The Swedish Taxonomy Initative & Biodiversity Infrastructure

The Swedish Species Information Centre (ArtDatabanken, SSIC) at the Swedish University of Agricultural Sciences (SLU) accumulates, analyses and disseminates information concerning Swedish species, habitats and ecosystems. The SSIC hosts the Swedish Taxonomy Initiative (STI) and produces the Swedish Red List. In addition, the SSIC is the leading partner within the Swedish LifeWatch (SLW) consortium, which cooperates with the Biodiversity Atlas Sweden (BAS) and the Living Atlas Community. The SSIC provides an open access biodiversity reporting and analysis infrastructure including for example the Swedish Species Observation System (artportalen.se), the Swedish taxonomic backbone (dyntaxa.se) and tools for species information including traits, terminology and species determination (artfakta.se). All systems, including the SLW Analysis Portal (analysisportal.se), rely on recognized standards to ensure interoperability and consist of databases, API:s and portals. The Artportalen platform now contains >69 000 000 georeferenced observations, along with 1 300 000 images, video or sound, of some 32 000 species from Sweden. The data are harvested by SLW and the Global Biodiversity Information Facility (GBIF). In addition to reports from NGOs and the general public, which generate >90% of the observations, a rapidly increasing number of Swedish governmental authorities and agencies are using the platform to store regional and local species inventories collected by standardized scientific methods. There are sophisticated systems for validation and to secure data quality, and the records are used by scientists as well as by county and municipality councils as a principle biodiversity resource in environmental planning and decision making. Data concerning some species considered to be particularly sensitive to disturbance are classified and not openly available. These data can be accessed via a hierarchy of access levels so as to enable such classified data to available to, for example, environmental officers and to be used in management purposes The SSIC has just launched new API:s, modules for improved reporting of species checklists and invasive species, and a new platform aggregating the services in a single web interface and based on responsive design and specific interfaces for different users (artfakta.se). Improvements are also to be made in the infrastructure of the Swedish taxonomic backbone, which now contains data for almost all Swedish species (more than 275 000 scientific names and 62 000 species). In 2002, when the Swedish Taxonomy Initiative (STI) was established, the SSIC was commissioned by the Swedish Parliament to identify all species of multicellular plants, fungi and animals in the country and to make the information available to scientists, conservationists and the public. The information is presented in the Artfakta platform and in a series of identification handbooks, The Encyclopedia of the Swedish Flora and Fauna. In addition, the STI supports barcoding activities, scientific courses and announces grants for museums and taxonomic research and inventories within poorly known organismal groups. The Swedish and Norwegian taxonomy initiatives work cooperatively to increase the collective knowledge of poorly known species and, as a result, more than 3 000 species new to Sweden and Norway have been found, approximately a third being new to science. The attempt to join forces between different Scandinavian counterparts via technical progress and to focus on digitalization and sharing information on species and communities from the same biogeographical region has proven a successful concept

Finnish Biodiversity Information Facility - Improving the Taxonomic Coverage and Deepening the Information Content Through Collaboration

The Finnish Biodiversity Information Facility FinBIF  (LINK: species.fi), operational since late 2016, is one of the more recent examples of comprehensive, all-inclusive national biodiversity research infrastructures. FinBIF integrates a wide array of biodiversity information approaches under the same umbrella. These include species information Fig. 1 (e.g. descriptions, photos and administrative attributes); citizen science platforms enabling recording, managing and sharing of observation data; an e-learning environment for species identification; management and sharing of restricted data among authorities; building a national DNA barcode reference library and linking it to species occurrence data; community-driven species identification support; large-scale and multi-technology digitisation of natural history collections; and IUCN Red Listing to conduct a periodic national assesment of the status of the threatened species. To improve the taxonomic coverage and the content of species information, FinBIF is starting a process to collaborate with the species information community at large, in order to collate already existing but not yet openly distributed information. This also means digitisation of information from analogue sources. In addition, the attempt is to join forces with Scandinavian counterparts, namely Artdatabanken (LINK: https://www.artdatabanken.se/) and Artsdatabanken (LINK: https://www.artsdatabanken.no/), for more efficient knowledge exchange within the countries sharing the same biogeographical region and thus similar species composition. The aim is also to reach politically high level agreement for deeper and wider commitment to collaborate in compiling, digitising and sharing relevant biodiversity information over the national borders.

Norwegian Taxonomy Initiative & Biodiversity Infrastructure

Norwegian Biodiversity Information centre (NBIC) shares information about Norwegian species, habitats and ecosystems. One of the key tasks is to maintain an updated taxonomical and nomenclatural backbone “Norwegian Taxonomic backbone” (Artsnavnebase) for species. Launched in 2009, the backbone contains more than 185 000 scientific names, as well as 45 000 names in Norwegian (two languages) and Northern Sami. “Norwegian Taxonomic backbone” delivers names and taxonomic information to scientific institutions and museums across the country and is used for both management and research purposes as well as by general public. Additionally, the database has contributed more than 33500 names to the construction of the Global Biodiversity Information Facility (GBIF) taxonomy. Another major task is the Norwegian Taxonomy Initiative (NTI) which was established in 2009 with the goal of improving knowledge about Norwegian biodiversity with special emphasis on poorly known species. In addition, the surveys provide information about distributions of species in Norway and their habitat requirements. NTI collaborates with Norwegian Barcode of Life (NorBOL) and contributes into building up a comprehensive library of standardized DNA sequences (DNA barcodes) and supports research school in biosystematics (ForBio). Swedish and Norwegian taxonomy initiatives work cooperatively to increase the collective knowledge on poorly known species, and as a result, more than 3 000 species new to the country in both Sweden and Norway has been found, of which about a third being new to science. NBIC is in a process of developing and collating a trait database “Trait bank” (Egenskapsbank) for Norwegian species and habitats. Trait bank will describe and combine information about species traits on morphology, physiology and ecology etc. The aim is to also store information about Norwegian habitat types described based on Nature in Norway -system and establish the connections between habitats and species using them. Species trait data relevant for Norwegian species will be extracted from existing databases and other data sources. The first information from this work will be made available through 2020 and is going to be useful for research, conservation and area planning

Practical Examples of Cooperation and of Visualizing Species Information: Species identification and invasive alien species (IAS)

The SLU Swedish Species Information Centre (SSIC, SLU Artdatabanken) accumulates, analyses and disseminates information concerning species and habitats occurring in Sweden. The work is frequently carried out in cooperation with various experts and non-governmental organisations. The SSIC produces the Swedish Red List of threatened species and works on commission by the Government and other authorities within the field of Swedish biodiversity, e.g. risk assessment of invasive alien species (IAS) and the Habitats Directive. Since 2002, when the Swedish Taxonomy Initiative (STI) was established, the SSIC is commissioned by the Swedish Parliament to identify and describe all species of multicellular plants, fungi and animals in Sweden and to make the information available to scientists, conservationists and the public. The SSIC provides an open access biodiversity reporting and analysis infrastructure including for example the Swedish Species Observation System, the Swedish taxonomic backbone Dyntaxa and tools for species information including traits, terminology and species identification (artfakta.se). All systems, including the Swedish LifeWatch (SLW) Analysis Portal, rely on recognized standards to ensure interoperability and consist of databases, APIs and web applications. In addition, the SSIC was the leading partner within the former SLW consortium and now cooperates in the Swedish Biodiversity Data Infrastructure and the Living Atlases Community.In the first example we show what data from Hygrophorus, one of the genera where taxon concepts are mapped within Fennoscandia, is available in the SSIC web applications and hence what kind of data could be shared, based on the ongoing collaboration within the Nordic Taxonomy Initiatives. The Hygrophorus data consists of a identification key, descriptions (characters, distribution, ecology), names & classification, nature conservation lists (for red listed species descriptions of threats, conservation measures and assessments). Furtheremore, there are different classfications for filter functions (e.g. landscape type, habitat, substrate, ecological group, mycorrhiza/symbiosis), an image gallery and observation maps generated from sightings. Most come from Artportalen, which in total contains more than 93,000,000 georeferenced observations, along with 3,000,000 images, videos or sounds of some 37,000 species from Sweden. Observation records are harvested by the national Species Observation System (SOS) (serving, amongst others, the Swedish authorities with data) and by the Global Biodiversity Information Facility (GBIF). The SSIC also offers tool for image-based species identification, collaborating with PlantNet and Artsoraklet/Naturalis.The second example demonstrates the Swedish network and collaboration on invasive alien species (IAS), which is another example of species information of international interest when it comes to sharing and vizualiazing data. In collaboration with the Swedish Environmental Protection Agency (Naturvårdsverket) and the Swedish Agency for Marine and Water Management (Havs- och vattenmyndigheten) a reporting system focusing firstly on the species listed in the IAS Regulation 1143/2014 (EU) has been developed in Sweden (invasivaarter.nu). Here, anyone can report an observation of one of these species, with information on geographic position, date and a photo. This information will be directed to a network of experts verifying both the species identification and the place, if necessary in dialogue with the reporting individual. Once verified occurrence data is published, responsible authorities (often County Administrative Boards, CABs) can carry out field checks and, if necessary, instigate appropriate eradication measures. A digital catalogue of such eradication methods is under development and collaboration between IAS coordinators in regional CABs is being established. The CABs have a separate tool for documentation of eradication measures and since the beginning of this year the complete digital chain is working, from observation to documentation of eradication measures taken. If/when measures are carried out (by CABs) this information is fed back from the CAB-tool into the database in SSIC where it is possible to search for and visualize this information

Linking Fennoscandian Species of Two Fungal Genera: A test case for linked open data

In Norway, Sweden and Finland, we all have our own taxonomy initiatives, mapping our biodiversity (Lahti and Skarp 2019, Sjödin Skarp 2019, Skarp et al. 2019). Together these countries make up most of Fennoscandia, sharing a large part of the fauna, flora and fungi. It was only natural for us to start cooperating through a Nordic Taxonomy Initiative, sharing expertise and knowledge. Our implementation of Linked Open Data (LOD) is a first step toward automated sharing of information about Fennoscandian species. By linking taxon concepts, we can share observations and facilitate our efforts to combat invasive alien species, as well as assessing conservation status of our native species (Liljeblad and Lahti 2019a, Liljeblad and Lahti 2019b).We picked the fungal genera Hygrophorus Fr. and Tricholoma (Fr.) Staude (Basiciomycetes: Agaricales) as test cases for matching species concepts between our countries. We downloaded lists of species from Checklistbank as a starting point, including synonym names and documenting the specific versions. However, the identifiers for these taxa are not independent of name and concept changes here, so this backbone was imported into taxonid.org. A spreadsheet with these taxa was then complemented with taxa from the three respective countries’ taxonomic databases.In Hygrophorus, there were 35 species with 28 present in Finland, 33 in Norway and 34 in Sweden. The mycologists among us discussed the full list during a virtual workshop and agreed upon how to interpret their respective taxonomies compared to the list at taxonid.org. Next, we copied the identifier for each species in taxonid.org to our respective national databases.Matching up all species of Hygrophorus took about 3 hours for 3 people, making for a total of 9 hours of effort excluding things such as exporting and preparing checklists for comparison. Adding the identifiers from taxonid.org into the respective national databases was a simple import of a maximum one hour each. We then did the same for the more species-rich genus Tricholoma.In the process, besides the links, we have established closer personal contact, synced our views on the taxonomy and had a chance to tidy up the nomenclature. When attempting to share more than taxonomic information, we have come to realize how our countries differ in usage of standard terms documenting residency, reproductive status as well as that of establishment means. For now, we will have to make do with a simple absence/presence, but having the actual taxon links is the prerequisite we are now starting to fulfill