Catalogue of project tools

eTOXsys

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Hpath is an ontology of histopathology terms used to describe observations made during mandatory animal studies conducted before first human testing. It was created based on existing scientific glossaries and complemented to cover the needs of the eTOX project. It was deposited in the public domain with the ambition to create a new common resource for the community.

The OntoBrowser tool was developed to manage ontologies and code lists. The primary goal of the tool is to provide an online collaborative solution for expert curators to map code list terms (sourced from multiple systems/databases) to preferred ontology terms. Other key features include visualisation of ontologies in hierarchical/graph format, advanced search capabilities, peer review/approval workflow and web service access to data.

Open IT platform that unlocks the information stored in Electronic Health Records for improving clinical research while fully respecting patient privacy and ensuring a high level of security.

Single platform linking many drug discovery data sources together so that users can easily see the relationships between compounds, targets, pathways, diseases and tissues. Data sources include ChEBI, ChEMBL, SureChEMBL, ChemSpider, ConceptWiki, DisGeNET, DrugBank, Gene Ontology, neXtProt, UniProt and WikiPathways.

Covers the key enabling technologies that underpin biotechnology research including enzyme discovery and engineering, systems and synthetic biology and biochemical and process engineering.

eTRIKS data catalogue

Code of practice on secondary use of medical data in scientific research projects.

Industry standard HTS screening facilities and a 500,000 compound library to screen any novel drug targets for free.

Standards Starter Pack

Procedures for dealing with data standards and standards stewardship.

 A chronological selection of recommended articles, a list of selected journals extracted from ISI Web of Knowledge with toxicology filtering, and finally, a section of interesting links, where all these resources are presented by alphabetic order and organized by categories. See Mol Inf 2013;32:24-35.

WEB-RADR

UK, Netherlands and Croatian smartphone apps developed, enabling patients, caregivers, and healthcare professionals to report adverse drug reactions (ADRs) and receive up-to-date information and news alerts.

Open, publicly-available, free-to-use platform for models on the discovery, development and usage of drugs and spanning PK, PD and disease models as well as the range from empirical to systems pharmacology/biology models.

The platform is indexed, fully searchable and supported by peer-review.

Interoperability Framework

The Interoperability Framework is an integrated infrastructure to enable efficient exchange and integration of models across modelling languages, existing and new tools.

Information about various computational methods for studying molecular binding kinetics, and the computational tools that employ them. KBbox is developed to be of use to researchers interested in applying these methods in their work. To help with this, KBbox provides an updated list of examples of published work, along with detailed tutorials to guide less experienced researchers.

RADAR-CNS

RADAR-base, a platform to support wearable device data

RADAR-base is an open-source platform that aims to support scientific research with wearable device data. It allows study participants to share their health data with clinicians and researchers in a secure way.  It enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access.

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This unified metrics toolkit can be used to comprehensively evaluate the sustainability of chemical and bio-chemical reactions based on a series of key parameters. The rationale behind the creation of the toolkit and description of the methodologies adopted is available as an open access publication and the Toolkit itself is available in the form of a user friendly excel spreadsheet in the supplementary information of the publication.

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This solvent selection guide differs from other available solvent ranking systems as it incorporates the assessment of bio-derived as well as classical solvents on a level playing field. The guide and associated methodology for its creation are provided in an open access publication. In addition, there is an associated Excel spreadsheet and online tool that will enable the user to rank a solvent not included in the list according to the guidelines outlined in the publication.

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Bronchiectasis patients registry

EMBARC is a pan-European network committed to promoting clinical research and education in bronchiectasis, through sharing of protocols, research idea and expertise. Central to this project is the creation of the European Bronchiectasis Registry, a collaboration open to all investigators around Europe caring for patients with bronchiectasis.

The lung clearance index (LCI) is a lung function parameter derived from the multiple-breath washout (MBW) test. LCI is being explored as a novel exploratory endpoint of lung disease severity and response to inhaled antibiotic therapy in patients with Cystic Fibrosis and Bronchiectasis. This online tool provides training in the use of MBW equipment and the interpretation of results.

A flexible framework supporting predictive modeling within the eTRANSAFE  project. Easily develop machine-learning models, for example QSAR-like models, starting from annotated collections of chemical compounds stored in standard formats (i.e. SDFiles). Transfer new models into a production environment where they can be used by web services to predict the properties of new compounds.

ADAPT- SMART

White paper

COMBACTE-MAGNET

EPI-Net platform

Online platform that provides timely access to data on emergence and spread of antimicrobial resistance (AMR) in humans and animal sector and healthcare-associated infections (HAI). The platform connects various national and international European surveillance systems for infections and outbreaks due to antibiotic resistant bacteria by linking microbiologic and epidemiological data.

PRO-active

Patient reported outcomes

Two patient reported outcome (PRO) instruments to capture physical activity (PA) data in patients with chronic obstructive pulmonary disease (COPD) in clinical trial settings: 1) D-PPAC (for daily data collection with a recall period of 1 day); and 2) C-PPAC (recall period of 7 days, intended to collect PA data during specified clinical study visits). The tools have been qualified by the European Medicines Agency.

Final qualification opinion

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Report on research-based suggestions for driving antibiotic development while ensuring access and sustainable use.

Report on quality indicators and quantity metrics of antibiotic use.

Commercially available

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

M Van Speybroeck, Janssen Pharmaceutica - mvspeybr [AT] its.jnj.com -  or PJ Visser, Maastricht University - pj.visser [AT] maastrichtuniversity.nl

Sample Collection and Management Manual

Manual to provide guidance through the sample collection and the different processing procedures that are to be performed within a clinical trial for pathogens detection. This serves as a template to facilitate development of clinical study-specific manuals.

Free

Community Engagement, Communications, and Technology for Clinical Trials in Outbreak Settings

Online, open access training resource relevant for anybody who is interested in community engagement, communications and enabling technologies for clinical trials in outbreak settings.

Harmonised Informed Consent Form (ICF) template to facilitate the secondary use of personal data

Harmonised ICF template for clinical studies and further research. Covers all information required by the General Data Protection Regulation (GDPR) within a traditional (non-electronic) informed consent document to be signed by patients or healthy volunteers before participating in a clinical study. The ICF aims to address the processing of personal data for (a) the conduct of a clinical study within a drug development programme (Part 1) and (b) future scientific research on personal data and biosamples collected in clinical studies, i.e. research beyond of the original drug development programme.

Toolkit for the identification, selection, and measurement of outcomes including in real-world settings

The toolkit proposes six main stages to develop Core Outcome Sets, from scoping to dissemination, with a focus on stakeholder input across all stages to ensure a wide range of perspectives are taken into account. Whilst the toolkit highlights any existing best practice to developing COS, it importantly also presents a range of methodological options which BD4BO projects can consider depending on the scope of the work and resources available.

Public webinar on outcomes standardisation

Webinar to introduce Core Outcome Sets (COS) and their role in harmonising outcomes generated in real world settings. Presentation of a toolkit giving methodological and practical guidance on developing COS, including for use in real world settings. Explanations of experiences from the different BD4BO projects including, for example, on involving patient perspectives in the standardisation of outcomes

ROADMAP Alzheimer’s Disease data cube

3D heat map assessment which allows the visualisation of the landscape on available Alzheimer’s disease data in Europe, together with their relevance for different stages of the disease.

Free