Deliverable Report D3.4 ISA-Tab templates for common bioselected set of assays

Data preparation is an activity pertinent to most of the NanoSafety Cluster (NSC) projects. The importance of standardized means for data logging and data sharing is acknowledged by both data providers and data users, but the current practice consists mostly of disparate efforts, resulting in incompatible files. The ISA-TAB (Investigation-Study-Assay) and ISA-TAB-Nano formats are cited in many projects, but not used due to several reasons, e.g. lack of user friendliness or the steep learning curve needed to adopt the format. Instead, variations of the ISA have appeared, such as the ISA-TAB-Logic templates, developed and released under open license by the NANoREG project. The ISA-TAB-Logic templates are Excel files, with a number of fields describing the material sample, physchem characterisation and bioassays. Various flavours of Excel templates are used or considered for adoption by several NSC projects. We have cleaned, annotated and created configuration files for the publicly released templates, enabling direct import into the database through a web browser or programmatically. Ontology annotation is ongoing, with close collaboration with eNanoMapper WP2. We developed tools to automatically generate ISA-JSONv1 (the new specification of ISA) from existing nanomaterial safety data. We also developed Material Schema extension for the new ISA-JSON specification, which is the counterpart of the “material file” in the ISA-Tab-Nano specification. To allow for easy adoption, we have created a documentation site, describing the developments above, accessible via the eNanoMapper tutorials repository at Github https://github.com/enanomapper/tutorials/tree/master/DataTemplates and via menu “Data templates” of the search application at https://search.data.enanomapper.net
Being able to read the Excel spreadsheets and write the internal data model into ISA-JSON files accomplishes the goal of automatically generating the ISA files, and enables exporting query results from the database in any desired format. The templates provided are coupled with configuration files, enabling import into the database through a simple web form or programmatically via Application Programming Interface. The use of the tools and templates described in this deliverable is also foreseen within the NSC projects enabling harmonized collection of data, which will eventually be compatible across projects.