Research Projects

Current projects

Phycobank (Aufbau einer globalen Registration und eines Indexes für Wissenschaftliche Namen und Typen von Algen)

PhycoBank is the registration system for nomenclatural acts (new names, new combinations and types) of algae. Algae are a very diverse group of organisms and are covered by the International Code of Nomenclature for algae, fungi and plants, ICN. PhycoBank will serve both the scientific phycological community and the international open access biodiversity information infrastructures.
 
During its first phase, the project developed a fully functional prototype of an annotation data repository for complex and cross-linked data including back-end server functionality, web services and an on-line user interface. Main objectives of the current project phase are (1) rolling out the software to major biodiversity portals in order to further establish the system and methodology in the domain and to gather user input for improving the interface and procedures. This will include extensions of the types of biodiversity content handled by the system and (2) extending the generic qualities of AnnoSys to further structured data formats including non-XML-based standards with machine readable explicit semantic concepts, and thus opening up the data gathered through AnnoSys for the Semantic Web and Open Data. This will also include the investigation and integration with other annotation systems based on the W3 Open Annotation Community Group standard.
 
The 3-year project (2016-2019) is funded by the LIS-Programme of the German Research Foundation (DFG).

Europeana Digital Service Infrastructure (DSI)

www.Europeana.eu is the cross-domain central portal to Europe’s digitized cultural and scientific heritage. The portal links to almost 50 million of digital objects from Europe’s museums, galleries, archives, libraries and audio-visual collections. Europeana’s vision is to make cultural heritage as easily accessible and as freely reusable as possible. The Europeana DSI project aims to ensure the continued operation of the Europeana Digital Service Infrastructure (DSI) and to facilitate the transition of the Europeana website from a portal to a multi-sided platform, offering a variety of services to data providers, end users and re-users. The Freie Universität Berlin on behalf the OpenUp! network is involved in Work Package 1 focussing on the innovation of the aggregation infrastructure. Key objectives are to make it easier for providers to add their content to the Europeana site; improve the quality of metadata and the quantity of digital objects available; and increase the amount of objects with open licencing conditions.
 
OpenUp! is a growing network of European institutions providing natural history objects to Europeana. This includes digitized specimens, natural history artwork, animal sounds, and videos. The OpenUp! natural history aggregator for Europeana is coordinated by the Freie Universität Berlin, Botanic Garden und Botanical Museum Berlin-Dahlem (BGBM). Collections provide standardised metadata via the BioCASe Provider Software (Biological Collection Access Service) or the GBIF Integrated Publishing Toolkit (IPT), feeding into the aggregation process that includes the harvest, transformation and transfer of metadata to Europeana. During the process scientific metadata items are enriched by literature references, geo names, and common names of plants and animals to increase the accessibility of objects by non-scientific users. So far, 23 partners from 12 European countries take part in the OpenUp! network and contribute 2.2 million records. Data providers benefit from reaching new audiences, increasing web traffic to institutional websites and gaining better visibility towards research funding organizations and within society.
 
The Europeana DSI project is funded under the Connecting Europe Facility (CEF) that supports trans-European networks and infrastructures in the sectors of transport, telecommunications and energy.

German Federation of Biological Data (GFBio) – Phase III

Environmental and biological research is becoming central to major societal challenges related to the Earth’s ecosystems and climate dynamics. To handle the scale and complexity of the scientific questions being addressed, there is a strong need to integrate knowledge because biological data are currently scattered and difficult to share. We propose here a coherent infrastructure to improve scientific data integration and preservation.
 
The project brings together national key players providing environmentally related biological data and services to develop the ‘German Federation of Biological Data’ (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research. The federation will build on proven data archiving infrastructures and workflows such as those of PANGAEA for environmental data and the resources of Germany's major natural history collection data repositories. The new infrastructure will improve and integrate these existing components within a common technological and organizational framework.
 
The infrastructure will addresses data management requirements of a large range of stakeholders including individual scientists, natural history collections as well as larger research networks. It will be capable to handle highly interdisciplinary heterogeneous data. Within the current project, special consideration will be given to genome data, ecological and environmental data as well as collection related data. Services provided by the GFBio will cover the full life cycle of research data from field or real time data acquisition to long term archiving and publication as well as analysis and re-use of these data.
 
The BGBM co-leads work package 3 (Data Access and Analyzes).
 
GFBio III (2018 - 2020) is funded by the German research Foundation (DFG).
 

SYNTHESYS, SYNTHESYS-2, SYNTHESYS-3 and SYNTHESYS Plus

SYNTHESYS aims to produce an accessible, integrated European resource for research users in the natural sciences. SYNTHESYS will create a shared, high quality approach to the management, preservation, and access to leading European natural history collections.

A core element in SYNTHESYS is to provide funded researcher visits (Access) to the 390,000,000 specimens housed by SYNTHESYS institutions. In particular, the 4,049,800 type specimens. Alongside the Access, a Joint Research Activity (JRA) aims to improve the quality of and increase access to digital collections and data within natural history institutions by developing virtual collections. Network Activities (NA) will provide enhanced quality and quantity of online collections information to virtual Users and will implement best practice benchmarks in collections care to raise standards and improve accessibility to collections for all physical Users.

The BGBM co-leads work package NA3 (Molecular Collections in the age of genomics - Standards & Processes) and leads task 4.2 (Adoption and development of the CETAF stable identifier framework).

SYNTHESYS Plus is the fourth iteration (1 February 2019 - 31 January 2023) of the SYNTHESYS programme, funded by the European Commission.

EvoBoGa (Pflanzensammlungen Botanischer Gärten: Lebendige Ressourcen für die integrative Evolutionsforschung)

EvoBoGa aims to develop a networked online catalogue for the living collections of participating botanic gardens. The BGBM provides te technical infrastructure which is based on software components developed by GBIF, BioCASe, and GGBN.
 
EvoBoGa  is funded by the German Ministry of Education and Research (2017 - 2019).
 

Permanent online resources

Coordination of the GBIF-D Node System and the Botanical Node

Germany is one of the founding nations of the Global Biodiversity Information Facility (GBIF). Main objective of the GBIF-D project is the focussed collection and mobilisation of suitable data within Germany's research community and natural history collections as well as of the available observation data.

The BGBM is coordinating this 6-partner project to ensure the technical and organisational cohesion of the eight Nodes in the German GBIF system:  

 

•             BGBM Berlin-Dahlem responsible for Coordination

•             DSMZ Braunschweig responsible for Bacteria & Archaea

•             BGBM Berlin-Dahlem responsible for Plants & Protists

•             BSM München responsible for Fungi & Lichens

•             MfN Berlin responsible for Insects

•             ZSM München responsible for Invertebrates II

•             Senckenberg Frankfurt responsible for Invertebrates III

•             ZFMK Bonn responsible for Vertebrates

•             MfN Berlin responsible for Fossils

 

The German Botanical Node of the Global Biodiversity Information Facility has been established at the BGBM in close collaboration with ten German botanical institutions and five other partner institutions as part of the German contribution to GBIF International. It represents all flowering plants, ferns, and mosses and also puts a special accent on algae and protists.The project at the BGBM supports the German botanical community in their efforts to mobilise botanical data using the BioCASE software and to create a German Virtual Herbarium.

 

OpenUp! - Opening up the European Natural History Heritage for EUROPEANA (link is external)

The institutions participating in OpenUp! will provide over one million multimedia objects from the natural history domain to Europeana, the European Virtual Library (www.europeana.eu (link is external)). OpenUp! is complementary to the eContentPlus project Biodiversity Heritage Library Europe, which mobilised digitised literature in the natural history domain. OpenUp! is an initiative of members of the Consortium of European Taxonomic Facilities (CETAF) and several European nodes of the Global Biodiversity Information Facility (GBIF).
The BGBM is responsible for the overall coordination of OpenUp! and provides high-quality herbarium images to the system. 

 

European Distributed Institute of Taxonomy - EDIT (link is external), Platform for Cybertaxonomy

The overall objective of EDIT was to integrate European taxonomic effort within the European Research Area and to build a world leading capacity. EDIT work-package 5 was lead by the BGBM and created the “Internet Platform for Cybertaxonomy”.

The EDIT Platform is an integrated software suite providing tools and support of the entire taxonomic workflow that leads to the creation of taxonomic monographs, checklists, flora and fauna treatments.
The software is further developed, promoted and sustained in the framework of several projects and as a core activity of the BGBM’s Biodiversity Informatics Research Group.

European Distributed Institute of Taxonomy – EDIT Cichorieae examplar group.

In the workpackage "Unifying revisionary taxonomy" of the EDIT project the BGBM created an exemplar site using the EDIT Platform for Cybertaxonomy (link is external). The Cichorieae network (link is external) is sustained by the BGBM’s Asterales Research Group.

DNA Bank Network and Global Genome Biodiversity Network (GGBN)

The Botanic Garden and Botanical Museum Berlin-Dahlem is a founding member and the coordinator of the DNA Bank Network (link is external). The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility (link is external)). It offers a worldwide unique concept based on GBIF and BioCASe (link is external). DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals).
In 2011 the Global Genome Biodiversity Network (link is external) has been founded by the DNA Bank Network, as well as GBIF, Smithsonian Institution, Natural History Museum London, Natural History Museum Denmark and many others. At present more than 29 DNA and tissue banks are GGBN members. The existing data portal of the DNA Bank Network will serve as the data portal for GGBN in the near future. The aim is to provide all available samples from all GGBN partners via this central data portal and to build a knowledge platform on non-human biobanking.
The GGBN/DNA Bank Network data portal is further developed, promoted and sustained in the framework of other projects and as a core activity of the BGBM’s Biodiversity Informatics Research Group.

PESI (link is external) /EU-Nomen

PESI stands for Pan-European Species directories Infrastructure. Authoritative species name registers are not only essential for taxonomy but important for information systems dealing with species of conservation, pest or commercial relevance as well. PESI enhances the quality and reliability of such European registers by integrating community networks of taxonomic experts into a joint work programme.
In the project (2008-2011, funded by the EU under FP7) the BGBM lead the integration of the European Register of Marine Species, Fauna Europaea and Euro+Med Plantbase into a joint information system. The joint PESI infrastructure is maintained with the partners as an activity of the BGBM’s Biodiversity Informatics Group and in projects such as EU-BON.

Digital specimen images at the Herbarium Berolinense (B)

Since 2004, high resolution digital camera equipment is used to produce digital images of herbarium specimens. The digitisation of type specimens and some of the important collections such as the Herbaria Willdenow and Bridel were and are funded by the Andrew W. Mellon foundation in the framework of the Global Plant Initiative.The German Virtual Herbarium is part of the GBIF-D project financed by the Federal Ministry of Research and Education, which also provided the funding for a large scale improvement of the underlying hardware in 2010. Contributing digitisation activities are also taking place as part of the BGBM’s loan system, and have been supported by the Association of Friends of the BGBM. (link is external)

A Biological Collection Access Service for Europe: BioCASE (link is external)

Originally a 35-partner research and development project co-ordinated by the BGBM, starting  Nov. 1, 2001 financed under the EU's 5th Framework Programme, Research Infrastructures until Jan. 31, 2005. Since then, the suit of software and activities in the area of has become one of . The BGBM is responsible for over-all co-ordination and for the development of the access system. The initiative is sustained in the framework of SYNTHESYS, GBIF-D and as a core activity of the BGBM’s Biodiversity Informatics Research Group.