Work Package 1: Management
WP1 (led by EMBL-EBI ) will provide the management infrastructure for PhenoMeNal. It will be coordinated by the EMBL-EBI, building on EMBL-EBI experience in the management of large consortia. It will make use of state of the art electronic communication methods, which will be integrated in the PhenoMeNal Virtual Research Environment.
- Efficiently manage the consortium activities to maximise PhenoMeNal impact.
- Organise all PhenoMeNal consortium and stakeholder meetings, as well as regular staff exchanges between the PhenoMeNal partners in collaboration with our consortium partners.
- Systematically document the decision-making process and decisions made in teleconferences, meetings and by mail exchange. This will be compiled regularly into PhenoMeNal consortium documentation.
- Minutes of kick-off meeting – D1.3
- Bi-annual progress report – D1.4.1
- Bi-annual progress report – D1.4.2
- Bi-annual progress report – D1.4.3
- Bi-annual progress report – D1.4.4
- Bi-annual progress report – D1.4.5
- Bi-annual progress report – D1.4.6
- Data management plan – D1.5.1
- Updated data management plan – D1.5.2
- Updated data management plan – D1.5.3
- MS1.1 – PhenoMeNal Project Plan
- MS1.2 – Initial release of Data Management Plan
Work Package 2: Sustainability of PhenoMeNal
WP2 (led by UL) will develop and implement plans to sustain the PhenoMeNal e-infrastructure beyond its initial 3-year funding period. Sustainability measures include building strong relationships to all stakeholders, to industry and to all parties developing components of the PhenoMeNal grid and virtual research environment.
- Mapping of e-infrastructures, users, investments for supporting policy developments in the field of metabolomics, biomarkers and biobanks.
- Establishing and maintaining relations with publishers for supporting data deposition services.
- Coordination with national and international related activities and support to the development of global and sustainable approaches in the field.
- Promotion of long-term sustainability, including the involvement of funders.
- Preparation of a business plan beyond the end of the project.
- Report on mapping of e-infrastructures, users, investments for supporting policy developments in the field of metabolomics, biomarkers and biobanks – D2.1
- A first version of the sustainability plan – D2.2
- Updated Report on mapping of e-infrastructures, users, investments for supporting policy developments in the field of metabolomics, biomarkers and biobanks – D2.3
- Business plan beyond the end of the project – D2.4
- Report on concrete sustainability measures taken by all partners – D2.5
- MS2.1 – Sustainability Plan released
Work Package 3: Dissemination and Outreach
WP3 (led by UoB) will establish close links between the PhenoMeNal consortium and the wider community in metabolomics, genomics and the biomedical community in order to establish a user base for the services offered. We will raise community awareness for the services provided by the PhenoMeNal consortium, from data and information mining, processing and analysis, but also for the use of omics technologies in a biomedical context, close to the clinic. Through the existing framework of the Metabolomics Society, we will ensure broad community input into the services developed by the PhenoMeNal consortium and the processing and data mining services for metabolomics provided by this consortium. We will provide online training in the grid, the tools and the data formats used in the PhenoMeNal grid.
- Establish extra-consortium links with other e-infrastructures, standards communities, publishers and funders
- Raise awareness for standards, services and tools provided by the PhenoMeNal grid
- Provide online training for users interested in the PhenoMeNal grid
- Arrange PhenoMeNal stakeholder meetings
- Report of the annual stakeholder meeting – D3.1.1
- Report of the annual stakeholder meeting – D3.1.2
- Report of the annual stakeholder
- Report on establishing and maintaining relations with publishers for supporting data deposition – D3.2
- Web-based Tutorial release 1 about “Metabolomics Data Deposition and Analysis through PhenoMeNal”, in the form of video clips – D3.3.1
- Web-based tutorial release 2 about “Metabolomics data deposition and analysis through PhenoMeNal”, in the form of video clips – D3.3.2
- Two training workshops on omics data deposition, grid processing, dissemination and access – D3.4.1
- Two training workshops on omics data deposition, grid processing, dissemination and access – D3.4.2
- MS3.1 – First web tutorial online
Work Package 4: Interfacing with Biomedical and European Infrastructures
WP4 (led by CIRMMP) will aim at maximising communications with European infrastructures with an interest in biomedical data generation and analysis (such as EGI, Elixir, BBMRI, IMI eTRIKS, INSTRUCT and any other relevant infrastructures resulting from the present and future calls) and those supported by NIH. The PhenoMeNal project, through this work package, will actively participate in the concertation activities, consultations and other meetings and events related to e-infrastructure. The objective is to optimise synergies between projects by providing input and receiving feedback from other stakeholders.
- Boost the offering of services by the PhenoMeNal e-infrastructure to the current large scale EU biomedical infrastructures, both physical and electronic, and their users.
- Align PhenoMeNal activities to the requirements of such infrastructures.
- Optimise synergies between projects by providing input and receiving feedback from working groups addressing activities of common interest.
- Establish communication channels and participate in meetings with other European biomedical and e-infrastructures, and those word-wide.
- Report on requirements for relevant research centres producing and/or consuming metabolomics data – D4.1
- Report describing the activity and output of working groups – D4.2
- Consensus agreement document from the working groups – D4.3
- Report on State-of-the -art and perspectives in the field – D4.4
Work Package 5: Operations and Maintenance of PhenoMeNal GRID/Cloud
WP5 (led by UU) will provide the foundation upon where data and analysis services are made possible to be used together on compute resources. It comprises the hardware (compute and storage) as well as middleware for federating queries and resources between sites, enabling the functions in the Virtual Research Community (VRC) portal developed in WP6. Of high importance is the documentation and packaging of infrastructure resources and configurations to allow for easy setup on partner systems, enabling a federated system.
- Establishment of the PhenoMeNal e-infrastructure
- Operations and maintenance of the PhenoMeNal VRC portal
- Maintenance and provisioning of the PhenoMeNal services in the PhenoMeNal e-infrastructure
- Build system with continuous integration, providing development snapshots of PhenoMeNal Virtual Machine Images – D5.1
- A beta-version of PhenoMeNal integration VMI capable of the proof-of-concept integration with other VMIs – D5.2
- Operational grid/cloud allowing for combining data, tools, and compute VMIs. Most services available. Functional integration with EGI federated cloud/grid for compute resources. Demonstrated analysis on private/sensitive data in secure environment – D5.3
- A federated cloud/grid system running on partners’ infrastructures for public data and tools. All services available. Operational installation at ICL clinical site for decision support. D5.4
MS5.1 – Operational Grid/Cloud
Work Package 6: PhenoMeNal Virtual Research Community Gateway
WP6 (led by EMBL-EBI) will create a PhenoMeNal Virtual Research Community (VRC) will be the central access point for all users. This is the online portal enabling user interactions, virtual machine distribution, access to compute resources and information exchange. Users can search for existing public datasets and perform online analysis. The VRC will interact with the PhenoMeNal middleware developed in WP5 to federate on-demand job requests between provisioned data, compute, and analysis resources. Expert help and training will be available through the VRC.
- Establishment of the PhenoMeNal Virtual Research Community (VRC) portal
- User Experience Document on VRC Design Guide – D6.1
- PhenoMeNal VRC (static) portal publicly available – D6.2
- Participating biobanks and repositories connected to the VRC – D6.4
- Training and online tutorial for the general use of PhenoMeNal – D6.5
- Report on available processes, methods and SOP’s deployed in the grid/cloud – D6.6
- Report on general usage of the VRC and grid/cloud – D6.7
Joint Research Activities
Work Package 7: Privacy and Ethics
WP7 (led by ICL) will ensure that all data collected and held within the project will comply with all local laws, regulations and ethics. All personal information will be processed in accordance with accepted Data Protection Principles outlined above. Responsibility for data will be with the host institution/data provider.
- Develop appropriate policies, procedures and management accountability and structures to provide a robust governance framework for information management.
- Raise awareness of information governance within the consortium and assure ongoing compliance.
- Provide a forum for information exchange on best practice in clinical data sharing and disclosure.
- Ensure that ethical standards and guidelines of Horizon2020 will be rigorously applied, regardless of the country in which the research is carried out.
- 1st Workshop on best practices in handling sensitive human data, taking into account national and Institutional legal policies – D7.1.1
- Workshop on best practices in handling sensitive human data, taking into account national and Institutional legal policies – D7.1.2
- Report on the policies and procedures for sensitive human data management – D7.2
- Evaluation report for the introduction of data provider form – D7.3
- Process to extract maximum information from sensitive datasets with minimum compromise, in collaboration with BBMRI and BioMedBridges – D7.4
- Report to the EC/REA with ethical approvals, informed consent forms and patient information material of datasets to be used within PhenoMeNal e-infrastructure development – D7.5
Work Package 8: Data provenance, Compliance, and Integrity
WP8 (led by UOXF) will ensure building a federated infrastructure, by essence, requires the stakeholders to agree on reporting and communication standards for messages and information to be reliably brokered and exchanged between systems. Contingent to a central demand to ensure data evaluation, audit and review imposes that provenance, traceability and integrity of data is delivered. WP8 will therefore develop a set of modular format specifications to achieve maximum efficiency during data exchange with each module focusing on specific component of data management, while retaining compatibility with existing community standards and addressing distinct and complementary scenarios of usage. Data safety and patient de-identification schemes developed in WP7 will be considered.
- Define metadata and data exchange standards, along with technical and user documentations.
- Implement and maintain PhenoMeNal reference implementations.
- Report on the community standards for reporting, access and integrity supported in the PhenoMeNal grid; to be disseminated in a dedicated BioSharing page via the project website – D8.1
- Modularised ISA model and format: biospecimen centric schema, corresponding xml schemas, reference implementation guidelines and validation rules – D8.2
- nmrML, mzML data exchange formats and associated terminologies for instrument raw data, with reference implementation guidelines and validation rules – D8.3
- Signal processing and data exchange format – D8.4
- Specifications for derived data matrices specifications and terminology for description of analysis and statistical results – D8.4.1
- Reference implementation guidelines and validation rules – D8.4.2
Work Package 9: Tools, Workflows, Audit and Data Management
WP9 (led by IPB) aims to develop and maintain the primary scientific- and technological tools and corresponding interfaces. We will support the data standards defined by WP8 and facilitate the interoperability of tools both within this consortium and those externally developed by the community. We will establish distributed tools for phenomics, metabolomics and bioinformatics processing pipelines and workflows, including longitudinal primary research data management (continuous availability to avoid data lock-in) and data audit mechanisms, as well as quality assurance schemes. Thus, this work package will produce several tailored VMIs which will be the basis for the service activities in WP5.
- Specify and integrate software pipelines and tools utilised in the PhenoMeNal e-Infrastructure into VMIs, adhering to data standards developed in WP8 and supporting the interoperability and federation middleware developed in WP5. Most tools will be already available (see table 1.1) and we will develop new applications to complete ‘missing links’ in pipelines. Although two explicit releases for VMIs are listed as deliverables below, we will use public repositories and continuous integration to always provide development snapshots of the infrastructure VMIs.
- Develop methods to scale-up software pipelines for high-throughput analysis, supporting distributed execution on e.g. local clusters, private clouds, federated clouds, or GRIDs.
- Add quality control and quality assurance to pipelines to ensure high quality and reliable data, keep an audit trail of intermediate steps and results.
- Develop methods to present and summarize the results of the pipelines in biomedical and disease contexts.
- Report on existing software tools, workflows and analytical pipelines initially supported in the PhenoMeNal grid – D9.1
- PhenoMeNal-Preprocess Virtual Machine Image to enable data producers to locally process raw data into standard formats supported in PhenoMeNal – D9.2.1
- PhenoMeNal-Data Virtual Machine image to enable sharing and dissemination of standardised and processed omics data to participating online repositories, like MetaboLights – D9.2.2
- Services Virtual Machine Image to facilitate the PhenoMeNal toolsets and pipelines, both locally and in the grid – D9.2.3
- Compute Virtual Machine Image to enable standardised compute capabilities for all the grid supplying partners – D9.2.4
- Portal Virtual Machine Image that is capable of integrating other PhenoMeNal VMIs (in local federated clouds) and make all functionality available via command-line, web-APIs, and graphical user interfaces – D9.2.5
- Report API access to PhenoMeNal resources – D9.3
- Updated report on existing software tools, workflows and analytical pipelines supported in PhenoMeNal – D9.4
- Updated preprocess virtual machine image 1 – D9.5.1
- Updated data processing virtual machine image 2 – D9.5.2
- Updated services virtual machine image 3 – D9.5.3
- Updated compute virtual machine image 4 – D9.5.4
- Updated portal virtual machine image 5 – D9.5.5