Dependent Types for Nominal Terms with Atom Substitutions

Nominal terms are an extended first-order language for specifying and verifying properties of syntax with binding. Founded upon the semantics of nominal sets, the success of nominal terms with regard to systems of equational reasoning is already well established. This work first extends the untyped language of nominal terms with a notion of non-capturing atom substitution for object-level names and then proposes a dependent type system for this extended language. Both these contributions are intended to serve as a prelude to a future nominal logical framework based upon nominal equational reasoning and thus an extended example is given to demonstrate that this system is capable of encoding various other formal systems of interest

Templates as a method for implementing data provenance in decision support systems

AbstractDecision support systems are used as a method of promoting consistent guideline-based diagnosis supporting clinical reasoning at point of care. However, despite the availability of numerous commercial products, the wider acceptance of these systems has been hampered by concerns about diagnostic performance and a perceived lack of transparency in the process of generating clinical recommendations. This resonates with the Learning Health System paradigm that promotes data-driven medicine relying on routine data capture and transformation, which also stresses the need for trust in an evidence-based system. Data provenance is a way of automatically capturing the trace of a research task and its resulting data, thereby facilitating trust and the principles of reproducible research. While computational domains have started to embrace this technology through provenance-enabled execution middlewares, traditionally non-computational disciplines, such as medical research, that do not rely on a single software platform, are still struggling with its adoption. In order to address these issues, we introduce provenance templates – abstract provenance fragments representing meaningful domain actions. Templates can be used to generate a model-driven service interface for domain software tools to routinely capture the provenance of their data and tasks. This paper specifies the requirements for a Decision Support tool based on the Learning Health System, introduces the theoretical model for provenance templates and demonstrates the resulting architecture. Our methods were tested and validated on the provenance infrastructure for a Diagnostic Decision Support System that was developed as part of the EU FP7 TRANSFoRm project

ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Exchange of research data and samples in biomedical research has become a common phenomenon demanding for their effective quality assessment. At the same time, several reports address reproducibility of research, where history of biological samples (acquisition, processing, transportation, storage, and retrieval) and data history (data generation and processing) defines their fitness for purpose, and hence their quality. The project aims at developing a comprehensive W3C PROV based provenance information standard intended for the biomedical research domain. The standard is being developed by the working group 5 ("data processing and integration") of the ISO (International Standardisation Organisation) technical committee 276 "biotechnology". The outcome of the project will be published in parts as international standards or technical specifications. The poster informs about the goals of the standardisation activity, presents the proposed structure of the standards, briefly describes its current state and outlines its future development and open issues

Towards a Common Standard for Data and Specimen Provenance in Life Sciences

The exchange of biological material and data has become an issue of major importance for research in biotechnology. At the same time, many reports indicate problems with quality, trustworthiness and reproducibility of research results, mainly due to poor documentation of data generation or collection of samples. Consequently, there is an urgent need for improved and standardized documentation of data and specimen used in research studies. In response to these issues, we are developing a provenance information standard for the biotechnology domain within the ISO Technical Committee 276 “Biotechnology”. The major objectives of the standard, now registered as ISO/WD 23494, are improved reproducibility of research results, enabling the assessment of the quality of biological samples and data, traceability and higher reliability of observations. We are convinced that the standardization project is of substantial interest to a broader audience, who we would also invite to comment and contribute to this comprehensive effort.Manuscript under consideration

Typed Nominal Rewriting

Nominal terms extend first-order terms with nominal features and as such constitute a meta-language for reasoning about the named variables of an object language in the presence of meta-level variables. This article introduces a number of type systems for nominal terms of increasing sophistication and demonstrates their application in the areas of rewriting and equational reasoning. Two simple type systems inspired by Church’s simply typed lambda calculus are presented where only well-typed terms are considered to exist, over which α-equivalence is then axiomatised. The first requires atoms to be strictly annotated whilst the second explores the consequences of a more relaxed de Bruijn-style approach in the presence of atom-capturing substitution. A final type system of richer ML-like polymorphic types is then given in the style of Curry, in which elements of the term language are deemed typeable or not only subsequent to the definition of alpha-equivalence. Principal types are shown to exist and an inference algorithm given to compute them. This system is then used to define two presentations of typed nominal rewriting, one more expressive and one more efficient, the latter also giving rise to a notion of typed nominal equational reasoning.</jats:p