Ismael Navas-Delgado

Intelligent client for integrating bioinformatics services

MOTIVATION In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem. RESULTS In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain. AVAILABILITY The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome.

Plant reproductive transcriptomes have been analyzed in different species due to the agronomical and biotechnological importance of plant reproduction. Here we presented an olive tree reproductive transcriptome database with samples from pollen and pistil at different developmental stages, and leaf and root as control vegetative tissues http://reprolive.eez.csic.es). It was developed from 2,077,309 raw reads to 1,549 Sanger sequences. Using a pre-defined workflow based on open-source tools, sequences were pre-processed, assembled, mapped, and annotated with expression data, descriptions, GO terms, InterPro signatures, EC numbers, KEGG pathways, ORFs, and SSRs. Tentative transcripts (TTs) were also annotated with the corresponding orthologs in Arabidopsis thaliana from TAIR and RefSeq databases to enable Linked Data integration. It results in a reproductive transcriptome comprising 72,846 contigs with average length of 686 bp, of which 63,965 (87.8%) included at least one functional annotation, and 55,356 (75.9%) had an ortholog. A minimum of 23,568 different TTs was identified and 5,835 of them contain a complete ORF. The representative reproductive transcriptome can be reduced to 28,972 TTs for further gene expression studies. Partial transcriptomes from pollen, pistil, and vegetative tissues as control were also constructed. ReprOlive provides free access and download capability to these results. Retrieval mechanisms for sequences and transcript annotations are provided. Graphical localization of annotated enzymes into KEGG pathways is also possible. Finally, ReprOlive has included a semantic conceptualisation by means of a Resource Description Framework (RDF) allowing a Linked Data search for extracting the most updated information related to enzymes, interactions, allergens, structures, and reactive oxygen species.

Systems biology metabolic modeling assistant

SUMMARY We present Systems Biology Metabolic Modeling Assistant (SBMM Assistant), a tool built using an ontology-based mediator, and designed to facilitate metabolic modeling through the integration of data from repositories that contain valuable metabolic information. This software can be used for the visualization, design and management of metabolic networks; selection, integration and storage of metabolic information; and as an assistant for kinetic modeling. AVAILABILITY SBMM Assistant for academic use is freely available at http://www.sbmm.uma.es.

Protopia: a protein-protein interaction tool

BackgroundProtein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data http://asp.uma.es.ResultsThe tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein.ConclusionThe tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks.

Sharing and executing linked data queries in a collaborative environment

MOTIVATION Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. RESULTS In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. AVAILABILITY The Bioqueries portal is freely accessible at http://bioqueries.uma.es. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

A design methodology for semantic Web database-based systems

The exponential growth in the volume of accessible information on the Web has led to the development of distributed systems, which share knowledge by making use of conceptualizations of specific domains generally defined by means of ontologies. Multiple conceptualizations may describe similar domains using different or overlapped terminologies. These issues should be taken into account when a new system is designed. However, they are not usually considered, leading to greater development time and effort. In order to tackle these problems, we propose an engineering approach for the development of new database-based systems starting from domain ontologies.

jMetalSP: A framework for dynamic multi-objective big data optimization

Abstract Multi-objective metaheuristics have become popular techniques for dealing with complex optimization problems composed of a number of conflicting functions. Nowadays, we are in the Big Data era, so metaheuristics must be able to solve dynamic problems that may vary over time due to the processing and analysis of several streaming data sources. As this is a new field, there is a need for software platforms to solve dynamic multi-objective Big Data optimization problems. In this paper, we present jMetalSP, which combines the multi-objective optimization features of the jMetal framework with the streaming facilities of the Apache Spark cluster computing system. Thus, existing state-of-the-art multi-objective metaheuristics can be easily adapted to deal with dynamic optimization problems that are fed by multiple streaming data sources. Moreover, these algorithms can take advantage of the parallel computing features of Spark. We describe the architecture of jMetalSP and show how it can be used to solve a dynamic bi-objective instance of the Traveling Salesman Problem (TSP) based on New York Citys real-time traffic data. We have also carried out an experimental study to assess the performance of the resultant jMetalSP application in a Hadoop cluster composed of 100 nodes.

kpath: integration of metabolic pathway linked data

In the last few years, the Life Sciences domain has experienced a rapid growth in the amount of available biological databases. The heterogeneity of these databases makes data integration a challenging issue. Some integration challenges are locating resources, relationships, data formats, synonyms or ambiguity. The Linked Data approach partially solves the heterogeneity problems by introducing a uniform data representation model. Linked Data refers to a set of best practices for publishing and connecting structured data on the Web. This article introduces kpath, a database that integrates information related to metabolic pathways. kpath also provides a navigational interface that enables not only the browsing, but also the deep use of the integrated data to build metabolic networks based on existing disperse knowledge. This user interface has been used to showcase relationships that can be inferred from the information available in several public databases. Database URL: The public Linked Data repository can be queried at http://sparql.kpath.khaos.uma.es using the graph URI “www.khaos.uma.es/metabolic-pathways-app”. The GUI providing navigational access to kpath database is available at http://browser.kpath.khaos.uma.es.

AMMO-Prot: amine system project 3D-model finder

BackgroundAmines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accumulated, which need to be integrated in order to be effective in the advance of biological knowledge in the field. For this purpose, a multidisciplinary group has started an ontology-based system named the Amine System Project (ASP) for which amine-related information is the validation bench.ResultsIn this paper, we describe the Ontology-Based Mediator developed in the Amine System Project (http://asp.uma.es) using the infrastructure of Semantic Directories, and how this system has been used to solve a case related to amine metabolism-related protein structures.ConclusionsThis infrastructure is used to publish and manage not only ontologies and their relationships, but also metadata relating to the resources committed with the ontologies. The system developed is available at http://asp.uma.es/WebMediator.

Solving Queries over Semantically Integrated Biological Data Sources

Mediators used to be developed as monolithic systems that envelop the data source’s information, such as its semantics and location. Furthermore, its architecture based on wrappers involves a high degree of coupling among the mediator’s components. This coupling does not allow sharing services with other organizations or the dynamic integration of new data sources, so they must be designed and developed for each problem to be solved. Therefore, wrappers must be re-designed and manually added for each mediation system, entailing a high development cost and reduced scalability. We propose an architecture for conceptual mediation in which the sources’ query capabilities are published as web data services. These services can be registered in one or more resource directories (Semantic Directories), which are the core of this architecture because they provide the needed flexibility and scalability for dynamic integration. Semantic Directories allow users to make more expressive queries and infer information from the ontology-explicit knowledge, which enables them to solve queries that a traditional mediator could not evaluate. Another key feature of this architecture is that it provides a way to achieve interoperability between applications in the Semantic Web context. We have applied it to the field of Bioinformatics, integrating biological data sources. We are developing a new application of our proposal for Digital Libraries, in order to solve biological problems for which biological data has to be obtained and used to search in digital libraries. This second application is an example of how we achieve interoperability between close or related domains using soft integration in our approach.Mediators used to be developed as monolithic systems that envelop the data source’s information, such as its semantics and location. It involves a high degree of coupling among the mediator’s components. This coupling does not allow sharing services with other organizations or the dynamic integration of new data sources. We propose an architecture for conceptual mediation in which the sources’ query capabilities are published as web data services. This architecture also provides a way to achieve interoperability between applications in the Semantic Web context.