Transformation Toolkit Research Articles

Development of a FHIR RDF data transformation and validation framework and its evaluation

Resource Description Framework (RDF) is one of the three standardized data formats in the HL7 Fast Healthcare Interoperability Resources (FHIR) specification and is being used by healthcare and research organizations to join FHIR and non-FHIR data. However, RDF previously had not been integrated into popular FHIR tooling packages, hindering the adoption of FHIR RDF in the semantic web and other communities. The objective of the study is to develop and evaluate a Java based FHIR RDF data transformation toolkit to facilitate the use and validation of FHIR RDF data. We extended the popular HAPI FHIR tooling to add RDF support, thus enabling FHIR data in XML or JSON to be transformed to or from RDF. We also developed an RDF Shape Expression (ShEx)-based validation framework to verify conformance of FHIR RDF data to the ShEx schemas provided in the FHIR specification for FHIR versions R4 and R5. The effectiveness of ShEx validation was demonstrated by testing it against 2693 FHIR R4 examples and 2197 FHIR R5 examples that are included in the FHIR specification. A total of 5 types of errors including missing properties, unknown element, missing resource Type, invalid attribute value, and unknown resource name in the R5 examples were revealed, demonstrating the value of the ShEx in the quality assurance of the evolving R5 development. This FHIR RDF data transformation and validation framework, based on HAPI and ShEx, is robust and ready for community use in adopting FHIR RDF, improving FHIR data quality, and evolving the FHIR specification.

Development of a genetic transformation toolkit for Brettanomyces bruxellensis.

Brettanomyces bruxellensis is usually considered a spoilage microorganism, responsible for significant economic losses during the production of fermented beverages such as wine, beer and cider, though for some styles of beer its influence is essential. In recent years, the competitiveness of this yeast in bioethanol production processes has brought to attention its broader biotechnological potential. Furthermore, the species has evolved key fermentation traits in parallel with Saccharomyces cerevisiae. Attempts to better understand B. bruxellensis physiology through genomics-driven research have been hampered by a lack of functional genomics tools. Genetic transformation for B. bruxellensis has only been developed recently and with limited efficiency. Here we describe gene transformation cassettes tailored for B. bruxellensis, which provide multiple drug-resistant markers and the ability to tag B. bruxellensis with different fluorescent proteins. All marker cassettes resulted in increased transformation efficiency compared to the maximum reported in literature, with one cassette, TDH1p natMX, showing five times greater efficiency. Transformation cassettes encoding fluorescent proteins enabled discrimination between subpopulations of transformed B. bruxellensis cells by flow cytometry and fluorescent microscopy. Thus, the genetic transformation toolkit described here unlocks several molecular applications such as strain tagging, insertional mutagenesis and potentially targeted gene deletion.

A Hamiltonian approach to Thermodynamics

In the present work we develop a strictly Hamiltonian approach to Thermodynamics. A thermodynamic description based on symplectic geometry is introduced, where all thermodynamic processes can be described within the framework of Analytic Mechanics. Our proposal is constructed on top of a usual symplectic manifold, where phase space is even dimensional and one has well-defined Poisson brackets. The main idea is the introduction of an extended phase space where thermodynamic equations of state are realized as constraints. We are then able to apply the canonical transformation toolkit to thermodynamic problems. Throughout this development, Dirac’s theory of constrained systems is extensively used. To illustrate the formalism, we consider paradigmatic examples, namely, the ideal, van der Waals and Clausius gases.

Embedded system design and code generation by using the DSL and T4

In the development trend of embedded technology, the methods of embedded system design are studied and widely utilized. This paper presents a new approach to design embedded system and generate code from models based on Domain Specific Language and Text Template Transformation Toolkit. We define three Domain Specific Languages, build the corresponding meta-models and develop our framework. The framework is to design the models of embedded system such as the architectural model and the component model. It is also to design the flow chart of embedded software. Based on the designed models, we apply the Text Template Transformation Toolkit to generate code from models automatically

Interactive Hull Form Transformations using Curve Network Deformation

This paper presents an approach to hull surface transformation based on identifying features in the form topology. The technique allows changes using both interactive mouse manipulation and numerical parameters. A rich transformation tool kit is created which allows the user to confidently make rapid hull changes in conjunction with existing surface definition techniques.

Transforming XML documents as schemas evolve

Database systems often use XML schema to describe the format of valid XML documents. Usually, this format is determined when the system is designed. Sometimes, in an already functioning system, a need arises to change the XML schemas. In such a situation, the system has to transform the old XML documents so that they conform to the new format and that as little information as possible is lost in the process. This process is called schema evolution . We have implemented an XML schema transformation toolkit within IBM Master Data Management Server (MDM). MDM uses XML documents to describe products that an enterprise may be offering to its clients. In this work we focus on evolving schemas rather than on integrating separate or heterogeneous data sources. Our solution includes an extendible schema matching algorithm that was designed with evolving XML schemas in mind and takes advantage of hierarchical structure of XML. It also includes a data transformation and migration method appropriate for environments where migration is performed in an abstraction layer above the DBMS. Finally, we describe a novel way of extending an XSLT editor with an XSLT visualization feature to allow the user's input and evaluation of the transformation.

Inference of Session Types From Control Flow

This is a study of a technique for deriving the session type of a program written in a statically typed imperative language from its control flow. We impose on our unlabelled session type syntax a well-formedness constraint based upon normalisation and explore the effects thereof. We present our inference algorithm declaratively and in a form suitable for implementation, and illustrate it with examples. We then present an implementation of the algorithm using a program analysis and transformation toolkit.

Artifact-centered operational modeling: Lessons from customer engagements

For almost a decade, the artifact-centered operational-modeling approach for modeling business operations, also referred to as the “business artifact method,” has been practiced and refined. This approach has been used in a variety of engagements, and each engagement has brought forth innovations that have enriched and strengthened the approach. In this paper, we describe three of these engagements in order to illustrate the method and highlight some of the lessons learned. The main objective of this paper is to establish the value of operational modeling in business transformation and to incorporate the lessons we have learned into a more comprehensive account of the method. We also describe the model-driven business transformation toolkit, which adds a unique value proposition to the method—the rapid and effective transformation of operational models into implementations that are manageable and can be monitored.

Toward a complete transformational toolkit for compilers

PIM is an equational logic designed to function as a “transformational toolkit” for compilers and other programming tools that analyze and manipulate imperative languages. It has been applied to such problems as program slicing, symbolic evaluation, conditional constant propagation, and dependence analysis. PIM consists of the untyped lambda calculus extended with an algebraic data type that characterizes the behavior of lazy stores and generalized conditionals. A graph form of PIM terms is by design closely related to several intermediate representations commonly used in optimizing compilers. In this article, we show that PIM's core algebraic component, PIM t , possesses a complete equational axiomatization (under the assumption of certain reasonable restrictions on term formation). This has the practical consequence of guaranteeing that every semantics-preserving transformation on a program representable in PIM t can be derived by application of PIM t rules. We systematically derive the complete PIM t logic as the culmination of a sequence of increasingly powerful equational systems starting from a straightforward “interpreter” for closed PIM t terms. This work is an intermediate step in a larger program to develop a set of well-founded tools for manipulation of imperative programs by compilers and other systems that perform program analysis.

Database reverse engineering: From requirements to CARE tools

This paper analyzes the requirements that CASE tools should meet for effective database reverse engineering (DBRE), and proposes a general architecture for data-centered applications reverse engineering CASE environments. First, the paper describes a generic DBMS-independent DBRE methodology, then it analyzes the main characteristics of DBRE activities in order to collect a set of desirable requirements. Finally, it describes DB-MAIN, an operational CASE tool developed according to these requirements. The main features of this tool that are described in this paper are its unique generic specification model, its repository, its transformation toolkit, its user interface, the text processors, the assistants, the methodological control and its functional extensibility. Finally, the paper describes five real-world projects in which the methodology and the CASE tool were applied.