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Cross-Section Activities

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AnnoSys: A generic annotation system for biodiversity data

The project´s main objective is to exemplarily develop a specification for an annotation data repository for networked and highly complex scientific data. It will be implemented using the example of collection and observation data in the botanic domain provided by the GBIF/BioCase system (currently over 50.8 million data sets, including 15 million data sets from natural history collection objects).

Analogical to the traditional, written annotation of natural history collection objects, e.g. concerning their taxonomic identity, a procedure is established for data available via the internet. This will allow annotations of single data sets as well as mass annotations for sets of collection objects.

Using the example of natural history collection data in the framework of GBIF-Germany the project develops solutions for several cross-domaine and domaine-specific problems and implements them in a pilot system. The issues include:

  • categorisation of annotations
  • access rights, rights of personality and rights of attribution of annotating scientists 
  • quality check
  • reference and linking of annotations
  • conception of a user-friendly system that encourages annotations
  • feedback to the distributed data providers
  • the potential use of the system in ongoing research projects for filtering of useable data from the overall system 
  • in general, the integration of data access on annotation data in the overall system of GBIF, BioCASE and GBIF-Germany.

The project is funded by the DFG.

 Further information: https://annosys.bgbm.fu-berlin.de/ 


BiNHum - Biodiversity Network of the Humboldt-Ring

Access and format of existing digital object data, alignment of established database systems and development of a joint data portal

BiNHum is a joint project of five natural history museums and research collections representing the Humboldt-Ring. These are the State Museums of Natural History Karlsruhe and Stuttgart, the Zoological Research Museum Alexander Koenig in Bonn, the Bavarian Natural History Collections in Munich, and the Botanic Garden and Botanical Museum Berlin-Dahlem.

The three-year project (2012-2015) will enforce collaboration and consolidate collection data of the Humboldt-Ring institutes and their associates by development of a joint data portal and efforts in data mining, standardisation, new data types as 3D images e.g., or data digitized by the sub-project MORPHYLL at the SMNS (DFG support code RO 3250/21, acquisition of ecophysiologically relevant morphometric data of fossil leaves), and data porting to current IT standards.

Additionally, the portal will provide all accessible data to international projects as GBIF.

The implementation of these tasks needs task sharing, so BiNHum is partitioned into four work packages:
WP 1: Coordination, data mining and porting (SMNS, SMNK, University of Ulm),
WP 2: Development of a data portal (ZFMK),
WP 3: Networking and data quality (BGBM),
WP 4: Diversity workbench as virtual environment for BiNHum (SNSB).
 


DiversityMobile – IBF 

The IBF project is based on the development of the Diversity Workbench Framework and will expand the platform by a software application (DiversityMobile) for smartphone and TabletPCs. The approach is to gain biological research data from the field by using a mobile device with GPS functionality and a digital imagery, sound and video option. Several user interfaces for two major biological communities allow biodiversity scientists and ecologists to gather and store monitoring data or complex biological data already in the field. The user interface of the mobile device is interchangeable and give access to taxonomic name, ecological descriptor, and general scientific term presets, and allows for selecting reference points in digitized topographic maps.

The gathered data are transferred to a data repository at the IT-Center of the Bavarian Natural History Collections (SNSB IT-Center) via data synchronisation between the databases involved and are further redistributed to end-users via various types of interfaces. Besides this integrated infrastructure, the data repository hosts schemata and generic interfaces for the data exchange between mobile applications, wrapper installations (ABCD schema) and external applications for data analysis and presentation (see IBF-datasets delivered to GBIF). The complete dataflow and working environment is built up in cooperation between four research groups. In the course of the development, new strategies of complex data access and structuring will be modelled and tested. This especially concerns multiple interrelations between organisms in a temporal and spatial context.

The project is in progress and funded by the Deutsche Forschungsgemeinschaft, Bereich Wissenschaftliche Literaturversorgungs- und Informationssysteme (DFG – LIS), entitled with "Setting up an Information Network on Biological Research Data gained in the Field up to the Sustainable Storage in a Primary Data Repository – IBF".

Lead and partners see homepage
 


DNA Bank Network

The scope of the DNA Bank Network (www.dnabank-network.org) is to facilitate access to genetic resources for biodiversity research. While participating DNA banks can make their well documented samples available via a shared portal scientists can search and order for voucher referenced DNA samples.

Accessible voucher specimens are the only reliable basis to verify the species identity of molecular sequences published in databases such as GenBank, EMBL, DDBJ, or BOLD. Although the deposition of vouchers in public research collection for taxonomic descriptions is general routine an equal diligence in molecular analysis is rather the exception than the rule.

Based on the GBIF/BioCASe concept and IT tools to gather primary biodiversity data from multiple dispersed database sources the Network now provides a unique opportunity to document biospecimens including high resolution images and furthermore to reference derived DNA samples dynamically with analysed specimen. Supplementing software components (DNA Module, ABCDDNA) to manage and transfer DNA sample data has been developed by the DNA Bank Network.

The DNA Bank Network started with four German partners with complementary collections and expertise: the Bavarian State Collection of Zoology, Munich (ZSM), the Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM), the German Collection of Microorganisms and Cell Cultures, Braunschweig (DSMZ), and the Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn.

The Network is currently funded the Deutsche Forschungsgemeinschaft DFG and will be maintained and developed by the partner institutions.

Lead and partners see homepage

 


EDAPHOBASE (GBIF Information System Soil Zoology)

The project (2009-2017, funded by the Federal Ministry of Education and Research of Germany (support codes 01LI0901A and 01LI1301A) further develops a soil zoology information system with comprehensive ecological and taxonomic query mechanisms. Edaphobase is an information system (data warehouse) dealing with the distribution and ecological preferences of soil invertebrates. It serves as a publicly available tool for biodiversity sciences and provides access to distributed collection data as well as data from literature. It is freely accessible via the Internet at http://portal.edaphobase.org.

In cooperation with GBIF-D partners the thematic network “soil zoology” is under development since 2014. This network will present information on ecology and biodiversity not of single taxonomic units but of various species that are commonly found in soil.

Here, in addition to information about the organisms themselves, data on correlated abiotic parameters will be offered as well as information on ecological niches, traits, and community structures. This thematic network within will serve as a repository to collect and make available additional data on organisms at the species level also from non- taxonomic (e.g., environmental) research groups. The thematic network will make accessible this data on a long term basis, e.g. for meta-analyses, taxonomically validated and updated as necessary via the EDIT Platform for Cybertaxonomy.

Lead and partners see homepage
 


 

OpenUp! – Opening Up the Natural History Heritage for Europeana

European natural history museums and botanical gardens hold a large amount of multimedia data in their collections, such as specimen images, movies, and animal sound files, all with a reference to an observation or collection event in nature. The EU-CIP ICT PSP project OpenUp! (2011-2014) mobilizes this multimedia information using existing information networks in the biodiversity research domain like BioCASe and GBIF  and links these networks to the digital library of Europe Europeana – a web portal that provides access to millions of books, paintings, films, museum objects and archival records that have been digitized throughout Europe. The project addresses a number of key issues, namely, technical interoperability, metadata standards, and adaptation of Europeana workflow and harvesting procedures. It also looks at best practices for rights' clearance and IPR management of natural history multimedia. In addition, there will be a multilingual enrichment of metadata to facilitate access by a wide European cultural audience.

Project members have committed to feed at least 1.1 million multimedia objects to Europeana by the end of the project. Once the information pathway from natural history collections and the GBIF/BioCASe networks of biological collections to Europeana is created, additional multimedia objects that will enter the GBIF network will be consistently provided to Europeana even after the end of the project duration in 2014.

Scientific Coordinators:
Dr. Petra Böttinger and Alexa Michel, M.Sc.
Botanic Garden and Botanical Museum Berlin-Dahlem

 

No Updates after 15.05.2014

AnnoSys als Annotationssystem in GBIF integriert

Virtuelles Herbarium Deutschland jetzt online

Das Virtuelle Herbarium Deutschland (http://vh.gbif.de), abgekürzt VH/de, ist ein neues Internet-Portal, das den freien Zugang zu umfangreichen Pflanzensammlungen aus deutschen Herbarien ermöglicht.

BioCASe Provider kann sich nun mit Excel-Dokumenten verbinden

Über den Biological Collection Access Service (BioCASe) werden Millionen Biodiversitätsdaten aus Deutschland an Biodiversitätsnetzwerke geliefert. Neuigkeiten gibt es aus der BioCASe-Entwicklung

Von Fischen bis zu Kleinalgen – kontinuierlicher Datenfluss von der Diversity Workbench zu GBIF

Seit 15 Jahren entwickelt das Datenzentrum am SNSB

 

Deutsche Datenbereitstellung für GBIF: immer auf dem aktuellsten Stand

Biodiversitätsdaten, die aus Deutschland an GBIF geliefert werden

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