Abstract
BackgroundUnderstanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field.MethodsOur two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed.ResultsThis work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent).ConclusionThe generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species.
Highlights
Understanding the genome, with all of its components and intrinsic relationships, is a great challenge
The experience accumulated with the analysis of both human genome data and citrus genome data has lead us to designing a unified conceptual schema of the genome that is intended to capture the essentials of the genome structure by identifying all of the relevant conceptual concepts that could represent the holistic knowledge associated to the genome regardless of the species. We envision this Conceptual Schema of the Genome (CSG) as a holistic artifact that provides a common conceptual background that could be used with any particular species by creating the conceptual view that satisfies the needs of any working domains
We have already identified and detailed our two existing conceptual schemes: the Conceptual Schema of the Human Genome (CSHG) to work with humans and the Conceptual Schema of the Citrus Genome (CSCG) to work with citrus
Summary
Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field. Regardless of the research area, it answers fundamental questions by identifying what concepts are relevant and their relationships with each other. Conceptual models make mental representations of the world explicit, which helps to establish common ontological frameworks that facilitate both communication and knowledge evolution in complex domains [2]. An example of such a convoluted and vast domain is genomics, where understanding the genome and all of its intrinsic relationships in order to decipher the code of life is a huge challenge. The genomic domain is a good candidate for applying CM techniques
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