Database development and implementation

Description of Tasks

1). Protocol Technical specification
2). Protocol management web services
3). Experimental data web services
4). Search services
5). ISA-Tab template development for common bio assays
6). Modules for linking and integration with third party databases


Database development and implementation

D3.1 Technical Specification and initial implementation of the protocol and data management web services
D3.2 Data Management System with extended search capabilities
D3.3 Modules and services for linking and integration with third party databases
D3.4 ISA-Tab templates for common bioselected set of assays


Idea Consult LTD


This WP will design, implement and provide the data infrastructure and search capabilities, supporting all aspects of ENM characterization, namely synthesis and processing, physicochemical characterization, LCA, environmental and health hazards assessment, high throughput and high content datasets. A web service for protocol management will allow uploading and linking to experimental protocols, which are likely to evolve and change quickly in the dynamic domain of ENMs. The database will employ a flexible data model, based on semantic technologies, OpenTox data services, ISA-TAB and the nano material ontology, developed and recommended by WP2. We will adopt a pragmatic approach, building a distributed set of data access services and linking existing databases. The database will be populated from public data, databases owned by consortia members (KI,VTT,UM) and other databases, recognized as essential during the WP1 requirement analysis.

Description of work

WP3 will build flexible data storage based on semantic web technologies and open source components, already proved to be efficient for supporting diverse data types. WP3 will design and implement web services for protocol management, experimental data upload, search and retrieval and will integrate with the Authentication and Authorization web service (WP5). It will provide a web services API for upload and retrieval of metadata and raw data in the form of file access and OpenTox dataset API, which could be directly used by WP4. WP3 will define ISA-TAB templates (with ontology annotations) for a set of assays, recommended by WP1. The assays will likely cover a) specific experimental methodologies for ENM manufacturing and physicochemical properties characterization, partly based on the OHT templates, relevant for ENMs b) exposure and life cycle assessment c) OHT for human and ecological hazard assessment, as the OECD guidance for these endpoints is considered largely applicable; d) high throughput and high content datasets identified by consortia members and WP1 requirement analysis. WP3 will implement modules for conversion of ISA-TAB into semantic web format, using and extending the open source tools developed previously by the consortium members (isa2rdf) and input from WP2 Ontology development.