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PubMed2006

Definition of an XML markup language for clinical laboratory procedures and comparison with generic XML markup.

BACKGROUND: Clinical laboratory procedure manuals are typically maintained as word processor files and are inefficient to store and search, require substantial effort for review and updating, and integrate poorly with other laboratory information. Electronic document management systems could improve procedure management and utility. As a first step toward building such systems, we have developed a prototype electronic format for laboratory procedures using Extensible Markup Language (XML). METHODS: Representative laboratory procedures were analyzed to identify document structure and data elements. This information was used to create a markup vocabulary, CLP-ML, expressed as an XML Document Type Definition (DTD). To determine whether this markup provided advantages over generic markup, we compared procedures structured with CLP-ML or with the vocabulary of the Health Level Seven, Inc. (HL7) Clinical Document Architecture (CDA) narrative block. RESULTS: CLP-ML includes 124 XML tags and supports a variety of procedure types across different laboratory sections. When compared with a general-purpose markup vocabulary (CDA narrative block), CLP-ML documents were easier to edit and read, less complex structurally, and simpler to traverse for searching and retrieval. CONCLUSION: In combination with appropriate software, CLP-ML is designed to support electronic authoring, reviewing, distributing, and searching of clinical laboratory procedures from a central repository, decreasing procedure maintenance effort and increasing the utility of procedure information. A standard electronic procedure format could also allow laboratories and vendors to share procedures and procedure layouts, minimizing duplicative word processor editing. Our results suggest that laboratory-specific markup such as CLP-ML will provide greater benefit for such systems than generic markup.

Clinical Laboratory Information Systems↗
PubMed1996

A Tcl-based SRS v. 4 interface.

A new SRS (Sequence Retrieval System) user interface has been developed for SRS v.4. Key features are the support of simple character-oriented (ASCII, VT100) terminals by coding in Tcl augmented by some dedicated Curses calls, support of graphics terminals in an X-Windows version by using the Tk extension to Tcl, and support of a client/server environment by using the TDP extension to Tcl. The Sequence Retrieval System (SRS) is a powerful tool for the fast extraction of information from flat file libraries (Etzold and Argos, 1993) and has rapidly established itself as a major research instrument for the bio-informatics community. Internally the system employs a query language, which is user accessible through either a command-line user interface, 'getz', or a more user friendly, character-oriented window interface. For SRS versions up to release v. 3, this window interface supported VT100-compatible terminals. Because of major changes in the underlying SRS libraries, the v. 3 interface became fully incompatible with the most recent version of SRS (v. 4.x). Thus the many users with only a simple terminal/terminal emulator connection were either deprived of access to SRS, or were forced to use the ASCII WWW client LYNX. This prompted us to develop a character-oriented SRS v. 4 window interface with the look and feel of its SRS v. 3.1 predecessor and coded to be as library independent as possible to maintain compatibility with future SRS releases. In addition, some 'extensions' were coded to widen the applicability to graphics terminals and to a client/server environment. At the time of preparation of this paper, the SRS interface described had been implemented in one form or another on most EM Bnet nodes and on all the platforms given in Table II. The code has been stored at the EMBL in Heidelberg, where it will be available, with installation instructions and scripts, as part of the SRS distribution.

Computer Graphics↗
PubMed1994

Macromolecular query language (MMQL): prototype data model and implementation.

Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu.

Amino Acid Sequence↗
PubMed2004

ICPC Multilingual Collaboratory: a Web- and Unicode-based system for distributed editing/translating/viewing of the multilingual International Classification of Primary Care.

The International Classification of Primary Care (ICPC) is a clinical classification containing 726 clinical concepts, available in over 20 languages, augmented by links to ICD-10 concepts. It is employed in clinical information systems in several European countries, Israel, Japan, and Australia. In translating ICPC, it has been challenging to manage the flow of multilingual information, maintain its quality, and optimize its portability, particularly in light of the numerous character encodings used to represent its content. The ICPC Multilingual Collaboratory (IMC) is a World Wide Web-based environment, created to allow the viewing, maintenance, and translation of ICPC content by a dispersed international editorial staff. Based upon open-source software, it represents ICPC content using the Unicode standard for character encoding. The system implements three interfaces to ICPC data: 1) a password-protected editorial interface which instantiates a hierarchical authority model and communication channels for review and control of content, including a means of up-loading new candidate translations; 2) an openly accessible read-only interface, with e-mail access to the editors (providing another level of content review); and, 3) a management interface for the system administrator. The completed system powerfully demonstrates the ability of the World Wide Web, open-source software, and Unicode to expedite and simplify international multilingual collaboration, even in a world in which Unicode support is incomplete on existing computing platforms.

Female↗
PubMed1997

WWW creates new interactive 3D graphics and collaborative environments for medical research and education.

Virtual Reality Modelling Language (VRML) is the start of a new era for medicine and the World Wide Web (WWW). Scientists can use VRML across the Internet to explore new three-dimensional (3D) worlds, share concepts and collaborate together in a virtual environment. VRML enables the generation of virtual environments through the use of geometric, spatial and colour data structures to represent 3D objects and scenes. In medicine, researchers often want to interact with scientific data, which in several instances may also be dynamic (e.g. MRI data). This data is often very large and is difficult to visualise. A 3D graphical representation can make the information contained in such large data sets more understandable and easier to interpret. Fast networks and satellites can reliably transfer large data sets from computer to computer. This has led to the adoption of remote tale-working in many applications including medical applications. Radiology experts, for example, can view and inspect in near real-time a 3D data set acquired from a patient who is in another part of the world. Such technology is destined to improve the quality of life for many people. This paper introduces VRML (including some technical details) and discusses the advantages of VRML in application developing.

Computer Communication Networks↗
PubMed1989

Computers in a human perspective: an alternative way of teaching informatics to health professionals.

An alternative way of teaching informatics, especially health informatics, to health professionals of different categories has been developed and practiced. The essentials of human competence and skill in handling and processing information are presented parallel with the essentials of computer-assisted methodologies and technologies of formal language-based informatics. Requirements on how eventually useful computer-based tools will have to be designed in order to be well adapted to genuine human skill and competence in handling tools in various work contexts are established. On the basis of such a balanced knowledge methods for work analysis are introduced. These include how the existing problems at a workplace can be identified and analyzed in relation to the goals to be achieved. Special emphasis is given to new ways of information analysis, i.e. methods which even allow the comprehension and documentation of those parts of the actually practiced 'human' information handling and processing which are normally overlooked, as e.g. non-verbal communication processes and so-called 'tacit knowledge' based information handling and processing activities. Different ways of problem solving are discussed involving in an integrated human perspective--alternative staffing, enhancement of the competence of the staff, optimal planning of premises as well as organizational and technical means. The main result of this alternative way of education has been a considerably improved user competence which in turn has led to very different designs of computer assistance and man-computer interfaces. It is the purpose of this paper to give a brief outline of the teaching material and a short presentation of the above mentioned results.(ABSTRACT TRUNCATED AT 250 WORDS)

Attitude to Computers↗
PubMed1995

Using intermediate states to improve the ability of the Arden Syntax to implement care plans and reuse knowledge.

The Arden Syntax is one of a few knowledge representation languages currently in use for clinical decision support. While some of these languages are being used in active patient care settings, none have gained widespread acceptance as a clinical tool. Prior attempts to represent temporally complex care plans in the Arden Syntax have revealed difficulties in representing and tracking series of consecutive time-oriented events and recommendations, in sharing and reusing knowledge and in dealing with unobtainable data. In an attempt to improve Arden's ability to deal with these problems and demonstrate the importance of these factors, the clinical event monitor has been adapted to store coded data representing Intermediate States in the Columbia Presbyterian Medical Center (CPMC) central data repository. The Intermediate States define the current state of the patient as laid out in the care plan. Four care plans were constructed. The findings include an improved ability to track complex series of events and recommendations over long periods of time. The knowledge generated by the electronic care plans was able to be reused by the care plan that generated it, by other elements of the knowledge base and by non-decision support applications. Modular development, facilitated by the changes, simplified dealing with data not available to the central data repository by aiding the implementation of those parts of the care plan for which sufficient data is available.

Artificial Intelligence↗
PubMed1988

Effects of pulmonary emphysema on QRS infarct size score.

Pulmonary emphysema can produce false-positive electrocardiographic (ECG) changes of anterior myocardial infarction (MI). This problem was not addressed in earlier studies of the Selvester 54 Criteria/32 Point QRS score for MI size. The purpose of this study was to examine an automated Hewlett Packard ECG Computer Language (HP-ECL) implementation of the QRS score in the following groups of subjects. Patients who had been studied for possible lung disease with pulmonary tests, including lung volumes, were divided into two groups: group 1 (n = 133), with abnormal tests (emphysema); and group 2 (n = 102), with normal tests (no emphysema). Two other groups were studied: group 3 (positive controls, n = 44), with greater than 3 QRS points for MI on ECG and documented coronary disease with wall motion abnormalities on angiography; and group 4 (negative controls, n = 146), 49 house staff and 97 clinically normal men. A frontal plane P axis greater than 65 separated 90% of patients with emphysema from those without. Of 133 patients with emphysema, 60 (45%) had greater than 3 QRS points for MI on ECG, mainly from Q criteria in aVL and V1-V3; decreased R criteria 1 in V2, V3, and V6; and abnormal R/S criteria in V4-V6. Using HP-ECL, the QRS score was readily modified so that when P axis was greater than 65 these MI size criteria were suppressed. This resulted in a more appropriate incidence of MI diagnoses: 2% (down from 45%) in emphysema patients, no change in specificity, and minor reduction in sensitivity to MI in infarct controls from 100% to 96%.(ABSTRACT TRUNCATED AT 250 WORDS)

Electrocardiography↗
PubMedDate not supplied

The SGML standardization framework and the introduction of XML.

Extensible Markup Language (XML) is on its way to becoming a global standard for the representation, exchange, and presentation of information on the World Wide Web (WWW). More than that, XML is creating a standardization framework, in terms of an open network of meta-standards and mediators that allows for the definition of further conventions and agreements in specific business domains. Such an approach is particularly needed in the healthcare domain; XML promises to especially suit the particularities of patient records and their lifelong storage, retrieval, and exchange. At a time when change rather than steadiness is becoming the faithful feature of our society, standardization frameworks which support a diversified growth of specifications that are appropriate to the actual needs of the users are becoming more and more important; and efforts should be made to encourage this new attempt at standardization to grow in a fruitful direction. Thus, the introduction of XML reflects a standardization process which is neither exclusively based on an acknowledged standardization authority, nor a pure market standard. Instead, a consortium of companies, academic institutions, and public bodies has agreed on a common recommendation based on an existing standardization framework. The consortium's process of agreeing to a standardization framework will doubtlessly be successful in the case of XML, and it is suggested that it should be considered as a generic model for standardization processes in the future.

Cohort Studies↗
PubMedDate not supplied

HIS/RIS/PACS integration: getting to the gold standard.

The technology for acquiring, storing, retrieving, displaying, and distributing images has advanced dramatically in recent years. The push is toward enterprise-wide image management solutions, where digital images from radiology, cardiology, and other "ologies" are seamlessly linked with information from clinical information systems and other databases, and they are accessed seamlessly from a single point of end-user interaction. The "gold standard" of system integration would provide the platform for improved workflow, patient throughput and patient safety, as well as decreased cost. Unfortunately, the gold standard remains elusive in most healthcare environments, even those with new systems. One of the earliest issues that plagued the progress of hospital information system/radiology information systems/picture archiving and communication systems (HIS/RIS/PACS) integration was a matter of language between Health Level-7 (HL7) and DICOM. This barrier was solved by the broker--a software and hardware device that accepts HL7 messages from the RIS then translates, or maps, the data to produce DICOM messages for transmission to the PACS. Technologist workflow requires patient and exam information from the RIS to flow to the modality. The broker provides support for this by taking advantage of the DICOM Modality Worklist (DMWL). Two primary problems are inherent in most brokered configurations. Workflow is driven by paper, and RIS information flows in 1 direction only, which leads to duplicative databases. Overcoming the limitations of HIS/RIS/PACS connectivity requires industry accepted communication protocols/rules. To facilitate this, the Integrating the Health Care Enterprise (IHE) initiative was developed. The goal of IHE is to provide end-users improved access to critical patient and clinical information across all systems within the healthcare delivery network. While the IHE initiative began to facilitate more efficient, predictable, and functional integration between disparate systems, vendors still had technology hurdles to overcome. System integration continues to be significantly hampered, not by technology limitations, but instead by business and political issues. In response to these challenges, several vendors have begun to offer consolidated RIS/PACS solutions and/or HIS/RIS/PACS solutions. Consequently, the prospect of the gold standard appears to be on the horizon. Single vendor consolidated systems are not, however, feasible for deployment in many healthcare organizations, and they are not necessarily the panacea.

Database Management Systems↗
PubMed2006

Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.

BACKGROUND: Approximately 30% of intubated preterm infants with respiratory distress syndrome (RDS) will fail attempted extubation, requiring reintubation and mechanical ventilation. Although ventilator technology and monitoring of premature infants have improved over time, optimal extubation remains challenging. Furthermore, extubation decisions for premature infants require complex informational processing, techniques implicitly learned through clinical practice. Computer-aided decision-support tools would benefit inexperienced clinicians, especially during peak neonatal intensive care unit (NICU) census. METHODS: A five-step procedure was developed to identify predictive variables. Clinical expert (CE) thought processes comprised one model. Variables from that model were used to develop two mathematical models for the decision-support tool: an artificial neural network (ANN) and a multivariate logistic regression model (MLR). The ranking of the variables in the three models was compared using the Wilcoxon Signed Rank Test. The best performing model was used in a web-based decision-support tool with a user interface implemented in Hypertext Markup Language (HTML) and the mathematical model employing the ANN. RESULTS: CEs identified 51 potentially predictive variables for extubation decisions for an infant on mechanical ventilation. Comparisons of the three models showed a significant difference between the ANN and the CE (p = 0.0006). Of the original 51 potentially predictive variables, the 13 most predictive variables were used to develop an ANN as a web-based decision-tool. The ANN processes user-provided data and returns the prediction 0-1 score and a novelty index. The user then selects the most appropriate threshold for categorizing the prediction as a success or failure. Furthermore, the novelty index, indicating the similarity of the test case to the training case, allows the user to assess the confidence level of the prediction with regard to how much the new data differ from the data originally used for the development of the prediction tool. CONCLUSION: State-of-the-art, machine-learning methods can be employed for the development of sophisticated tools to aid clinicians' decisions. We identified numerous variables considered relevant for extubation decisions for mechanically ventilated premature infants with RDS. We then developed a web-based decision-support tool for clinicians which can be made widely available and potentially improve patient care world wide.

Birth Weight↗
PubMed2003

Presenting XML-based medical discharge letters according to CDA.

UNLABELLED: The HL7 Clinical Document Architecture (CDA) is an important XML-based standard for the representation of clinical documents. OBJECTIVES: The use of Markup Languages could satisfy the demands of involved healthcare staff as well as the needs of patients, to receive an overview of the patient's treatment during the hospital stay. The standardization efforts of different groups dealing with this problem have demonstrated progress, but have not, as yet, achieved a routinely usable result. In particular, differentiating information according to a hierarchical order has not been published to date. METHODS: A retrospective analysis of 60 discharge letters from a cardiology ward (ward A) as well as 60 discharge letters from a gastroenterology ward (ward B) were extracted from the central hospital information system, by taking every fifth discharge letter issued over a one year period. RESULTS: An XML-based prototype for medical discharge letters has been put in place representing the required information units and information elements. By means of an XSL-stylesheet, a detailed representation of the conventional discharge letter has been produced that is platform independent and permits the recurrent use of information units. CONCLUSIONS: Through the introduction of definitions like information elements and information units, progress in the development of CDA level two and three might be realized. We present a method by which discharge letters can be used by an Internal Medicine Department. This concept is implemented in a XML-based prototype allowing a special view on XML data to generate this document type.

Aged↗
PubMed2002

Building a bioinformatics ontology using OIL.

This paper describes the initial stages of building an ontology of bioinformatics and molecular biology. The conceptualization is encoded using the ontology inference layer (OIL), a knowledge representation language that combines the modeling style of frame-based systems with the expressiveness and reasoning power of description logics (DLs). This paper is the second of a pair in this special issue. The first described the core of the OIL language and the need to use ontologies to deliver semantic bioinformatics resources. In this paper, the early stages of building an ontology component of a bioinformatics resource querying application are described. This ontology (TaO) holds the information about molecular biology represented in bioinformatics resources and the bioinformatics tasks performed over these resources. It, therefore, represents the metadata of the resources the application can query. It also manages the terminologies used in constructing the query plans used to retrieve instances from those external resources. The methodology used in this task capitalizes upon features of OIL-The conceptualization afforded by the frame-based view of OIL's syntax; the expressive power and reasoning of the logical formalism; and the ability to encode both handcrafted, hierarchies of concepts, as well as defining concepts in terms of their properties, which can then be used to establish a classification and infer relationships not encoded by the ontologist. This ability forms the basis of the methodology described here: For each portion of the TaO, a basic framework of concepts is asserted by the ontologist. Then, the properties of these concepts are defined by the ontologist and the logic's reasoning power used to reclassify and infer further relationships. This cycle of elaboration and refinement is iterated on each portion of the ontology until a satisfactory ontology has been created.

Algorithms↗
PubMed2003

MedCIRCLE: collaboration for Internet rating, certification, labelling and evaluation of health information on the World-Wide-Web.

We describe MedCIRCLE, an EU-funded semantic web project to implement the first steps towards a global, collaborative rating and guidance system for health information proposed in the MedCERTAIN project. In MedCIRCLE, three European gateway sites for consumer health information will implement the metadata vocabulary HIDDEL (Health Information Disclosure, Description and Evaluation Language). HIDDEL allows portals and gateways to make the results of their evaluations accessible as XML/RDF. The three participating national portals are: AQUMED (Agency for Quality in Medicine) patienten-information, de, COMB (Official Medical College of Barcelona) and CISMeF, a quality-controlled health gateway developed at Rouen University Hospital. Other health subject gateways, accreditation, or rating services are invited to join the collaboration simply by implementing HIDDEL on their gateways. Widespread implementation HIDDEL will allow intelligent agents or client-side software to harvest statements and opinions about the trustworthiness of other websites, assisting users in selecting trustworthy websites. The MedCIRCLE project builds on, expands and continues work on rating health information on the Internet piloted within the MedCERTAIN project. While MedCERTAIN provided the core technologies and software for rating and "trustmarking" health information, MedCIRCLE is built around these technologies and involves a wider medical community to assess health information, demonstrating the power of collaborative and interoperable evaluations in a semantic web environment. MedCIRCLE is a project with the overall objective to develop and promote technologies able to guide consumers to trustworthy health information on the Internet, to establish a global web of trust for networked health information, and to empower consumers to positively select high quality health information on the web. Other aims include refinement and expansion of HIDDEL, to become a standard vocabulary and interchange format for self- and third-party ratings of health information.

Europe↗
PubMed2006

Duke Surgery Research Central: an open-source Web application for the improvement of compliance with research regulation.

BACKGROUND: Although regulatory compliance in academic research is enforced by law to ensure high quality and safety to participants, its implementation is frequently hindered by cost and logistical barriers. In order to decrease these barriers, we have developed a Web-based application, Duke Surgery Research Central (DSRC), to monitor and streamline the regulatory research process. RESULTS: The main objective of DSRC is to streamline regulatory research processes. The application was built using a combination of paper prototyping for system requirements and Java as the primary language for the application, in conjunction with the Model-View-Controller design model. The researcher interface was designed for simplicity so that it could be used by individuals with different computer literacy levels. Analogously, the administrator interface was designed with functionality as its primary goal. DSRC facilitates the exchange of regulatory documents between researchers and research administrators, allowing for tasks to be tracked and documents to be stored in a Web environment accessible from an Intranet. Usability was evaluated using formal usability tests and field observations. Formal usability results demonstrated that DSRC presented good speed, was easy to learn and use, had a functionality that was easily understandable, and a navigation that was intuitive. Additional features implemented upon request by initial users included: extensive variable categorization (in contrast with data capture using free text), searching capabilities to improve how research administrators could search an extensive number of researcher names, warning messages before critical tasks were performed (such as deleting a task), and confirmatory e-mails for critical tasks (such as completing a regulatory task). CONCLUSION: The current version of DSRC was shown to have excellent overall usability properties in handling research regulatory issues. It is hoped that its release as an open-source application will promote improved and streamlined regulatory processes for individual academic centers as well as larger research networks.

Academic Medical Centers↗
PubMed2001

[Specific nature of the software used to construct simulations: physiologically-based toxicokinetic models].

Building of the physiologically-based toxicokinetic (PBTK) models is based on the application of simulation languages, such as advanced continuous simulation language (ACSL). The aim of this study was to develop the principles of constructing the fundamental model and the models dedicated to chemicals found in the work environment (e.g. trimethylbenzene (TMB) isomers present in the petrochemical, paint and lacquer and related industries). The fundamental model is based on four main compartments (fat tissues, richly perfused tissue, slowly perfused tissue and liver) and six auxiliary compartments (lungs, venous blood, arterial blood, body weight, inhaled air and exhaled air). The basic element of the PBTK model comprises blocks containing definitions of variables and constants supplemented by the following parameters: command, calculated, transferred and resulted. The models dedicated to various chemicals and organisms are built by a suitable modification of the fundamental model. All sets of command parameters values for the organism, chemical and simulation are written in the text files and loaded before or during the simulation. The empirical data obtained in experiments with volunteers are used in a similar way. The specimen dedicated model was built for 1,2,3-TMB (hemimellitene). 2,3-Dimethylbenzoic acid (2,3,-DMBA) (a hemimelitene metabolite) excretion rate data obtained from an experiment during which volunteers were exposed to hemimellitene at 25 at 100 mg/m3 were compared with the results of the computer simulation. A high convergence of the comparable values was obtained. Simulations were also made for exposure periods of one week and one month. The results confirmed the experiment-based recommendations on the assessment of the occupational exposure. The application of the new physiologically-based toxicokinetic models renders it possible to forecast toxic chemical (or it metabolite) concentrations corresponding to the concentrations of those chemicals in the workplace atmosphere.

Body Fluid Compartments↗
PubMed2005

The tissue micro-array data exchange specification: a web based experience browsing imported data.

BACKGROUND: The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel and Microsoft Word are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. RESULTS: Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. CONCLUSION: Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA.

AIDS-Related Complex↗