The eNanoMapper database for nanomaterial safety information

Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR)

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations

Collaborative development of predictive toxicology applications

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals

METER.AC: Live Open Access Atmospheric Monitoring Data for Bulgaria with High Spatiotemporal Resolution

Detailed atmospheric monitoring data are notoriously difficult to obtain for some geographic regions, while they are of paramount importance in scientific research, forecasting, emergency response, policy making, etc. We describe a continuously updated dataset, METER.AC, consisting of raw measurements of atmospheric pressure, temperature, relative humidity, particulate matter, and background radiation in about 100 locations in Bulgaria, as well as some derived values such as sea-level atmospheric pressure, dew/frost point, and hourly trends. The measurements are performed by low-power maintenance-free nodes with common hardware and software, which are specifically designed and optimized for this purpose. The time resolution of the measurements is 5 min. The short-term aim is to deploy at least one node per 100 km2, while uniformly covering altitudes between 0 and 3000 m asl with a special emphasis on remote mountainous areas. A full history of all raw measurements (non-aggregated in time and space) is publicly available, starting from September 2018. We describe the basic technical characteristics of our in-house developed equipment, data organization, and communication protocols as well as present some use case examples. The METER.AC network relies on the paradigm of the Internet of Things (IoT), by collecting data from various gauges. A guiding principle in this work is the provision of findable, accessible, interoperable, and reusable (FAIR) data. The dataset is in the public domain, and it provides resources and tools enabling citizen science development in the context of sustainable development

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

Deliverable Report D5.4 User application for importing NanoSafety Cluster data

The aim of this work is to analyze and choose technical options to implement application and user interfaces for the import of available data from various EU Nanosafety Cluster (EU NSC) projects. Applications are subjected to integrated testing (Task 5.2) and, depending on licenses, data are released for user testing and evaluation (Task 1.4). eNanoMapper has been in contact with various NanoSafety Cluster projects for importing data. Most of this data is expected to be provided as spreadsheets for which a general framework has been developed. We engaged with the following EU Nanosafety Cluster projects: 1. With NANoREG (WP6) we are working on exporting data from their literature capturing database into eNanoMapper and back again, and annotating fields and content with the eNanoMapper ontology along the way. NANoREG also provided confidential Excel templates used to gather data within NANoREG WP2, WP4 and WP5. 2. ModNanoTox was provided as MS Excel spreadsheet files, containing 86 assays with more than 100 different endpoints affecting 45 species. We developed a dedicated command line application, built on top of the configurable spreadsheet data parser, which enables parsing the entire ModNanoTox data and importing into the database. The annotation of fields and content with the eNanoMapper ontology is ongoing. 3. COST Action MODENA agreed to share data with eNanoMapper and provided the Excel files to eNanoMapper. The data was collected for training purposes. This data was first reviewed by MODENA and provided to eNanoMapper as an Excel spreadsheet, containing information on the nanomaterials (NM) identification, characterization, assay performed, test conditions and a few toxicity parameters (ECs). Additionally, MODENA provided Excel templates used within the project to gather literature data (one Excel file per material). These individual templates are then summarized into the spreadsheet for training purposes described above. The MODENA templates are similar (but not exactly the same) to MARINA templates. 4. MARINA project has published an exhaustive paper on the in vitro assessment using representative JRC nanomaterials. Data to be imported refers to the in vitro toxicity of six NMs and was evaluated in 12 cellular models representing 6 different target organs/systems (immune system, respiratory system, gastrointestinal system, reproductive organs, kidney and embryonic tissues). The toxicity assessment was conducted using 10 different assays for cytotoxicity, embryotoxicity, epithelial integrity, cytokine secretion and oxidative stress. In addition, MARINA participant provided confidential Excel templates used to gather the data within the projects, covering variety of physicochemical characterisation experiments and bioassays. 5. NANoPUZZLES project provided confidential data templates, designed to resemble ISA-TAB-Nano structure. NANoPUZZLES plans to release the data with CC-BY license after the end of the project. 6. Exhaustive data on physico-chemical properties of representative nanomaterials used in various EU Nanosafety Cluster projects (e.g. ENPRA, MARINA, and NANoREG) are publicly available via the EC-JRC reports, (https://ec.europa.eu/jrc/en/publications)

Complementary visualization of perfSONAR network performance measurements

Research backbone networks are currently used by a variety of scientists and research projects interested in maximizing the benefit they receive in using the networks. Therefore, it is highly desirable for them to get access to network performance monitoring data which is prepared to serve their needs. The perfSONAR measurement framework, which is jointly developed by the EU-funded GN2 JRA1 project, Internet2, and ESnet, has developed a prototype for measuring a variety of network performance metrics such as utilization, one-way delay, one-way delay variation, packet loss, available bandwidth, and others. Corresponding measurements are currently carried out in the contributing research networks in a prototypical manner and will be installed on a regular basis in the future. For the visualization of measurements a set of tools is under development which is in the focus of this paper. The design of the tools is carried out to serve the interests of the broad user community and uses best practices gained from a survey of visualization possibilities

Deliverable Report D5.5 User application for searching and downloading eNanoMapper data

Searching and downloading nanomaterial data was identified from requirements analysis as one of the top priority use cases for users within the Nano Safety community. The search modes include both free text and structured search, which appeal to different types of users. The typical structured search requires combining queries on chemical composition and query on physicochemical characterization and bioassay outcomes. The preferred way of displaying the search result is a summary, with a subsequent drill down for details. This deliverable describes a user friendly free text search application (http://search.data.enanomapper.net), provides examples of using the API for searching the eNanoMapper database via R, and examples of building visual summaries with Javascript. Download of substances and studies as well as search results is enabled via REST API calls. The download formats supported include JSON, spreadsheets (XLSX) and semantic formats (RDF/XML, N3, JSON-LD). The web pages at http://data.enanomapper.net provide download links for user convenience. A blog post, describing how to use the different database search functionalities and an example of measurement representations in a semantic format are provided as Annexes

Summary of the Spring 2014 NSC Database Survey

<p>The NanoSafety Cluster Database working group organized in Spring 2014 a survey for the community to summarize the current state of databases and including questions of a more technical nature. This survey is a first in a biannual continuous effort and attempt to collect, organise and share up-to-date information about NanoSafety related databases worldwide. For example, it included questions about application programming interfaces, database schema, supported input and output formats, etc. This document summarizes the responses we received before August 2014.</p