Requirement analysis for the DiSSCo research infrastructure

DiSSCo – the Distributed System of Scientific Collections – will mobilise, unify and deliver bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. At present DiSSCo has 115 partners from 21 countries across Europe. The DiSSCo research infrastructure will enable critical new insights from integrated digital data to address some of the world's greatest challenges, such as biodiversity loss, food security and impacts of climate change. A requirement analysis for DiSSCo was conducted to ensure that all of its envisioned future uses are accommodated through a large survey using epic user stories. An epic user story has the following format: As [e.g. scientist] I want to [e.g. map the distribution of a species through time] so that I [e.g. analyse the impact of climate change] for this I need [e.g. all georeferenced specimens records through time] Several consultation rounds within the ICEDIG community resulted in 78 unique user stories that were assigned to one, or more, out of seven recognized stakeholder categories: - Research, - Collection management, - Technical support, - Policy, - Education, - Industry, and - External. Each user story was assessed for the level of collection detail it required; four levels of detail were recognised: Collection, Taxonomic, Storage unit, and Specimen level. Furthermore, it was assessed whether the future envisioned use of digitised natural history collections were possible without the DiSSCo research infrastructure. Subsequently 1243 identified stakeholders were invited to review the DiSSCo user stories through a Survey Monkey questionnaire. Additionally, an invitation for review was posted in several Facebook groups and announced on Twitter. A total of 379 stakeholders responded to the invitation, which led to 85 additional user stories for the envisioned use of the DiSSCo research infrastructure. In order to assess which component of the DiSSCo data flow diagram should facilitate the described user story, all user stories were mapped to the five phases of the DiSSCo Data Management Cycle (DMC), including data: - acquisition, - curation, - publishing, - processing, and - use. At present, the user stories are being analysed and the results will be presented in this symposium

Requirement analysis for the DiSSCo research infrastructure

DiSSCo – the Distributed System of Scientific Collections – will mobilise, unify and deliver bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. At present DiSSCo has 115 partners from 21 countries across Europe. The DiSSCo research infrastructure will enable critical new insights from integrated digital data to address some of the world's greatest challenges, such as biodiversity loss, food security and impacts of climate change. A requirement analysis for DiSSCo was conducted to ensure that all of its envisioned future uses are accommodated through a large survey using epic user stories. An epic user story has the following format: As [e.g. scientist] I want to [e.g. map the distribution of a species through time] so that I [e.g. analyse the impact of climate change] for this I need [e.g. all georeferenced specimens records through time] Several consultation rounds within the ICEDIG community resulted in 78 unique user stories that were assigned to one, or more, out of seven recognized stakeholder categories: - Research, - Collection management, - Technical support, - Policy, - Education, - Industry, and - External. Each user story was assessed for the level of collection detail it required; four levels of detail were recognised: Collection, Taxonomic, Storage unit, and Specimen level. Furthermore, it was assessed whether the future envisioned use of digitised natural history collections were possible without the DiSSCo research infrastructure. Subsequently 1243 identified stakeholders were invited to review the DiSSCo user stories through a Survey Monkey questionnaire. Additionally, an invitation for review was posted in several Facebook groups and announced on Twitter. A total of 379 stakeholders responded to the invitation, which led to 85 additional user stories for the envisioned use of the DiSSCo research infrastructure. In order to assess which component of the DiSSCo data flow diagram should facilitate the described user story, all user stories were mapped to the five phases of the DiSSCo Data Management Cycle (DMC), including data: - acquisition, - curation, - publishing, - processing, and - use. At present, the user stories are being analysed and the results will be presented in this symposium

Traitplasticityseedlingsmosssoil

To assess the plasticity of the morphological traits, we compared the morphological traits based on seedlings from Experiment 2 (grown on soil) with values measured on seedlings in Experiment 1 under contrasting moisture condition

exp_2a_13C_15N_harvest_and_t0_macroinvertebrates

See first tab for informatio

Towards a Global Collection Description Standard

With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'

Traitsandsurvival

Traits assessed in Experiment 2 were used to relate to seedling survival in Experiment 1. This file contains trait data from experiment 2 and seedling survival of seven conifer species in experiment 1 kept under contrasting moisture conditions (Dry, Wet

germination

To assess germination, we introduced seeds to Experiment 1 in the third week, corresponding to the time when pot water contents had stabilized. Three seeds were placed around the seedling of the same species, on the capitulum of a moss individual, using 3 x 140 = 420 seeds in total. Germination was checked twice a week until harvest, 5 weeks later. We considered a seed germinated when the integument had broken and a ‘shoot’ of at least 1 mm had emerged from the seed

Seedlingtraitdataexperiment2

Experiment 2 Morphological traits were assessed independently of Experiment 1. We grew tree seedlings under optimal conditions by planting pre-grown 4 weeks old tree seedlings ( see plant material) into the center of a (10 cm wide) pot, using a density of one seedling per pot. The pots were filled with sterilized organic soil, watered daily and kept under the same glasshouse light and humidity conditions as Experiment 1. Pots were arranged in five replicated blocks. Both the blocks and the pots within a block were randomly moved once a week. For more information on columnheadings see Table 1 in the associated M

Mossgrowth and seedling performance

The file contains growth and survival of seedlings grown on moss in experiment 1 as well as the moss growth itsel

Future Challenges in Digitisation of Private Natural History Collections

Specimens held in private natural history collections form an essential, but often neglected part of the specimens held worldwide in natural history collections. When engaging in regional, national or international initiatives aimed at increasing the accessibility of biodiversity data, it is paramount to include private collections as much and as often as possible. Compared to larger collections in national history institutions, private collections present a unique set of challenges: they are numerous, anonymous, small and diverse in all aspects of collection management. In ICEDIG, a design study for DiSSCo these challenges were tackled in task 2 "Inventory of content and incentives for digitisation of small and private collections" under Workpackage 2 "Inventory of current criteria for prioritization of digitization". First, we need to understand the current state and content of private collections within Europe, to identify and tackle challenges more effectively. While some private collections will duplicate material already held in public collections, many are likely to fill more specialised or unusual niches, relevant to the particular collector(s). At present, there is little evidence about the content of private collections and this needs to be explored. In 2018, a European survey was carried out amongst private collection owners to gain more insight in the volume, scope and degree of digitisation of these collections. Based on this survey, all of the respondents’ collections combined are estimated to contain between 9 and 33 million specimens. This is only the tip of the iceberg for private collections in Europe and underlines the importance of these private collections. Digitisation and sharing collection data are activities that are overall considered important among private collection owners. The survey also showed that for those who have not yet started digitising their collection, the provision of tools and information would be most valuable. These and other highlights of the survey will be presented. In addition, protocols for inventories of private collections will be discussed, as well as ways to keep these up to date. To enhance the inclusion of private collections in Europe’s digitisation efforts, we recognise that we mainly have to focus on the challenges regarding the ‘how’ (work-process), and the sharing of information residing in private collections (including ownership, legal issues, sensitive data). Where necessary, we will also draw attention to the ‘why’ (motivation) of digitisation. A communication strategy aimed at raising awareness about digitisation, offering insight in the practicalities to implement digitisation as well as providing answers to issues related to sharing information, is an essential tool. Elements of a communication strategy to further engage private collection owners will be presented, as will conclusions and recommendations. Finally, digitisation and communication aspects related to private collection owners will need to be tested within the community. Therefore, a pilot project is currently (2018-2019) being carried out in Estonia, Finland and the Netherlands to digitise private collections in a variety of settings. Preliminary results will be presented, zooming in on different approaches to include data from private collections in the overall (research) infrastructures