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NA 3 (SYNTHESYS 3) – Innovation, Impact and sustainability

The overall aim of NA3 is to ensure that SYNTHESYS3 has a clear pathway to impact by making certain that outputs are well publicised to, and utilised by, the broader research and development community – and that the work undertaken and benefits created continue beyond the life of the project. Moreover, the outputs assist in the delivery of other key European initiatives including, but not limited to, LifeWatch.

The overall aim of NA3 is to ensure that SYNTHESYS3 has a clear pathway to impact by making certain that outputs are well-publicised to, and utilised by, the broader research and development community, and that the work undertaken and benefits created continue beyond the life of the project. Moreover, the outputs assist in the delivery of other key European initiatives including, but not limited to, LifeWatch.

NA3 seeks to meet these goals through 3 broad objectives:

  1. Innovation
  2. Impact
  3. Sustainability

Objective 1: Innovation

Participants: NHM (lead), RBGK, RBGE, CSIC, NHMW, RMCA, NMP, VU

Task 1.1 Engagement of Scientific Advisory Board (SAB)

NHMMT will seek opinion and target engagement of external specialists as required to ensure that the work undertaken, particularly the JRA, remains relevant and is utilising the most up-to-date technology available.

Confirmed and potential SAB Members include:

  • Rod Page: Bioinformatician, Uni of Glasgow
  • Gregor Hagedorn: Bioinformatician, Julius Kühn-Institute,
  • Donald Holbern: Exec Sec GBIF
  • Scott Miller: IBOL, Science Steering Cttee member
  • Chris Norris: President of SPNHC
  • Deb Paul: iDigBio, Digitisation and Technology Specialist
  • Sarah Simons: CABI
  • Steve Welch: Knowledge Transfer Network
  • Pieter Holtzhausen: Stellenbosch University

Further members may be co-opted as required during the life of the project.

Task 1.2 Foster relationships with industry and support technological development

Should there be innovation in the wider imaging field that merits further commercial development, NA3 will be responsible for identifying new industrial collaborators to take this forward. The initial step will be to seek advice from the SAB.  Working alongside the JRA, NA3 will support the technological developments of SYNTHESYS3 by gathering User feedback on the application of software, allowing the technology to be further developed to better meet User needs.

Task 1.3 Pilot Study into optimal digitisatoin technologies and equipment

In collaboration with the JRA, a pilot project will review operational aspects of access to new forms of digitised images. The study will seek to identify which digitisation techniques and equipment provide virtual collections that are most suitable to permit research on particular specimens. The pilot will involve gathering data from Participants on their current digitisation facilities and needs, plus a literature review and questionnaire on how their equipment has been used and their successes and challenges. The JRA will undertake further research on the use potential of key digitisation equipment with Participants that currently lack optimal facilities. Results will be fed back to manufacturers where appropriate to be used in their future R&D to develop new tools fit for market. An output of the pilot study will be a digitisation work flow that can support Users/collection managers when requesting/accessing surrogate collections for their research needs. Institutions can also benefit from the results when considering which new equipment to purchase for their infrastructure.

Task 1.4 Pilot study into optimal crowdsourcing processes for NH institutions

In collaboration with the JRA, a two-phase pilot project will be completed. Phase 1 will identify the most appropriate target groups for crowdsourcing. The review will include general public, amateur taxonomists/retired experts and other researchers. It will identify 'Power Users' from current users of collection facilities, and data mine social media for active users with a clear interest in biodiversity. They will then be approached to engage in the crowdsourcing website development and testing. Phase 2 will look at the most appropriate and engaging projects for crowdsourcing. Results will feed into development of the crowdsourcing website (JRA 2.2) and can be used by other NH organisations.

Objective 2: Impact 

Participants: NMP (Lead), NHM, RBGK, MNHN, UCPH, CSIC, NRM, NCB, BGBM, MfN, HNHM, RMCA

Task 2.1 Promotion & Dissemination

This task is concerned with promoting outputs of SYNTHESYS3 within and outside Europe. This includes promotion of CSAT internationally, allowing further adoption in third countries, and promotion of the crowdsourcing website to appropriate stakeholders.  The immediate European NH community will be reached by CETAF and the CPB. Wider dissemination of outputs can be achieved using international networking groups such as SPNHC, TDWG, GBIF and ISBER.

Task 2.2 Improved access to collections and contribution to ERA

Improve access to virtual and new physical collections by making all data outputs freely available and open access. For peer-to-peer use the key portal for specimen data will be GBIF. For a wider audience including the public and media the newly accessible data will be made available on established open access outlets, e.g. Europeana. Working alongside NA2, NH institutions will be enabled to make their DNA barcodes available via EBI (www.ebi.ac.uk/). In addition, DNA, RNA and proteomes will be made available following the best practices of ISBER.

Objective 3: Sustainability 

Participants: NMP (Lead), NHM, RBGK, RBGE, MNHN, UCPH, CSIC, NRM, NCB, BGBM, MfN, NHMW, HNHM, RBINS, RMCA, SGN, SMNS

Task 3.1. Meeting the future needs of Users of NH institutions

In 2008, the EU-funded EDIT project held a symposium on future trends in taxonomy for the 21st century. This will be used as a baseline document and workshop will be held on the sustainability of NH collections, and will result in a roadmap for European NH institutions to progress in a unified manner to meet the changing demands of research.

Task 3.2. Facilitating Access beyond SYNTHESYS3

The improvements to NH virtual collections as a result of improved digitisation methods will, over time, change the face of Access and reduce the need for lengthy physical visits. NH institutions will increasingly be able to send digital surrogates that are of excellent research quality. This new form of access will be of benefit not only to the European research community but also to researchers in Third Countries who wish to undertake collaborative research with European scientists using collections based in Europe. Sustainability of post-project physical access to physical collections will also be progressed, and this requires an intellectual effort and unified approach from Europe’s NH collections-holding institutions.

Task 3.3. Collaboration with iDigBio on training for the future

It is recognised that in order to build a sustainable future for digitisation of NH collections it is critical to collaborate with other large-scale digitisation programmes on training people in new technological advances in digitisation. This task aims to link with the iDigBio programme funded by the National Science Foundation in the USA to prioritise and provide training in these new technologies. A joint workshop with iDigBio will be organised to provide training for digitisation software including that developed in the JRA Task 1.1.

Task 3.4. Sustainable use of SYNTHESYS3 outputs

In order to ensure uptake and a lasting legacy for the outputs of the SYNTHESYS3 project, a range of actions have been identified:

The CETAF Digitisation Working Group were approached and have agreed to maintain the online handbook

  • “Recommendations: Collections Management Policy on Digital Data” which was created within the framework of the NA2, Objective 1, Task 1.1 "Develop policies for virtual CM and integrate JRA outputs". There will be a formal handover once this first version of the handbook is finalised.
  • A series of short videos providing information and instruction on tools and protocols for the digitisation and management of new collections, including the use of the digitisation software developed in the JRA Task 1.1, the use of stable URIs for specimen images and the use of tea-bags for collecting organic material in silica gel for DNA extraction.
  • Discussion with other organisations including CETAF, iDigBio and JSTOR about the development of onlineresources to encourage new audiences for Natural History collections.

Promotion of JRA and NA Outputs (Dels 3.1 & 3.2)

Summary report of NA dissemination activities

Summary report of JRA dissemination activities

Review of optimal digitisation technologies and equipment (Del 3.3, November 2014)

This review summarises some of the main components and underlying issues with respect to digitisation workflows as evidenced from questionnaire responses from SYNTHESYS partners, as well as providing some key recommendations based on these findings.

Summary findings include the prioritisation for collection digitisation, pre-digitisation curation steps, the range of equipment used, imaging standards used, limits to the rates of digitisation and data storage.  This report acknowledges the wide variety of approaches, requirements and equipment needs for natural history specimen collection digitisation, recognising that “a one size fits all” approach is not a viable solution. However, a number of common themes were present throughout all of the responses to the questionnaire, which helped formulate key recommendations.

Read the report in full here.

A digitisation work flow template that can support Users/collection managers when requesting/accessing surrogate collections for their research needs has been developed for the NHM.  More are expected to follow as the project progresses.  View the template work flow here and the appendix here.

Further work on comparison of imaging systems is provided in a report: "Imaging specimens at higher magnification: comparison of imaging systems".  Read the report in full here.

Crowdsourcing reports (Del 3.4, August 2014)

These 2-part reports provide a review of crowdsourcing and citizen science in biodiversity research, and recommendations for developing a crowdsourcing strategy for natural history collections.

Phase 1: Crowdsourcing and Citizen science in biodiversity research

Phase 2: Making molehills out of mountains: crowdsourcing digital access to natural history collections

Sustainability workshop - "Meeting the Future Needs of Users" (Del 3.5, October 2015)

This workshop examined traditional, non-conventional and potential uses and user groups of NH collections with the aim of assessing potential opportunities for use, challenges and limitations, feasibility and benefits of open collections, and promotion of innovative uses and potential new user groups.  Points of discussion and outcomes have been detailed in a meeting report.

European Roadmap (Del 3.6, June 2016)

SYNTHESYS3 project staff reviewed 26 use cases demonstrating use of collections, expertise and services within European Natural History to address a range of societal challenges, in order to build a foundation for a roadmap for a European NH institution access policy. The use cases and research findings can be seen in the deliverable report.

SPNHC Symposium (Del 3.7, June 2016)

SYNTHESYS3 collaborated with iDigBio, GBIF and CETAF to organise 3 days of talks at the 31st Annual meeting of the Society for the Preservation of Natural History. These focused on coordinating efforts to realise global digitisation and data access for biological collections. SPNHC was attended by 300 participants from 31 countries.

Deliverable report.

SYNTHESYS & iDigBio joint workshop: Selected tools for automated metadata capture from specimen images (Del 3.8, June 2016)

This workshop was hosted by BGBM in June 2016 and aimed to deliver practical training and discussion around 3 automated metadata capture tools: Inselect, ABBYY FineReader, and Symbiota.

A summary of the workshop and results of a survey can be read here.

JRA Instruction Videos (Del 3.9, June 2017)

A series of short videos were prepared to provide information and instruction on tools and protocols for digitisation and management of new collections (molecular & digital).

The videos were as follows:

1. Tea-bags for collection organic material in silica gel for DNA extraction

2. Stable URIs for specimen images

3. Digitisation software Inselect

Subtitles in French, Spanish and Portuguese were also developed for video 1., to increase accessibility.

Does digitisation of natural history collections reduce the need for physical access and physical loans? 

Read the report on this SYNTHESYS survey and analysis here.

Improving access to collections: read guidelines on sharing data via four major data aggregators (Europeana, GBIF, EMBL-EBI and ISBER) here.