Tools developed by the HEAP team
FAIR data self-assessment service
The Self Assessment Service (SAS) is an on-line questionnaire to guide researchers on how Findable, Accessible, Interoperable and Reusable (FAIR) their data is.
FAIR toolbox
A modular component-based toolkit for life sciences. Open-source software is combined with ID- and user-management to record data provenance graphs to enable implementation of research workflows in a FAIR manner.
Hopsworks exposome Platform as a Service
PaaS for distributed management and analysis of exposome data. GDPR compliant, sharable data, bioinformatics tools and analysis pipelines. Provides Machine Learning out of the box.
Exposome Toolbox
The HEAP tools are part of EHEN's virtual exposome toolbox, which is a signposting hub for the tools developed by the European Human Exposome Network projects. They include data models, guidelines and protocols,
Learning resources from the HEAP team
In this series of short videos, join the HEAP researchers, FAIR frog and Data Gator on a data management journey, starting with an introduction to data management for researchers, and ending with a presentation of the key features of the HEAP platform.
Scientific publications
Published in the journal Environmental Epidemiology in December 2021, the HEAP project paper introduces the HEAP informatics platform that will integrate an Infrastructure as a Service (IaaS: computational resources services for storage and computation) and a Platform as a Service (PaaS: software services for managing and analyzing data).
Epigenetics
Published in the journal Genome Biology in February 2022 by the Work Package 8 team from the University of Innsbruck.
The findings imply that there are multiple epigenetic clocks, many of which are tissue-specific, and that the differential tick rate between these clocks may be an informative surrogate measure of disease risk.
GDPR and joint controllership
Published in Open Research Europe in June 2022 by the Work Package 2 team from MLCF Foundation.
Proposal for a ‘funnel-and-sieves’ model for deciding who are joint controllers under GDPR legislation for the data processing in research consortia and who are not.
Artificial intelligence
Published in the journal Computer in July 2021 by the Work Package 7 team from the Medical University of Graz and the Work Package 2 team from MLCF Foundation.
Practical guidelines for those applying artificial intelligence to provide a concise checklist to a wide group of stakeholders.
Published in the journal Computer in February 2022 by the Work Package 7 team from the Medical University of Graz.
An argument for using causability in medical artificial intelligence (AI) to develop and evaluate future human–AI interfaces.
Published in the journal IEEE in February 2022 by the Work Package 7 team from the Medical University of Graz.
A 5-step approach for developing personas to support human-centered design of AI applications, with practical examples from personas development for AI solutions for digital pathology.
Published in the journal New Biotechnology in September 2022 by the Work Package 7 team from the Medical University of Graz.
Description of concepts and examples of how explainability and causability are essential to demonstrate scientific validity, as well as analytical and clinical performance for future AI-based IVDs.
Metagenomics
Published in the journal Nature, Scientific Reports in July 2022 by the Work Package 3 team from the Karolinska Institute.
Description of “HPV-meta”, the first open-source pipeline aiming to specifically detect HPV transcripts in RNA sequencing data.
Published in the journal Multidisciplinary Digital
Publishing Institute (MDPI) in 2022.
Identification of a microbiome signature for predicting the risk of colorectal cancer, that was validated in a new study, Colorectal Cancer Screening (COLSCREEN).
Consumer purchase data
Published in the journal BMJ Open in June 2022 by the Work Package 4 team from the Statens Serum Institut, Copenhagen.
Protocol for a population-based inception cohort study aiming to investigate the underlying mechanisms for the heterogeneous course of IBD, including need for, and response to, treatment. Environmental factors and quality of life will be assessed using questionnaires and, when available, automatic registration of purchase data.
Biobanking
Published by Springer Nature Switzerland in March 2022 by the Work Package 7 team from the Medical University of Graz.
Standards and tools for biospecimen quality management must be democratised for biorepositories in a variety of settings to have a truly global impact on research.
Project reports and public deliverables
This document defines the life cycle and governance framework for all data to be collected, processed and generated during the HEAP project.
This document provides guidance for the development and use of the Reference Architecture within the Human Exposome Assessment Platform (HEAP). It describes the technical architecture, data and metadata flow and means for accessing data in the platform.
The HEAP project reports are all available on Zenodo...
- Heimo Muller, Roxana Merino, Stefan Negru, Martin Boeckhout, Evert-Neb van Veen. (May, 2020). Human Exposome Assessment Platform - Data Management Plan. Public deliverable 7.1. Update Jan 2023 (Version Final deliverable). Zenodo. https://doi.org/10.5281/zenodo.7572272
- Arroyo, Sara, Merino, Roxana, Pimenoff, Ville, Bala, Piotr. (December, 2022). Ontology and semantic metadata for metagenomic profiles and tools for NGS data management. Public deliverable 9.3. Zenodo. https://doi.org/10.5281/zenodo.7540992
- Górski, Łukasz Górski, Mroczek, Magdalena, Nowicki, Marek, Bala, Piotr. (February, 2022). AI based alignment free (agnostic) taxonomic classification. Public deliverable 9.2. Zenodo. https://doi.org/10.5281/zenodo.7520385
- Szymkiewicz, Szymon, Bala, Piotr. (December, 2020). Bacterial and viral metagenomics. Public deliverable 9.1. Zenodo. https://doi.org/10.5281/zenodo.7520376
- Zhang, Allison, Pimenoff, Ville. (December, 2022). Exposome and metabolomics analysis pipelines. Public deliverable 5.3. Zenodo. https://doi.org/10.5281/zenodo.7499184
- Zhang, Allison, Snyder, Michael, Pimenoff, Ville. (December, 2020). Improved wearable Personal Exposome Monitors (PEMs). Public deliverable 5.1. Zenodo. https://doi.org/10.5281/zenodo.7499101
- Trier Møller, Frederik, Ewes, Caroline, Wilkowski, Bartlomiej, Chong, Steven, Grønborg Junker, Thor. (December, 2022). Consumer cohort - secure platform and recruitment. Public deliverable 4.1. Zenodo. https://doi.org/10.5281/zenodo.7499081
- Coombs, Heather, Kozlakidis, Zisis, Berger, Anouk. (December, 2022). Knowledge and Information - Phase 1 report. Public deliverable 11.3. Zenodo. https://doi.org/10.5281/zenodo.7499065
- Ormenisan, Alex, Mukhedkar, Dhananjay, Arroyo, Sara, Pimenoff, Ville, Zhang, Allison, Trier Møller, Frederik, Herzog, Chiara, Bala, Piotr. (December, 2022). HEAP Knowledge Engine. Public deliverable 6.2. Zenodo. https://doi.org/10.5281/zenodo.7498973
- Coombs, Heather, Berger, Anouk, Kozlakidis, Zisis. (December, 2021). Knowledge and Information Sharing Plan. Public deliverable 11.2. Zenodo. https://doi.org/10.5281/zenodo.7498916