Abteilung Datenbanken Leipzig - Publikationen

Finding Cross Genome Patterns in Annotation Graphs

Mon, 23 Apr 2012 13:55:55 +0200

Benik, J.; Chang, C.; Raschid, L.; Vidal, M. E.; Palma, G.; Thor, A. (2012-06)
DILS 2012 (accepted for publication)

Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where concepts such as genes and proteins are annotated with controlled vocabulary terms from ontologies. Scientists are interested in analyzing or mining these annotations, in synergy with the literature, to discover patterns. Further, annotated datasets provide an avenue for scientists to explore shared annotations across genomes to support cross genome discovery. We present a tool, PAnG (Patterns in Annotation Graphs), that is based on a complementary methodology of graph summarization and dense subgraphs. The elements of a graph summary correspond to a pattern and its visualization can provide an explanation of the underlying

How do Ontology Mappings Change in the Life Sciences?

Mon, 16 Apr 2012 14:58:24 +0200

Groß, A.; Hartung, M.; Thor, A.; Rahm, E. (2012-04)
CoRR abs/1204.2731

Mappings between related ontologies are increasingly used to support data integration and analysis tasks. Changes in the ontologies also require the adaptation of ontology mappings. So far the evolution of ontology mappings has received little attention albeit ontologies change continuously especially in the life sciences. We therefore analyze how mappings between popular life science ontologies evolve for different match algorithms. We also evaluate which semantic ontology changes primarily affect the mappings. We further investigate alternatives to predict or estimate the degree of future mapping changes based on previous ontology and mapping transitions.

Effective Mapping Composition for Biomedical Ontologies

Mon, 07 May 2012 11:01:44 +0200

Hartung, M.; Groß, A.; Kirsten, T.; Rahm, E. (2012-05)
Semantic Interoperability in Medical Informatics @ ESWC 2012

There is an increasing need to interconnect biomedical ontologies. We investigate a simple but promising approach to generate mappings between ontologies by reusing and composing existing mappings across intermediate ontologies. Such an approach is especially promising for highly interconnected ontologies such as in the life science domain. There may be many ontologies that can be used for composition so that the problem arises to find the most suitable ones providing the best results.

COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies

Fri, 11 May 2012 11:51:34 +0200

Hartung, M.; Groß, A.; Rahm, E. (2012-04-10)
Accepted for publication in Journal of Biomedical Informatics

Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management.

Beiträge zur dynamischen Lastbalancierung in parallelen Datenbanksystemen

Fri, 30 Mar 2012 17:36:36 +0200

Märtens, H. (2008)
Dissertation, Univ. Leipzig

Diese Arbeit untersucht ausgewählte Problemstellungen der dynamischen Lastbalancierung
in parallelen Datenbanksystemen (PDBS). Betrachtet wird die möglichst gleichmäßige Verteilung von Arbeitslasten zur Laufzeit komplexer analytischer Anfragen. Das Hauptproblem besteht in der eingeschränkten Vorhersagbarkeit sogenannter Skew-Effekte, die verschiedene Arten von Lastungleichgewichten beschreiben und deren Bekämpfung der Schlüssel zur gleichmäßigen Verteilung und effizienten Abarbeitung von Arbeitslasten ist. In der Arbeit werden sowohl empirische als auch analytische Untersuchungsmethoden angewandt. Der Schwerpunkt der Untersuchung liegt dabei auf sogenannten Shared-Disk-Systemen, die sich durch eine gemeinsame Plattenspeicheranbindung auszeichnen; diese Architekturen haben in früheren Forschungen vergleichsweise wenig Beachtung gefunden. Über die eigentliche Lastverteilung hinaus betrachtet die Arbeit ausgewählte Aspekte der dynamischen Allokation von Zwischenergebnissen komplexer Anfragen.

Event-Oriented Dynamic Adaptation of Workflows: Model, Architecture and Implementation

Fri, 30 Mar 2012 14:59:27 +0200

Müller, R. (2002)
Dissertation, Univ. Leipzig

Workflow management is widely accepted as a core technology to support long-term business processes in heterogeneous and distributed environments. However, conventional workflow management systems do not provide sufficient flexibility support to cope with the broad range of failure situations that may occur during workflow execution. In particular, most systems do not allow to dynamically adapt a workflow due to a failure situation, e.g., to dynamically drop or insert execution steps.

Schnelle Transaktionen: DBMS-Leistungsvergleich mit TPC-Benchmarks

Fri, 30 Mar 2012 14:06:17 +0200

Rahm, E. (1993)
IX

Zur Leistungsbewertung von Datenbank- und Transaktionssystemen ziehen Hersteller häufig
Benchmarks heran. Vergleiche sind jedoch erst mit standardisierten Messungen, wie sie das
Herstellerkonsortium Transaction Processing Council definiert hat, aussagekräftig. Immer mehr Spitzenplätze nehmen Datenbanksysteme unter Unix ein

Evolution and merging of real-life ontologies

Thu, 29 Mar 2012 15:45:28 +0200

Rahm, Erhard (2011-06)
Proc. SEBD Conf. (Invited Talk)

Ontologies are in wide-spread use in diverse domains. In life sciences, many large ontologies are used to annotate biomedical entities and perform analysis tasks such as functional profiling or term enrichment. On the web, simple ontologies such as web directories or product catalogs are heavily used for improved content categorization and search. These ontologies are subject to significant reorganizations and other evolutionary changes. There is thus an increasing need to better deal with ontology evolution, in particular to support the automatic detection of evolution mappings

PAnG - Finding Patterns in Annotation Graphs

Wed, 16 May 2012 16:29:32 +0200

Anderson, P.; Thor, A.; Benik, J.; Raschid, L.; Vidal, M.-E. (2012-05)
SIGMOD 2012 (demo paper)

Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences and health sciences, where concepts of interest such as genes, proteins or clinical trials are annotated with controlled vocabulary terms from multiple ontologies. Scientists are interested in analyzing or mining these annotations, in synergy with the literature, to discover patterns.

Nah gekoppelte Rechnerarchitekturen für ein DB-Sharing-System

Fri, 30 Mar 2012 12:00:15 +0200

Rahm, Erhard (1986)
Proc. Architektur von Rechensystemen (ARCS)

Als DB-Sharing bezeichnet man die gemeinsame Benutzung einer Datenbank durch
Datenbank-Verwaltungssysteme (DBVS) auf einem System lose bzw. nahe gekoppelter
Prozessoren. Das wesentliche Entwurfsziel solcher Mehrrechner-Datenbanksysteme
ist die annähernd lineare Erhöhung des Durchsatzes im Transaktionsbetrieb bei nur wenig verlängerten Antwortzeiten im Vergleich zum 1-Rechner-Fall. Weiterhin wird eine deutliche Verbesserung der Verfügbarkeit des Systems für die DB-Verarbeitung angestrebt.