Chairs

Davorka Hackenberger
Department of Biology, University of Osijek, Croatia
davorka(at)biologija.unios.hr

Jiří Schlaghamerský
Terrestrial Invertebrate Research Group, Department of Botany and Zoology, Faculty of Science, Masaryk University, Czech Republic
jiris(at)sci.muni.cz

Description

Standardised vocabularies and data curation are essential for data comparability and common re-use as well as database credibility. They are thus a prerequisite to all other Action activities. The major goals of WG1 will be the development of peer-review protocols for standardised data vocabularies as well as scientific and data-management quality-assessment procedures. 

• Standardised and well-defined vocabularies and formats for data fields to be covered in the data warehouse will be defined, building from existing data fields and implementing the Essential Biodiversity Variables. 
• A minimum data set will be specified, including taxon, site of occurrence, observation date, observer/source, methodology (what, where, when, who, how), promoting future data identification and re-use. 
• Essential environmental metadata will be defined, otherwise rarely collected within soil biodiversity surveys yet dramatically increasing the value of biodiversity data. 
• Pre-existing hierarchal “authority lists” for spatial-data detail and thematic resolution of qualitative data fields (i.e., soil or habitat types) will be amended, expanded and agreed upon, allowing high data comparability. 
• Harmonisation with European standards will be achieved by agreement with the INSPIRE directive as well as available global standards relevant to soil biodiversity, i.e., FAO guidelines, WRB and ISO standards. 

WG1 works closely with WG2 as well as WG5 to achieve a consensus on all terminologies, proposing thesauri for translation from national vocabularies.

The second main task of WG1 will be to develop procedures and protocols for data quality control, including data-harmonisation based on the standardised vocabularies and formats above. Building from existing procedures, a resource-efficient quality-control workflow will be defined and tested for high error recognition while minimising personal requirements. Both technical and content-oriented quality control will be considered. 

• For necessary final manual quality control, data review boards analogous to journals’ editorial boards will be established.
• Taxonomic review boards will also be established, drawing from Action participants as well as external experts. Building from national and international databases and checklists, they will achieve a consensus on a basic taxonomic backbone and definition of valid species’ nomenclatures. 
• In addition to procedures and review boards geared to quality control prior to data import, procedures and software for data control, curation and correction after import into the data warehouse (WG2) will be reviewed and improved. 

By developing principles for the harmonisation, use and mapping of existing information on soil biodiversity in Europe, the quality of the data will increase the credibility of use by all partners, stakeholders and end-users. 

Intended outcomes

WG1 will provide standardised vocabularies, protocols and checklists for soil-biodiversity data. These will be made available to all data providers, users and stakeholders at European and national levels. (2) The definition of data curation and quality-control processes, establishing viable paths for data correction and harmonizing metadata for individual datasets to comply with overall criteria.

Chairs

Cristina Fiera
Institute of Biology Bucharest, Romanian Academy, Romania
cfiera2013(at)gmail.com

Aino Juslén
Biodiversity Informatics, University of Helsinki, Finland
aino.juslen(at)helsinki.fi

Description

Taxonomists and ecologists in individual European countries as well as several EU projects have been collecting soil biodiversity data for decades. This represents a vast pool of soil biodiversity data throughout Europe, much of which is publically unavailable (“file-drawer” problem). A key goal of WG2 is to identify these data sources as well as to establish the procedures and tools necessary for collecting and integrating past, present and future data in a pan-European data warehouse.

• A major task lies in the identification of existing datasets throughout Europe, their availability as well as degree of digitalisation and formats. Datasets will be evaluated for compliance to vocabularies, available data fields, formats etc. set in WG1. The collection of descriptive and environmental metadata of datasets will be evaluated and ensured. Guidelines for rendering these datasets compatible to a common data warehouse will be developed. 
• A principle task is to develop methodologies for building capacity for digitizing data only available on paper. Training courses and workshops will offer assistance in building digitalisation capacity and use of data-upload software tools. Larger datasets available in digital form will be exemplarily collated by partners having access to them through their networks. These will represent the basis for testing and improving data-upload tools, quality-control procedures (WG1) as well as data evaluation and assessment routines (WG6).

Preparing and importing data to external databases is beyond the range of people’s daily work tasks. Software tools for data upload are currently being developed and tested to ease this task. These tools allow data in various digital formats to be entered to the platform foreseen by the Action. 

• WG2 will test this software for the exemplary data with WG1, evaluate its efficiency and deliver guidance for its further development. During further development of the upload software, stress will therefore be laid on its uncomplicated use to ease time demands placed on data upload. 
• For larger databases allowing a continual future data-upload, Darwin Core data-exchange formats (wrapper software) already in place will be evaluated and further developed. 
• For these software tools, WG2 will also work in close cooperation with WG4 in improving user interfaces. 

A data policy (incl. data-sharing agreement) has been developed prior to the Action. It sets terms-of-use for the data warehouse, describes how data from providers is maintained and curated, and defines an intellectual property rights (IPR) policy offering data providers hierarchical public data-accessibility possibilities for their data, including embargo periods for unpublished data. It has been legally checked and complies with recent EU data-protection legislation. 

• WG2 will evaluate this policy, especially considering EU legal developments regarding data protection and information security, compare it with data policies of other biodiversity databases and provide guidance for its amendment and expansion. 
• During dataset identification, WG2 will assess this data policy with data providers to assure that their IPRs are adequately met. 
• Recommendations for confirming and securing authorship for data providers whose data is utilised by users (i.e., via DOIs) will be given. 

A final data policy will be legally checked for compliance with (inter-)national data-protection legislation.

Intended Outcomes

(1) A catalogue of available datasets across Europe, including (2) guidelines and requirements for harmonizing and rendering these datasets compatible to a pan-European data warehouse. (3) Tested software tools for comfortable data import. (4) A formal, legally checked data policy protecting data providers’ IPRs.

Chairs

Mickaël Hedde
UMR Eco & Sols, INRA Montpellier, France
mickael.hedde(at)versailles.inra.fr

Ryszard Laskowski
Institute of Environmental Sciences, Jagiellonian University Kraków, Poland
ryszard.laskowski(at)uj.edu.pl

Description

Soil biodiversity’s contribution to ecosystem services can be derived from species’ functional traits. A main goal for a future data warehouse is to query, map and assess functional biodiversity derived from trait information of species for which occurrence data is available. A number of Action participants as well as national and international trait databases maintain species’ trait information. A main goal of WG3 is to assess, harmonise and collate available trait data for use in the data warehouse.

WG3 will retrieve trait data from existing databases hosted by Action participants, expanding them where possible. A main task is to harmonise trait data and create a consensus on nomenclature and units, paying careful attention to what has already been learned by leading experts when establishing their own databases and evaluating trait data. Available thesauri for trait data will be brought together, assessed and where necessary expanded and amended.

To map and assess functional biodiversity, a data warehouse must link traits to species, which are linked to field-level biodiversity data. The data-warehouse platform foreseen for the Action is currently developing the software routines to link trait-data to species and to aggregate species occurrence data based on trait information, which can then be used for evaluation and assessment routines. WG3 will evaluate these software modules and produce guidance for further development of software-based biodiversity evaluation and assessment based on trait data. WG3 will work together with WG5 to ensure that the trait data being collated are relevant to the needs of end users. 

Identified trait datasets for relevant species will be exemplarily added to the data warehouse platform to test software routines. WG3 will thereby identify soil organisms possessing key functional traits that can indicate soil ecosystem services, while simultaneously being responsive to drivers of environmental change in different habitats.

Intended Outcomes

(1) A comprehensive catalogue of trait data associated with soil-dwelling species will be provided. (2) Guidelines for how trait data can be directly linked to species in a data warehouse, including how such data is indirectly linked to sites of occurrence, will be developed. (9) Guidelines for how trait data can be made available for query and analysis in the data warehouse and used for assessment tools will be offered.

Chairs

Ismael Navas-Delgado
Khaos Research Group, ITIS Software, University of Malága, Spain
ismael(at)uma.es

Vesna Tunguz
Faculty of Agriculture, University of East Sarajevo, Bosnia & Herzegovina
vesna.tunguz(at)gmail.com

Description

The foreseen pan-European data warehouse will be complex and offer multiple functionalities. The “easy” collection of data, operation of query and data-aggregation routines as well as use of assessment tools requires user-friendly and intuitive interfaces despite data-warehouse complexity. This will determine the database’s success, is key to its adoption and broad use and is therefore of vital importance. The main goal of WG4 is the development of user-friendly and intuitive user interfaces (GUIs) and represents cross-cutting activities to, i.e., WG2, WG3 and WG6. WG4 will ensure that user-friendly interfaces enable combinations of data across taxonomic and functional groups over spatial scales to be easily accessed and evaluated. 

All GUIs of the existing software platform will be assessed and necessary improvements and additions recommended. WG4 will evaluate the data-import software (WG2) and offer recommendations for improvement of its user interface, also considering the suggestions of WG2 for improvements and development of this tool. To ensure that users and stakeholders can easily access information needed for scientific questions, management of soil resources and policy decisions (WG5), WG4 will assess the existing interfaces for queries (filters) and compilation (incl. download) of available data, as well as data-analysis modules. Simulations of improved GUIs (”Mock-ups”) will be drafted.

WG4 will be responsible for regular consultations with all potential users to improve interface quality and easiness of use. WG4 will work closely with the software developers employed by the Action participants to guarantee coherence between interface construction and underlying data-manipulation and -analysis routines. In all GUIs, emphasis will be placed on intuitive use, striving to integrate different understandings and mentalities of Action participants. Training courses will assist in the usage of the data warehouse and its tools, providing important input for improving the GUIs.

Intended Outcomes

(1) A catalogue of recommendations and sample solutions for changes in existing software-user interfaces as well as new interfaces developed. (2) Mock-ups of potential GUIs with explanations of how biologically or policy oriented users view and approach these interfaces will be prepared. (3) Ontologies for Edaphobase’s vocabularies and data fields will be developed, allowing better networking linkages with other databases and software tools.

Chairs

Marjetka Suhadolc
Department of Agronomy, University of Ljubljana, Slovenia
Marjetka.Suhadolc(at)bf.uni-lj.si

Stephan Jänsch
ECT Oekotoxikologie GmbH, Germany
s-jaensch(at)ect.de

Description

The added value of a pan-European data warehouse lies in its use for applied purposes, i.e. for national and EU soil-management and -protection goals, as well as basic science. The sustainability of the data warehouse will also depend on its acceptability and use by local, national and European agencies and end users. The goal of WG5 is to involve stakeholders and end users in the development of the data warehouse and its tools, securing its adaptation to stakeholders’ needs.

A first task of WG5 will be to involve agencies, stakeholders and other potential end-users at national and EU levels involved in soil biodiversity and/or soil management and protection. WG5 will develop a questionnaire to determine stakeholders’ and end-users’ needs for soil-management and –protection tasks as well as for biodiversity issues. Stress will be placed on how a pan-European data warehouse can help with their individual tasks, rather than how they can help soil biodiversity research. The survey will help determine, i.e., 1) data evaluation and usage needs; 2) conditions and requirements for sharing data collected, i.e., in state-run monitoring programs; as well as 3) the possibilities, constraints and particularities of stakeholders and national agencies concerning international cooperation.

Stakeholder and end-user involvement will guide identification of data availability (WG2 & WG6) as well as development of data-collection, data-evaluation and assessment routines (WG6), including the GUIs for their “easy” use (WG5). Users and stakeholders will be invited as ad hoc participants to ensure broad adoption of the data warehouse and its tools. Workshops with stakeholders and end users will guide development of the pan-European data warehouse. Training courses with this user group will assist in the use of the data warehouse and its tools. Courses will be in open access format, including invitation of the media for broader coverage and increasing awareness of the general public.

Intended Outcomes

(1) A catalogue of relevant local, national and European agencies, including contact information and analyses of their pragmatic interests and needs. (2) Associated lists of data availability, data and assessment needs. (3) Requirements and conditions for cooperation with national and European agencies.

Chairs

Marko Debeljak
Department of Knowledge Technologies, Jozef Stefan Institute, Slovenia
marko.debeljak(at)ijs.si

Andrey Zaytsev
Department of Animal Ecology, Justus-Liebig-University Giessen, Germany
andrey.zaytsev(at)allzool.bio.uni-giessen.de

Description

EU Directives guiding the development of assessment and decision-making support tools of the data warehouse have different requirements. The definition of biodiversity baselines and thresholds for comparison within monitoring studies are needed for directives requiring the determination of impacts on, or minimizing risks to biodiversity, soil quality and/or the environment in general (i.e., many “industrial” and “agricultural” directives). Directives not explicitly mentioning soil biodiversity and functions, but stressing soil conditions and concentrations of specific elements influenced by biotically driven processes (i.e., Nitrate Directive) or explicitly stating protection of soil functions and ESS (i.e., CAP) require a functional biodiversity approach (WG3). Many directives demand monitoring and/or corresponding databases, for which the data warehouse can serve. WG6 will work together closely with WG5 to ensure that the data-evaluation tools of the warehouse will be tailored to the needs of end-users. The key goals of WG6 are to determine which results assessment tools must offer stakeholders, to secure the corresponding data linkages within the data warehouse and to establish software algorithms needed for developing assessment tools.

WG6 will determine how data can be analysed and visualised to meet these needs. As the spatial coverage of soil biodiversity data is patchy, determining baselines and thresholds must derive the potential soil biodiversity from existing data and environmental metadata. The data available in the warehouse for developing appropriate assessment tools will be evaluated and tested with modelling techniques such as general dissimilarity modelling, regression and classification techniques and will be focussed on GIS methodologies. Working together with WG3 (Traits), WG6 will evaluate how species groups can be aggregated by specific traits to determine potential functional biodiversity using the aforementioned methodologies. For functional relationships, correlation methods relating the distribution of functional groups with, i.e., N- and C-content of soils, greenhouse-gas emissions, etc. (available from national and European agencies) will be evaluated. A major task of WG6 will therefore be on establishing guidelines for how data must be queried (filtered) and assembled and which statistical algorithms are appropriate for allowing automated evaluation and visualisation.

Case studies will be developed to determine the usefulness and applicability of the data in the data warehouse and the suggested evaluation algorithms. Options include a hypothetical ecotoxicological higher-tier assessment of a relevant pesticide, determining reference values/areas for the distribution or abundance of specific organisms at risk, and/or testing performance of a third-tier investigation of a contaminated site, following the TRIAD approach. Other test case studies can relate the distribution of functional soil biodiversity to external distribution information on soil N- and C-content, greenhouse-gas emissions, etc. Further, the provision of background information including temporal trends for Red-List-applications can be tested. The details will be elaborated by WG6 together with WG5.

Intended Outcomes

(1) A register of the results to be delivered by assessment tools will be developed. (2) The necessary algorithms for analysing and visualizing soil-biodiversity data will be compiled. (3) The appropriate correlation procedures for linking the distribution of functional biodiversity with soil and habitat parameters will be defined. (4) Case studies will test the recommended assessment tools.

Chairs

Žaklina Marjanović
Department of Life Sciences, Institute for Multidisciplinary Research, Belgrade University, Republic of Serbia
zaklina(at)yahoo.com

Anne Winding
Department of Environmental Science, Aarhus University, Denmark
aw(at)envs.au.dk

Description

The objectives of this WG are to integrate morphological, ecological and molecular data of soil microorganisms into Edaphobase. This will be achieved in a stepwise manner.

1. We will focus on taxonomic morphological data on fungal fruit bodies and microbial molecular data based on DNA sequencing, i.d. Operational Taxonomic Units (OTU), Sequence Variance etc. at lowest possible taxonomic level (genus level). Functional genes (DNA or RNA) analyses based on the closest match possible. For this, Edaphobase needs taxonomic trees of microorganisms such as bacteria, fungi, archaea, oomycetes, and protists.
2. For analyses of functional traits, Edaphobase has to be modified to have such data included. This can be achieved by including data based on functional analyses such as enzymatic activities, soil respiration, microbial and metabolic quotients, soil microbial biomass and phospholipid fatty acid (PLFA) content. Environmental variables such as pH, nutrient availablity or texture can be easily incorporated in EUdaphobase as well.

Tasks

The existing data have to be standardized in order to match the Edaphobase data model regarding taxonomy and ecological data, while Edaphobase has to be modified to accommodate molecular data. Initially, WG7 will establish and discuss with WG1 standardised and well-defined vocabularies and formats for data fields to be covered in the Edaphobase data warehouse. 

WG7 will specify a minimum data set as described in WG2: Guideline for requesting data for EUdaphobase – draft 2019-11-10.docx and What kind of data does EUdaphobase need.docx, including taxon, i.d. OTU, site of occurrence including soil type and land-use practice, sampling date, soil depth, source, methodology if available (DNA extraction method, sequencing platform, variable region amplified, primers used, other repository where the data are stored such as NCBI), promoting future data identification and re-use. This will include but not be limited to introducing specific attributes/variables in the existing EUdaphobase system. After the integration of microbial molecular data in EUdaphobase, integration and combined analyses of microbial, soil fauna and physical/chemical data will be made possible. 

The second main task of WG7 will be to develop procedures and protocols for data integration. By developing principles for the harmonisation, use and mapping of existing information on soil biodiversity in Europe, the quality of the data will increase the credibility of use by all partners, stakeholders and end-users. An important additional issue to be addressed in WG7 in collaboration with WG1–WG3 is how data from microbiological and soil fauna databases can be integrated, which has never been achieved before. Integration of microbial data already deposited in other databases such as data from UNITE, LUCAS and EU projects as EcoFINDERS should be made possible.

Intended Outcomes

WG7 will (1) provide of standardised vocabularies, protocols and checklists for microbial soil-biodiversity data. These will be made available to all data providers, users and stakeholders at European and national levels. (2) Data quality-control processes for microbial data will be defined, which harmonize metadata for individual datasets to comply with overall criteria.