Group work is an essential part of modern health care. Although there have been advances in the technology of communication, these have not necessarily led to efficient and effective communication ...among collaborating health-care professionals. Instead, barriers such as varied organizational cultures, different training backgrounds, and varied time schedules can overwhelm technological solutions and impede efficient communication. We focus on one particular sort of collaboration, that of group work around a clinical trial protocol, where the collaboration is asynchronous and the participants are geographically distributed. In this work setting, we have applied a computer-supported cooperative work (CSCW) approach in two distinct ways. First, we used observational methods to uncover and understand a complex set of communication behaviors and needs. Second, we used participatory design and iterative prototyping to design a system that aims to improve communication and work flow among these collaborators. We found that these methods work well in tandem—our observational study helped better inform our design, and our prototyping cycles provided additional insight into the work. More specifically, we were able to identify a set of communication problems in the work that led us to specify a set of design desiderata for systems that support asynchronous collaboration around an evolving medical document.
Detailed problem lists that comply with JCAHO requirements are important components of electronic health records. Besides improving continuity of care electronic problem lists could serve as ...foundation infrastructure for clinical trial recruitment, research, biosurveillance and billing informatics modules. However, physicians rarely maintain problem lists. Our team is building a system using MetaMap and UMLS to automatically populate the problem list. We report our early results evaluating the application. Three physicians generated gold standard problem lists for 100 cardiology ambulatory progress notes. Our application had 88% sensitivity and 66% precision using a non-modified UMLS dataset. The systemâs misses concentrated in the group of ambiguous problem list entries (Chi-square=27.12 p<0.0001). In addition to the explicit entries, the notes included 10% implicit entry candidates. MetaMap and UMLS are readily applicable to automate the problem list. Ambiguity in medical documents has consequences for performance evaluation of automated systems.
We introduce Chalkboard, a prototype tool for representing and displaying cell-signaling pathway knowledge, for carrying out simple qualitative reasoning over these pathways, and for generating ...quantitative biosimulation code. The design of Chalkboard has been driven by the need to quickly model and visualize alternative hypotheses about uncertain pathway knowledge. Chalkboard allows the biologists to test in silico the implications of various hypotheses. To fulfill this need, chalkboard includes (1) a rich ontology of pathway entities and interactions, which is ultimately informed by the basic chemistry and physics among molecules, and (2) a form of qualitative reasoning that computes causal chains and feedback loops within the network of entities and reactions. We demonstrate Chalkboard's capabilities in the domain of APP proteolysis, a pathway that plays a key role in the pathogenesis of Alzheimer's disease. In this pathway (as is common), information is incomplete and parts of the pathways are conjectural, rather than experimentally verified. With Chalkboard, we can carry out in silico perturbation experiments and explore the consequences of different conjectural connections and relationships in the network. We believe that pathway reasoning capabilities and in silico experiments will become a critical component of the hypothesis generation phase of modern biological research.
We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformat-ics modeling of biological structures and the ...bio-simulation modeling of biological processes. Where-as modeling anatomical entities is relatively well-studied, representing the physics-based semantics of biosimulation and biological processes remains an open research challenge. The OPB bridges this semantic gap-linking the semantics of biosimulation mathematics to structural bio-ontologies. Our design of the OPB is driven both by theory and pragmatics: we have applied systems dynamics theory to build an ontology with pragmatic use for annotating biosimulation models.
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field ...still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.
XML has become the default standard for data exchange among heterogeneous data sources, and in January 2007 XQuery (XML Query language) was recommended by the World Wide Web Consortium as the query ...language for XML. However, XQuery is a complex language that is difficult for non-programmers to learn. We have therefore developed XGI (XQuery Graphical Interface), a visual interface for graphically generating XQuery. In this paper we demonstrate the functionality of XGI through its application to a biomedical XML dataset. We describe the system architecture and the features of XGI in relation to several existing querying systems, we demonstrate the system's usability through a sample query construction, and we discuss a preliminary evaluation of XGI. Finally, we describe some limitations of the system, and our plans for future improvements.
The semantic web is envisioned as an evolving set of local ontologies that are gradually linked together into a global knowledge network. Many such local "application" ontologies are being built, but ...it is difficult to link them together because of incompatibilities and lack of adherence to ontology standards. "Reference" ontologies are an emerging ontology type that attempt to represent deep knowledge of basic science in a principled way that allows them to be re-used in multiple ways, just as the basic sciences are re-used in clinical applications. As such they have the potential to be a foundation for the semantic web if methods can be developed for deriving application ontologies from them. We describe a computational framework for this purpose that is generalized from the database concept of "views", and describe the research issues that must be solved to implement such a framework. We argue that the development of such a framework is becoming increasingly feasible due to a convergence of advances in several fields.
Biosimulation models have the potential to improve our understanding of biological function, and ultimately could support disease diagnosis and prioritize treatment options. Here we identify ...characterizing features of computational models and a subset of considerations that may be taken into account when determining the appropriate simulation platform to support research needs.
...biological information from a new experiment may raise the importance of a variable hidden within a component. ...it becomes difficult to anticipate what information in a component should be ...exposed or hidden by an interface.\n For example, while one annotator may refer to the concept "D-glucose" from the ChEBI knowledge base 19, another may refer to the term "Glucose" from the Systematized Nomenclature of Medicine--Clinical Terms resource (SNOMED-CT 20). ...critical challenges for SAIM modeling include incentivizing model curators to annotate at this level of detail and developing intuitive software that minimizes annotation costs.
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