Workshop

E ffective Mapping Composition for Biomedical Ontologies

Authors: 
Hartung, M.; Gross, A.; Kirsten, T.; Rahm, E.
Year: 
2012
Venue: 
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 fi nd the most suitable ones providing the best results.

Automating Database Schema Evolution in Information System Upgrades

Authors: 
Curino, Carlo; Moon, Hyun J.; Zaniolo, Carlo
Year: 
2009
Venue: 
Hot Topics In Software Upgrade

The complexity, cost, and down-time currently created by the database schema evolution process is the source of incessant problems in the life of information systems and a major stumbling block that prevent graceful upgrades. Furthermore, our studies shows that the serious problems encountered by traditional information systems are now further exacerbated in web information systems and cooperative scientific databases where the frequency of schema changes has increased while tolerance for downtimes has nearly disappeared.

Using annotations from controlled vocabularies to find meaningful associations

Authors: 
W. Lee, L. Raschid, P. Srinivasan, N. H. Shah, D. L. Rubin, N. F. Noy
Year: 
2007
Venue: 
Proc. DILS

This paper presents the LSLink (or Life Science Link) methodology that provides users with a set of tools to explore the rich Web of interconnected and annotated objects in multiple repositories, and to identify meaningful associations. Consider a physical link between objects in two repositories, where each of the objects is annotated with controlled vocabulary (CV) terms from two ontologies. Using a set of LSLink instances generated from a background dataset of knowledge we identify associations between pairs of CV terms that are potentially significant and may lead to new knowledge.

Efficient Management of Biomedical Ontology Versions

Authors: 
Kirsten, T; Hartung, M; Gross, A; Rahm, E
Year: 
2009
Venue: 
4th Intl. Workshop on Ontology Content (Part of the OTM Conferences & Workshops)

Ontologies have become very popular in life sciences and other domains. They mostly undergo continuous changes and new ontology versions are frequently released. However, current analysis studies do not consider the ontology changes reflected in different versions but typically limit themselves to a specific ontology version which may quickly become obsolete. To allow applications easy access to different ontology versions we propose a central and uniform management of the versions of different biomedical ontologies.

Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes

Authors: 
Gross, A; Hartung, M; Kirsten, T; Rahm, E
Year: 
2009
Venue: 
6th Intl. Workshop on Data Integration in the Life Sciences (DILS)

Ontology-based annotations associate objects, such as genes and proteins, with well-defined ontology concepts to semantically and uniformly describe object properties. Such annotation mappings are utilized in different applications and analysis studies whose results strongly depend on the quality of the used annotations. To study the quality of annotations we propose a generic evaluation approach considering the annotation generation methods (provenance) as well as the evolution of ontologies, object sources, and annotations.

Rule-based Management of Schema Changes at ETL sources

Authors: 
Papastefanatos, G.; Vassiliadis, P.; Simitsis, A.; Sellis, T.; Vassiliou, Y.
Year: 
2009
Venue: 
Workshop on Managing Evolution of Data Warehouses (MEDWa 2009)

In this paper, we visit the problem of the management of inconsistencies emerging on ETL processes as results of evolution operations occurring at their sources. We abstract Extract-Transform-Load (ETL) activities as queries and sequences of views. ETL activities and its sources are uniformly modeled as a graph that is annotated with rules for the management of evolution events. Given a change at an element of the graph, our framework detects the parts of the graph that are affected by this change and highlights the way they are tuned to respond to it.

Management of the Evolution of Database-Centric Information Systems

Authors: 
Vassiliadis, P.; Papastefanatos, G.; Sellis, T.; Vassiliou, Y.
Year: 
2007
Venue: 
In International Workshop on Database Preservation (PresDB 07)

Hecataeus: A Framework for Representing SQL Constructs as Graphs

Authors: 
Papastefanatos, G.; Kyzirakos, K; Vassiliadis, P.; Vassiliou, Y.
Year: 
2005
Venue: 
In 10th International Workshop on Exploring Modeling Methods for Systems Analysis and Design - EMMSAD '05 (in conjunction with CAISE'05)

Traditional modeling techniques typically focus on the static part of databases and ignore their dynamic part (e.g., queries or data-centric workflows). In this paper, we first introduce and sketch a graph-based model that that uniformly captures relations, views, constraints and queries. We then present Hecataeus, a tool for implementing and visualizing the above framework

An Approach to Heterogeneous Data Translation based on XML Conversion.

Authors: 
Papotti, Paolo; Torlone, Riccardo
Year: 
2004
Venue: 
CAiSE Workshops: Web Information Systems Modeling (WISM)

In this paper, we illustrate a preliminary approach to the
translation of Web data between heterogeneous formats. This work fits
into a larger pro ject whose aim is the development of a tool for the man-
agement of data described according to a large variety of formats used on
the Web and the (semi)automatic translation of schemes and instances
from one model to another. Data translations operate over XML repre-
sentations of instances and rely on a uniform representation of models
that we call metamodel. The metamodel shows structural diversities and

Improving search and navigation by combining Ontologies and Social Tags

Authors: 
Bindelli, Silvia; Criscione, Claudio; Curino, Carlo A.; Drago, Mauro L.; Eynard, Davide; Orsi, Giorgio
Year: 
2008
Venue: 
OTM Workshop: Ambient Data Integration

The Semantic Web has the ambitious goal of enabling complex autonomous applications to reason on a machine-processable version of the World Wide Web. This, however, would require a coordinated effort not easily achievable in practice. On the other hand, spontaneous communities, based on social tagging, recently achieved noticeable consensus and diffusion.

X-SOM: A Flexible Ontology Mapper

Authors: 
Curino, Carlo A.; Orsi, Giorgio; Tanca, Letizia
Year: 
2008
Venue: 
DEXA Workshop

System interoperability is a well known issue, especially for heterogeneous information systems, where ontology-based representations may support automatic and user-transparent integration. In this paper we present X-SOM: an ontology mapping and integration tool. The contribution of our tool is a modular and extensible architecture that automatically combines several matching techniques by means of a neural network, performing also ontology debugging to avoid inconsistencies.

Managing the History of Metadata in support for DB Archiving and Schema Evolution

Authors: 
Curino, Carlo A.; Moon, Hyun J.; Zaniolo, Carlo
Year: 
2008
Venue: 
ECDM

Modern information systems, and web information systems in particular, are faced with frequent database schema changes, which generate the necessity to manage such evolution and preserve their history.

Information Systems Integration and Evolution: Ontologies at Rescue

Authors: 
Curino, Carlo A.; Tanca, Letizia; Zaniolo, Carlo
Year: 
2008
Venue: 
STSM

The life of a modern Information System is often characterized by (i) a push toward integration with other systems, and (ii) the evolution of its data management core in response to continuously changing application requirements. Most of the current proposals dealing with these issues from a database perspective rely on the formal notions of mapping and query rewriting.

Management von Ontologien in den Lebenswissenschaften

Authors: 
Hartung, M.
Year: 
2008
Venue: 
20. Workshop über die Grundlagen von Datenbanken (GvDB)

Die Bedeutung bzw. der praktische Nutzen von Ontologien zeigt sich insbesondere in den Lebenswissenschaften. Durch die gestiegene Akzeptanz und Anwendung von Ontologien stellt deren Management mehr und mehr ein wichtiges Problem dar. Aus diesen Grund werden die ständige Weiterentwicklung (Evolution) von Ontologien und die starke Heterogenität bezüglich ihrer Formate in diesem Beitrag näher betrachtet. Im speziellen versucht ein erster Ansatz verschiedene Ontologien über eine Middleware in Gridumgebungen zu integrieren, um Gridnutzern bzw.

Alignment of biomedical ontologies using life science literature

Authors: 
Tan, H; Jakoniene, V; Lambrix, P; J Aberg, N
Year: 
2006
Venue: 
Workshop on Knowledge Discovery in Life Science Literature

In recent years many biomedical ontologies have been developed
and many of these ontologies contain overlapping information.
To be able to use multiple ontologies they have to be aligned. In this
paper we propose strategies for aligning ontologies based on life science
literature. We propose a basic algorithm as well as extensions that take
the structure of the ontologies into account. We evaluate the strategies
and compare them with strategies implemented in the alignment system
SAMBO. We also evaluate the combination of the proposed strategies
and the SAMBO strategies.

COMA++: Results for the Ontology Alignment Contest OAEI 2006

Authors: 
Massmann, S.; Engmann, D.; Rahm, E.
Year: 
2006
Venue: 
International Workshop on Ontology Matching, collocated with the 5th ISWC-2006; Athens, Georgia, USA

This paper summarizes the OAEI Contest 2006 results for the matching tool
COMA++. The study shows that a generic schema matching system can also
effectively solve complex ontology matching tasks.

Management of Executable Schema Mappings for XML Data Exchange

Authors: 
Pankowski, T.
Year: 
2006
Venue: 
EDBT 2006 Workshop

Executable schema mappings between XML schemas are essential
to support numerous data management tasks such as data exchange,
data integration and schema evolution. The novelty of this paper
consists in a method for automatic generation of automappings (automorphisms)
from key constraints and value dependencies over XML
schemas, and designing algebraic operations on mappings and schemas
represented by automappings. During execution of mappings some missing
or incomplete data may be inferred. A well-defined executable semantics

Reducing the Cost of Validating Mapping Compositions by Exploiting Semantic Relationships

Authors: 
Dragut, E.; Lawrence, R.
Year: 
2006
Venue: 
LNCS 4275

Defining and composing mappings are fundamental operations required in any data sharing architecture (e.g. data warehouse, data integration). Mapping composition is used to generate new mappings from existing ones and is useful when no direct mapping is available. The complexity of mapping composition depends on the amount of syntactic and semantic information in the mapping. The composition of mappings has proven to be inefficient to compute in many situations unless the mappings are simplified to binary relationships that represent “similarity” between concepts.

A Framework for Aligning Ontologies

Authors: 
Lambrix, P; Tan, H
Year: 
2005
Venue: 
Proc. 3rd Int Workshop on Principles and Practice of Semantic Web Reasoning. Springer LNCS 3703

Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies and thus the ontologies need to be aligned. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed.

Conceptual XML Schema Evolution --- the CoDEX Approach for Design and Redesign

Authors: 
Klettke, M.
Year: 
2007
Venue: 
BTW Workshop “Model Management und Metadaten-Verwaltung”, Aachen

Most available approaches for XML schema evolution spec-
ify the evolution steps for an XML schema or a DTD. This article will
show that schema evolution can also be realized on a conceptual model.
Schema evolution always requires propagating the changes to the XML
documents that are already associated to the schema. This article sug-
gests a method for conceptual schema evolution concerning all these
subtasks. It is implemented in a tool called CoDEX (Conceptual Design
and Evolution of XML schemas).

A Coevolution Approach for Database Schemas and Related Ontologies

Authors: 
Kupfer, Andreas; Eckstein, Silke; Neumann, Karl; Mathiak, Brigitte
Year: 
2006
Venue: 
19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)

Ontologies are one of the key technologies for data integration and meta-databases, by connecting databases on a semantical level. Still, everything fails when one of the database schemas changes: specific parts of the ontology have to be reconstructed by hand. We propose an approach that allows the database schema and the ontology to change and evolve, without ever losing their connection to each other. We call that \"coevolution\". Coevolution cannot be completely automated, as data definition languages do not define the change of semantical concepts, but only technical schema changes.

Oasis: A Mapping and Integration Framework for Biomedical Ontologies

Authors: 
Song, Guanglei ; Qian, Yu; Liu, Ying ; Zhang, Kang
Year: 
2006
Venue: 
19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)

More and more ontologies are emerging across bioinformatics domains to represent and define domain knowledge, such as gene ontology, anatomy ontology and disease ontology. To integrate these heterogeneous ontologies is becoming critically important for applications utilizing multiple ontologies. Because the entities described in the ontology often overlap with other entities in other ontologies, a mapping between two corresponding terms is required and becoming the key to the integration of heterogeneous ontologies.

Query Reformulation for the XML standards XPath, XQuery and XSLT

Authors: 
Groppe, S., Boettcher, S.
Year: 
2004
Venue: 
XSW 2004 - The Workshop on XML Technologies for the Semantic Web, Berlin, Germany, October 2004.

Whenever transformation of data is used to bridge the gap of different data formats, and a query is given in the destination format, query reformulation can speed up the transformation of data. We achieve this speed-up in transformation when only the required data segment, described by the computed reformulated query, is transformed. Whenever the required section of data is not too large, query reformulation allows transformation on demand, even when the input data is large.

Change Management for a Temporal Versioned Object-Oriented Database

Authors: 
Galante, R de Matos; Edelweiss, N; Santos, CS dos
Year: 
2003
Venue: 
Proc. ER Workshop ECDM, LNCS 2784

In this paper, we propose a schema versioning mechanism to manage the schema evolution in temporal object-oriented databases. The schema evolution management uses an object-oriented data model that supports temporal features and versions definition - the Temporal Versions Model - TVM. One interesting feature of our proposal is that TVM is used to control not only the schema versioning, but also the storage of extensional database and propagation of the changes performed on the objects.

Supporting database evolution: Using ontologies matching

Authors: 
Lammari, N.; Akoka, J.; Comyn-Wattiau, I.
Year: 
2003
Venue: 
Proc. Object-Oriented Information Systems, LNCS 2817

In this paper, we propose a methodology for managing database evolutions by exploiting two ontologies. The first ontology describes the changes occurring in a database application. The second one aims at characterizing techniques and tools useful for database change management. We propose an algorithm performing ontologies matching and its application to identify appropriate techniques and tools for a given database change.

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