Retrieval, alignment, and clustering of computational models based on semantic annotations

Abstract

As the number of computational systems biology models increases, new methods are needed to explore their content and build connections with experimental data. In this Perspective article, the authors propose a flexible semantic framework that can help achieve these aims.

Controlled vocabularies and semantics in systems biology

“…As such, modelers may decide to reuse portions of existing models as building blocks. Annotation of model components with SBO terms can be used in model search strategies (Schultz et al , 2011). Annotation of existing models with TEDDY terms is also potentially an effective way of discovering components of interest by allowing queries such as ‘ Find a model of MAPK cascade that oscillates ’ or ‘ Find a model of MAPK cascade that can exhibit bistability .’ We anticipate that the same procedure will also make TEDDY extremely useful for synthetic biology, where modularity is seen as a core feature in the construction of novel systems from composable parts.…”

BioModels: Content, Features, Functionality, and Use

“…Furthermore, it is also possible to analyze the individual model components, based on their semantic annotations, across the set of all models. This allows the clustering of related models (by shared components), and can be used to further assist in efficient search strategies . Semantic information can also be used to generate human‐readable and queryable forms of curated models .…”

In Silico Cell: Challenges and Perspectives

“…Разработка таких автоматизированных «конструкторов» in silico позволили бы не только ускорить процесс создания различных вариантов «электронной клетки» (прототипов новых бактериальных штаммов-продуцентов с заранее заданными физиологическими, метаболическими и другими свойствами) и анализа их динамических свойств, но и значительно облегчила интеграцию, представление комплексных математических моделей живых систем на различных уровнях их иерархической организации. Однако, создание подобных компьютерных систем возможно только при наличии общепринятых стандартов представления, аннотации и семантического анализа математических моделей [60,61], что также не является до конца решенной проблемой в этой области.…”