scholarly journals Enabling Semantic Queries Across Federated Bioinformatics Databases

2019 ◽  
Author(s):  
Ana Claudia Sima ◽  
Tarcisio Mendes de Farias ◽  
Erich Zbinden ◽  
Maria Anisimova ◽  
Manuel Gil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Integration ◽  
Heterogeneous Data ◽  
Biological Data ◽  
Data Sources ◽  
Biological Knowledge ◽  
Biological Databases ◽  
Semantic Level ◽  
Sparql Endpoint ◽  
Link Type

MotivationData integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.ResultsWe introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: 1) Bgee, a gene expression relational database; 2) OMA, a Hierarchical Data Format 5 (HDF5) orthology data store, and 3) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialised RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.Project URLhttp://biosoda.expasy.org, https://github.com/biosoda/bioquery

scholarly journals Enabling semantic queries across federated bioinformatics databases

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Ana Claudia Sima ◽  
Tarcisio Mendes de Farias ◽  
Erich Zbinden ◽  
Maria Anisimova ◽  
Manuel Gil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Data Integration ◽  
Heterogeneous Data ◽  
Biological Data ◽  
Data Sources ◽  
Biological Knowledge ◽  
Biological Databases ◽  
Semantic Level ◽  
Sparql Endpoint ◽  
Description Framework

Abstract Motivation: Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly. However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases. Results: We introduce an ontology-based federated approach for data integration. We applied this approach to three heterogeneous data stores that span different areas of biological knowledge: (i) Bgee, a gene expression relational database; (ii) Orthologous Matrix (OMA), a Hierarchical Data Format 5 orthology DS; and (iii) UniProtKB, a Resource Description Framework (RDF) store containing protein sequence and functional information. To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx. We then show how the relational data in Bgee can be expressed as a virtual RDF graph, instantiating GenEx, through dedicated relational-to-RDF mappings. By applying these mappings, Bgee data are now accessible through a public SPARQL endpoint. Similarly, the materialized RDF data of OMA, expressed in terms of the Orthology ontology, is made available in a public SPARQL endpoint. We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores. Finally, we lay the groundwork to enable nontechnical users to benefit from the integrated data, by providing a natural language template-based search interface.

Design and Implementation of Oilfield Heterogeneous Data Integration Model Based on Ontology

2014 ◽  
Vol 912-914 ◽  
pp. 1201-1204
Author(s):  
Gang Huang ◽  
Xiu Ying Wu ◽  
Man Yuan
Keyword(s):  
Data Integration ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Semantic Heterogeneity ◽  
Integration Model ◽  
Integration Framework ◽  
Heterogeneous Data Integration ◽  
Semantic Level ◽  
Heterogeneous Data Sources ◽  
Semantic Difference

This paper provides an ontology-based distributed heterogeneous data integration framework (ODHDIF). The framework resolves the problem of semantic interoperability between heterogeneous data sources in semantic level. By metadatas specifying the distributed, heterogeneous data and by describing semantic information of data source , having "ontology" as a common semantic model, semantic match is established through ontology mapping between heterogeneous data sources and semantic difference institutions are shielded, so that semantic heterogeneity problem of the heterogeneous data sources can be effectively solved. It provides an effective technology measure for the interior information of enterprises to be shared in time accurately.

Research and Application on Oilfield Product Heterogeneous Data Integration Based on Ontology

2014 ◽  
Vol 530-531 ◽  
pp. 809-812
Author(s):  
Gang Huang ◽  
Xiu Ying Wu ◽  
Man Yuan ◽  
Rui Fang Li
Keyword(s):  
Data Integration ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Distributed Data ◽  
Semantic Heterogeneity ◽  
Gas Industry ◽  
Heterogeneous Data Integration ◽  
Semantic Level ◽  
Heterogeneous Data Sources ◽  
Integrated Operations

The Oil & Gas industry is moving forward with Integrated Operations (IO). There are different ways to achieve data integration, and ontology-based approaches have drawn much attention. This paper introduces an ontology-based distributed data integration framework (ODDIF). The framework resolves the problem of semantic interoperability between heterogeneous data sources in semantic level. By metadatas specifying the distributed, heterogeneous data and by describing semantic information of data source , having "ontology" as a common semantic model, semantic match is established through ontology mapping between heterogeneous data sources and semantic difference institutions are shielded, so that semantic heterogeneity problem of the heterogeneous data sources can be effectively solved. The proposed method reduces developing difficulty, improves developing efficiency, and enhances the maintainability and expandability of the system.

scholarly journals Machine learning can differentiate venom toxins from other proteins having non-toxic physiological functions

2016 ◽  
Vol 2 ◽  
pp. e90 ◽  
Author(s):  
Ranko Gacesa ◽  
David J. Barlow ◽  
Paul F. Long
Keyword(s):  
Machine Learning ◽  
Sequence Data ◽  
Biological Data ◽  
Biological Databases ◽  
Web Based ◽  
Physiological Functions ◽  
Link Type ◽  
Venom Toxins ◽  
Venomous Animals ◽  
Toxin Protein

Ascribing function to sequence in the absence of biological data is an ongoing challenge in bioinformatics. Differentiating the toxins of venomous animals from homologues having other physiological functions is particularly problematic as there are no universally accepted methods by which to attribute toxin function using sequence data alone. Bioinformatics tools that do exist are difficult to implement for researchers with little bioinformatics training. Here we announce a machine learning tool called ‘ToxClassifier’ that enables simple and consistent discrimination of toxins from non-toxin sequences with >99% accuracy and compare it to commonly used toxin annotation methods. ‘ToxClassifer’ also reports the best-hit annotation allowing placement of a toxin into the most appropriate toxin protein family, or relates it to a non-toxic protein having the closest homology, giving enhanced curation of existing biological databases and new venomics projects. ‘ToxClassifier’ is available for free, either to download (https://github.com/rgacesa/ToxClassifier) or to use on a web-based server (http://bioserv7.bioinfo.pbf.hr/ToxClassifier/).

scholarly journals Integração, Relacionamento e Representação de Dados em Cidades Inteligentes: Uma Revisão de Literatura

2018 ◽  
Author(s):  
Larysse Silva ◽  
José Alex Lima ◽  
Nélio Cacho ◽  
Eiji Adachi ◽  
Frederico Lopes ◽  
...  
Keyword(s):  
Decision Making ◽  
Literature Review ◽  
Data Integration ◽  
Smart Cities ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Application Development ◽  
Continuous Integration ◽  
Heterogeneous Data Sources ◽  
Computational Systems

A notable characteristic of smart cities is the increase in the amount of available data generated by several devices and computational systems, thus augmenting the challenges related to the development of software that involves the integration of larges volumes of data. In this context, this paper presents a literature review aimed to identify the main strategies used in the development of solutions for data integration, relationship, and representation in smart cities. This study systematically selected and analyzed eleven studies published from 2015 to 2017. The achieved results reveal gaps regarding solutions for the continuous integration of heterogeneous data sources towards supporting application development and decision-making.

Semantic-Based Geospatial Data Integration With Unique Features

2019 ◽  
pp. 254-277 ◽  
Author(s):  
Ying Zhang ◽  
Chaopeng Li ◽  
Na Chen ◽  
Shaowen Liu ◽  
Liming Du ◽  
...  
Keyword(s):  
Data Integration ◽  
High Performance ◽  
Data Access ◽  
Heterogeneous Data ◽  
Geospatial Data ◽  
Experimental Results ◽  
Data Sources ◽  
Data Format ◽  
Access Protocols ◽  
Data Source

Since large amount of geospatial data are produced by various sources, geospatial data integration is difficult because of the shortage of semantics. Despite standardised data format and data access protocols, such as Web Feature Service (WFS), can enable end-users with access to heterogeneous data stored in different formats from various sources, it is still time-consuming and ineffective due to the lack of semantics. To solve this problem, a prototype to implement the geospatial data integration is proposed by addressing the following four problems, i.e., geospatial data retrieving, modeling, linking and integrating. We mainly adopt four kinds of geospatial data sources to evaluate the performance of the proposed approach. The experimental results illustrate that the proposed linking method can get high performance in generating the matched candidate record pairs in terms of Reduction Ratio(RR), Pairs Completeness(PC), Pairs Quality(PQ) and F-score. The integrating results denote that each data source can get much Complementary Completeness(CC) and Increased Completeness(IC).

Semantic Web and Geospatial Unique Features Based Geospatial Data Integration

2019 ◽  
pp. 230-253
Author(s):  
Ying Zhang ◽  
Chaopeng Li ◽  
Na Chen ◽  
Shaowen Liu ◽  
Liming Du ◽  
...  
Keyword(s):  
Semantic Web ◽  
Data Integration ◽  
High Performance ◽  
Data Access ◽  
Heterogeneous Data ◽  
Geospatial Data ◽  
Data Sources ◽  
Modeling Process ◽  
Translation Function ◽  
Data Source

Since large amount of geospatial data are produced by various sources and stored in incompatible formats, geospatial data integration is difficult because of the shortage of semantics. Despite standardised data format and data access protocols, such as Web Feature Service (WFS), can enable end-users with access to heterogeneous data stored in different formats from various sources, it is still time-consuming and ineffective due to the lack of semantics. To solve this problem, a prototype to implement the geospatial data integration is proposed by addressing the following four problems, i.e., geospatial data retrieving, modeling, linking and integrating. First, we provide a uniform integration paradigm for users to retrieve geospatial data. Then, we align the retrieved geospatial data in the modeling process to eliminate heterogeneity with the help of Karma. Our main contribution focuses on addressing the third problem. Previous work has been done by defining a set of semantic rules for performing the linking process. However, the geospatial data has some specific geospatial relationships, which is significant for linking but cannot be solved by the Semantic Web techniques directly. We take advantage of such unique features about geospatial data to implement the linking process. In addition, the previous work will meet a complicated problem when the geospatial data sources are in different languages. In contrast, our proposed linking algorithms are endowed with translation function, which can save the translating cost among all the geospatial sources with different languages. Finally, the geospatial data is integrated by eliminating data redundancy and combining the complementary properties from the linked records. We mainly adopt four kinds of geospatial data sources, namely, OpenStreetMap(OSM), Wikmapia, USGS and EPA, to evaluate the performance of the proposed approach. The experimental results illustrate that the proposed linking method can get high performance in generating the matched candidate record pairs in terms of Reduction Ratio(RR), Pairs Completeness(PC), Pairs Quality(PQ) and F-score. The integrating results denote that each data source can get much Complementary Completeness(CC) and Increased Completeness(IC).

Inference of Gene Regulatory Networks by Topological Prior Information and Data Integration

Biotechnology ◽  
2019 ◽  
pp. 265-304
Author(s):  
David Correa Martins Jr. ◽  
Fabricio Martins Lopes ◽  
Shubhra Sankar Ray
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Prior Information ◽  
Heterogeneous Data ◽  
Data Sources ◽  
Expression Data ◽  
Heterogeneous Data Sources ◽  
Gene Regulatory

The inference of Gene Regulatory Networks (GRNs) is a very challenging problem which has attracted increasing attention since the development of high-throughput sequencing and gene expression measurement technologies. Many models and algorithms have been developed to identify GRNs using mainly gene expression profile as data source. As the gene expression data usually has limited number of samples and inherent noise, the integration of gene expression with several other sources of information can be vital for accurately inferring GRNs. For instance, some prior information about the overall topological structure of the GRN can guide inference techniques toward better results. In addition to gene expression data, recently biological information from heterogeneous data sources have been integrated by GRN inference methods as well. The objective of this chapter is to present an overview of GRN inference models and techniques with focus on incorporation of prior information such as, global and local topological features and integration of several heterogeneous data sources.

Semantic-Based Geospatial Data Integration With Unique Features

2018 ◽  
pp. 393-416
Author(s):  
Ying Zhang ◽  
Chaopeng Li ◽  
Na Chen ◽  
Shaowen Liu ◽  
Liming Du ◽  
...  
Keyword(s):  
Data Integration ◽  
High Performance ◽  
Data Access ◽  
Heterogeneous Data ◽  
Geospatial Data ◽  
Experimental Results ◽  
Data Sources ◽  
Data Format ◽  
Access Protocols ◽  
Data Source

Since large amount of geospatial data are produced by various sources, geospatial data integration is difficult because of the shortage of semantics. Despite standardised data format and data access protocols, such as Web Feature Service (WFS), can enable end-users with access to heterogeneous data stored in different formats from various sources, it is still time-consuming and ineffective due to the lack of semantics. To solve this problem, a prototype to implement the geospatial data integration is proposed by addressing the following four problems, i.e., geospatial data retrieving, modeling, linking and integrating. We mainly adopt four kinds of geospatial data sources to evaluate the performance of the proposed approach. The experimental results illustrate that the proposed linking method can get high performance in generating the matched candidate record pairs in terms of Reduction Ratio(RR), Pairs Completeness(PC), Pairs Quality(PQ) and F-score. The integrating results denote that each data source can get much Complementary Completeness(CC) and Increased Completeness(IC).

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