Danish Biodiversity Information Facility Status and Future

“GBIF will do for biodiversity information what the printing press did for the sharing of recorded information during the Renaissance - it will make recorded knowledge the common property of everyone, not just the elect few. Even better, GBIF will do it electronically, so the resource will be dynamic, interactive, and ever-evolving” - GBIF Strategic Plan 2007-2011

Introduction This document outlines the rationale for building a mechanism to provide global and unified internet access to the world's supply of primary scientific data on biodiversity. The document further describes what has been done to engage in such a huge endeavour and in particular Denmark’s current and future role in the Global Biodiversity Information Facility (GBIF1). GBIF carries out its work through a coordinating secretariat and through the concerted efforts of its participants. GBIF participants sign a Memorandum of Understanding (MoU), and Denmark was among the first to sign in 2001. GBIF participants include over 70 countries and international organisations – among the latter the Convention on Biological Diversity, the Consortium for the Barcode of Life, the Catalogue of Life partnership, the Biodiversity Information Standards (TDWG), and the Nordic Gene Bank may be mentioned. The GBIF secretariat is hosted by the University of Copenhagen. The Danish Natural Science Research Council (DNSRC) pays Denmark’s annual contribution to GBIF. Each GBIF participant contributes to the work through a node. DanBIF (Danish Biodiversity Information Facility2) was founded in 2001 as Denmark’s GBIF node. The DanBIF secretariat is housed at the Natural History Museum of Denmark, University of Copenhagen. DanBIF is co-financed by the DNSRC and the Faculty of Science, University of Copenhagen. The current funding period for DanBIF terminates June 30, 2008. The purpose of this document is hence to provide information for DNSRC on the status and future plans of DanBIF.

Rationale Why a Global Biodiversity Information Facility? Global biodiversity is a handy phrase describing the genetic variety and ecological associations for all the species on the Earth. Biodiversity research is, more than most other types of research, dependant on huge amounts of primary data. The simplest primary data needed are of the form “species X was collected or observed on location Y at time Z”. Other types of primary data include genetic data such as DNA sequences and ecological data such as population sizes. The amount of species-level primary data alone is astronomical, countable in the billions. These data are scattered among numerous private and public collections, libraries, research and museum databases, etc., all over the World. The majority of these data are not at present easily accessible. But, as within other fields of science, a digital revolution is taking place through greatly enhanced tools and media for electronic capture, storage and processing of biodiversity data. In parallel, and by the systematic use of databases, the Internet is evolving into a research tool whereby the species-level data may be combined in analyses with data from multiple levels of biological organisation, e.g. molecular or ecological sensor-web data, and with geospatial and climate data. Such an integrated research methodology is needed to solve the increasingly complex research questions taking, for

1 www.gbif.org 2 www.danbif.dk 1 example, a systems-level approach to changes in biodiversity. Finding the right data in the exponentially growing multitude of data (data-mining) is a huge and continuously growing challenge for biodiversity researchers. It is the mission of GBIF to facilitate unified digital access to and global dissemination of primary biodiversity data, so that people from all countries can benefit from the use of the information. At the time of writing (November 20, 2007) 140 million primary biodiversity data are available through the newly launched 2nd version of the GBIF data portal3. GBIFs ambition is to reach the first 1 billion records of primary data by the end of the year 20084. To reach this goal, and thereby becoming the necessary tool for basic and applied biodiversity research, GBIF is strongly dependant on contributions from its participants (Appendix 1). The GBIF secretariat in Copenhagen can do little more than coordinate the efforts of its participants. Each participant of GBIF is obliged to set up a participant node which helps to make biodiversity data from distributed providers available for search and query through the GBIF data portal and to develop tools for analysing these data.

Why a Danish Biodiversity Information Facility? Denmark has a strong biodiversity research tradition, and as a result, a very large body of primary data is available in Danish collections, archives and databases. These include “national data”, i.e., data on organisms living in Denmark, but also “global data” concerning the rest of the World, collected by Danish researchers. The national data are, in addition to being useful for basic research, also needed for managers of natural resources and policy- makers if they want their decisions to be based on results from the most accurate scientific analyses. The global data are similarly useful both for basic and applied research not only in Denmark, but all over the World. The basic goal of DanBIF is to actively contribute to GBIF through the development of easy and unified access to Danish national and global biodiversity data. However, DanBIF has a broader scope. It also provides a forum for Danish biodiversity researchers to meet and inspire one another through international conferences, sponsored by DanBIF, on topical biodiversity themes. The overall functions of DanBIF include: 1) Contributing to the development and operation of GBIF and its IT-infrastructure. 2) Guiding Danish users of biodiversity resources to access and utilise the global network of knowledge and data. 3) Making Danish biodiversity data available for search through the GBIF portal. 4) Organising activities within the Danish research network to facilitate cross-cutting research projects within biodiversity.

Function 1. Contributing to the development and operation of GBIF and its IT infrastructure

Being part of the GBIF network of members GBIF functions through the data provided by members to the GBIF portal, and through their ideas and the recommendations they contribute, including tools for reliable and reproducible data analyses. With its active participation in the GBIF Governing Board and NODES Committee activities, DanBIF plays an important direct role in the operation and development of GBIF.

3 http://data.gbif.org 4 Inaugural speech of the newly appointed director of the GBIF secretariat, Dr. Nicolas King, http://www.gbif.org/Stories/STORY1194436774 2 DanBIF is the mechanism by which Denmark coordinates and sustains its global data- sharing activities. The DanBIF secretariat encourages, supports and coordinates the contribution of data by Danish providers, and maintains the required information technology (IT) infrastructure and expertise for this purpose. The secretariat acts as the information gateway between the GBIF network and the Danish biodiversity science community. During the prototype phase of GBIF (2001 through 2006), DanBIF significantly contributed (Appendix 2) to the primary objective of GBIF in building a critical mass of biodiversity data. In doing this, a proof of concept was established for the GBIF data portal. Moving beyond this largely technical vision, the operational phase of GBIF now takes a much more user- focused approach, implementing an enhanced phase, in which GBIF will embody a dynamic worldwide community, able to respond to the needs of both scientific and applied users of biodiversity information. As outlined in the GBIF strategic and operational plans for 2007- 20115, GBIF works to accomplish its goals through three main themes: Content, Informatics and Participation. These themes are reflected in the functions, achievements and future plans of DanBIF. To reach the targets for content, regarding both quantity of records and usefulness through adequate taxonomic, temporal and spatial coverage of data, a new decentralised implementation of GBIF is taking place. Implicit in this decentralised model is a more prominent role for GBIF Nodes, particularly as regards expediting the establishment and consolidation of national, regional, and thematic “BIFs” (biodiversity information facilities) to mirror GBIF activities at more local levels (Appendix 1). This approach will also aid to obtain greater tangible benefits of GBIF at the national and local levels. Future plans for DanBIF include engaging in this decentralisation by: • Mediating the benefits of GBIF by actively promoting and advancing the national scientific and applied use of the GBIF data portal. • Collecting and conveying feedback from stakeholders regarding the portal’s ongoing development of web-services and functionality. • Targeting national data sharing and digitisation efforts to aid in solving specific research questions. DanBIF engages in partnerships with other existing GBIF nodes to exchange knowledge and IT tools6, or to provide GBIF-funded mentoring services7 for the development of new GBIF nodes. A previous mentoring effort concerned Ghana and future plans include Tanzania through the GBIF Capacity Enhancement Programme for Developing Countries8. Future plans for DanBIF include: building a regional "BIF" with the Nordic countries (NordBIN). Plans for concerted efforts in the functional network of NordBIN include: • Combined species inventories including Globally Unique Identifiers (GUIDs) for specimens and names. • Common approach to providing information about species to the Encyclopedia of Life9 and to GBIF Species Banks. • Cooperation on outreach and support through joint efforts in approaching new potential data providers of new data types that are part of larger cross-national thematic networks (e.g. the genebanks). • Sharing of GIS and Web Mapping resources, experiences, and of GIS datasets on topography and administrative layers (county, landscape, roads, lakes...), eco-types, eco- regions, etc.

5 www.gbif.org/GBIF_org/GBIF_Documents/strategic_plans.pdf 6 Poland, Spain, Sweden, US 7 Capacity building, training and transfer of knowledge and IT-tools 8 CEPDEC, www.gbif.org/Stories/STORY1173278313 9 http://eol.org/home.html 3 • Joint feedback to the global GBIF network or the GBIF secretariat on areas such as development of the GBIF data portal and participation in the GBIF campaigns. Campaigns aim to achieve extended societal and scientific benefits with biodiversity data through support of collaborations developing a specific product that meets the needs of a well-defined user group10. In addition to playing an active role in the international work of GBIF, DanBIF collaborates with and contributes to several regional and international biodiversity networks and scientific forums (Appendix 3).

Development and maintenance of the IT infrastructure Approach and objectives The development and maintenance of DanBIF as an advanced electronic access system to biodiversity resources is based on input from 5 areas of investigation and organisation: 1) Organisation of information flow to create and be part of the GBIF information system • Development, implementation, and maintenance of common procedures to network and share collection data across a network of institutional data nodes and collections, including digitisation of information (see Function 3). 2) Collections Metadata Inventory development • Evaluation of existing Danish collections, including those not yet digitised, followed by the creation of an extendible, searchable metadata inventory catalogue, allowing for adequate representation of information. 3) User interface and data indexing • Development of web-based user interfaces. • Creation of a national index of unit-level11 biodiversity data from Danish collections, to be used by GBIF in the new decentralised mode of operation, as well as by newly developed or applied applications from a wide array of national/local science and applied users of biodiversity data. 4) Sustainable and expandable biodiversity information service for Denmark • A new system developed in concert with its users which for the first time enables access to information on Danish and worldwide collection resources in an integrated and concerted way. 5) User needs • The DanBIF network provides a link to hundreds of Danish researchers and other users of biodiversity data and thus constitutes a significant source for feedback on user interests. Expected impacts DanBIF establishes the most comprehensive infrastructure to access unit-level biodiversity data associated with Danish natural history collections; using innovative data exchange techniques and taking into account the requirements of actual users. DanBIF significantly improves the accessibility of unit-level information, thus improving the base for species-level research projects and their short and long-term functional reliability. Furthermore, unit-level information includes a time dimension in addition to the spatial and taxonomic aspects. It can thus directly improve our knowledge of environmental and climatic changes both in Denmark and worldwide. Future plans for DanBIF include: • To build a network of institutional nodes and data nodes with common procedures for sharing collection data in Denmark and across the countries participating in GBIF, overcoming the barriers presented by different levels of IT application, lack of interdisciplinary communication, isolated solutions, and local differences in the

10 www.gbif.org/News/NEWS1168530273 11 Unit-level data are information related to collection objects (physical specimens and observations) in contrast to species information describing general group (taxon) characteristics. 4 organisation of biological collections. • To develop and implement techniques to provide unified access to the distributed information resources with an intuitive user friendly interface, adaptable to different user groups. • Further development and application of the metadata inventory system based on geographical, taxonomic, biogeographical, palaeontological and ecological terminologies and classifications. The system will have an integrated search engine and intuitive user interface supporting a wide array of users with diverse constraints in both hardware and software. • Linking and automated indexing of the distributed online biodiversity resources, thereby overcoming the major obstacles of the heterogeneity of available collection information and the diversity of collection databasing and publishing technologies. • Development and implementation of an operational methodology to increase the production of research results in biodiversity informatics.

Function 2. Guiding Danish users of biodiversity resources to access and utilise the global network of knowledge and data

DanBIF aspires to be the main Danish entrance to the global network of biodiversity knowledge including primary biodiversity data as well as other resources in institutions, organisations, networks, websites etc. In order to achieve this goal DanBIF: • has built a network of contact persons in Denmark. • has developed the DanBIF portal to be a central biodiversity information gateway. • raises awareness in the public, among decision makers and others of the importance of biodiversity research, data and knowledge sharing. • organises conferences and network meetings with focus on biodiversity research and knowledge dissemination (see Function 4). • collaborates with others who work on biodiversity projects, education, and knowledge dissemination.

The DanBIF Community DanBIF has identified basic and applied research institutions in Denmark that will provide biodiversity data to DanBIF and GBIF. In addition, DanBIF is contacting and encouraging new data providers and users within private research companies and industry, governmental agencies and the regions and municipalities. Data users (researchers) and data providers to DanBIF are organised as members of a network. Members are kept informed about DanBIF activities and GBIF developments. Members have the opportunity to meet regularly at conferences and other DanBIF gatherings (see Function 4). In addition to a nationwide data provider network, DanBIF also aims to build a research network contributing to the development of a “biodiversity knowledge synergy forum”. Such a forum may engender cross-disciplinary research in biodiversity subjects, as well as broader use of biodiversity data in basic and applied research, industry, and nature resource management. The DanBIF network currently includes 32 researchers representing 14 institutions12. Members are appointed by DNSRC after nomination from their institutions and are obliged to contribute to the dissemination of knowledge about DanBIF and to assist in providing

12 http://www.danbif.dk/About_DanBIF/fol627402 5 biodiversity datasets to DanBIF and GBIF. The DanBIF circle includes people other than network members (e.g., data providers) who wish to receive news about DanBIF and GBIF activities. Everyone can join the DanBIF circle, and members are not committed in any way. Many circle members act as ambassadors for DanBIF in their scientific community and in broader audiences. The DanBIF circle currently encompasses 127 people in 43 institutions, companies and organisations. Future plans for DanBIF include: identifying and recruiting further potential network and circle members. Hence, in continuation of our previous dealings with biologists in the Danish counties, DanBIF will move forward and try to establish a network of contact persons in the municipalities and the new Environmental Centres, with focus on data providers and data use. Biodiversity data from the national survey programmes (e.g. NOVANA), and other sources are published on the portal “Danish Nature Data”13. DanBIF plans to explore possibilities of data provision from this portal to the GBIF data portal. In the context of e.g. climate change research, fast and global access to biodiversity data from local/regional surveys is important in order to document changes in the distribution of certain species, and the GBIF data portal provides the framework to accomplish this.

The DanBIF Portal and related websites The DanBIF portal14 serves as the main Danish gateway to biodiversity data and knowledge. The portal is public and bilingual (Danish and English). It contains information about DanBIF, links to other Danish and international biodiversity research resources, and news about Danish and international biodiversity research and events. The portal provides services for Danish biodiversity researchers, e.g. mapping services. In addition to the main portal, DanBIF is involved in developing and maintaining several other websites (Appendix 4): • Separate websites for each DanBIF conference. • Naturhistorisk Guide (Natural History Guide). Portal (in Danish) informing the public about natural history organisations, museums, institutions, botanical and zoological gardens, journals and magazines, education, natural history websites, etc. • Danish Biodiversity Research Platform. The Danish Biodiversity Research Platform was erected in the framework of the European Platform for Biodiversity Research Strategy15. • ISOBIS – International School of Biodiversity Sciences. Future plans for DanBIF include: Developing a "tool box" for biodiversity researchers as part of the portal and further developing the portal to inform the broader public of biodiversity subjects.

Raising awareness of the importance of biodiversity research, digitisation and biodiversity data sharing DanBIF uses several means of disseminating knowledge about the work of GBIF and DanBIF. Activities include: • One or two DanBIF newsletters per year, published on the DanBIF portal and announced by email to the DanBIF community, as well as other relevant persons and forums. • Articles in scientific magazines (including popular ones) and the newsletters of relevant scientific communities. • Contact to the press, press releases and articles in newspapers, occasionally radio and TV interviews.

13 Danmarks Naturdata, www.naturdata.dk 14 www.danbif.dk 15 www.epbrs.org/, provides a European arena for three-way discussions between policy, scientific, and funding organisations, contributing to the development of biodiversity research at the national and European levels. 6 • Coverage on relevant websites. • Lectures to scientific forums and exhibitions in, for example, zoological and botanical gardens and museums. Future plans for DanBIF include: further developing the biodiversity exhibition concept with posters and interactive computer shows for display in natural history museums, zoological gardens, etc.

Function 3. Making Danish biodiversity data available for search through the GBIF portal

Mobilising data During its first phase 2001 through 2007, DanBIF has explored and mobilised a considerable number of Danish datasets on national and global biodiversity (Appendix 2 and 5). DanBIF continues to identify datasets and resources and will keep encouraging the data providers to make their datasets available for the benefit of the community through the DanBIF and GBIF network. However, since the most readily accessible datasets have now been made available, securing a steady pipeline of data being digitised and mobilised through the GBIF system is going to require additional funding. DanBIF has taken the first small step in this direction by supporting digitisation of a collection with a small amount of seed money (Appendix 6, DBL freshwater gastropod and mollusc collection). Future plans for DanBIF include: mobilising more collections as useful digital datasets for search and analysis through the GBIF portal. The datasets listed in Appendix 5 and 6 are being cleaned, formatted and georeferenced by DanBIF, in collaboration with the data holders. But an unexplored majority of collections need a major effort in digitisation from scratch16. Digitising all relevant data would be a huge task. Hence, setting priorities for the effort should be clearly based on needs to solve specific research questions. Countries that have already developed long-term plans for digitisation17 recognise that it takes a massive financial investment in manpower and IT-tools, and a substantial contribution of expert knowledge housed by the natural history museums, to digitise collection data for research. DanBIF operates in the intersection between cutting-edge IT- technologies for internet databases and digitisation, biodiversity research, and the collections of observations and specimens. Hence, DanBIF constitutes an optimal infrastructure to handle such a mobilisation of Danish primary biodiversity data. By way of its network of members, DanBIF is in the position to identify research projects in dire need of base-line biodiversity data. Through a recent call for interest to the network, DanBIF received proposals to digitise a number of collections within 4 projects (Appendix 7) during the next 3 years. All proposed projects contribute to casting light on factors impacting current biodiversity on either a national, regional or global scale. Furthermore, two of the projects contribute to the objectives of the Convention on Biological Diversity and GBIF through repatriation of biodiversity data from the Eastern Arc Mountains18 in Tanzania. Provided that DanBIF obtains the proposed funding, it has been agreed that the 4 projects outlined in Appendix 7 will be planned and carried out in close collaboration with the Centre for Macroecology and Evolution, a “Programme of Excellence” (2008-2013, lead by Professor Carsten Rahbek), under the University of Copenhagen. The multi-disciplinary centre applies new cutting-edge modelling tools and novel data for direct testing of

16 Database input of specimen label data, validation of species names, georeferencing of collecting-locality names, pictures of specimens when relevant. 17 Australia, Canada (www.acadiau.ca/whatsnew/newsrelease/2007/herbarium_1feb.html) , Netherlands, Spain and Sweden 18 The Eastern Arc is an old mountain range running along the coast of southern Kenya and Tanzania. 7 hypotheses19 to explain large-scale temporal and spatial distribution patterns of biological diversity on Earth. In a synergistic framework, the centre will elucidate the relative importance of different historical and contemporary factors in shaping the current patterns. This will allow for more precise predictions of the future distribution of diversity, based on developments in land use and climate change as well as the improved management of biological ecosystems, both today and in the future. The models to be applied utilise several groups of data20, for which the DanBIF digitisation projects will contribute important distributional data from selected areas.

Data integration and hosting DanBIF and GBIF aim to provide unified access to biological collection information in Denmark and worldwide. Currently, the knowledge base held in Danish collections is largely under-utilised because its highly distributed, heterogeneous, and complex scientific nature obstructs efficient retrieval. Data integration and networking efforts exist, but functional networks are restricted to the local or institutional level or to narrowly defined biological sub- disciplines. The challenge of data integration lies in connecting larger scale collection networks with single collection databases through the GBIF and subsequently the DanBIF network. To achieve that, DanBIF implements standard semantic interfaces for the data sources to be accessed by the system and provides a solid index for the GBIF domain. Furthermore, in order to facilitate the integration of data islands and orphan datasets21, DanBIF provides data hosting services, assuring at the same time a reliable, uninterrupted connection of these sources to the system. The datasets are physically hosted on central servers at the DanBIF secretariat, while the maintenance and administration of these resources are decentralised through a web-based interface, leaving the control over the information supply in the hands of the information providers.

Facilitating data identification and collection by supplying databases, georeferencing tools, and data cleaning tools For unit-level data identification and integration it is necessary to improve our knowledge of existing collections (metadata) including those which are not yet digitised. The challenge lies in the provision of adequate standardised metadata, which, on the one hand, do not violate the complex and changing scientific22 and political/historical23 concepts involved, but which also allows user-friendly access to the information contained in biological collections. To tackle this, DanBIF has developed a metadata inventory system, initially to be used for identification and classification of collections, but now being expanded with further modules for indexing, search, retrieval and analyses of the metadata. DanBIF is taking an active role in the process of initiating data collection by direct support to those groups holding the data. DanBIF assists by building and setting up efficient database systems, both locally and web-based, for online data registration, involving biological groups like plants, fungi, spiders, beetles and ants. DanBIF assists in the process of data cleaning and georeferencing, and a web-based service for georeferencing of Danish collections, supplying both latitude/longitude information and UTM field code, has been created. DanBIF helps researchers in making their data available online by encouraging, developing and hosting local data portals (see Appendix 4 for full list of services). Future plans for DanBIF include: Publishing a toolbox of services to facilitate digitisation of all types of biodiversity data, including: Databases containing sound data structures for the collection of primary data; databases with taxonomical information for all organism groups;

19 Belonging to categories of ecological, evolutionary and historical (area & climate change) hypotheses 20 Contemporary data on the distribution of species and environmental factors; Contemporary data on environmental factors; Historical climatic data; Historical data on species distributions; Phylogenetic information on species evolutionary history. 21 Usually spreadsheets and lists or singular unconnected desktop databases 22 taxonomy, ecology, palaeontology 23 geography 8 services for easy georeferencing of both old and newly generated records; database tools for assisting in cleaning of older data (thereby making the data fit for modern systems); and guidelines on how to collect older, paper-based information in digitised systems. DanBIFs vision includes becoming the primary place to retrieve information on how to collect, maintain and publish biodiversity data in Denmark by acting as a central resource and service centre for data holders and datasets.

Legal basis and best practice for the common access system within DanBIF and GBIF The provision of data to a common access service implies legal questions of intellectual property rights, copyright, database copyright etc. This is a very complicated area in itself, made even more intricate by the questions on rights about biological materials which have surfaced in connection with the Convention on Biological Diversity. Such legal considerations may present an impediment with respect to data provision for some collection owners. DanBIF will not solve these questions. However, DanBIF will devise common policy guidelines as well as model data access and proposition agreements, which can be used by Danish data nodes and institutions where considered necessary. DanBIF properly credits data providers by retaining intellectual property rights of original data in the hands of originators.

Function 4. Organising activities for a Danish research network to facilitate cross-cutting research projects within biodiversity

Meetings organised by DanBIF serve 1) to make Danish researchers aware of the potential for scientific use of the global data resource made available by GBIF, and 2) as a vehicle by which new, cross-cutting topics and directions in biodiversity may be explored.

Conferences DanBIFs international conferences serve as an important forum for Danish and international biodiversity researchers and other related scientists to share ideas on cutting-edge topics in biodiversity. Until now, 4 conferences on different biodiversity subjects have been arranged, with international experts as speakers and broad, international scientific audiences (Appendix 8). The broad coverage of biodiversity-related subjects on the conferences is in line with the development in GBIF of a broader approach that includes data from a much wider spectrum of sources than just specimens and observational data originating in natural history collections, as well as data that relate to biodiversity at many more levels than the organismic one, from molecular through ecosystem. Creating biodiversity informatics systems that cover the whole range requires much new analysis and synthesis of concepts originating in the various sub-disciplines. The series of DanBIF conferences can be seen as Denmark’s contribution to developing the fully functional phase of GBIF, apart from its intrinsic value in promoting cutting edge science in biodiversity informatics. Future plans for DanBIF include: Continuing the suite of international conference on biodiversity-related themes. Already a further 4 conferences have been planned for the years 2008 to 2011 (Appendix 8). Final remarks The above account shows that DanBIF cannot really be regarded as a project extending from year x to year y, but rather should be seen as a (semi-)permanent infrastructure for biodiversity research in Denmark and elsewhere.

9 DanBIF Budget (excluding overheads) Cost pr. year DKK DanBIF secretariat Salary DanBIF secretariat 4 staff (Manager/International relations; Informatics; Databases and Collections; Public relations, outreach, conferences) 2,000,000 IT infrastructure (hardware, software, training, external support and development) 350,000 Public relations, outreach, conference and travel expenditures 280,000 Total 2,630,000

Cost to complete digitisation Cost pr. projects year DKK DKK Digitisation projects: Tanzania Perching Birds (Project duration 1 year) 325,000 325,000 Tanzania Terrestrial Arthropods (Project duration 3 year) 450,000 1,350,000 Denmark Flora & Fauna (Project duration 3 year) 5,325,000 15,975,000 Greenland Flora & Fauna (Project duration 3 year) 270,000 810,000 Total 6,370,000 18,460,000

TOTAL YEARLY COSTS FOR A DanBIF SECRETARIAT AND A CONTINUOUS DIGITISATION EFFORT IN DENMARK 9,000,000

10 11 12 Appendix 2

Danish datasets made available for search through the GBIF portal (http://data.gbif.org) by DanBIF

Dataset name Institution/company/organisation Number of records The AAU Herbarium Herbarium of the University of 120.728 Database Aarhus Arthropod fauna in christmas KU LIFE 3.491 tree plantations Botanical Museum, Natural History Museum of 46.933 Copenhagen, Mycology Denmark Herbarium Botanical Museum, Natural History Museum of 6.957 Copenhagen, the Lichen Denmark Herbarium Botanical Museum, Natural History Museum of 47.342 Copenhagen, the Phycology Denmark Herbarium Botanical Museum, Natural History Museum of 21.619 Copenhagen, Database of Denmark type specimens Botanical Museum, Denmark, Natural History Museum of 3.299 Database of registrations of Denmark red listed plants Botany registration database Danish amateur botanists 7.939 by Danish botanists Bryotropha (Lepidoptera: Natural History Museum of 9.899 Gelechiidae) in Western Denmark Palaearctic. ConDidact public insect ConDidact 4.085 surveys (danske-dyr.dk), spiders (2004) and butterflies (2005) Crustacea species in ZMUC Natural History Museum of 7.968 Denmark Danish Mycological Society, Danish Mycological Society 80.558 fungal records database Danish waterbugs (Insecta: Natural History Museum of 17.596 Hemiptera-Heteroptera: Denmark & Natural History Gerromorpha + Museum, Aarhus Nepomorpha) Den store paddejagt ("The ConDidact & Friluftsrådet 1.286 great amphibian survey") (2007) Den store sneglejagt ("The ConDidact 2.174 great snail-hunt") (2006) Entomology Department Natural History Museum of 14.472 Collections, ZMUC Denmark Fungal Specimens collected HabitatVision 17.788 by HabitatVision (Jacob Heilmann-Clausen)

13 Fungi on beech (Fagus HabitatVision 5.202 sylvatica) wood, Halland, Sweden Galapagos grasses and University of Aarhus 490 sedges Galathea II, Danish Deep Natural History Museum of 1.825 Sea Expedition 1950-52 Denmark Herbarium Faeroense The Faroese Museum of Natural 12.844 History Marine Benthic Fauna List, Marine Biological Laboratory, 577 Læsø, Denmark Department of Biology, University of Copenhagen MycoKey - online photos MycoKey 3.700 (fungi) Nivå Bay species list, Marine Biological Laboratory, 770 Sjælland, Denmark Department of Biology, University of Copenhagen P. V. Lund collection in Natural History Museum of 88 ZMUC, Copenhagen Denmark Pilularia Globulifera Natural History Museum of 230 distribution map in Denmark Denmark Priest Pot species list, Marine Biological Laboratory, 1.320 Cumbria, Britain Department of Biology, University of Copenhagen Tanzanian Vertebrate Natural History Museum of 24 Collection Denmark The Danish Newt Collection Natural History Museum of 557 Denmark The Danish Royal Veterinary KU LIFE 24.797 and Agricultural University's Arboretum The Fish Collection Natural History Museum of 70.229 Denmark Western Palearctic migrants Natural History Museum of 25.333 in continental Africa Denmark In all: 562.120

14 Appendix 3

Collaborating with and contributing to regional and international biodiversity networks and scientific forums In addition to playing an active role in the international work of GBIF (see Function 1), DanBIF takes part in a number of European or international initiatives: European Network of Biodiversity Information (ENBI, http://www.enbi.info/forums/enbi/index.php) – An EU funded thematic network (2003-2005). DanBIF led a work package about “making biodiversity data in European repositories globally available”. The Biological Collections Access Service for Europe (BioCase, http://www.biocase.org/). – The Natural History Museum of Denmark is regional focal point for BioCASE. The DanBIF Secretariat functions as de facto Danish secretariat for BioCASE, and DanBIF’s network meeting in 2004 was at the same time a Danish BioCASE meeting. Biodiversity Information Standards (TDWG, http://www.tdwg.org/), formerly known as the Taxonomic Database Working Group, is a non-profit scientific and educational association that is affiliated with the International Union of Biological Sciences. TDWG now focuses on the development of standards for the exchange of biological/biodiversity data. DanBIF is an active institutional member of the TDWG international association with the aim to: - Develop, adopt and promote the most suitable standards and guidelines for the recording and exchange of biodiversity data from Danish collections. - Promote the use of international standards through the most appropriate and effective means in Denmark. - Act as a forum for discussion between Danish scientists and the international association. Future plans for DanBIF include: Collaboration/synergy with new and upcoming European and international initiatives such as • LIFEWATCH (http://www.lifewatch.eu/) • SpeciesBase (http://www.speciesbase.org) • Pan-European Species-directories Infrastructure (PESI, no website yet) • Encyclopedia of Life (and http://www.lifewatch.eu/) • Collaboration, knowledge exchange and sharing of benefits in building a functional network of the Nordic countries' GBIF nodes (NordBIN, no website yet) - see Function 1

15 Appendix 4

Data portals and web services developed/hosted by DanBIF

Service Description Address DanBIF The homepage of DanBIF and its http://www.danbif.dk organisation activities, with links to all relevant projects portal and affiliates. DanBIF Websites for the DanBIF conferences. http://www.danbif.dk/conference2002 conference http://www.danbif.dk/conference2004 websites http://www.danbif.dk/conference2006 http://www.danbif.dk/conference2007 http://www.danbif.dk/conference2008 Naturhistorisk Portal to natural history relevant societies, http://www.naturhistoriskguide.dk Guide organisations, groups, etc. Danish Erected in the framework of the European http://www.danbif.dk/bioplatform Biodiversity Platform for Biodiversity Research Research Strategy, aiming to provide a national Platform arena for three-way discussions between policy, scientific and funding organisations. ISOBIS Homepage of International School of http://www.isobis.org Biodiversity Sciences. Fungal DanBIF staff has developed a mapping http://www.svampe.dk/svampefund mapping service for the Danish Mycological service Society online registration database ”Svampefund”. Registrations of fungus observations are plotted dynamically onto maps. Additionally, DanBIF has been involved in developing the method for data input in the same system. The Databases over distributions of http://130.225.211.158/subsaharanaf Copenhagen vertebrates in Sub-Saharan Africa have rica/subsaharan.htm databases of been compiled over more than eleven African years at the Zoological Museum, (will eventually move to another vertebrates University of Copenhagen, through a address, but can then be found via broad collaboration with other institutions DanBIF homepage) and researchers. DanBIF staff has developed the homepage with mapping service. Danish Spider Distribution of Danish spiders. DanBIF (http://130.225.211.158/spidermap/s Catalogue staff has developed the homepage with pidermap.htm mapping service. (will eventually move to another address, but can then be found via DanBIF homepage). Danish A system of databases containing both Not publicly available yet Coleoptera taxonomical and distributional information Catalogue (maps) on Danish coleopteran (beetles), maintained by the coleopterological community in cooperation with coleopterologists from the Natural History Museum of Denmark.

16 Database of Data from a century of Danish bird ringing Not publicly available yet the Danish has recently been published in a Bird Ringing monumental work. DanBIF staff is in Centre close cooperation with the Bird Ringing Centre developing an online searchable version containing all the basic data. Bird registry DanBIF staff has developed an online Not publicly available database registry system, used for digitising bird specimens and registrations in the Natural History Museum of Denmark, Zoological Museum. DanBIF is hosting the system on a local server. Mapping UTM 10 x 10 km squares of Denmark. http://www.danbif.dk/serv/fol823781/ service Many mapping projects of Danish doc991856 Denmark biodiversity are based on the UTM square system. Unfortunately maps with these squares pre-printed are hard to find. DanBIF has developed an online service to find and show the position of the squares in Denmark. Danish Service for finding lat/long and UTM http://www.danbif.dk/serv/fol823781/ Coordinate coordinates for Denmark. In this service doc230971 Finder developed by DanBIF, the user by clicking on a scalable map can get to coordinates in latitude/longitude and UTM square of a position anywhere in Denmark. UTM Denmark has a local aberration regarding http://www.danbif.dk/serv/fol823781/f conversion the UTM system. The border between ol477792) table zone 32 and 33 is positioned through Denmark. This has resulted in the development of a ”corrected” system, where zone 32 was extrapolated to cover all of Denmark, introducing a further level of confusion regarding which system has been used by who. DanBIF is supplying an excel sheet that contains the formula for transforming the extrapolated zone 32 coordinates into the true zone 32/33 coordinates and into the correct latitude/longitude values used by e.g. The GBIF system.

17 Appendix 5

Danish datasets currently being processed by DanBIF for availability through the GBIF portal (http://data.gbif.org)

Dataset name Description Estimated number of records DOFbasen Observation database of Danish 5.000.000 bird recordings, maintained by the Danish Ornithological Society Danish Spider Catalogue Specimens and observations of 20.000 Danish spiders from the Natural History Museum and by the arachnological community Aphids of Fennoscandia Distributional registrations of 9.000 Aphids in Fennoscandia, published by Ole E. Heie in six volumes of Fauna Entomologica Scandinavica Reptile collection at the Database of the reptile specimens 13.000 Zoological Museum, Natural in the Zoological Museum History Museum of Denmark collection, covering about 2/3 of the total reptile specimens Copenhagen Databases of Databases over distributions of 500.000 African vertebrates vertebrates in Sub-Saharan Africa (of these just about 50.000 have been compiled over more are primary observation than eleven years at the Zoological data) Museum, Natural History Museum of Denmark, through a broad collaboration with other institutions and researchers Danish Bird Ringing Centre Registrations of recoveries of birds 100.000 ringed in Denmark or by Danish bird ringers Danish Ants in the collections Database of specimens of ants in 11.000 of the Zoological Museum, the Zoological Museum collections Natural History Museum of Denmark Danish Coleoptera Catalogue Distributional registrations in 11 24.000 zootopographical regions of all Danish Coeloptera Checklist of Danish DanBIF is in the process of 25.000 biodiversity collecting and joining checklists, monographs and databases to form an all-species inventory for Denmark Coleoptera from Djursland Database of Coleoptera, registered 79 as part of master’s thesis, AAU Klaus Hermansen butterfly Database and photos of butterfly 135 database recordings by Klaus Hermansen (Lepidopterological Society, Copenhagen)

18 Appendix 6

Data collection projects initiated by DanBIF

Dataset name Description Estimated number of records Seidenfaden Orchid DanBIF has structured the data input in the 10.000 Database registration of all material from the orchid specialist Gunnar Seidenfaden at the Botanical Museum, Natural History Museum of Denmark. A student has been trained by DanBIF and is now scanning drawings and slides of the specimens. This material will be available online with technical assistance from DanBIF Galathea II, the DanBIF has digitised the specimens 1.825 published recorded and described in the Galathea Project homepage: specimens Reports 1-20. With assistance from DanBIF, http://www.zmuc.dk/inverwe the articles in Galathea Reports relevant to b/Galathea/index.html this has been scanned and transformed into pdf files available online P. V. Lund material DanBIF initiated registration and illustration 88 in the Zoological of a part of the rich P. V. Lund material from Project homepage: Museum, Natural Lagoa Santa in Brazil http://www.zmuc.dk/VerWeb History Museum of /lund/lund_mammals.html Denmark Danish waterbugs in DanBIF has contributed with a volunteer 17.596 the collections of the who has digitised the specimens Zoological Museum, Natural History Museum of Denmark Danish Coleopteran DanBIF has built database structures for 24.000 Catalogue digitising the information previous on paper and contributes with a volunteer who, together with a volunteer from the Coleopteran community, at the moment is digitising the records Danish Spider DanBIF financed a workshop with Danish 20.000 Catalogue arachnologists to discuss and plan how to build a joint database platform for spider registrations Bird registration from The light from lighthouses traps birds that 1030 Danish lighthouses get killed and it has been a long tradition in Denmark to report such dead birds to the Zoological Museum, Natural History Museum of Denmark. This century-long information is currently being digitised by a DanBIF volunteer Danish Ants in the A volunteer supplied and trained by DanBIF, 11.000 collections of the has digitised the specimens of ants in the Zoological Museum, Zoological Museum collections Natural History Museum of Denmark

19 Zoological Museum Amber containing animals. DanBIF has 2.500 amber collection, created a database for registration of the Natural History specimens in the amber collection of the Museum of Denmark Natural History Museum of Denmark, and contributes with a volunteer, who at the moment is digitising the information Danish herbarium at DanBIF has built a database for registration 60.000 KU LIFE (Faculty of of the herbarium specimens of the KU LIFE Life Sciences) herbarium of Danish plants. An employee at LIFE is doing the registration, based on training by DanBIF staff DBL freshwater DanBIF has with a small grant initiated the 20.000 gastropod and digitisation of the freshwater gastropod and mollusc collection mollusc collection at the Mandahl Barth Research Centre for Biodiversity and Health (former Danish Bilharziose Laboratory). The digitisation process and data structure is planned and accomplished in close cooperation with DanBIF staff

20 Appendix 7

Digitisation projects planned by DanBIF for the first years from 2008 onwards.

These projects are DanBIF’s first priorities for digitisation projects and are all connected with analytical research projects which are already ongoing or will start in the near future. The timeline for execution of the digitisation projects will depend on available funds, cf. the budget outline in the main document.

Digitisation project 1: Speciation processes in biodiversity hotspots – Perching Birds of the Eastern Arc Mountains1, Tanzania Professor Jon Fjeldså, Zoological Museum, Natural History Museum of Denmark The Zoological Museum holds a unique collection of tissue samples from birds. Perching Birds (Passeriformes) constitute more than 60% of the World’s bird species. In a large-scale project2 with Genoscope in Paris, The Natural History Museum in Stockholm and The Museum of Vertebrate Zoology at Berkeley University, the Perching Birds’ spatial proliferation on Earth during the past 70 mio. years is being studied. The project investigates the Perching Birds’ evolutionary history, diversity and speciation process, incorporating the data on diversity and distribution patterns in the modelling carried out at the Centre for Macroecology & Evolution. Focus is set on how tropical biodiversity hotspots are correlated with the special conditions that mountain areas such as the Eastern Arc constitute for survival of relict populations of species. Digitisation of approximately 8000 specimens is needed for distributional data. Data also constitute e-vouchers (photos, label data) necessary to document the tissue samples.

Digitisation project 2: Geographic patterns of biological diversity – Terrestrial Arthropods3 of the Eastern Arc Mountains, Tanzania Associate Professors Thomas Pape & Nikolaj Scharff, Zoological Museum, Natural History Museum of Denmark The project aims at launching the first large-scale specimen-level data capture for animals occurring in the Eastern Arc Mountains. Geographic patterns of biological diversity in the Eastern Arc Mountains and their underlying patterns will be studied in the Centre for Macroecology and Evolution. However, distributional data available in museums world-wide are currently limited to low-diverse groups of organisms such as vertebrates and higher plants. Long term inventory work carried out by the Natural History Museum of Denmark since the 1980’ies has made this institution the major depository of birds, snakes, and terrestrial arthropods3 from the Eastern Arc. Unfortunately, very little of this material has been digitally recorded, and overall exceedingly little specimen-level data from the Eastern Arc is currently available through the GBIF portal. The purpose of the present project is to compile at least 50.000 records representing at least 5000 identified animal species of the Eastern Arc, to be entered in the analyses carried out at the Centre for Macroecology & Evolution.

1 The Eastern Arc is an old mountain range running along the coast of southern Kenya and Tanzania. The forests are among the oldest and most stable on the African continent, and the combination of a high fragmentation (natural and man-made), high species-richness, high degree of endemism, and high pressures from an encroaching human population makes a biotic documentation exceedingly appropriate. This ‘inland archipelago’ is rapidly gaining a reputation at least matching that of the Galapagos Islands. New amphibians, reptiles, birds and mammals are being discovered at a surprisingly high rate, including a new genus and new species of primate described as recently as 2005. 2 Danish research component financed by DNSRC 3 The arthropods (phylum Arthropoda) constitute over 90% of the animal kingdom. Terrestrial arthropods include groups such as insects, spiders, scorpions, mites, centipedes and millipedes.

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Digitisation project 3: Distribution of species in Denmark – underlying processes and patterns A wide group of researchers from institutions with natural history collections in Denmark The fauna, flora, and fungi of Denmark are relatively well known, but we know little about WHICH species exist WHERE and WHY. The pattern of species diversity and distributions in Denmark is complicated by the fact that although the country is small it lies in the intersection of three biogeographical zones, the Boreal, the Atlantic and the Continental zones. The basic which-where- why is scientifically interesting in itself, but this knowledge is also an absolute prerequisite for setting priorities for a national strategy for biodiversity4 in the light of both how to deal with possible effects of climate change, and for our obligation to the Convention on Biological Diversity year 2010 target5 of a significant reduction of the current rate of biodiversity loss6. To gain insight into causes and factors influencing the diversity and distribution, historical data held by the Natural History Museum of Denmark are needed. The priority list of groups of organisms to be digitised include higher plants, mosses, hover flies, ground beetles, butterflies and spiders, altogether 755.000 specimens representing 2700 species.

Digitisation project 4: Modelling climate change effects on species distributions and diversity using the flora and fauna data of Greenland A wide group of researchers from the Natural History Museum of Denmark The Natural History Museum of Denmark holds a large and unique collection of zoological and botanical specimens from Greenland. Digitisation of these specimens will provide the base-line data for creating contemporary species distributions in Greenland which are needed by the Centre for Macroecology and Evolution in order to model the effects of climate change on biodiversity. The models will make projections of the effect of climate both backwards and forwards in time. Part of the digitisation process will include extracting the relevant material from its current scattered position in the collections, quantifying the number of specimens to be digitised in that process. The project will enhance the geographical coverage of GBIF-served data. Exceedingly little specimen- level data from Greenland is presently available through the GBIF portal and this should be improved also to meet upcoming needs for data from this area by research projects within the International Polar Year framework7. The priority list of groups of organisms to be digitised include higher plants, mosses, and terrestrial arthropods, altogether 390.000 specimens.

4 National Strategy for Biodiversity hearing, by the Danish Board of Technology at: http://www.tekno.dk/subpage.php3?article=1418&language=dk&category=6&toppic=kategori6 5 http://www.cbd.int/2010-target/default.shtml 6 Biodiversity year 2010 – how do we reach the goals? – by the Danish Board of Technology at: http://www.tekno.dk/subpage.php3?article=1399&language=dk&category=5&toppic=kategori5 7 IPY 2007-2009 see http://www.ipy.org/index.php?/ipy/about/

22 Appendix 8

DanBIF International Conferences

DanBIF has organised a series of conferences on different biodiversity subjects and cutting- edge science with international experts as speakers and broad, international scientific audiences. We have planned a series of six international conferences, one each year from 2006 to 2011, that will strengthen the theoretical basis for developing informatics systems for research in biodiversity.

DanBIF Conference 2002: Conference on Biodiversity Informatics www.danbif.dk/conference2002

DanBIF Conference 2004: Conference on Molecular Biodiversity www.danbif.dk/conference2004

DanBIF Conference 2006: Biodiversity at the Ecosystem Level www.danbif.dk/conference2006

DanBIF Conference 2007: Biodiversity Informatics and the Barcode of Life www.danbif.dk/conference2007

DanBIF Conference 2008: Biodiversity Informatics and Climate Change Impacts on Life www.danbif.dk/conference2008

DanBIF Conference 2009: Biodiversity Informatics and the level of Populations

DanBIF Conference 2010: Biodiversity Informatics and the Origin of Life

DanBIF Conference 2011: Biodiversity Informatics and the Problem of Scale

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