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UW-SIG Projects


Projects are chosen based on several criteria: 1) funding opportunities, 2) interested collaborators, 3) relevance to general issues of structural informatics.

In most cases the project should present difficult informatics issues, which if solved, would generalize towards a structural information framework. It is also an important goal of our group to develop practical applications from these projects. These applications will not only be of use in biomedicine, but will also provide valuable feedback necessary for improvement.

We are currently focusing on these major projects:

These projects are described below, and a separate alphabetical list of subprojects is also available.

The Ontology Views Project

Research into the generation and utilization of application specific views of reference ontologies. The principle goals of the Ontology Views Project are to:

  1. create application ontologies as views over reference ontologies
  2. embed these views as queryable web services

In developing these methods we will pursue the following specific aims, in collaboration with the National Center for Biomedical Ontology (NCBO) and the UW computer science department:

The Foundational Model of Anatomy Ontology

Led by Onard Mejino

Symbolic representation of anatomy ranging from the macroscopic to molecular level. Over 75,000 concepts representing all structures visible to 1 mm, and many structures at the microscopic and molecular levels, are arranged in various ontologies using the Protege frame-based knowledge acquisition tool. The ontologies are then made available by various servers listed below. The FMA is one of the largest computer-based knowledge sources in the biomedical sciences.

Related subprojects:

Emily A relation-centric query interface for the FMA.
Foundational Model Explorer This JSP-based webapp is designed to facilitate navigation of the data contained with in the Foundational Model of Anatomy.
Foundational Model of Anatomy DB This database stores the data representing the relationships and entities of the Foundational Model of Anatomy, which is authored using the 'Protege' application.
OQAFMA Server OQAFMA. A query engine for the FMA that is optimized for certain types of queries, such as transitive closures. Takes StruQL query as input, returns XML result.

Biosimulation Project

Led by Dan Cook

Application Model Ontology (AMO) Project

Biosimulations are available in competing computational environments (e.g., JSim, Fortran, MatLab) yet models semantics are implicit in the mathematics or, at best, embedded in in-line code annotations. Recognizing the need to reuse and integrate such biosimulation models, we propose the Application Model Ontology (AMO) as a light-weight framework for ApplModels that are machine-readable symbolical representation for indexing and merging biosimulation models.

Ontology of Physics for Biology (OPB) Project

We are developing the Ontology of Physics for Biology (OPB) as a reference ontology of those aspects of classical physics that are essential for representing, annotating and encoding quantitative models of biological processes. The OPB will be essential for annotating, reusing and generating code for the libraries of biosimulation models that will be required for comprehensive multiscale simulations of humans.


Recognizing the potential benefits to human health that can be realized from applying and advancing the field of biomedical computing, the Biomedical Information Science and Technology Initiative (BISTI) was launched at the NIH in April 2000. This initiative is aimed at making optimal use of computer science and technology to address problems in biology and medicine.

Related SIG subprojects:

CELO Customizable Electronic Laboratory Online (CELO) is a Web-based Data Management System Builder for Biomedical Research Laboratories.
Eye Lab Image Repository The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. This web tool allows the researchers to add their images to a repository facilitating data management and organization.

The Digital Anatomist Information System

Symbolic representations for anatomy, as exemplified by the Foundational Model of Anatomy, are combined with spatial or image-based representation in a distributed information system. Various structural information servers access the spatial and symbolic resources, and various authoring and end-user client programs implement several applications. Among these applications are a foundational model explorer (FME), a graphical query engine to the FMA called Emily, a StruQL-based query engine for the FMA called OQAFMA, a natural language front-end that composes StruQL queries, a Lisp-based FMA server, a web-based image manager, FMA-based image retrieval, interactive atlases of anatomy, and a dynamic 3-D scene generator.

Current work is aimed at combining many of these separate applications into an Anatomy Explorer that will use the FMA as the basis for integrating and accessing various distributed anatomy resources.

Related subprojects:

AnnoteImage A Java tool for creating IML, an XML format for storing textual annotations to images. The annotation model is one of outlined regions, identified by labels, and colored 'strings' and 'pins'. The IML schema also allows for some limited metadata about the annotations. IML was based on an existing lisp-like format used in our web-based interactive anatomy atlases.
BodyGen A tool for reconstructing 3D anatomy models from serial sections.
Digital Anatomist Atlases Digital Anatomist Atlases are a set of C-based cgi scripts that allow web access to a series of anatomical atlases, ie, images with associated anatomical outlines and captions
Digital Anatomist Jigsaw Puzzle A Java Web Start(tm) application that takes a DA image and presents the various segments contained therein as puzzle pieces to be assembled.
Dynamic Scene Generator The 3D Scene Generator dynamically constructs composite scenes of anatomical models and integrates anatomical knowledge into the GUI for model selection.
Image Manager WIRM Repository The Image Manager WIRM Repository is a WIRM-based repository for images which allows user- and group-based permissions and can maintain hierarchical collections of images (subcollections).
Skandha4 A 3D graphics programming environment.
Who Wants to Be A (Digital) Anatomist? A Java Web Start(tm) application that quizes the user on the anatomical segments contained in a Digital Anatomist image in the spirit of "Who Wants to Be A Millionaire?"

Web Interfacing Repository Manager, a high-level programming environment for developing web information systems.

Biolucida Next generation Dynamic Scene Generator in Java, with output to interactive VRML, and planned access to databases.

The UW Human Brain Project

An on-line information system for managing and visualizing data about the human brain. In this case a structural model is used as a framework for organizing other information.

Related subprojects:

Brain Browser Web Interface The Brain Browser Web Interface is a Java applet that allows users to view reconstructed brain models and associated stimulation mappings.
Brain Map WIRM Repository The Brain Map WIRM Repository ('Bmap Repo') is a WIRM-based repository which manages data relating to the stimulation sites on the surface of the brain.
Brain Visualizer Graphics Server Graphics server for the Brain Visualizer. Uses Slisp for input and output.
Seedpod A model-driven data management tool
X_Batch A toolbox developed for batch processing of functional MRI data in SPM2. It utilizes Dartmouth fMRI Data Management Tool to document file processing steps. All information is stored in Protege ontology software.
XBrain The XBrain project is designed to allow fellow researchers to query SIG's Brain Mapping Database. The query language to use is XQuery, and the results are turned in XML. Written in JSP.
MindSeer Formerly BrainJ3D.  It is a visualization tool for multimodality brain imaging data.  It includes a high-performance standalone version and a client/server mode for use with a central data repository.
DXBrain DXBrain is a lightweight distributed data integration system for the UW Human Brain Project data network. Data sources are integrated at the query level, via distributed XQueries.
DXQP The Distributed XQuery Processor (DXQP) takes XQueries as input, breaks them down into targetted query snippets, sends these queries snippets to the appropriate source wrappers, and then combines the source results into a unified XML result document.
WIX WIX (Web Interface for XQuery) is a simple service that allows users to submit an XQuery to query an XML document. The servlet interface for submitting XQueries is simple and efficient and can easily be called from any programming language, other instances of XQuery, or an HTML form. WIX is used by DXBrain.

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