Applying Conceptual Modeling to Better Understand the Human Genome

Román, José Fabián Reyes; Pastor, Óscar; Casamayor, Juan Carlos; Valverde, Francisco

doi:10.1007/978-3-319-46397-1_31

Cited by 38 publications

(14 citation statements)

References 5 publications

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“…To achieve what we refer to as the "Smart Data" perspective presented in this article, we need a conceptual structure in which to store each piece of genomic data in the right place, regardless of the data's origin. To accomplish this goal, we propose the use of the Conceptual Schema of the Human Genome (CSHG) [17], [18].…”

Section: The Conceptual Schema Of the Human Genomementioning

confidence: 99%

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Smart Data for Genomic Information Systems: the SILE Method

Palacio

López

2018

CSIMQ

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During the last two decades, data generated by Next Generation Sequencing Technologies have revolutionized our understanding of human biology and improved the study on how changes (variations) in the DNA are involved in the risk of suffering a certain disease. A huge amount of genomic data is publicly available and frequently used by the research community in order to extract meaningful and reliable gene-disease relationships. However, the management of this exponential growth of data has become a challenge for biologists. Under such a Big Data problem perspective, they are forced to delve into a lake of complex data, spread in over one thousand heterogeneous repositories, represented in multiple formats and with different levels of quality; but when data are used to solve a concrete problem only, a small part of that "data lake" is really significant; this is what we call the "smart" data perspective. By using conceptual models and the principles of data quality management, adapted to the genomic domain, we propose a systematic approach called the SILE method to move from a Big Data to a Smart Data perspective. The aim of this approach is to populate an Information System with genomic data which are sufficiently accessible, informative and actionable to extract valuable knowledge.

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Section: The Conceptual Schema Of the Human Genomementioning

confidence: 99%

“…This characteristic helps the experts in the domain to understand the structure of the information without the need of studying the internal schema of each repository. The CSHG has five main parts, each one related to a specific domain view [17]:…”

Section: The Conceptual Schema Of the Human Genomementioning

confidence: 99%

Smart Data for Genomic Information Systems: the SILE Method

Palacio

López

2018

CSIMQ

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“…Our recent work focuses on exploring how essential CM is for improving domain understanding and guiding the design and development of Genome Information Systems (GeIS) [34]. The main result is an initial Conceptual Schema of the Human Genome (CSHG).…”

Section: Introductionmentioning

confidence: 99%

Towards the Understanding of the Human Genome: A Holistic Conceptual Modeling Approach

et al. 2020

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Understanding the human genome is a great scientific challenge, whose achievement requires effective data manipulation mechanisms. The non-stop evolution of both new knowledge and more efficient sequencing technologies generates a kind of genome data chaos. This chaos complicates the use of computational resources that obtain data and align them into specific actions. Conceptual modelbased techniques should play a fundamental role in turning data into actionable knowledge. However, current solutions do not give a crucial role in the task of modeling that it should have to obtain a precise understanding of this domain. Hundreds of different data sources exist, but they have heterogeneous, imprecise, and inconsistent data. It is remarkably hard to have a unified data perspective that covers the genomic data from genome to transcriptome and proteome, which could facilitate semantic data integration. This paper focuses on how to design a conceptual model of the human genome that could be used as the key artifact to share, integrate, and understand the various types of datasets used in the genomic domain. We provide a full conceptual picture of relevant data in genomics and how semantic data integration is much more effective by conceptually integrating the diverse types of existing data. We show how such a conceptual model has been built, focusing on the conceptual problems that were solved to adequately model concepts whose knowledge is under constant evolution. We show how the use of the initial versions of the conceptual model in practice has allowed us to identify new features to incorporate in the model, achieving a continuous improvement process. The current version is ready to be used as the key artifact in projects where conceptually combining multiple levels of data helps to provide valuable insights that would be hard to obtain without it.

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“…El MCGH v2 omite por lo tanto la denominada "Genome view", centrándose en una descripción más precisa sobre el modelo genérico del genoma para recopilar toda la información relevante sobre el genoma. En esta versión se decidió organizarlo en cinco vistas principales [112]: 1. Structural view: esta vista se compone de los elementos básicos de la secuencia de ADN (describe la estructura del genoma), 2.…”

Section: Eliminación Del Banco De Datos De Genomas Individualesunclassified

“…b) Se utiliza un framework orientado a servicios [179], el cual mejora aspectos de interoperabilidad e integración. c) VarSearch utiliza una proyección del MCGH [112], por lo que depende de un paradigma orientado a modelos en lugar de un paradigma orientado a los datos. d) Proporciona una interfaz web funcionalmente completa, con la capacidad de descargar resultados en formatos de fichero -de salida estándar-, que posteriormente pueden ser procesados por herramientas de terceros.…”

Section: Trabajos Relacionadosunclassified

Diseño Y Desarrollo De Un Sistema De Información Genómica Basado en Un Modelo Conceptual Holístico Del Genoma Humano

Roman¹,

Fabian²

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Porque para Dios no hay nada imposible." Lucas 1:37 "Y sabemos que a los que aman a Dios, todas las cosas les ayudan a bien, esto es, a los que conforme a su propósito son llamados." Romanos 8:28 A Dios A mi familia A ti mi reina, mi amada esposa… "El que no vive para servir, no sirve para vivir." Teresa de Calcuta Marcos 10:45 "El que no ama, no ha conocido a Dios; porque Dios es amor." 1 Juan 4:8 Mediante el uso de este Modelo Conceptual holístico del Genoma Humano se busca comprender y mejorar el compromiso ontológico con el dominio-genómico-, y desarrollar Sistemas de Información Genómicos apoyados en Modelo Conceptuales para ayudar a la toma de decisiones en el entorno bioinformático.

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Applying Conceptual Modeling to Better Understand the Human Genome

Cited by 38 publications

References 5 publications

Smart Data for Genomic Information Systems: the SILE Method

Smart Data for Genomic Information Systems: the SILE Method

Towards the Understanding of the Human Genome: A Holistic Conceptual Modeling Approach

Diseño Y Desarrollo De Un Sistema De Información Genómica Basado en Un Modelo Conceptual Holístico Del Genoma Humano

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