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Showing papers presented at "Semantic Web Applications and Tools for Life Sciences in 2012"


Proceedings Article
28 Nov 2012
TL;DR: It is argued that good workflow design is a prerequisite for repairing a workflow, or redesigning an equivalent workflow pattern with new components, and the semantic tooling that is being developed in the Workflow4Ever project to support these best practices are presented.
Abstract: In this position paper we present a set of best practices for workflow design to prevent workflow decay and increase reuse and re-purposing of scientific workflows. MyExperiment provides access to a large number of scientific workflows. However, scientists find it difficult to reuse or re-purpose these workflows for mainly two reasons: workflows suffer from decay over time and lack sufficient metadata to understand their purpose. We argue that good workflow design is a prerequisite for repairing a workflow, or redesigning an equivalent workflow pattern with new components. We present a set of best practices for workflow design and the semantic tooling that is being developed in the Workflow4Ever (Wf4Ever) project to support these best practices.

30 citations


Proceedings ArticleDOI
01 Jan 2012
TL;DR: A prototype of a multi-signal pipeline for reconstructing provenance is described and preliminary results of reconstructing dependencies between documents in the context of clinical guidelines and associated documents are shown.
Abstract: Understanding the provenance of clinical guidelines is important for both practitioners and researchers as it allows for deeper understanding of the provided recommendations and could potentially provide a basis for updating guidelines. Often such provenance is incomplete or unavailable. We describe a prototype of a multi-signal pipeline for reconstructing provenance and show preliminary results of reconstructing dependencies between documents in the context of clinical guidelines and associated documents. 1 Prototype description Broadly, we target the problem of reconstructing provenance of files in a shared folder setting, in which several authors can create or edit files at different moments, and only standard filesystem metadata is available. In a previous work [3] we proposed a content-based approach that is able to reconstruct provenance automatically, leveraging several similarity measures and edit distance algorithms, which are then adapted and integrated them into a multi-signal pipeline. Here, we present an improved version of this prototype applied to a clinical guideline and associated biomedical documents. The architecture of our prototype is shown in Fig. 1.

6 citations


Proceedings Article
01 Jan 2012
TL;DR: An effective framework of building standardized Semantic Web RESTful services on ICD-11 linked data, which would be useful to support I CD-11 revision is developed.
Abstract: For the beta phase of the 11th revision of International Classification of Diseases (ICD-11), the World Health Organization (WHO) intends to accept public input through a distributed model of authoring. To enable social computation and collaboration among broader communities, it is imperative but remains challenging to have an open-data access solution for ICD-11 contents. The objective of the present study is to describe our experiences and challenges on building the Simple Knowledge Organization System (SKOS) compliant Semantic Web RESTful services that aim to support the authoring application development of ICD-11. We propose a framework of building such services, which is composed of four layers: a semantic normalization layer, a semantic repository layer, a semantic services layer and an application layer. For the prototype implementation, we first generated the normalized ICD-11 linked RDF data through utilizing WHO ICD URI scheme and SKOS RDF data model. We used the Linked Data API and developed simple RESTful services for the standardized ICD-11 contents. We performed a preliminary evaluation on the usefulness of the system in terms of the feasibility of the services and its potential in support of building the Common Terminology Services 2 (CTS2) compliant services. In conclusion, we developed an effective framework of building standardized Semantic Web RESTful services on ICD-11 linked data, which would be useful to support ICD-11 revision.

3 citations


Proceedings Article
01 Jan 2012
TL;DR: In this paper, a lightweight ontology for representing annotations of declarative evidence based clinical guidelines is presented, which provides the means to connect clinical questions and associated recommendations to underlying evidence, and can capture strength and quality of recommendations and evidence.
Abstract: This paper describes a lightweight ontology for representing annotations of declarative evidence based clinical guidelines. We present the motivation and requirements for this representation, based on an analysis of several guidelines. The ontology provides the means to connect clinical questions and associated recommendations to underlying evidence, and can capture strength and quality of recommendations and evidence, respectively. The ontology was applied in the conversion of manual annotations to RDF and used as part of a prototype clinical decision support system.

3 citations