and consortia, whereas we also actively gather data sets from various public sources.
Data submissions to ArrayExpress which use MAGE-TAB can accurately describe a wider range of experiment types compared with those submitted using the MIAMExpress web interface, and are usually quicker and easier to complete for larger experiments.
The PRIDE submission workflow is summarized in Figure 3. Due to the difficulty caused by the existing high heterogeneity in data formats, the PRIDE Converter application (http://code.google.com/p/pride-converter) was developed for streamlining data submissions to PRIDE (11).
