ELIXIR-NL is involved in a new Implementation Study that aims to dramatically improve the reusability of public proteomics datasets. This will be achieved by substantially increasing the amount and quality of technical and biological annotations for datasets stored in the PRIDE database. The study will start on 1 June 2018 and run for a one year period.
Merlijn van Rijswijk (DTL Technologies Programme Manager) explains: “Ten ELIXIR nodes are involved in this new Implementation Study. It is coordinated by EMBL-EBI. Peter Horvatovich of Groningen University and Magnus Palmblad of the LUMC represent ELIXIR-NL.”
PRIDE
The PRIDE database is the world-leading repository for mass spectrometry proteomics data. It is one of ELIXIR’s core data resources. The proteomics community is widely embracing open data policies. As an illustration, PRIDE received 2,443 dataset submissions in 2017. Reuse and reanalysis of these data continue to grow, e.g., around 295 TBs of data were downloaded from PRIDE in 2017. However, proteomics data reuse is currently constrained by the limited technical and biological annotations that are available for PRIDE datasets. A user-friendly mechanism is required for users to improve the quality of the annotation of the datasets.
Four objectives
The Implementation Study has four objectives. First, the ELIXIR nodes will develop an a posteriori annotation system for PRIDE, for technical and biological metadata, which will leverage the unique synergies of already existing tools and pipelines developed by different ELIXIR nodes. Second, they will create data structures that can capture the most-frequently used experimental designs in proteomics studies. Third, an appropriate API will be built to allow annotation tools to be developed easily. Fourth, they will reach out to actively involve the whole proteomics community in the annotation process. Taken together, this should dramatically improve the reusability of public proteomics datasets.
More information
About ELIXIR Implementation Studies
Implementation Studies are short technical projects to inform future service development, drive standards adoption, and connect ELIXIR’s 21 Nodes. The projects are funded through the budget of the ELIXIR Hub and form part of ELIXIR’s ongoing activities in a particular Platform or Community. They are proposed by Platforms, agreed with the ELIXIR Heads of Nodes committee, and approved by the ELIXIR Board. Read more.
About proteomics and ELIXIR
Proteomics activities are well-represented within Europe and ELIXIR nodes. ELIXIR recently started a Proteomics Community.