Database Interoperability Research Articles

Looking forward: Applying an ecological model web to assess impacts of climate change

Climate change is a major threat to the world's protected areas, yet the difficulty of making good predictions of the impacts of change constrains management, planning, and policy making. An important factor limiting development of these predictions is the inability of existing computer models, which simulate ecosystem and related processes, to easily exchange information. The ecological Model Web, now in the early stages of development, addresses this limitation. The Model Web will be an open-ended network of interoperable computer models and databases that use web services to communicate with one another and with end-users. Analogous to the World Wide Web, it will grow organically and opportunistically within a framework of broad goals and high-level standards. Making it easier for models to communicate will increase their collective power and the breadth of questions they can address, while providing web access to their results will facilitate greater extraction of societal benefits by managers, policy makers, and the public.

Improving the evidence base for international comparative research

Industrial societies today produce abundant data fed by the statistical system, social research, market research and administrative data. This is increasingly complemented by processing data produced from sources like commercial transactions. Looking at societies in an international comparative perspective, however, we find many incoherent patterns or even white spots on the globe. Nevertheless, we can observe encouraging progress over past decades. The pioneers of the data movement worked towards an international network of data infrastructures that were conceived as building blocks in a system of social observation. Gaps in the statistical data base had to be filled by sample surveys from social research. This resulted in a network of social science data services to preserve and process the data collected to make them available for secondary analysis, and systematic efforts to continuously collect data comparative by design and to make them available as a public good to the scientific community at large. Increasingly we can observe a rapprochement that has been taking place between social policy and social research since the turn of the millennium. Facing the challenges of globalisation we cannot however, overlook the fact that in spite of all progress, social science data have been collected predominantly with a national perspective, are not well integrated and – even if they are technically and legally accessible – do not easily lend themselves to comparison between nations or periods of time. International data programmes may well profit from the methodological standardisation and harmonisation of measurements as well as from technical progress towards the easier access to and interoperability of data bases. These processes will profit much, if growing efforts to agree on data policies and funding perspectives for international and transcontinental cooperation succeed.

Solutions for data integration in functional genomics: a critical assessment and case study

The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.

Genebanks in the post-genomic age: Emerging roles and anticipated uses

Genebanks assemble, preserve and distribute genetic resources that are critical for research on biological diversity in a changing world. Traditional users of genebanks for crop improvement and rare specimen preservation are now joined by scientists from increasingly diverse disciplines who need access to broad collections of quality-assured materials with good physical integrity plus accurate phenotypic, genotypic, ecological and provenance data. The changing role of genebanks requires a critical evaluation of the genebanking process to ensure that different conservation targets (ranging from biological communities to transcription elements) are adequately captured and maintained ex situ and made available in a useful form. To meet the needs of diverse users, genebanks require better methods to preserve viability, greater emphasis on wild-collected germplasm and enhanced interoperability of databases among various collections-based institutions. The impact of genebanks is contingent on our ability to anticipate future uses and applications of genetic resources in the broadest context.

A Framework of Environmental Modelling and Information Sharing for Urban Air Pollution Control and Management

More effective environmental pollution control and management are needed due to the increasing environmental impacts from a range of human activities and the growing public demands for a better living environment. Urban air pollution is a serious environmental issue that poses adverse impacts on the health of people and the environment in most metropolitan areas. In this paper, we propose a geoinformatics augmented framework of environmental modelling and information sharing for supporting effective urban air pollution control and management. This framework is outlined in terms of its key components and processes including: 1) an integrated, adaptive network of sensors for environmental monitoring; 2) a set of distributed, interoperable databases for data management; 3) a set of intelligent, robust algorithms and models for environmental modelling; 4) a set of flexible, efficient user interfaces for data access and information sharing; and 5) a reliable, high capacity, high performance computing and communication infrastructure for integrating and supporting other framework components and processes.

SenseLab: new developments in disseminating neuroscience information

This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab's unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources.

A dynamic approach to make CDS/ISIS databases interoperable over the internet using the OAI protocol

PurposeA dynamic approach to making legacy databases, like CDS/ISIS, interoperable with OAI‐compliant digital libraries (DLs).Design/methodology/approachThere are many bibliographic databases that are being maintained using legacy database systems. CDS/ISIS is one such legacy database system. It was designed and developed specifically for handling textual data. Over the years, many databases have been developed using this package. There is, however, no mechanism supported by the package for seamless interoperability of databases. The open archives initiative (OAI) addresses the issue of interoperability by using a framework to facilitate the discovery of content stored in distributed archives or bibliographic databases through the use of the OAI Protocol for Metadata Harvesting (OAI‐PMH). The protocol is becoming a de facto standard for interoperability of DLs. Many of the legacy database systems that are in use today, to the best of our knowledge, for various reasons, are not OAI‐compliant. This makes it difficult for the legacy databases to share their metadata automatically. There are two possible approaches to make legacy databases OAI‐compliant – static and dynamic. In this paper, we discuss the dynamic approach to make CDS/ISIS databases OAI‐compliant.FindingsThe dynamic approach is a simple way to make legacy databases OAI‐compliant so that they become interoperable with other OAI‐compliant DLs.Research limitations/implicationDeveloping a general‐purpose tool to make legacy databases OAI‐compliant may be difficult as the driver software needed for database connectivity may not be easily available. Also, the structure of the databases are likely be so varied that identifying the fields that make up the databases programmatically will be very challenging.Originality/valueProvides a dynamic approach to making legacy databases interoperable with OAI‐compliant libraries.

Interoperability of police databases within the EU: An accountable political choice?

This article discusses the interoperability of police databases in the EU with reference to the 24 November 2005 Communication from the Commission to the Council and the European Parliament on improved effectiveness, enhanced interoperability and synergies among European databases in the area of Justice and Home Affairs. The different levels of interoperability are identified. Straightforward interoperability within the EU is distinguished from four more controversial levels of interoperability, such as interoperability with atypical systems and interoperability with systems outside the EU. On the basis of this analysis the question of the desirability and suitability interoperability is addressed, followed by a discussion of the necessary guarantees to be included. Contrary to what is often suggested, interoperability is a highly sensitive political issue. The attempt of the Commission's 2005 Communication, to make it look like a mere technical issue does not create the right context for a serious and in-depth discussion.

Sustaining a digital collection after the grants: the Early Washington Maps Project

PurposeAims to provide an overview of methods for digitizing maps, the creation and preservation of a digital collection, interoperable database construction, and an examination of the real costs associated with maintaining a digital collection.Design/methodology/approachThis paper is an examination of the tools, metadata choices, work with Open Archives Initiative (OAI) research projects, and sustainability costs, associated with a digital project of 946 dynamic historic cartographic images.FindingsThe Early Washington Maps project demonstrates how multiple tools may be integrated and interoperability between databases achieved. Realistic costs associated with digital collections and practical reference techniques are described.Practical implicationsThis is an extremely common‐sense discussion of digital library issues for library professionals planning or enhancing digital collections.Originality/valueThe paper describes ideas for enhancing access to digital collections during and after a grant award.

Standardization initiatives in the (eco)toxicogenomics domain: a review

The purpose of this document is to provide readers with a resource of different ongoing standardization efforts within the ‘omics’ (genomic, proteomics, metabolomics) and related communities, with particular focus on toxicological and environmental applications. The review includes initiatives within the research community as well as in the regulatory arena. It addresses data management issues (format and reporting structures for the exchange of information) and database interoperability, highlighting key objectives, target audience and participants. A considerable amount of work still needs to be done and, ideally, collaboration should be optimized and duplication and incompatibility should be avoided where possible. The consequence of failing to deliver data standards is an escalation in the burden and cost of data management tasks.

웹 서비스를 이용한 바이오 서열 정보 데이터베이스 및 통합 검색 시스템 개발

Recently, the rapid development of biotechnology brings the explosion of biological data and biological data host. Moreover, these data are highly distributed and heterogeneous, reflecting the distribution and heterogeneity of the Molecular Biology research community. As a consequence, the integration and interoperability of molecular biology databases are issue of considerable importance. But, up to now, most of the integrated systems such as link based system, data warehouse based system have many problems which are keeping the data up to date when the schema and data of the data source are changed. For this reason, the integrated system using web service technology that allow biological data to be fully exploited have been proposed. In this paper, we built the integrated system if the bio sequence information bated on the web service technology. The developed system allows users to get data with many format such as BSML, GenBank, Fasta to traverse disparate data resources. Also, it has better retrieval performance because the retrieval modules of the external database proceed in parallel.

Book Review

Analysing gene expression, edited by S. Lorkowski and P. Cullen. 2003. Weinheim, Germany: Wiley-VCH. $335.

The ESF Programme on Functional Genomics workshop on ‘Data Integration in Functional Genomics: Application to Biological Pathways’

We report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases.

Interoperability of CABRI services and biochemical pathways databases

Common Access to Biological Resources and Information (CABRI) service is a ‘one-stop-shop’ for materials that are collected by a number of European culture collections that engage themselves in a quality service for the scientific community by adhering to Quality Guidelines for the management of resources and related information. It includes collections' catalogues that can be searched in an SRS implementation. A simple search facility, including a synonym search and a shopping cart, is also available. Within the European Biological Resource Centres Network (EBRCN) project, an extension and improvement of the catalogues' information is under way. This includes adding links to bibliographic databanks and sequence databases. Revision of ‘in-house’ controlled vocabularies used by data annotators is under way, in order to improve the setting up of external links, and new links to biochemical pathways databases are being set up for some of the catalogues.

Semantic conflict resolution ontology (SCROL): an ontology for detecting and resolving data and schema-level semantic conflicts

Establishing semantic interoperability among heterogeneous information sources has been a critical issue in the database community for the past two decades. Despite the critical importance, current approaches to semantic interoperability of heterogeneous databases have not been sufficiently effective. We propose a common ontology called semantic conflict resolution ontology (SCROL) that addresses the inherent difficulties in the conventional approaches, i.e., federated schema and domain ontology approaches. SCROL provides a systematic method for automatically detecting and resolving various semantic conflicts in heterogeneous databases. SCROL provides a dynamic mechanism of comparing and manipulating contextual knowledge of each information source, which is useful in achieving semantic interoperability among heterogeneous databases. We show how SCROL is used for detecting and resolving semantic conflicts between semantically equivalent schema and data elements. In addition, we present evaluation results to show that SCROL can be successfully used to automate the process of identifying and resolving semantic conflicts.

Biological nomenclatures: a source of lexical knowledge and ambiguity.

There has been increased work in developing automated systems that involve natural language processing (NLP) to recognize and extract genomic information from the literature. Recognition and identification of biological entities is a critical step in this process. NLP systems generally rely on nomenclatures and ontological specifications as resources for determining the names of the entities, assigning semantic categories that are consistent with the corresponding ontology, and assignment of identifiers that map to well-defined entities within a particular nomenclature. Although nomenclatures and ontologies are valuable for text processing systems, they were developed to aid researchers and are heterogeneous in structure and semantics. A uniform resource that is automatically generated from diverse resources, and that is designed for NLP purposes would be a useful tool for the field, and would further database interoperability. This paper presents work towards this goal. We have automatically created lexical resources from four model organism nomenclature systems (mouse, fly, worm, and yeast), and have studied performance of the resources within an existing NLP system, GENIES. Using nomenclatures is not straightforward because issues concerning ambiguity, synonymy, and name variations are quite challenging. In this paper we focus mainly on ambiguity. We determined that the number of ambiguous gene names within the individual nomenclatures, across the four nomenclatures, and with general English ranged from 0%-10.18%, 1.187%-20.30%, and 0%-2.49% respectively. When actually processing text, we found the rate of ambiguous occurrences (not counting ambiguities stemming from English words) to range from 2.4%-32.9% depending on the organisms considered.

A universal legal framework as a prerequisite for database interoperability.

A universal legal framework as a prerequisite for database interoperability.

Information management for microarray experimental data

Today, proficiency in generating microarray data is fast overcoming the capacity for storing and analysing this data. Although there are some existing microarray databases, they have their own storage structure and implementation. In addition, those proposed databases might use the different terminologies to describe the same domain or concepts. As a result, these could lead to a limitation in the sharing of data with other laboratories and the combination of other experimental results. Here, we proposed the integrated information management architecture for microarray experimental data. Unlike the past work on database interoperation in the bioinformatics community, this database design will take into account the important issues in microarray data integration including a lack of a common shared microarray-ontology and having dynamic data representation of the microarray data sources.

ON USING REMOTE USER DEFINED FUNCTIONS AS WRAPPERS FOR BIOLOGICAL DATABASE INTEROPERABILITY

Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide effort in genomics research has resulted in a powerful collection of publicly available sequence analysis tools. These tools often require specialized local services and domain knowledge to function correctly, rendering them unlikely candidates for integration into remote database applications. Thus, integration of heterogeneous "functions" still remains an open problem. Providing a reasonable framework for seamless integration of these tools with database query engines will enable application developers to exploit and harness the power of these effective analysis tools. In this paper, we present an integration framework for such tools by enabling access to them in a user transparent way as part of database queries. In our system, such online tools are abstracted as remote user defined functions (RUDF). An extended SQL DDL language, called the Internet Function Definition Language (IFDL), is presented for the specification and definition of RUDFs. The interface between database system and the Internet is implemented using a layer based on a language called the Hyper Text Query Language (HTQL). The separation of IFDL, DDL, HTQL and SQL DML offers several optimization opportunities and makes it possible to develop an architecture for interoperability of heterogeneous databases with RUDFs in more simple and efficient ways.

Database interoperability through state-based logical data independence

Computer supported cooperative work (CSCW) involving business-to-business transactions depends more and more upon database interoperability. The design of interbusiness CSCW when the businesses are already operating independent systems depends either upon effective reverse engineering (to properly discover the semantics underlying each organisation's systems and through that to develop appropriate matches for interbusiness software), or upon sufficiently rich semantic models and good database management system support for logical data independence (to allow database updating through a logical view). This paper takes the second approach, presenting a rich semantic data model that the authors have been developing and have used successfully in a number of major consultancies, and a new approach to logical data independence and view up datability based on that model. We show how these approaches support database interoperability for business-to-business transactions and, for CSCW within an organisation, how they support federated databases.