Semantic processing of EHR data for clinical research

There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.Comment: Accepted for publication in Journal of Biomedical Informatics, 2015, preprint versio

Implicit quantification made explicit : how to interpret blank nodes and universal variables in Notation3 Logic

Since the invention of Notation3 Logic, several years have passed in which the theory has been refined and applied in different reasoning engines like Cwm, EYE, and FuXi. But despite these developments, a clear formal definition of Notation3’s semantics is still missing. This does not only form an obstacle for the formal investigation of that logic and its relations to other formalisms, it has also practical consequences: in many cases the interpretations of the same formula differ between reasoning engines. In this paper we tackle one of the main sources of that problem, namely the uncertainty about implicit quantification. This refers to Notation3’s ability to use bound variables for which the universal or existential quantifiers are not explicitly stated, but implicitly assumed. We provide a tool for clarification through the definition of a core logic for Notation3 that only supports explicit quantification. We specify an attribute grammar which maps Notation3 formulas to that logic according to the different interpretations and thereby define the semantics of Notation3. This grammar is then implemented and used to test the impact of the differences between interpretations on practical cases. Our dataset includes Notation3 implementations from former research projects and test cases developed for the reasoner EYE. We find that 31% of these files are understood differently by different reasoners. We further analyse these cases and categorize them in different classes of which we consider one most harmful: if a file is manually written by a user and no specific built-in predicates are used (13% of our critical files), it is unlikely that this user is aware of possible differences. We therefore argue the need to come to an agreement on implicit quantification, and discuss the different possibilities

The pragmatic proof: hypermedia API composition and execution

Machine clients are increasingly making use of the Web to perform tasks. While Web services traditionally mimic remote procedure calling interfaces, a new generation of so-called hypermedia APIs works through hyperlinks and forms, in a way similar to how people browse the Web. This means that existing composition techniques, which determine a procedural plan upfront, are not sufficient to consume hypermedia APIs, which need to be navigated at runtime. Clients instead need a more dynamic plan that allows them to follow hyperlinks and use forms with a preset goal. Therefore, in this paper, we show how compositions of hypermedia APIs can be created by generic Semantic Web reasoners. This is achieved through the generation of a proof based on semantic descriptions of the APIs' functionality. To pragmatically verify the applicability of compositions, we introduce the notion of pre-execution and post-execution proofs. The runtime interaction between a client and a server is guided by proofs but driven by hypermedia, allowing the client to react to the application's actual state indicated by the server's response. We describe how to generate compositions from descriptions, discuss a computer-assisted process to generate descriptions, and verify reasoner performance on various composition tasks using a benchmark suite. The experimental results lead to the conclusion that proof-based consumption of hypermedia APIs is a feasible strategy at Web scale.Peer ReviewedPostprint (author's final draft

RDF Surfaces: Computer Says No

Logic can define how agents are provided or denied access to resources, how to interlink resources using mining processes and provide users with choices for possible next steps in a workflow. These decisions are for the most part hidden, internal to machines processing data. In order to exchange this internal logic a portable Web logic is required which the Semantic Web could provide. Combining logic and data provides insights into the reasoning process and creates a new level of trust on the Semantic Web. Current Web logics carries only a fragment of first-order logic (FOL) to keep exchange languages decidable or easily processable. But, this is at a cost: the portability of logic. Machines require implicit agreements to know which fragment of logic is being exchanged and need a strategy for how to cope with the different fragments. These choices could obscure insights into the reasoning process. We created RDF Surfaces in order to express the full expressivity of FOL including saying explicitly ‘no’. This vision paper provides basic principles and compares existing work. Even though support for FOL is semi-decidable, we argue these problems are surmountable. RDF Surfaces span many use cases, including describing misuse of information, adding explainability and trust to reasoning, and providing scope for reasoning over streams of data and queries. RDF Surfaces provide the direct translation of FOL for the Semantic Web. We hope this vision paper attracts new implementers and opens the discussion to its formal specification