title: ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.
abstract: BACKGROUND
  With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized.
  
  
  OBJECTIVE
  In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries.
  
  
  METHODS
  The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information.
  
  
  RESULTS
  The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software models.
  
  
  CONCLUSIONS
  ART-ML can be used as a reference ML model in multiscale simulations of plaque formation and progression, incorporating all scales of the biological processes.
authors.affiliation: Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, FORTH, Ioannina, Greece.
authors.forename: E C
authors.initials: EC
authors.lastname: Karvounis
authors.forename: T P
authors.initials: TP
authors.lastname: Exarchos
authors.forename: E
authors.initials: E
authors.lastname: Fotiou
authors.forename: A I
authors.initials: AI
authors.lastname: Sakellarios
authors.forename: D
authors.initials: D
authors.lastname: Iliopoulou
authors.forename: D
authors.initials: D
authors.lastname: Koutsouris
authors.forename: D I
authors.initials: DI
authors.lastname: Fotiadis
mesh_terms: D050197:Atherosclerosis / Q000503:physiopathology; D002318:Cardiovascular Diseases / Q000503:physiopathology*; D006801:Humans; D020407:Internet; D008955:Models, Cardiovascular; D011381:Programming Languages