Understanding the Semantic Links among Heterogeneous Biological Data Sources

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.

Download Full-text

Challenges in Integrating Biological Data Sources

Journal of Computational Biology ◽

10.1089/cmb.1995.2.557 ◽

1995 ◽

Vol 2 (4) ◽

pp. 557-572 ◽

Cited By ~ 81

Author(s):

S.B. DAVIDSON ◽

C. OVERTON ◽

P. BUNEMAN

Keyword(s):

Biological Data ◽

Data Sources

Download Full-text

PATH-BASED SYSTEMS TO GUIDE SCIENTISTS IN THE MAZE OF BIOLOGICAL DATA SOURCES

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720006002375 ◽

2006 ◽

Vol 04 (05) ◽

pp. 1069-1095 ◽

Cited By ~ 31

Author(s):

SARAH COHEN-BOULAKIA ◽

SUSAN DAVIDSON ◽

CHRISTINE FROIDEVAUX ◽

ZOÉ LACROIX ◽

MARIA-ESTHER VIDAL

Keyword(s):

Biological Data ◽

Data Sources ◽

Single Experiment ◽

Novel Technologies ◽

Biological Resources ◽

Wet Lab ◽

Points Of View ◽

Growing Network ◽

The Way

Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer. Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data. In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.

Download Full-text

The PlaNet Consortium: A Network of European Plant Databases Connecting Plant Genome Data in an Integrated Biological Knowledge Resource

Comparative and Functional Genomics ◽

10.1002/cfg.374 ◽

2004 ◽

Vol 5 (2) ◽

pp. 184-189 ◽

Cited By ~ 3

Author(s):

H. Schoof ◽

R. Ernst ◽

K. F. X. Mayer

Keyword(s):

Data Exchange ◽

Data Representation ◽

Data Models ◽

Biological Data ◽

Plant Genome ◽

Data Sources ◽

Direct Access ◽

Biological Knowledge ◽

Database Integration ◽

Complex Data

The completion of theArabidopsisgenome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration ofArabidopsisand other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.

Download Full-text

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

Journal of Computational Biology ◽

10.1089/cmb.2012.0273 ◽

2013 ◽

Vol 20 (4) ◽

pp. 344-358 ◽

Cited By ~ 33

Author(s):

Hua Wang ◽

Heng Huang ◽

Chris Ding ◽

Feiping Nie

Keyword(s):

Protein Interactions ◽

Nonnegative Matrix ◽

Biological Data ◽

Data Sources ◽

Protein Protein Interactions

Download Full-text

Clustering Genes Using Heterogeneous Data Sources

International Journal of Knowledge Discovery in Bioinformatics ◽

10.4018/jkdb.2010040102 ◽

2010 ◽

Vol 1 (2) ◽

pp. 12-28 ◽

Cited By ~ 3

Author(s):

Erliang Zeng ◽

Chengyong Yang ◽

Tao Li ◽

Giri Narasimhan

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

Incomplete Data ◽

Clustering Algorithm ◽

Biological Data ◽

Exploratory Analysis ◽

Data Sources ◽

Modular Organization ◽

Constrained Clustering ◽

Expression Data

Clustering of gene expression data is a standard exploratory technique used to identify closely related genes. Many other sources of data are also likely to be of great assistance in the analysis of gene expression data. This data provides a mean to begin elucidating the large-scale modular organization of the cell. The authors consider the challenging task of developing exploratory analytical techniques to deal with multiple complete and incomplete information sources. The Multi-Source Clustering (MSC) algorithm developed performs clustering with multiple, but complete, sources of data. To deal with incomplete data sources, the authors adopted the MPCK-means clustering algorithms to perform exploratory analysis on one complete source and other potentially incomplete sources provided in the form of constraints. This paper presents a new clustering algorithm MSC to perform exploratory analysis using two or more diverse but complete data sources, studies the effectiveness of constraints sets and robustness of the constrained clustering algorithm using multiple sources of incomplete biological data, and incorporates such incomplete data into constrained clustering algorithm in form of constraints sets.

Download Full-text