Waldeyr Mendes Cordeiro da Silva

A terpenoid metabolic network modelled as graph database

Terpenoids are involved in interactions such as signalling for communication intra/inter species, signalling molecules to attract pollinating insects, and defence against herbivores and microbes. Owing to their chemical composition, many terpenoids possess vast pharmacological applicability in medicine and biotechnology, besides important roles in ecology, industry and commerce. Metabolic networks are composed of metabolic pathways, they allow us to represent the metabolism of an organism. The biosynthesis of terpenes has been widely studied over the years, and it is well known that they can be synthesised from two metabolic pathways: mevalonate pathway (MVA) and non-mevalonate pathway (MEP). On the other hand, genome-scale reconstruction of metabolic networks faces many challenges, including organisational data storage and data modelling, to properly represent the complexity of systems biology. Recent NoSQL database paradigms have introduced new concepts of scalable storage and data queries. With regard to biological data, the use of graph databases has grown because of its versatility. In this paper, we propose 2Path, a graph database designed to represent terpenoid metabolic networks. It is modelled in such a way so that it preserves important terpenoid biosynthesis characteristics.

A methodology for quality assurance for business process modeling with BPMN: A case study for the SIGEPE software

During the development of computer systems, business process modeling is a phase that delivers important firsthand inputs for requirements engineering. The goal of business process mapping is to understand, improve and organize the activities of the process to ensure efficient and correct implementation. Quality in business process modeling can decisively influence the software quality. Internal quality analysis is made in-house, for the development process, while external quality analysis is made for the final product and satisfaction of the end consumer. Quality assurance comes from quality attributes verified with checklists in iterative cycles. Then, process mapping contributes both to producing consistent artifacts to better communications within the project. This article presents a methodology for quality assurance of process modeling that can be applied for the development of large computer systems. The methodology was used in a complex case study, with the mapping of business processes using BPMN, to develop a system for human resources management within the Ministry of Planning, Budget and Management (MPOG) in Brazil.

GRAPHED: A Graph Description Diagram for Graph Databases

Within recent years, graph database systems have become very popular and deployed mainly in situations where the relationship between data is significant, such as in social networks. Although they do not require a particular schema design, a data model contributes to their consistency. Designing diagrams is one approach to satisfying this demand for a conceptual data model. While researchers and companies have been developing concepts and notations for graph database modeling, their notations focus on their specific implementations. In this paper, we propose a diagram to address this lack of a generic and comprehensive notation for graph database modeling, called GRAPHED (Graph Description Diagram for Graph Databases). We verified the effectiveness and compatibility of GRAPHED in a case study in fraud identification in the Brazilian government.

Human-Computer Interaction Communicability Evaluation Method Applied to Bioinformatics.

Quality measures have different focuses and importance for distinct roles, like developers, maintainers, purchasers and end users. The focus of a quality evaluation may be internal, external quality or quality in use. This last one is the quality of the software product from the user’s point of view. Computer systems must satisfy determined quality criteria to assure interface characteristics of interest to their users and several evaluation methods can be applied to different objectives of quality in use. In bioinformatics, creating visual tools that can adequately represent the complexity and volume of biological data while preserving a high level of usability is a challenge. It is difficult to combine both interface usability and data expressiveness, particularly with heterogeneous and very connected data. 2Path is a case in point, this is a database of metabolic networks for terpenoid biosynthesis. Using evaluation by observation through Communicability Evaluation Method (CEM), we measured the following quality criteria for an interface designed for 2Path: usability, user experience, accessibility, and communicability. The users were monitored during the use of the system, some of their utterances using the system were identified and mapped. We present here the results obtained and the perspectives of a new interface that aims to meet the post-evaluation requirements fully.

An evaluation of data replication for bioinformatics workflows on NoSQL systems

Many research projects in bioinformatics may be viewed as scientific workflows. Biologists often run multiple times the same workflow with different parameters in order to refine their data analysis. These executions generate a large volume of files with different formats, which need to be stored for future evaluations. New database models, like NoSQL systems, could be considered to deal with large volumes of data, particularly in distributed systems. This work presents a data replication impact assessment from the execution of scientific workflows for two NoSQL database management systems: Cassandra and MongoDB.

Software documentation quality: A case study for the software documentation of SIGEPE

Requirements determine the correct construction of software and are frequently represented explicitly in the accompanying documentation in ways that vary according to the adopted software process. The documentation is typically written in natural language and can contain elements such as figures, tables or a more formal description. The quality assurance of artifacts written in natural language has advanced significantly since the mid-70s. SIGEPE makes use of checklists with criteria weighted by both form and content. The quality assurance team conducts periodic and individual checks on strategically selected projects. In little over a year, there was a noticeable improvement in the quality of the documentation and it was possible to identify the most common points of success and failure. This paper describes a Case Study to verify the quality of the elements of SIGEPE documentation.

A Method for Quality Assurance for Business Process Modeling with BPMN

Within the development of computer systems, the goal of business process mapping is to understand, improve, and organize the process activities to ensure efficient and correct implementation for releasing important firsthand inputs for requirements engineering. These inputs can be improved by process modeling. The quality of business process modeling can decisively influence the software quality. Internal quality analysis is done in-house, for the development process, while external quality analysis is done for the final product and satisfaction of the end consumer. Therefore, process modeling contributes to the production of consistent artifacts inorder to improve communications within the project. A way to assure quality comes from quality attributes verified with checklists in iterative cycles. Process mapping, then, contributes both to producing consistent artifacts and to improving communications within the project.

An Argumentation Theory-Based Multiagent Model to Annotate Proteins

Many computational and experimental methods have been proposed for predicting functions performed by proteins. In silico methods are time and resource-consuming, due to the large amount of data used for annotation. Moreover, computational predictions for protein functions are usually incomplete and biased. Although some tools combine different annotation strategies to predict functions, biologists (human experts) have to use their knowledge to analyze and improve these predictions. This complex scenario presents suitable features for a multiagent approach, e.g., expert knowledge, distributed resources, and an environment that includes different computational methods. Also, argumentation theory can increase the expressiveness of biological knowledge of proteins, considering inconsistencies and incompleteness of information. The main goal of this work is to present an argumentation theory-based multiagent model to annotate proteins, called ArgMAS-AP. Additionally, we discuss a theoretical example with real data to evaluate the suitability of our model.

Graph Databases in Molecular Biology

In recent years, the increase in the amount of data generated in basic social practices and specifically in all fields of research has boosted the rise of new database models, many of which have been employed in the field of Molecular Biology. NoSQL graph databases have been used in many types of research with biological data, especially in cases where data integration is a determining factor. For the most part, they are used to represent relationships between data along two main lines: (i) to infer knowledge from existing relationships; (ii) to represent relationships from a previous data knowledge. In this work, a short history in a timeline of events introduces the mutual evolution of databases and Molecular Biology. We present how graph databases have been used in Molecular Biology research using High Throughput Sequencing data, and discuss their role and the open field of research in this area.

2Path: A terpenoid metabolic network modeled as graph database

Terpenoids are involved in interactions as signaling for communication intra/inter species, signal molecules to attract pollinating insects, and defense against herbivores and microbes. Due to their chemical composition, many terpenoids possess vast pharmacological applicability in medicine and biotechnology, besides important roles in ecology, industry and commerce. The biosynthesis of terpenes has been widely studied over the years, and it is well known that they can be synthesized from two metabolic pathways: mevalonate pathway (MVA) and non-mevalonate pathway (MEP). On the other hand, genome-scale reconstruction of metabolic networks faces many challenges, including organizational data storage and data modeling, to properly represent the complexity of systems biology. Recent NoSQL database paradigms have introduced new concepts of scalable storage and data queries. Among them graph databases, which are versatile enough to cope with biological data. In this paper, we propose 2Path, a graph database model designed to represent terpenoid metabolic networks, with thousands of secondary metabolism reactions, such that it preserves important terpenoid biosynthesis characteristics.