Skip to main content

Synthesis of systematic resources

Periodic Reporting for period 1 - SYNTHESYS PLUS (Synthesis of systematic resources)

Période du rapport: 2019-02-01 au 2020-07-31

European natural science collections (NSCs) are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – mapping a sustainable future for ourselves and the natural systems on which we depend. Since 2004 SYNTHESYS has been an essential instrument supporting this community, underpinning new ways to access and exploit collections, harmonising policy and providing significant new insights for thousands of researchers.

SYNTHESYS+ aims to unify operations and access for European NSCs by:

1. Transforming the fragmented access model of European NSCs into a central facility and support new forms of virtual access within an integrated, data-driven, pan-European RI;
2. Coordinating formal and professional training activities to enhance data skills and competencies for scientists;
3. Running a robust joint research programme enabling scientists to benefit from new digital and genomic RIs to deliver data-driven scientific innovation;
4. Developing common policies, harmonising digital and molecular processes in alignment to national and international standards;
5. Working towards the establishment of a shared international vision of bringing together all global NSCs as an integrated RI.
Networking Activities (NA):

NA2 is harmonising, grouping and disseminating best practices already adopted by European NSCs. Data on existing policies, best practices and standards has been analysed to identify gaps, and support a toolkit for institutions to self-assess digital collections policies. NA2 has delivered a fully functional pilot dashboard (Deliverable 2.2) that provides a dynamic window on NSCs for stakeholders as well as a tool for digitisation prioritisation. Training activities are also being developed in NA2 via the DEST platform (Distributed European School of Taxonomy) to be delivered in early 2021.

NA3 has developed, launched, and evaluated a survey on biobank standards and best practices covering areas including specimen collection; preservation methods; sample retrieval, material request and shipment; emergency plans; safety and security; data standards and policies. The results will help to develop a handbook (due September 2022).

NA4 is working on providing data standards and processes to improve collections data interoperability. A standards compliance dashboard has been developed and a critical new standard (Minimum Information on Digital Specimens) is under construction that allows the assessment of the level of digitisation of a specimen. Work is also proceeding to add stable identifiers for specimen collectors, and rollout the International Image Interoperability Framework (IIIF) to discover image resources associated with specimens. A handbook on identifier management for curators (Deliverable 4.2) serves as a guideline to collections managers/curators to implement a stable identifier for physical specimens.

NA5 activities are working to bring major international stakeholders together to help develop the global collections research agenda. A consultation has reinforced the wide international interest in addressing increased standardisation and collaboration on NSC data. To expand geographic involvement, an NA5 call was opened inviting submission of proposals for projects that further develop digitisation of and access to NSCs in priority regions. NA5 also aims to align services with the Catalogue of Life (CoL) and its partner biodiversity data initiatives (CoL+) plus establish a communication channel with the European Environmental Agency.

Joint Research Activities (JRA):

JRA1 is developing an integrated European Loans and Visits System (ELViS) to support access applications and track outputs from NSCs. ELViS was taken into production for the 1st Virtual Access (VA) call in February 2020. Wireframes have also been created for the implementation of the TA workflow for the 3rd TA Call in spring 2021.

The key objectives of JRA2 are to support and enhance the technical infrastructure and institutional capacity to undertake and process Collection on Demand requests. VA coordinators have been appointed by each participating VA institution in order to support digitisation requests and facilitate digital access. A report on cost models used for digitisation on demand has been completed, while work to develop routine laboratory protocols and workflows for DNA Sequencing on Demand has also proceeded under JRA2.

JRA3 is developing the Specimen Data Refinery (SDR) that combines data capture technologies to harvest, organise, analyse and enhance information in a cloud-based platform for processing specimen images and their labels. A report has been compiled and published gathering data on associated AI technologies (Deliverable 8.1).

Two calls for Trans-national Access (TA) have been held to date, resulting in the award of 3,017 days of researcher access to 21 SYNTHESYS+ institutions across 13 countries. Whilst COVID-19 has had a major impact on international travel and therefore the entire TA programme, 1,435 user days of access have already taken place, resulting in 191 outputs in progress or published.

SYNTHESYS+ has delivered a new Virtual Access (VA) programme, providing digitisation on demand services to a significantly expanded user community. VA supported an ‘ideas call’ to test the process, after which the first VA call took place in 2020, resulting in 30 full digitisation requests of which 5 have been prioritised for funding.
SYNTHESYS+ is working to unlock information in NSCs and link it to other datasets to drive novel, integrative research and provide an incredibly powerful research tool for understanding the past, present and future of the natural world.

SYNTHESYS+ is acting to broaden the direct beneficiaries of NSCs, both geographically and across disciplines, via VA alongside the (physical) TA pillar of the project. Our ELViS system lowers overheads for NSC users and administrators. Complementary work packages address gaps in standards around managing molecular (NA3) and digital (NA4) information. Both are developing a more complete corpus of standards to be incorporated into international organisational policies and practices. A dedicated work package (NA5) is focusing on internationalisation and the expansion of our user community.

Physical users of the collections (via SYNTHESYS+ TA) are addressing global research issues including environmental and climate change and climate modelling. Users are delivering new and improved baseline bio- and geo-diversity data, working with expert hosts to generate and add value to existing collections.

SYNTHESYS+ is acting as a critical transition project for the Distributed System of Scientific Collections (DiSSCo - a new pan-European RI was accepted by the ESFRI ( for inclusion in the 2018 roadmap. SYNTHESYS+ undertaking the groundwork for DiSSCo to migrate a loosely joined network of access providers into an integrated and self-sustainable system of European collections.
SYNTHESYS+ European Loans and Visits System