Periodic Reporting for period 3 - SYNTHESYS PLUS (Synthesis of systematic resources)
Reporting period: 2022-02-01 to 2023-07-31
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+ has unified operations and access for European NSCs by:
1. Transforming the fragmented access model of European NSCs into a central facility and supporting 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.
SYNTHESYS+ has unified operations and access for European NSCs by:
1. Transforming the fragmented access model of European NSCs into a central facility and supporting 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 has harmonised, grouped and disseminated policies and best practices adopted by European NSCs. Deliverables include a toolkit for NSCs to self-assess digital collections policies, a fully functional dashboard providing a dynamic window on NSCs, and a catalogue with recommendations for development of training programmes.
NA3 has developed, implemented and disseminated standardised best practices to support sequencing and biobanking activities including specimen collection, preservation methods, sample retrieval, material request and shipment, emergency plans, safety and security, data standards and policies. NA3 publications describe policy aspects of material handling that require compliance with existing laws and regulations, and contain a standardised system of naming and semantically defining legal and contractual terms associated with using biodiversity collections.
NA4 has provided 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) constructed. Publications include a handbook on identifier management for curators serving as a guideline to collections managers on stable identifiers for physical specimens, and an implementation manual for the International Image Interoperability Framework (IIIF) identifiers in the community.
NA5 activities have brought major international stakeholders together to help develop the global collections research agenda. Consultations have reinforced the wide international interest in increased standardisation and collaboration on NSC data. To expand geographic involvement, regional support staff have worked in SE Asia to increase regional biodiversity data availability, strengthen regional capacity, develop skills in biodiversity data mobilisation, and facilitate exchange of guidance, best practices and expertise. Services have been aligned with the Catalogue of Life (CoL) and partner biodiversity data initiatives (CoL+) and the European Environmental Agency.
Joint Research Activities (JRA):
JRA1 has developed an integrated European Loans and Visits System (ELViS) to support access applications to NSCs and has been in production for 2 Virtual Access (VA) calls and 2 Trans-national Access (TA) calls, used by >1,300 researchers to date. Besides providing the novel workflow implementation for digitisation on demand, ELViS provides descriptions of NSCs and their (227) research and digitisation facilities for which access can be requested, as well as a workflow that allows communication between different stakeholders.
JRA2 has enhanced technical infrastructure and institutional capacity to undertake Collection on Demand requests. Data pipelines and standard workflows have been developed to enable online access to complex digital content such as micro-CT datasets, and datasets derived by several imaging techniques (micro-CT, surface scanning, photogrammetry, photo-stacking, multispectral imaging). Published reports include cost models for digitisation on demand, and identification of successful, cost effective and scalable laboratory workflows for DNA specimens recovered from NSCs, which can be applied in future to develop feasible and routine Sequencing on Demand services.
JRA3 has developed 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. Reports have been published gathering data on associated AI technologies, summarising tools and services development, and describing how the SDR integrates with wider architecture plus approaches to documentation and evaluation.
JRA4 has provided the digitisation services provided through the SYNTHESYS+ VA. VA coordinators appointed by each participating institution have supported digitisation requests and facilitated digital access, and teams of digitisers, data managers and curators have worked together to provide digital content for 10 high priority research projects.
Access:
Despite coinciding with European-wide COVID lockdowns, 4 calls for Trans-national Access (TA) were held, resulting in 6,464 days of researcher access to 21 SYNTHESYS+ NSCs in 13 countries, resulting in >1,000 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. Two VA calls took place resulting in 62 digitisation requests of which 10 were prioritised for funding. Over 215,500 specimens have now been digitised on behalf of the user community.
NA2 has harmonised, grouped and disseminated policies and best practices adopted by European NSCs. Deliverables include a toolkit for NSCs to self-assess digital collections policies, a fully functional dashboard providing a dynamic window on NSCs, and a catalogue with recommendations for development of training programmes.
NA3 has developed, implemented and disseminated standardised best practices to support sequencing and biobanking activities including specimen collection, preservation methods, sample retrieval, material request and shipment, emergency plans, safety and security, data standards and policies. NA3 publications describe policy aspects of material handling that require compliance with existing laws and regulations, and contain a standardised system of naming and semantically defining legal and contractual terms associated with using biodiversity collections.
NA4 has provided 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) constructed. Publications include a handbook on identifier management for curators serving as a guideline to collections managers on stable identifiers for physical specimens, and an implementation manual for the International Image Interoperability Framework (IIIF) identifiers in the community.
NA5 activities have brought major international stakeholders together to help develop the global collections research agenda. Consultations have reinforced the wide international interest in increased standardisation and collaboration on NSC data. To expand geographic involvement, regional support staff have worked in SE Asia to increase regional biodiversity data availability, strengthen regional capacity, develop skills in biodiversity data mobilisation, and facilitate exchange of guidance, best practices and expertise. Services have been aligned with the Catalogue of Life (CoL) and partner biodiversity data initiatives (CoL+) and the European Environmental Agency.
Joint Research Activities (JRA):
JRA1 has developed an integrated European Loans and Visits System (ELViS) to support access applications to NSCs and has been in production for 2 Virtual Access (VA) calls and 2 Trans-national Access (TA) calls, used by >1,300 researchers to date. Besides providing the novel workflow implementation for digitisation on demand, ELViS provides descriptions of NSCs and their (227) research and digitisation facilities for which access can be requested, as well as a workflow that allows communication between different stakeholders.
JRA2 has enhanced technical infrastructure and institutional capacity to undertake Collection on Demand requests. Data pipelines and standard workflows have been developed to enable online access to complex digital content such as micro-CT datasets, and datasets derived by several imaging techniques (micro-CT, surface scanning, photogrammetry, photo-stacking, multispectral imaging). Published reports include cost models for digitisation on demand, and identification of successful, cost effective and scalable laboratory workflows for DNA specimens recovered from NSCs, which can be applied in future to develop feasible and routine Sequencing on Demand services.
JRA3 has developed 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. Reports have been published gathering data on associated AI technologies, summarising tools and services development, and describing how the SDR integrates with wider architecture plus approaches to documentation and evaluation.
JRA4 has provided the digitisation services provided through the SYNTHESYS+ VA. VA coordinators appointed by each participating institution have supported digitisation requests and facilitated digital access, and teams of digitisers, data managers and curators have worked together to provide digital content for 10 high priority research projects.
Access:
Despite coinciding with European-wide COVID lockdowns, 4 calls for Trans-national Access (TA) were held, resulting in 6,464 days of researcher access to 21 SYNTHESYS+ NSCs in 13 countries, resulting in >1,000 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. Two VA calls took place resulting in 62 digitisation requests of which 10 were prioritised for funding. Over 215,500 specimens have now been digitised on behalf of the user community.
SYNTHESYS+ has successfully unlocked information in NSCs and linked 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+ has broadened the direct beneficiaries of NSCs, both geographically and across disciplines, via the VA and TA pillars of the project. Our ELViS system lowers overheads for NSC users and administrators. Complementary work packages addressed gaps in standards around managing molecular (NA3) and digital (NA4) information. Both have developed a more complete corpus of standards to be incorporated into international organisational policies and practices. A dedicated work package (NA5) has focused 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 have, and continue to, deliver new and improved baseline bio- and geo-diversity data, working with expert hosts to generate and add value to existing collections.
SYNTHESYS+ has acted as a critical transition project for the Distributed System of Scientific Collections (DiSSCo, http://dissco.eu) a pan-European RI on the ESFRI (http://esfri.eu) 2018 roadmap. SYNTHESYS+ has undertaken the groundwork for DiSSCo to migrate a loosely joined network of access providers into an integrated and self-sustainable system of European collections.
SYNTHESYS+ has broadened the direct beneficiaries of NSCs, both geographically and across disciplines, via the VA and TA pillars of the project. Our ELViS system lowers overheads for NSC users and administrators. Complementary work packages addressed gaps in standards around managing molecular (NA3) and digital (NA4) information. Both have developed a more complete corpus of standards to be incorporated into international organisational policies and practices. A dedicated work package (NA5) has focused 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 have, and continue to, deliver new and improved baseline bio- and geo-diversity data, working with expert hosts to generate and add value to existing collections.
SYNTHESYS+ has acted as a critical transition project for the Distributed System of Scientific Collections (DiSSCo, http://dissco.eu) a pan-European RI on the ESFRI (http://esfri.eu) 2018 roadmap. SYNTHESYS+ has undertaken the groundwork for DiSSCo to migrate a loosely joined network of access providers into an integrated and self-sustainable system of European collections.