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  • Assessing the socio-economic impact...

  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Walton, Stephanie; Livermore, Laurence; Bánki, Olaf; Cubey, Robert; +66 Authors

    This report reviews the current state-of-the-art applied approaches on automated tools, services and workflows for extracting information from images of natural history specimens and their labels. We consider the potential for repurposing existing tools, including workflow management systems; and areas where more development is required. This paper was written as part of the SYNTHESYS+ project for software development teams and informatics teams working on new software-based approaches to improve mass digitisation of natural history specimens.

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    Research Ideas and Outcomes
    Journal . Article
    License: CC BY
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Research Ideas and Outcomes
    Article . 2020
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Research Ideas and O...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      Research Ideas and Outcomes
      Journal . Article
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      Research Ideas and Outcomes
      Article . 2020
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    Authors: Laurence Livermore; Paul Brack; Ben Scott; Stian Soiland-Reyes; +1 Authors

    Over the past three years, we have been developing the Specimen Data Refinery (SDR) to automate the extraction of data from specimen images as part of the SYNTHESYS project (Walton et al. 2020). The SDR provides an easy to deploy, open source, web-based interface to multiple workflows that enable a user to create new or enhance existing natural history specimen records. The SDR uses the Galaxy workflow platform as the basis for managing data analysis, and where possible, using existing Galaxy community tools and approaches (Jalili et al. 2020, Hardisty et al. 2022). We have developed a library of domain-specific tools including semantic segmentation, optical character recognition, hand-written text recognition, barcode reading and natural language processing. These tools have been designed to work on standardised images of specimens, specifically herbarium sheets, pinned insects and microscope slides. In this presentation, we provide our technical approach in developing the SDR, including the Galaxy workflow platform, application deployment, and tool interoperability, using FAIR digital objects (e.g., RO-Crates and openDigital Specimen objects (Soiland-Reyes et al. 2022, Addink and Hardisty 2020)). We present an evaluation of the tools, including segmentation, text recognition, and others, and the new challenges in using the resulting data from both a technical and social perspective.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hardy, Helen; Knapp, Sandra; Allan, E. Louise; Berger, Frederik; +40 Authors

    The SYNTHESYS consortium has been operational since 2004, and has facilitated physical access by individual researchers to European natural history collections through its Transnational Access programme (TA). For the first time, SYNTHESYS+ will be offering virtual access to collections through digitisation, with two calls for the programme, the first in 2020 and the second in 2021. The Virtual Access (VA) programme is not a direct digital parallel of Transnational Access - proposals for collections digitisation will be prioritised and carried out based on community demand, and data must be made openly available immediately. A key feature of Virtual Access is that, unlike TA, it does not select the researchers to whom access is provided. Because Virtual Access in this way is new to the community and to the collections-holding institutions, the SYNTHESYS+ consortium invited ideas through an Ideas Call, that opened on 7th October 2019 and closed on 22nd November 2019, in order to assess interest and to trial procedures. This report is intended to provide feedback to those who participated in the Ideas Call and to help all applicants to the first SYNTHESYS+Virtual Access Call that will be launched on 20th of February 2020.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hal; MĂ©moires en Sci...arrow_drop_down
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    Research Ideas and Outcomes; ZENODO
    Other literature type . Article . 2020 . Peer-reviewed
    License: CC BY
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    Research Ideas and Outcomes
    Article . 2020
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      Research Ideas and Outcomes; ZENODO
      Other literature type . Article . 2020 . Peer-reviewed
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      Article . 2020
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    Authors: Casino, Ana; Raes, Niels; Addink, Wouter; Woodburn, Matt;

    Natural Science Collections (NSCs) contain specimen-related data from which we extract valuable information for science and policy. Openness of those collections facilitates development of science. Moreover, virtual accessibility to physical containers by means of their digitization will allow an exponential increase in the level of available information. Digitization of collections will allow us to set a comprehensive registry of reliable, accurate, updated, comparable and interconnected information. Equally, the scope of interested potential users will largely expand and so will the different levels of granularity required by researchers, institutions and governmental bodies. Meeting diverse needs entails a special effort in data management and data analysis to extract, digest and present information on a compressed but still precise and objective-oriented format. The Collections Digitisation Dashboard (CDD) underpins such an attempt. The CDD stands as a practical tool that specifically aims to support high-level decisions with a wide coverage of data, by providing a visual, simplified and structured arrangement that will allow discovery of key indicators concerning digitization of bio- and geodiversity collections. The realm of possible approaches to the CDD covers levels of digitization, collection exceptionality, resourceavailability and many others. Still all those different angles need to be aligned and processed at once to provide an overall overview of the status of NSCs in the digitization process and analyse its further development. The CDD is a powerful mechanism to identify priorities, specialisation lines together with regional development, gaps and niches and future capabilities as well, and strengths and weaknesses across collections, institutions, countries and regions. It can perfectly underpin measurable and comparable assessments, with evolution indexes and progress indicators, all under an overarching homogenous approach. The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure, currently in its preparatory phase, is built on top of the largest ever community of collections-related institutions across Europe and anchored on the Consortium of European Taxonomic Facilities (CETAF). It aims to provide a unique virtual access point to NSCs by facilitating a large and massive digitisation effort throughout Europe. Setting up priorities and specialization areas is pivotal to its success. To that end, the DiSSCo CDD will provide a valuation tool to summarize and showcase NSC's digitization status on a first-hand visualization. Different projects and initiatives will contribute, jointly and on a synergetic basis, to the production of the DiSSCo CDD. The ICEDIG project will address its basics features, terms of classification and tiers of information, and will produce a prototype and a set of recommendations on how to better attempt a massive dashboard by collating specific collections-based information and defining global strategic representations. CETAF working groups on collections and digitization will provide the desired homogeneity in describing and capturing the different implementation requirements from the users’ perspectives, which will be complemented by the contributions made under the umbrella of the COST Action MOBILISE. The Action will use networking activities to identify the right standards and policies to enable enlarging the scope of the DiSSCo CDD and its broader implementation by linking to the TDWG criteria and adopted standards. Complementarily, the ELViS platform to be developed under the SYNTHESYS+ project will provide the right virtual environment. Furthermore, SYNTHESYS+ will address the assessment capabilities of the CDD to enable the visual representation becoming a practical assessment mechanism and endow it with a dynamic feature for analysis over the time. The DiSSCo CDD will thus become an instrumental mechanism for decision-taking that will be embedded into the clustering initiative of products and services provided to the EOSCby the ENVRI-FAIR project in the environmental domain.

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    Authors: Walton, Stephanie; Livermore, Laurence; Bánki, Olaf; Cubey, Robert; +10 Authors

    Tools and services evaluation speadsheet

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    ZENODO
    Dataset . 2020
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      ZENODO
      Dataset . 2020
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Smith, Vincent; Gorman, Kristina; Addink, Wouter; Arvanitidis, Christos; +108 Authors

    European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. 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, while fostering the development of new approaches to face urgent societal challenges. SYNTHESYS+ is a fourth iteration of this programme, and represents a step change in the evolution of this community. For the first time SYNTHESYS+ brings together the European branches of the global natural science organisations (GBIF https://www.gbif.org/, TDWG https://www.tdwg.org/, GGBN http://www.ggbn.org/ggbn_portal/ and CETAF https://cetaf.org/) with an unprecedented number of collections, to integrate, innovate and internationalise our efforts within the global scientific collections community. Major new developments addressed by SYNTHESYS+ include the delivery of a new virtual access programme, providing digitisation on demand services to a significantly expanded user community; the construction of a European Loans and Visits System (ELViS) providing, for the first time, a unified gateway to accessing digital, physical and molecular collections; and a new data processing platform (the Specimen Data Refinery), applying cutting edge artificial intelligence to dramatically speed up the digital mobilisation of natural history collections. The activities of SYNTHESYS+ form a critical dependency for DiSSCo - the Distributed System of Scientific Collections (https://dissco.eu/), which is the European Research Infrastructure for natural science collections, under the ESFRI umbrella. DiSSCo will undertake the maintenance and sustainability of SYNTHESYS+ products at the end of the programme.

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    ZENODO; Research Ideas and Outcomes
    Article . Other literature type . 2019 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Woolland, Oliver; Brack, Paul; Soiland-Reyes, Stian; Scott, Ben; +1 Authors

    Specimen Data Refinery (SDR) is a developing platform for automating transcription of specimens from natural history collections (Hardisty et al. 2022). SDR is based on computational workflows and digital twins using FAIR Digital Objects. We show our recent experiences with building SDR using the Galaxy workflow system and combining two FDO methodologies with open digital specimens (openDS) and RO-Crate data packaging. We suggest FDO improvements for incremental building of digital objects in computational workflows. SDR workflows SDR is realised as the workflow system Galaxy (Afgan et al. 2018) with SDR tools installed. An Open Research challenge is that some tools have machine learning models with a commercial licence. This complicates publishing to Galaxy toolshed, however we created Ansible scripts to install equivalent Galaxy servers, including tools and dependencies, accounts and workflows. SDR workflows are published in WorkflowHub as FDOs. We implemented the use case De novo digitization in Galaxy (Brack et al. 2022). Shown in Fig. 1 the workflow steps exchange openDS JSON (Hardisty et al. 2019), for incremental completion of a digital specimen. Initial stages build a template openDS from a CSV with metadata and image references – subsequent analysis completes the rest of the JSON with regions of interest, text digitised from handwriting, and recognized named entities. Galaxy can visualise outputs of each step (Fig. 2), important to make the FDOs understandable by domain experts and to verify accuracy of SDR. We are adding workflows for partial stages, e.g. detection of regions (Livermore and Woolland 2022a) and hand-written text recognition (Livermore and Woolland 2022b), which we'll combine with scalability testing and wider testing by project users. Additional workflows will enhance existing FDOs and use new tools such as barcode detection of museums’ internal identifiers. We are now ready to publish digital specimens as FAIR Digital Objects, with registration into DiSSCO repositories, PID assignment and workflow provenance. However, even at this early stage we have identified several challenges that need to be addressed. FDO lessons We highlight the De novo use case because this workflow is exchanging partial FDOs – openDS objects which are not fully completed and not yet assigned persistent identifiers. openDS schemas are still in development, therefore SDR uses a more flexible JSON schema where only the initial metadata (populated from CSV) are required. Each step validates the partial FDO before passing it to the underlying command line tool. Although workflow steps exchange openDS objects, they cannot be combined in any order. For instance, named entity recognition requires digitised text in the FDO. We can consider these intermediate steps as sub-profiles of an FDO Type. Unlike hierarchical subclasses, these FDO profiles are more like ducktyping. For instance a text detection step may only require the regions key, but semantically there is no requirement for an OpenDSWithText to be a subclass of OpenDSWithRegion, as text also can be transcribed manually without regions. Similarly, we found that some steps can be executed in parallel, but this requires merging of partial FDOs. This can be achieved by combining JSON queries and JSON Schemas, but indicates that it may be more beneficial to have FDO fragments as separate objects. Adding openDS fragment steps would however complicate workflows. Several of our tools process the referenced images, currently https URLs in openDS. We added a caching layer to avoid repeated image downloading, coupled with local file-paths wiring in the workflow. A similar challenge occurs if accessing image data using DOIP, which unlike HTTP, has no caching mechanisms. RO-Crate lessons Galaxy is developing support for importing and exporting Workflow Run Crates, a profile of RO-Crate (Soiland-Reyes et al. 2022b) to captures execution history of a workflow, including its definition and intermediate data (De Geest et al. 2022). SDR is adopting this support to combine openDS FDOs with workflow provenance, as envisioned by Walton et al. (2020). Our prototype de novo workflow returns results as a ZIP file of openDS objects. End-users should also get copies of the referenced images and generated visualisations, along with workflow execution metadata. We are investigating ways to embed the preliminary Galaxy workflow history before the final step, so that this result can be an enriched RO-Crate. Conclusions SDR is an example of machine-assisted construction of FDOs, which highlight the needs for intermediate digital objects that are not yet FDO compliant. The passing of such “local FDOs” is beneficial not just for efficiency and visual inspection, but also to simplify workflow composition of canonical workflow building blocks. At the same time we see that it is insufficient to only pass FDOs as JSON objects, as they also have references to other data such as images, which should not need to be re-downloaded. Further work will investigate the use of RO-Crate as a wrapper of partial FDOs, but this needs to be coupled with more flexible FDO types as profiles, in order to restrict “impossible” ordering of steps depending on particular inner FDO fragments. A distinction needs to be made between open digital specimens that are in “draft” state and those that can be pushed to DiSSCo registries. We are experimenting with changing the SDR components into Canonical Workflow Building Blocks (Soiland-Reyes et al. 2022a) using the Common Workflow Language (Crusoe et al. 2022). This gives flexibility to scalably execute SDR workflows on different compute backends such as HPC or local cluster, without the additional setup of Galaxy servers.

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    Authors: Haston, Elspeth; Chapman, Cat;

    The digitisation standard, MIDS (Minimum Information about a Digital Specimen), has been developed to provide a clear definition for the level of digitisation of the specimens held in natural science collections. The standard comprises three levels of digitisation: Level 1 (Basic) is equivalent to a virtual cabinet or drawer in the collection; Level 2 (Regular) provides information needed for most research; Level 3 (Extended) provides all information on the specimen itself as well as links to associated resources. Level 1 (Basic) is equivalent to a virtual cabinet or drawer in the collection; Level 2 (Regular) provides information needed for most research; Level 3 (Extended) provides all information on the specimen itself as well as links to associated resources. A pre-digitisation Level 0 (Bare) allows for the citation of the specimen and the attachment of additional information. The standard has been developed through the collaboration of people representing digitisation, curation, data management, software development and research. The development has been coordinated within the TDWG MIDS Task Group. The aim has been to develop a standard that will fulfill the needs of those managing digitisation programmes (e.g., estimating costs, priorities) as well as the users of the digitised specimens (e.g., informing potential data users of a collection’s data richness).

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Walton, Stephanie; Livermore, Laurence; Bánki, Olaf; Cubey, Robert; +66 Authors

    This report reviews the current state-of-the-art applied approaches on automated tools, services and workflows for extracting information from images of natural history specimens and their labels. We consider the potential for repurposing existing tools, including workflow management systems; and areas where more development is required. This paper was written as part of the SYNTHESYS+ project for software development teams and informatics teams working on new software-based approaches to improve mass digitisation of natural history specimens.

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    Authors: Laurence Livermore; Paul Brack; Ben Scott; Stian Soiland-Reyes; +1 Authors

    Over the past three years, we have been developing the Specimen Data Refinery (SDR) to automate the extraction of data from specimen images as part of the SYNTHESYS project (Walton et al. 2020). The SDR provides an easy to deploy, open source, web-based interface to multiple workflows that enable a user to create new or enhance existing natural history specimen records. The SDR uses the Galaxy workflow platform as the basis for managing data analysis, and where possible, using existing Galaxy community tools and approaches (Jalili et al. 2020, Hardisty et al. 2022). We have developed a library of domain-specific tools including semantic segmentation, optical character recognition, hand-written text recognition, barcode reading and natural language processing. These tools have been designed to work on standardised images of specimens, specifically herbarium sheets, pinned insects and microscope slides. In this presentation, we provide our technical approach in developing the SDR, including the Galaxy workflow platform, application deployment, and tool interoperability, using FAIR digital objects (e.g., RO-Crates and openDigital Specimen objects (Soiland-Reyes et al. 2022, Addink and Hardisty 2020)). We present an evaluation of the tools, including segmentation, text recognition, and others, and the new challenges in using the resulting data from both a technical and social perspective.

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    Authors: Hardy, Helen; Knapp, Sandra; Allan, E. Louise; Berger, Frederik; +40 Authors

    The SYNTHESYS consortium has been operational since 2004, and has facilitated physical access by individual researchers to European natural history collections through its Transnational Access programme (TA). For the first time, SYNTHESYS+ will be offering virtual access to collections through digitisation, with two calls for the programme, the first in 2020 and the second in 2021. The Virtual Access (VA) programme is not a direct digital parallel of Transnational Access - proposals for collections digitisation will be prioritised and carried out based on community demand, and data must be made openly available immediately. A key feature of Virtual Access is that, unlike TA, it does not select the researchers to whom access is provided. Because Virtual Access in this way is new to the community and to the collections-holding institutions, the SYNTHESYS+ consortium invited ideas through an Ideas Call, that opened on 7th October 2019 and closed on 22nd November 2019, in order to assess interest and to trial procedures. This report is intended to provide feedback to those who participated in the Ideas Call and to help all applicants to the first SYNTHESYS+Virtual Access Call that will be launched on 20th of February 2020.

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    Research Ideas and Outcomes; ZENODO
    Other literature type . Article . 2020 . Peer-reviewed
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    Research Ideas and Outcomes
    Article . 2020
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      Research Ideas and Outcomes; ZENODO
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    Authors: Casino, Ana; Raes, Niels; Addink, Wouter; Woodburn, Matt;

    Natural Science Collections (NSCs) contain specimen-related data from which we extract valuable information for science and policy. Openness of those collections facilitates development of science. Moreover, virtual accessibility to physical containers by means of their digitization will allow an exponential increase in the level of available information. Digitization of collections will allow us to set a comprehensive registry of reliable, accurate, updated, comparable and interconnected information. Equally, the scope of interested potential users will largely expand and so will the different levels of granularity required by researchers, institutions and governmental bodies. Meeting diverse needs entails a special effort in data management and data analysis to extract, digest and present information on a compressed but still precise and objective-oriented format. The Collections Digitisation Dashboard (CDD) underpins such an attempt. The CDD stands as a practical tool that specifically aims to support high-level decisions with a wide coverage of data, by providing a visual, simplified and structured arrangement that will allow discovery of key indicators concerning digitization of bio- and geodiversity collections. The realm of possible approaches to the CDD covers levels of digitization, collection exceptionality, resourceavailability and many others. Still all those different angles need to be aligned and processed at once to provide an overall overview of the status of NSCs in the digitization process and analyse its further development. The CDD is a powerful mechanism to identify priorities, specialisation lines together with regional development, gaps and niches and future capabilities as well, and strengths and weaknesses across collections, institutions, countries and regions. It can perfectly underpin measurable and comparable assessments, with evolution indexes and progress indicators, all under an overarching homogenous approach. The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure, currently in its preparatory phase, is built on top of the largest ever community of collections-related institutions across Europe and anchored on the Consortium of European Taxonomic Facilities (CETAF). It aims to provide a unique virtual access point to NSCs by facilitating a large and massive digitisation effort throughout Europe. Setting up priorities and specialization areas is pivotal to its success. To that end, the DiSSCo CDD will provide a valuation tool to summarize and showcase NSC's digitization status on a first-hand visualization. Different projects and initiatives will contribute, jointly and on a synergetic basis, to the production of the DiSSCo CDD. The ICEDIG project will address its basics features, terms of classification and tiers of information, and will produce a prototype and a set of recommendations on how to better attempt a massive dashboard by collating specific collections-based information and defining global strategic representations. CETAF working groups on collections and digitization will provide the desired homogeneity in describing and capturing the different implementation requirements from the users’ perspectives, which will be complemented by the contributions made under the umbrella of the COST Action MOBILISE. The Action will use networking activities to identify the right standards and policies to enable enlarging the scope of the DiSSCo CDD and its broader implementation by linking to the TDWG criteria and adopted standards. Complementarily, the ELViS platform to be developed under the SYNTHESYS+ project will provide the right virtual environment. Furthermore, SYNTHESYS+ will address the assessment capabilities of the CDD to enable the visual representation becoming a practical assessment mechanism and endow it with a dynamic feature for analysis over the time. The DiSSCo CDD will thus become an instrumental mechanism for decision-taking that will be embedded into the clustering initiative of products and services provided to the EOSCby the ENVRI-FAIR project in the environmental domain.

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