In clinical studies, researchers must often maintain a freezer inventory of biosamples. Existing software packages, designed to track and manage freezer inventory, are not always suitable for small laboratories. We present a lightweight, low cost, alternative that's more appropriate for small studies with limited resources.
The biological and biomedical communities have been developing highly
structured, rich data sets for representing, analyzing and integrating complex biomed-
ical knowledge on the semantic web. However, the complexity of the query languages
that have been developed to access these resources makes it diﬃcult for non-technical
users to explore the data sets that have been developed, limiting the utility and wide-
spread adoption of both the data sets and the query languages. We present VIQUEN,
a graphical query engine designed to allow users to express sophisticated queries, which
are then compiled into a more complex underlying query language. After the...
Brinkley, James F.; Detwiler, Landon T.
We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written...
In this dissertation, I present three browsers that I have developed for the purpose
of exploring, understanding, and analyzing models, simulations, and ontologies in
biology and medicine. The ﬁrst browser visualizes multidimensional simulation data
as an animation. The second browser visualizes the equations of a complex model as
a network and puts structure and organization on top of equations and variables. The
third browser is an ontology viewer and editor, directly intended for the Foundational
Model of Anatomy (FMA), but applicable to other ontologies as well. This browser
has two contributions. First, it is a lightweight deliverable that lets someone...
Shaker, Ronald; Hertzenberg, Xenia; Brinkley, James
Research data from a single clinical study is often spread across multiple applications and systems. We present a reusable, lightweight, secure framework for automatically integrating and querying study data from heterogeneous sources in order to answer routine, operational questions for researchers.
Shaw, Marianne; Detwiler, Landon T; Noy, N. F.; Brinkley, James F; Suciu, Dan
Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages.
Wynden, Rob; Solbrig, Harold; Tu, Samson; Brinkley, James F
A common definition of value set will be provided and fully characterized relative to its proposed uses. We will describe, compare, and contrast several approaches to specifying and referencing value sets in a stable manner over time. The term “value set”, although ubiquitous within biomedical informatics has no common definition and has yet to be fully described in a formal manner. It is essential for the design and launch of new ontologies, biomedical informatics applications and data sharing environments that a common and well-‐ understood definition of “value set” is provided. It is also essential that options and trade-‐offs be...
Nichols, Nolan; Detwiler, Landon T; Franklin, Joshua D; Brinkley, James F
Operational Quality Control (QC) checks are standard practice in clinical trials and ensure ongoing compliance with the study protocol, standard operating procedures (SOPs) and Good Clinical Practice (GCP). We present a method for defining QC checks as distributed queries over case report forms (CRF) and clinical imaging data- sources. Our distributed query system can integrate time-sensitive information in order to populate QC checks that can facilitate discrepancy resolution workflow in clinical trials.
Detwiler, Landon T; Brinkley, James F
We present a method for defining value sets as queries over ontologies (ontology views), and a mechanism for evaluating such queries. In particular we demonstrate an approach utilizing reusable template queries and parameterized URLs. We illustrate this method using an example from the Ontology of Clinical Research (OCRe).
Franklin, Joshua D; Guidry, Alicia F; Brinkley, James F
The data collection process for clinical trials can be a tedious and error-prone process, and even a barrier to initiating small-scale studies. Electronic Data Capture (EDC) software can meet the need for faster and more reliable collection of data, but these informatics solutions can also be difficult to for researchers to set up. Establishing a full-featured commercial Clinical Trials Management System (CTMS) ecosystem is not realistic due to current institutional resource constraints. As an alternative solution, our Biomedical Informatics core (BMI) provided the technical expertise to pilot each EDC system in partnership with research teams and performed a qualitative evaluation...
There are many ways to use computer systems to record the information generated during the course of clinical trials. The Electronic Data Capture, or EDC, systems have a range of features from a simple basic functionality to sophisticated and complex specialty systems. The costs of these systems also vary from very expensive proprietary products to a recent trend of Open Source software that is distributed without a license fee. Traditionally, academic projects have made use of existing software resources like spreadsheets and Microsoft Access databases. This guide will present information on the low cost options using existing software or Open...
Brinkley, James F; Turner, Jessica A; Detwiler, Landon T; Mejino, Jose L V; Martone, Maryanne E; Rubin, Daniel L
We demonstrate the usefulness of the Foundational Model of Anatomy (FMA) ontology in reconciling different neuroanatomical parcellation schemes in order to facilitate automatic annotation and “intelligent” querying and visualization over a large multisite fMRI study of schizophrenic versus normal controls.
Detwiler, Landon T; Shaw, Marianne; Brinkley, James F
Like views in relational databases, ontology views are expressed as queries, but over source ontologies rather than tables. To enhance the reusability of such views, we are constructing a view Query Manager application. The Query Manager allows queries to be edited, executed, and stored for reuse. View queries are discoverable by searching the Query Manager's metadata catalog. The Query Manager also supports the storage of materialized view results upon which further queries may be issued.
Mejino, Jose L V; Detwiler, Landon T; Turner, Jessica A; Martone, Maryann E; Rubin, Daniel L; Brinkley, James F
In this study we focused on empowering RadLex with an ontological framework and additional content derived from the Foundational Model of Anatomy Ontology1 thereby providing RadLex the facility to correlate the different standards used in annotating neuroradiological image data. The objective of this work is to promote data sharing, data harmonization and interoperability between disparate neuroradiological labeling systems.
Nichols, Nolan; Perlmutter, Aaron; Mejino, Jose L V; Brinkley, James F
Our current effort focuses on representing connectivity relationships between gray and white matter structures in the Foundational Model of Anatomy Ontology (FMA). There are a number of terms used that imply either structural or functional relationship, but the semantics have not been made formally explicit in the ontology. In this work we propose a set of definitions to disambiguate and clarify the terminologies describing the types of connectivity relationships that exist between gray and white matter structures at different levels of granularity.
Shen, Terry H; Detwiler, Landon T; Tarczy-Hornoch, Peter; Cadag, Eithon; Carlson, Christopher S
Genome wide association studies (GWAS) are an important approach to understanding the genetic mechanisms behind human diseases. Single nucleotide polymorphisms (SNPs) are the predominant markers used in genome wide association studies, and the ability to predict which SNPs are likely to be functional is important for both a priori and a posteriori analyses of GWA studies. This article describes the design, implementation and evaluation of a family of systems for the purpose of identifying SNPs that may cause a change in phenotypic outcomes. The methods described in this article characterize the feasibility of combinations of logical and probabilistic inference with...
Turner, Jessica A; Mejino, Jose L V; Brinkley, James F; Detwiler, Landon T; Lee, Hyo Jong; Martone, Maryann E; Rubin, Daniel L
The annotation of functional neuroimaging results for data sharing and re-use is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA) to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus). This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural...
John H, Gennari; Maxwell L, Neal; Brian E, Carlson; Daniel L, Cook
Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semi- automatically merge models to more effectively build larger, multi-scale models. How- ever, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demon- strates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate...
Neal, Maxwell L; Gennari, John H; Arts, Theo; Cook, Daniel L
As a case-study of biosimulation model integration, we describe our experiences applying the SemSim methodology to integrate independently-developed, multiscale models of cardiac circulation. In particular, we have integrated the CircAdapt model (written by T. Arts for MATLAB) of an adapting vascular segment with a cardiovascular system model (written by M. Neal for JSim). We report on three results from the model integration experience. First, models should be explicit about simulations that occur on different time scales. Second, data structures and naming conventions used to represent model variables may not translate across simulation languages. Finally, identifying the dependencies among model variables...
Kalet, Ira; Mejino, Jose L V; Wang, Vania; Whipple, Mark; Brinkley, James F
Biomedical ontologies are envisioned to be usable in a range of research and clinical applications. The requirements for such uses include formal consistency, adequacy of coverage, and possibly other domain specific constraints. In this report we describe a case study that illustrates how application specific requirements may be used to identify modeling problems as well as data entry errors in ontology building and evolution. We have begun a project to use the UW Foundational Model of Anatomy (FMA) in a clinical application in radiation therapy planning. This application focuses mainly (but not exclusively) on the representation of the lymphatic system...