Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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Profile of On-Line Anatomy Information Resources: Design and Instructional Implications

This study is based on a review of 40 on-line anatomy web resources compiled from sites selected from our own searches as well as sites reviewed and published by an external group (Voiglio et al., 1999, Surg. Radiol. Anat. 21:65-68; Frasca et al., 2000, Surg. Radiol. Anat. 22:107-110). The purpose of our survey was to propose criteria by which anatomy educators could judge the characteristics of the currently available web-based resources for incorporation into the courses they teach. Each site was reviewed and scored based on a survey matrix that included four main categories: 1). site background information, 2). content components, 3). interactivity features, and 4). user interface design components. The average score of the reviewed sites was 3.3 of the total possible score of 10, indicating the limited use of computer-based design features by the majority of sites. We found, however, a number of programs in each of the survey categories that could serve as prototypes for designing future on-line anatomy resources. From the survey we conclude that various design features are less important than the comprehensiveness, depth, and logical organization of content. We suggest that the content should be sufficient for supporting explicitly defined educational objectives, which should target specific end-user populations. The majority of anatomy programs currently accessible on-line fall short of these requirements. There is a need for a coordinated and synergistic effort to generate a comprehensive anatomical information resource that is of sufficient quality and depth to support higher levels of learning beyond the memorization of structure names. Such a resource is a prerequisite for meaningful on-line anatomy education

Paroxysmal Nocturnal Hemoglobinuria: New Thoughts

I have tried to summarize some of the facts we know, and some questions we need to ask in a disease which, although it is not common, probably is not as rare as we once thought. Once the diagnosis is made, one must be very careful in tending to the patients, since there are instances in which they react much differently than would normal people--either by the hemolytic episode or with other complications. This is especially true with regard to surgery, which may be extremely dangerous in these patients. The post-operative course may be complicated by thrombosis, infections, and other forms of morbidity. Identification of these patients is important, simple, and relatively helpful in their care

The Digital Anatomist Information System and Its Use in the Generation and Delivery of Web-Based Anatomy Atlases

Advances in network and imaging technology, coupled with the availability of 3-D datasets such as the Visible Human, provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a half year period from June 1995–January 1997, the on-line atlases were accessed by over 33,000 sites from 94 countries, with an average of over 4000 ‘‘hits’’ per day, and 25,000 hits per day during peak exam periods. The atlases have been linked to by over 500 sites, and have received at least six unsolicited awards by outside rating institutions. The flexibility of the software framework has allowed the information system to evolve with advances in technology and representation methods. Possible new features include knowledge-based image retrieval and tutoring, dynamic generation of 3-D scenes, and eventually, real-time virtual reality navigation through the body. Such features, when coupled with other on-line biomedical information resources, should lead to interesting new ways for managing and accessing structural information in medicine

An Ontology-based Image Repository for a Biomedical Research Lab

We have developed a prototype web-based database for managing images acquired during experiments in a biomedical research lab studying the factors controlling cataract development. Based on an evolving ontology we are developing for describing the experimental data and protocols used in the lab, the image repository allows lab members to organize image data by multiple attributes. The use of an ontology for developing this and other tools will facilitate intercommunication among tools, and eventual data sharing with other researchers

OQAFMA Querying Agent for the Foundational Model of Anatomy: a Prototype for Providing Flexible and Efficient Access to Large Semantic Networks

The development of large semantic networks, such as the UMLS, which are intended to support a variety of applications, requires a exible and e cient query interface for the extraction of information. Using one of the source vocabularies of UMLS as a test bed, we have developed such a prototype query interface. We rst identify common classes of queries needed by applications that access these semantic networks. Next, we survey STRUQL, an existing query language that we adopted, which supports all of these classes of queries. We then describe the OQAFMA Querying Agent for the Foundational Model of Anatomy (OQAFMA), which provides an e cient implementation of a subset of STRUQL by pre-computing a variety of indices. We describe how OQAFMA leverages database optimization by converting STRUQL queries to SQL. We evaluate the exibility and e ciency of our implementation using English queries written by anatomists. This evaluation veri es that OQAFMA provides exible, e cient access to one such large semantic network, the Foundational Model of Anatomy, and suggests that OQAFMA could be an e cient query interface to other large biomedical knowledge bases, such as the Uni ed Medical Language System

Design of an Anatomy Information System

Biology and medicine rely fundamentally on anatomy. Not only do you need anatomical knowledge to understand normal and abnormal function, anatomy also provides a framework for organizing other kinds of biomedical data. That’s why medical and other health sciences students take anatomy as one of their first courses. The Digital Anatomist Project undertaken by members of the University of Washington Structural Informatics Group aims to “put anatomy on a computer” in such a way that anatomical information becomes as fundamental to biomedical information management as the study of anatomy is to medical students. To do this we need to develop methods for representing anatomical information, accessing it, and reusing it in multiple applications ranging from education to clinical practice. This development process engenders many of the core research areas in biological structural informatics, which we have defined as a subfield of medical informatics dealing with information about the physical organization of the body. By its nature, structural information proves highly amenable to representation and visualization by computer graphics methods. In fact, computer graphics offers the first real breakthrough in anatomical knowledge representation since publication of the first scholarly anatomical treatise in 1546, in that it provides a means for capturing the 3D dynamic nature of the human body. In this article we explain the nature of anatomical information and discuss the design of a system to organize and access it. Example applications show the potential for reusing the same information in contexts ranging from education to clinical medicine, as well as the role of graphics in visualizing and interacting with anatomical representations

A Relation-Centric Query Engine for the Foundational Model of Anatomy

The Foundational Model of Anatomy (FMA), a detailed representation of the structural organization of the human body, was constructed to support the development of software applications requiring knowledge of anatomy. The FMA's focus on the structural relationships between anatomical entities distinguishes it from other current anatomical knowledge sources. We developed Emily, a query engine for the FMA, to enable users to explore the richness and depth of these relationships. Preliminary analysis suggests that Emily is capable of correctly processing real world anatomical queries provided they have been translated into a constrained form suitable for processing by the query engine

Problems and Solutions with Integrating Terminologies into Evolving Knowledge Bases

We have merged two established anatomical terminologies with an evolving ontology of biological structure: the Foundational Model of Anatomy. We describe the problems we have encountered and the solutions we have developed. We believe that both the problems and solutions generalize to the integration of any legacy terminology with a disciplined ontology within the same domain