GeneConnector: Unlocking the full potential of Genbank metadata

Authors

Keywords:

Genbank, NCBI, Mycology, Phytopathology, GOPHY, Genomics

Abstract

Genbank currently stands as one of the most significant global repositories of genetic information. However, despite its vast quantity and diversity of data, a considerable portion of the existing records suffer from disjointed and often lacking metadata, failing to provide the necessary context of their acquisition. In light of this, we propose GeneConnector, a tool that harnesses shared information among multiple records of the same specimen in Genbank, aiming to enhance the completeness of poorly annotated nodes across various information domains. To demonstrate the tool’s capabilities, we conducted a comprehensive review and aggregation of available data using the Genbank database of Genera of Phytopathogenic Fungi (GOPHY). Through our evaluation, we observed substantial gains in information by analyzing shared data among nodes connecting Genbank specimen records, resulting in impressive increments ranging from 2% to a remarkable 60%. Our approach empowers users to make precise, straightforward, and accurate assessments of the context associated to results, facilitated by two metrics that gauge the current level of data annotation and the potential information gain achievable following our evaluation.

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Author Biographies

Samuel Galvão Elias, Universidade de Brasília, UnB, Brasilia, Brazil

I am a biologist/microbiologist and I value multi- and interdisciplinary approaches. As a biologist, my main focus is on mycology, and I have a strong knowledge of bacteriology as well. As a bioinformatician, I have experience in analyzing molecular data of various types. I also have expertise in analyzing microbial diversity, including community experimentation across a wide range of taxonomic groups. Additionally, I have extensive knowledge in molecular phylogenetics of eukaryotes and prokaryotic groups, along with experience in post-phylogenetics. In terms of Data Science, I have expertise in analyzing diverse classes of data, including univariate to multivariate, unifactorial to multifactorial, and categorical to continuous data. As a developer, I have experience in web application development (monolithic and distributed), embedded systems, desktop applications, and data pipelines both within and outside the field of bioinformatics. My language stack includes Python, R, Rust, Golang, JavaScript, and TypeScript, with experience in single and multithreaded development, single and multicore programming, concurrent programming, and parallel programming. I am involved in the architecture and development of stateful and stateless applications, native to cloud environments, with a focus on Kubernetes. Some of my main open-source projects include \href{https://github.com/sgelias/mycelium}{Mycelium} (Rust), an API gateway currently under development that focuses on permissioning in distributed environments, and \href{https://github.com/sgelias/blutils}{Blutils} (Rust), a tool for optimizing the execution process and analysis of Blast results.

Debora Cervieri Guterres, Federal University of Viçosa, Viçosa, Brazil

Dr. Debora Cervieri Guterres holds a Ph.D. in Phytopathology from the University of Brasília (UnB, 2018), a Master's degree in Environmental Sciences from the Federal University of Bahia (UFBA, 2013), and specializes in Environmental Management from FJC (2009). Additionally, earned a degree in Agronomist Engineering from FASB (2012) and holds a Bachelor's degree in Business Administration with a focus on Foreign Trade from FASB (2007).
With a diverse academic background, Debora has expertise in the fields of Phytopathology, Mycology, Etiology, and the Diversity and Taxonomy of Fungi. She has conducted extensive research in these areas, contributing to the understanding and management of plant diseases. Currently, Debora is engaged in a postdoctoral internship at the Federal University of Viçosa, further expanding her knowledge and expertise in the field.

Robert Weingart Barreto, Federal University of Viçosa, Viçosa, Brazil

He is an agronomist (UFRRJ) with a strong academic background in mycology. He obtained an MSc in Pure and Applied Taxonomy (Mycology) from the University of Reading in 1986 and went on to complete his Ph.D. in Botany (Mycology) at the same institution, along with the International Institute of Mycology (currently CAB International) in 1991. Following his doctoral studies, he pursued postdoctoral research focusing on molecular taxonomy of fungi at the esteemed Centraalbureau voor Schimmelcultures.
Currently, he holds the position of full professor in the Department of Phytopathology at the Federal University of Viçosa, where he is actively involved in teaching various courses in the field of mycology, plant disease diagnosis, and biological control. Since its establishment in 1998, he has been the dedicated Coordinator of the Plant Disease Clinic - DFP/UFV, ensuring effective management and treatment of plant diseases.
With extensive experience in mycology, his research interests encompass a wide range of topics. His expertise lies in the areas of biological control of weeds, fungal taxonomy, phytopathology, diagnosis of fungal diseases in plants, and the study of fungal biodiversity in Brazilian ecosystems. As an accomplished researcher, he has made significant contributions to these fields and is recognized as a leading figure in the discipline.
Furthermore, he holds the esteemed position of the current president of the Brazilian Society of Mycology, where he actively promotes collaboration and advances in mycological research. Through his leadership, he plays a pivotal role in shaping the direction of mycology in Brazil and fostering connections within the scientific community.

Helson Mário Martins do Vale, University of Brasília, Brasilia, Brazil

He holds a degree in Agricultural Sciences from the Federal Rural University of Rio de Janeiro (2002), a master's degree in Agricultural Microbiology from the Federal University of Lavras (2005) and a PhD in Agricultural Microbiology from the Federal University of Viçosa (2009), post-doctorate in metagenomics of endophytic fungi at the Ruhr-Universität Bochum, Germany. He is currently Associate Professor D, Level II at the University of Brasília (UnB) and Head of the Department of Phytopathology. He works in undergraduate disciplines of Agronomy courses (Microbiology and Phytopathogenic Micro-organisms); Biology (Mycology) and Environmental Sciences (Microbial Diversity and Biological Collections) and postgraduate disciplines in the Phytopathology (Molecular Techniques) and Microbial Biology (Microbial Ecology) courses at UnB. He has experience in the area of Agronomy and Biology, with emphasis on Agricultural Microbiology, working mainly on the following topics: Biological Nitrogen Fixation, Microbial Ecology, Metagenomics, Next Generation Sequencing (NGS), Yeast Diversity in Brazilian Ecosystems, Molecular Diversity and Characterization of Epiphytic and Endophytic Microorganisms.

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Published

2024-01-16

How to Cite

Galvão Elias, S., Cervieri Guterres, D., Weingart Barreto, R., & Mário Martins do Vale, H. (2024). GeneConnector: Unlocking the full potential of Genbank metadata. IEEE Latin America Transactions, 22(2), 99–105. Retrieved from https://latamt.ieeer9.org/index.php/transactions/article/view/8241

Issue

Vol. 22 No. 2 (2024): Ordinary Issue

Section

Computing