WP7: Bioinformatics and databases

Coordination:
Erik Bongcam-Rudloff
Uppsala University
 
Description
Bioinformatics and databases (WP7). The Proteinbinders portal (KTH) will contain detailed binder QC data (WP2,3) and facilitate user access to the resource. Database tools will prioritise binders with greatest potential in biomarker detection for specific cancer types (VTT). Functional proteomics data (WP6) will be centralised in the IntAct database (EBI). Protocols will be publicly accessible through the MolMeth resource (UU).
Objectives
This WP will co-ordinate the Affinomics data management and provide the following key public resources:

  1. Protein Binders, a community-based portal for validated protein binder information, and a central entry point for information on all binding reagents developed in Affinomics as well as community-contributed binder validation information.
  2. AffinomicsSelect, a publicly accessible toolkit for prioritisation of target selection and binder development.
  3. The IntAct molecular interaction database, providing a central entry point for interaction and pathway information generated within Affinomics as well as other EU projects and literature curation, with direct links to the reagents used in relevant experimens.
  4. The Molmeth database of experimental protocols and SOPs for binder applications used to generate data in Proteinbinders and IntAct and beyond.
  5. The PSI-PAR community standard for the representation of affinity binder properties as the integrative framework for data exchange and communication between and beyond the above Affinomics resources. The project databases will also be the first point of contact for user access to the resource, providing initial binder catalogue and detailed assessment information prior to a request for material. Duration: Months 1 – 60

Partners
UU, EMBL EBI, VTT, UTOV, KTH