Aufbau und Nutzung des Fachinformationssystems Geologie im Niedersächsischen Bodeninformationssystem NIBIS

Digital data from various scientific fields is stored in separate information systems („FIS geology“, „FIS pedology“, etc.) in the Lower Saxony Geo-Information System NIBIS so that it can be processed and interpreted; this is necessary to meet increasing demand for soil-relevant information for decision-making and planning purposes. The necessary work will be considerably accelerated and its quality improved by setting up and actually using such a tool. A detailed account is given of the Lower Saxony Geo-Information System NIBIS, in particular how the data base is set up and how the NIBIS is used in cases where concrete problems occured.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.