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Towards interoperability in genome databases:: The MAtDB (MIPS Arabidopsis thatiana database) experience

COMPARATIVE AND FUNCTIONAL GENOMICS 2003年第2期4卷 255-258页

作者： Schoof, H Tech Univ Munich Lehrstuhl Genomorientierte Bioinformat Wissensch Zentrum D-85350 Freising Weihenstephan Germany

Increasing numbers of whole-genome sequences are available, but to interpret them fully requires more than listing all genes. Genome databases are faced with the challenges of integrating heterogenous data and enabling data mining. In comparison to a data warehousing approach, where integration is achieved through replication of all relevant data in a unified schema, distributed approaches provide greater flexibility and maintainability. These are important in a field where new data is generated rapidly and our understanding of the data changes. interoperability between distributed data sources allows data maintenance to be separated from integration and analysis. Simple ways to access the data can facilitate the development of new data mining tools and the transition from model genome analysis to comparative genomics. With the MIPS Arabidopsis thaliana genome database (MAtDB, http://***/proj/that/db) our aim is to go beyond a data repository towards creating an integrated knowledge resource. To this end, the Arabidopsis genome has been a backbone against which to structure and integrate heterogenous data. The challenges to be met are continuous updating of data, the design of flexible data models that can evolve with new data, the integration of heterogenous data, e.g. through the use of ontologies, comprehensive views and visualization of complex information, simple interfaces for application access locally or via the Internet, and knowledge transfer across species. Copyright (C) 2003 John Wiley Sons, Ltd.

关键词： bioinformatics genome database data integration data mining database interoperability BioMOBY

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A Novel Framework for RDF Schema Extraction in NoSQL databases Using Sentence-BERT

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IEEE Access 2025年 13卷 88243-88254页

作者： Belefqih, Saad Barchane, Mohammed Zellou, Ahmed Benlahmar, El Habib Mohammed v University in Rabat Software Project Management Research Team Ensias Rabat Morocco Hassan Ii University Laboratory of Information Technology and Modeling Faculty of Sciences Ben m'Sick Casablanca Morocco

NoSQL databases, known for their flexibility and scalability, have become pivotal in handling diverse and unstructured data. However, their schema-less nature introduces significant challenges in metadata management, query optimization, and data integration. This research presents a novel schema extraction framework that captures the structural and semantic complexity of NoSQL databases. By integrating constraints, logical rules, and Sentence-BERT embeddings, the proposed approach generates semantically enriched schemas that ensure accuracy, coherence, and usability. Experimental evaluation highlights its adaptability across diverse datasets, demonstrating improvements in semantic precision, data integration, and metadata quality. The framework provides a practical solution for bridging schema-less and structured database workflows, enhancing interoperability and analytics capabilities. © 2013 IEEE.

关键词： database interoperability NoSQL databases RDF SBERT Schema Discovery Semantic Enrichment Transformers Unstructured Data Processing

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Mapping RDF databases to Property Graph databases

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IEEE ACCESS 2020年 8卷 86091-86110页

作者： Angles, Renzo Thakkar, Harsh Tomaszuk, Dominik Univ Talca Fac Engn Dept Comp Sci Curico 3340000 Chile OSTHUS GmbH D-52068 Aachen Germany Univ Bialystok Inst Informat PL-15245 Bialystok Poland Univ Bonn Informat Dept 3 D-53115 Bonn Germany

RDF triplestores and property graph databases are two approaches for data management which are based on modeling, storing and querying graph-like data. In spite of such common principle, they present special features that complicate the task of database interoperability. While there exist some methods to transform RDF graphs into property graphs, and vice versa, they lack compatibility and a solid formal foundation. This paper presents three direct mappings (schema-dependent and schema-independent) for transforming an RDF database into a property graph database, including data and schema. We show that two of the proposed mappings satisfy the properties of semantics preservation and information preservation. The existence of both mappings allows us to conclude that the property graph data model subsumes the information capacity of the RDF data model.

关键词： database interoperability direct mapping RDF property graph

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Specifying global behaviour in database federations

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INFORMATION SYSTEMS 1998年第3-4期23卷 217-233页

作者： Vermeer, MWW Apers, PMG Univ Twente Ctr Telemat & Informat Technol NL-7500 AE Enschede Netherlands

We discuss the impact of locally implemented behaviour on global behaviour specification in a federation of object-oriented databases. In particular, given a specification of an integrated view of a number of component databases, we discuss the process of determining the global methods that are implicitly implemented by a given set of local methods on these component databases. To this end, we develop the notions of objectivity and subjectivity of local methods, indicating whether the execution of a local method affects the global view exactly as it affects the local database, behaviour equivalences between local methods, indicating whether local methods of different components have similar effect, and behaviour concurrences, indicating whether local methods respond to the same event. These notions can be used as a basis for tools supporting the engineering activity of specifying global behaviour in database federations. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

关键词： multidatabases database interoperability semantic heterogeneity method specification

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Uniform techniques for deriving similarities of objects and subschemes in heterogeneous databases

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IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 2003年第2期15卷 271-294页

作者： Palopoli, L Saccà, D Terracina, G Ursino, D Univ Mediterranea Reggio Calabria DIMET I-89100 Reggio Di Calabria Italy Univ Calabria DEIS I-87036 Arcavacata Di Rende CS Italy

The availability of automatic tools for inferring semantics of database schemes is useful to solve several database design problems such as, that of obtaining Cooperative Information Systems or Data Warehouses from large sets of data sources. In this context, a main problem is to single out similarities or dissimilarities among scheme objects (interscheme properties) [7]. This paper presents graph-based techniques for a uniform derivation of interscheme properties including synonymies, homonymies, type conflicts, and subscheme similarities. These techniques are characterized by a common core: the computation of maximum weight matchings on some bipartite weighted graphs derived using a suitable metrics to measure semantic closeness of objects, The techniques have been implemented in a system prototype. Several experiments conducted with it, and (in part) accounted for in the paper, confirmed the effectiveness of our approach.

关键词： synonymies homonymies type conflicts subscheme similarities derivation of database semantics heterogeneous databases database interoperability

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Semantic heterogeneity resolution in federated databases by metadata implantation and stepwise evolution

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VLDB JOURNAL 1999年第2期8卷 120-132页

作者： Aslan, G McLeod, D Univ So Calif Dept Comp Sci Los Angeles CA 90089 USA

A key aspect of interoperation among data-intensive systems involves the mediation of metadata and ontologies across database boundaries. One way to achieve such mediation between a local database and a remote database is to fold remote metadata into the local metadata, thereby creating a common platform through which information sharing and exchange becomes possible. Schema implantation and semantic evolution, our approach to the metadata folding problem, is a partial database integration scheme in which remote and local (meta)data are integrated in a stepwise manner over time. We introduce metadata implantation and stepwise evolution techniques to interrelate database elements in different databases, and to resolve conflicts on the structure and semantics of database elements (classes, attributes, and individual instances). We employ a semantically rich canonical data model, and an incremental integration and semantic heterogeneity resolution scheme. In our approach, relationships between local and remote information units are determined whenever enough knowledge about their semantics is acquired. The metadata folding problem is solved by implanting remote database elements into the local database, a process that imports remote database elements into the local database environment, hypothesizes the relevance of local and remote classes, and customizes the organization of remote metadata. We have implemented a prototype system and demonstrated its use in an experimental neuroscience environment.

关键词： federated databases semantic hetrogeneity resolution database interoperability database integration schema evolution

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Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen

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GLYCOBIOLOGY 2021年第11期31卷 1510-1519页

作者： Navelkar, Rahi Owen, Gareth Mutherkrishnan, Venkatesh Thiessen, Paul Cheng, Tiejun Bolton, Evan Edwards, Nathan Tiemeyer, Michael Campbell, Matthew P. Martin, Maria Vora, Jeet Kahsay, Robel Mazumder, Raja George Washington Univ Dept Biochem & Mol Biol Med Ctr 2300 1 St NW Washington DC 20052 USA European Bioinformat Inst EMBL EBI European Mol Biol Lab Cheminformat & Metab Hinxton CB10 1SD Cambs England NLM Natl Ctr Biotechnol Informat NIH 8600 Rockville Pike Bethesda MD 20894 USA Georgetown Univ Dept Biochem & Cellular Biol 3900 Reservoir RD NW Washington DC 20007 USA Univ Georgia Dept Biochem & Mol Biol Complex Carbohydrate Res Ctr 315 Riverbend Rd Athens GA 30602 USA Univ Georgia Dept Chem 315 Riverbend Rd Athens GA 30602 USA Griffith Univ Inst Glyc Glyc 1G26-1 Parklands Dr Southport Qld 4215 Australia European Bioinformat Inst EMBL EBI European Mol Biol Lab Wellcome Trust Genome Campus Cambridge CB10 1SD England

Glycans play a vital role in health, disease, bioenergy, biomaterials and bio-therapeutics. As a result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at the EMBL-EBI and NCBI to facilitate access to important annotations at a global level. GlyTouCan is a comprehensive archival database that contains glycans obtained primarily through batch upload from glycan repositories, glycoprotein databases and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence and citations. databases like ChEBI and PubChem were designed to accommodate complete atomistic structures with well-defined chemical linkages. As a result, they cannot easily accommodate the structural ambiguity inherent in glycan databases. Consequently, there is a need to improve the organization of glycan data coherently to enhance connectivity across the major NCBI, EMBL-EBI and glycoscience databases. This paper outlines a workflow developed in collaboration between GlyGen, ChEBI and PubChem to improve the visibility and connectivity of glycan data across these resources. GlyGen hosts a subset of glycans (similar to 29,000) from the GlyTouCan database and has submitted valuable glycan annotations to the PubChem database and integrated over 10,500 (including ambiguously defined) glycans into the ChEBI database. The integrated glycans were prioritized based on links to PubChem and connectivity to glycoprotein data. The pipeline provides a blueprint for how glycan data can be harmonized between different resources. The current PubChem, ChEBI and GlyTouCan mappings can be downloaded from GlyGen (https://***).

关键词： database interoperability glycan annotations glycoinformatics

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Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

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CANCER INFORMATICS 2009年 8卷 75-86页

作者： Pantazatos, Spiro Li, Jianrong Pavlidis, Paul Lussier, Yves Columbia Univ Dept Physiol & Cellular Biophys New York NY 10027 USA Columbia Univ Biomed Informat New York NY USA Univ Chicago Dept Med Ctr Biomed Informat Chicago IL 60637 USA Univ British Columbia Dept Psychiat Vancouver BC Canada

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT (R)). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as "List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes". Precision of the NLP-derived coding of the unstructured phenotypes in each dataset was 88% (n = 50), and precision of the semantic mapping between these terms across datasets was 98% (n = 100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets.

关键词： computational ontologies phenotypes database interoperability Mediated Schema SNOMED

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Exploring attribute correspondences across heterogeneous databases by mutual information

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JOURNAL OF MANAGEMENT INFORMATION SYSTEMS 2006年第4期22卷 305-336页

作者： Zhao, HM Soofi, ES Univ Wisconsin Sch Business Adm Milwaukee WI 53201 USA

Identifying attribute correspondences across heterogeneous databases is a critical and time-consuming step in integrating the databases. Past research has applied correlation analysis techniques to explore correspondences between attributes. These techniques, however, are appropriate for numeric attributes that are linearly related. This paper proposes an information-theoretic approach to exploring correspondences between attributes in heterogeneous databases. The proposed approach is applicable to character attributes, as well as to numeric attributes, regardless whether or not they are linearly related. It overcomes some serious shortcomings of previous approaches based on correlation analysis and has much broader applicability. The proposed procedure samples both matching and nonmatching pairs of records from the databases under consideration, applies matching functions to compare pairs of attributes, and then uses the mutual information to measure the dependency between a matching function as applied to a pair of attributes and the class (i.e., matching or nonmatching) of a pair of records. A high mutual information index implies a potential attribute correspondence, which is presented to the analyst for further evaluation. The paper also presents some empirical results demonstrating the utility of the proposed approach.

关键词： attribute correspondence attribute matching composite information systems database interoperability heterogeneous databases information theory interorganizational systems mutual information

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The design and implementation of a corporate householding knowledge processor to improve data quality

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JOURNAL OF MANAGEMENT INFORMATION SYSTEMS 2003年第3期20卷 41-69页

作者： Madnick, S Wang, R Xian, X MIT United States Department of Information Technology Sloan School of Management United States Department of Engineering Systems School of Engineering MIT Information Quality Program United States MIT Total Data Qual. Mgmt. Program Department of Electrical Engineering Computer Science Honor Society National Engineering Honor Society United States Natl. Society of Collegiate Scholars Oracle Corporation United States

Advances in corporate householding are needed to address certain categories of data quality problems caused by data misinterpretation. In this paper, we first summarize some of these data quality problems and our more recent results from studying corporate householding applications and knowledge exploration. Then we outline a technical approach to a corporate householding knowledge processor (CHKP) to solve a particularly important type of corporate householding problem-entity aggregation. We illustrate the operation of the CHKP by using a motivational example in account consolidation. Our CHKP design and implementation uses and expands on the COntext INterchange (COIN) technology to manage and process corporate householding knowledge.

关键词： context mediation corporate household corporate householding database interoperability data quality enterprise knowledge management

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