Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Guideline-based decision support in medicine : modeling guidelines for the development and application of clinical decision support systems

Guideline-based Decision Support in Medicine Modeling Guidelines for the Development and Application of Clinical Decision Support Systems The number and use of decision support systems that incorporate guidelines with the goal of improving care is rapidly increasing. Although developing systems that are both effective in supporting clinicians and accepted by them has proven to be a difficult task, of the systems that were evaluated by a controlled trial, the majority showed impact. The work, described in this thesis, aims at developing a methodology and framework that facilitates all stages in the guideline development process, ranging from the definition of models that represent guidelines to the implementation of run-time systems that provide decision support, based on the guidelines that were developed during the previous stages. The framework consists of 1) a guideline representation formalism that uses the concepts of primitives, Problem-Solving Methods (PSMs) and ontologies to represent guidelines of various complexity and granularity and different application domains, 2) a guideline authoring environment that enables guideline authors to define guidelines, based on the newly developed guideline representation formalism, and 3) a guideline execution environment that translates defined guidelines into a more efficient symbol-level representation, which can be read in and processed by an execution-time engine. The described methodology and framework were used to develop and validate a number of guidelines and decision support systems in various clinical domains such as Intensive Care, Family Practice, Psychiatry and the areas of Diabetes and Hypertension control

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Development of a conceptual framework for integrated analysis and assessment of agricultural systems in SEAMLESS-IF

Production Economics,

Methodological and empirical progress and challenges in integrated assessment of agricultural systems and policies

In this contribution we first present a methodology for integrated assessment of agricultural systems (SEAMLESS Integrated Framework), illustrate its application in an integrated assessment of high commodity prices and then discuss its flexibility and limitations. From there we take a broader view and reflect on key scientific and empirical questions with respect to the development of research tools for the integrated assessment of agricultural systems.agricultural systems, integrated assessment, modelling, Agricultural and Food Policy, Farm Management,

Training materials for different categories of users

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use, Production Economics, Teaching/Communication/Extension/Profession,