Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.This paper has been partially supported by the MESOLAP (TIN2010-14860) and GEODAS-BI (TIN2012-37493-C03-03) projects from the Spanish Ministry of Education and Competitivity. Alejandro Maté is funded by the Generalitat Valenciana under an ACIF grant (ACIF/2010/298)

An authoring tool for decision support systems in context questions of ecological knowledge

Decision support systems (DSS) support business or organizational decision-making activities, which require the access to information that is internally stored in databases or data warehouses, and externally in the Web accessed by Information Retrieval (IR) or Question Answering (QA) systems. Graphical interfaces to query these sources of information ease to constrain dynamically query formulation based on user selections, but they present a lack of flexibility in query formulation, since the expressivity power is reduced to the user interface design. Natural language interfaces (NLI) are expected as the optimal solution. However, especially for non-expert users, a real natural communication is the most difficult to realize effectively. In this paper, we propose an NLI that improves the interaction between the user and the DSS by means of referencing previous questions or their answers (i.e. anaphora such as the pronoun reference in “What traits are affected by them?”), or by eliding parts of the question (i.e. ellipsis such as “And to glume colour?” after the question “Tell me the QTLs related to awn colour in wheat”). Moreover, in order to overcome one of the main problems of NLIs about the difficulty to adapt an NLI to a new domain, our proposal is based on ontologies that are obtained semi-automatically from a framework that allows the integration of internal and external, structured and unstructured information. Therefore, our proposal can interface with databases, data warehouses, QA and IR systems. Because of the high NL ambiguity of the resolution process, our proposal is presented as an authoring tool that helps the user to query efficiently in natural language. Finally, our proposal is tested on a DSS case scenario about Biotechnology and Agriculture, whose knowledge base is the CEREALAB database as internal structured data, and the Web (e.g. PubMed) as external unstructured information.This paper has been partially supported by the MESOLAP (TIN2010-14860), GEODAS-BI (TIN2012-37493-C03-03), LEGOLANGUAGE (TIN2012-31224) and DIIM2.0 (PROMETEOII/2014/001) projects from the Spanish Ministry of Education and Competitivity. Alejandro Maté is funded by the Generalitat Valenciana under an ACIF grant (ACIF/2010/298)

A framework for enriching Data Warehouse analysis with Question Answering systems

Business Intelligence (BI) applications allow their users to query, understand, and analyze existing data within their organizations in order to acquire useful knowledge, thus making better strategic decisions. The core of BI applications is a Data Warehouse (DW), which integrates several heterogeneous structured data sources in a common repository of data. However, there is a common agreement in that the next generation of BI applications should consider data not only from their internal data sources, but also data from different external sources (e.g. Big Data, blogs, social networks, etc.), where relevant update information from competitors may provide crucial information in order to take the right decisions. This external data is usually obtained through traditional Web search engines, with a significant effort from users in analyzing the returned information and in incorporating this information into the BI application. In this paper, we propose to integrate the DW internal structured data, with the external unstructured data obtained with Question Answering (QA) techniques. The integration is achieved seamlessly through the presentation of the data returned by the DW and the QA systems into dashboards that allow the user to handle both types of data. Moreover, the QA results are stored in a persistent way through a new DW repository in order to facilitate comparison of the obtained results with different questions or even the same question with different dates.This paper has been partially supported by the MESOLAP (TIN2010-14860), GEODASBI (TIN2012-37493-C03-03), LEGOLANG-UAGE (TIN2012-31224) and DIIM2.0 (PROMETEOII/2014/001) projects from the Spanish Ministry of Education and Competitivity. Alejandro Maté is funded by the Generalitat Valenciana under an ACIF grant (ACIF/2010/298)

The improvement of analytics in massive open online courses by applying data mining techniques

The continuous increase in the number of open online courses has radically changed the traditional sector of education during the last years. These new learning approaches are very difficult to manage by using traditional management methods. This is one of the challenges in order to improve the new massive open online courses. In this paper, we propose a big data modelling approach, considering information from a big data analysis perspective, finding out which are the most relevant indicators in order to guarantee the success of the course. This novel approach is described along the paper using the case study of an open online course offered at our university. We describe the lessons learned in this work with the objective of providing general tools and indicators for other online courses. This will enhance the analysis and management of this kind of courses, contributing to their success.This work has partially funded by the project GEODAS-BI (TIN2012-37493-C03-03) from the Ministry of Economy and Competitiveness (MINECO). Alejandro Maté is funded by a Vali+D grant (APOSTD/2014/064)

A Novel Multidimensional Approach to Integrate Big Data in Business Intelligence

The huge amount of information available and its heterogeneity has surpassed the capacity of current data management technologies. Dealing with huge amounts of structured and unstructured data, often referred as Big Data, is a hot research topic and a technological challenge. In this paper, the authors present an approach aimed to enable OLAP queries over different, heterogeneous, data sources. Their approach is based on a MapReduce paradigm, which integrates different formats into the recent RDF Data Cube format. The benefits of their approach are that it is capable of querying different sources of information, while maintaining at the same time, an integrated, comprehensive view of the data available. The paper discusses the advantages and disadvantages, as well as the implementation challenges that such approach presents. Furthermore, the approach is evaluated in detail by means of a case study.This work has been funded by the Spanish Ministry of Economy and Competitiveness under the project Grant GEODAS-BI (TIN2012-37493-C03-03)

Contemporary use of cefazolin for MSSA infective endocarditis: analysis of a national prospective cohort

Objectives: This study aimed to assess the real use of cefazolin for methicillin-susceptible Staphylococcus aureus (MSSA) infective endocarditis (IE) in the Spanish National Endocarditis Database (GAMES) and to compare it with antistaphylococcal penicillin (ASP). Methods: Prospective cohort study with retrospective analysis of a cohort of MSSA IE treated with cloxacillin and/or cefazolin. Outcomes assessed were relapse; intra-hospital, overall, and endocarditis-related mortality; and adverse events. Risk of renal toxicity with each treatment was evaluated separately. Results: We included 631 IE episodes caused by MSSA treated with cloxacillin and/or cefazolin. Antibiotic treatment was cloxacillin, cefazolin, or both in 537 (85%), 57 (9%), and 37 (6%) episodes, respectively. Patients treated with cefazolin had significantly higher rates of comorbidities (median Charlson Index 7, P <0.01) and previous renal failure (57.9%, P <0.01). Patients treated with cloxacillin presented higher rates of septic shock (25%, P = 0.033) and new-onset or worsening renal failure (47.3%, P = 0.024) with significantly higher rates of in-hospital mortality (38.5%, P = 0.017). One-year IE-related mortality and rate of relapses were similar between treatment groups. None of the treatments were identified as risk or protective factors. Conclusion: Our results suggest that cefazolin is a valuable option for the treatment of MSSA IE, without differences in 1-year mortality or relapses compared with cloxacillin, and might be considered equally effective