Cross-Section Activities

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.

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 (2010-2013, funded by the Federal Ministry of education and Research) will develop a soil zoology information system with comprehensive ecological and taxonomic query mechanisms. The system will serve as a publicly available tool for biodiversity sciences and give access to distributed collection data as well as data from literature.

Lead and partners see homepage

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

12.12.2011