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PubMed2005

Development of a deterministic XML schema by resolving structure ambiguity of HL7 messages.

Health level 7 (HL7) is a standard for medical information exchange. It defines data transfers for the application systems in the healthcare environment. Alternatively, the extensible markup language (XML) is a standard for data exchange using the Internet. If exchange messages follow the content and the sequence defined by HL7 and are expressed in the XML format, the system may benefit from the advantages of both standards. In creating the XML schema, we found ambiguities in HL7 message structures that cause the XML schema to be non-deterministic. These ambiguous expressions are summarized within 12 structures and can be replaced with equivalent or similar unambiguous structures. The finite state automata are used to verify expression equivalence. Applying this schema, an XML document may eliminate redundant segment group definitions and make the structure simple and easy to reproduce. In this paper, we discuss the methods and our experience in resolving ambiguous problems in HL7 messages to generate a deterministic XML schema.

Health Status↗
PubMed2004

The development of MML (Medical Markup Language) version 3.0 as a medical document exchange format for HL7 messages.

Medical Markup Language (MML), as a set of standards, has been developed over the last 8 years to allow the exchange of medical data between different medical information providers. MML Version 2.21 used XML as a metalanguage and was announced in 1999. In 2001, MML was updated to Version 2.3, which contained 12 modules. The latest version--Version 3.0--is based on the HL7 Clinical Document Architecture (CDA). During the development of this new version, the structure of MML Version 2.3 was analyzed, subdivided into several categories, and redefined so the information defined in MML could be described in HL7 CDA Level One. As a result of this development, it has become possible to exchange MML Version 3.0 medical documents via HL7 messages.

Medical Informatics Applications↗
PubMed1998

Molecular modeling information transfer with VRML: from small molecules to large systems in bioscience.

The suitability of the Virtual Reality Modeling Language (VRML) for the communication of scientists via the internet is demonstrated with recent results from computer assisted cancer research: I. Substrate channels in cytochrome P450 enzymes. II. Binding properties of the wild type and mutated p53 tumor suppressor protein. Complex 3D molecular models were used to visualize new insights in the active site access of cytochrome P450 enzymes and in the p53 protein-DNA binding achieved by the use of computational methods. These 3D models of biomolecular systems were transferred into VRML scenarios. Additional implemented features allow users to receive related information interactively. With these examples it is shown that VRML provides an efficient method for scientific information exchange by the use of complex 3D molecular models.

Binding Sites↗
PubMed1999

XML and its impact on content and structure in electronic health care documents.

Worldwide information networks have the requirement that electronic documents must be easily accessible, portable, flexible and system-independent. With the development of XML (eXtensible Markup Language), the future of electronic documents, health care informatics and the Web itself are about to change. The intent of the recently formed ASTM E31.25 subcommittee, "XML DTDs for Health Care", is to develop standard electronic document representations of paper-based health care documents and forms. A goal of the subcommittee is to work together to enhance existing levels of interoperability among the various XML/SGML standardization efforts, products and systems in health care. The ASTM E31.25 subcommittee uses common practices and software standards to develop the implementation recommendations for XML documents in health care. The implementation recommendations are being developed to standardize the many different structures of documents. These recommendations are in the form of a set of standard DTDs, or document type definitions that match the electronic document requirements in the health care industry. This paper discusses recent efforts of the ASTM E31.25 subcommittee.

Medical Records Systems, Computerized↗
PubMed2002

A Prolog-based centroid algorithm for isovolume extraction from finite element torso simulations.

Computer modeling and simulation of the human torso provides a rapid and non-invasive means to observe the effects of implanted defibrillators. The objective of this study was to improve a method of extracting data from an implanted defibrillator simulation for subsequent visualization. Electrical quantities, such as the potential and gradient fields, are computed at points throughout various regions of a three-dimensional (3-D) torso model via a finite element solution. Software is then implemented in the Prolog language to extract and visualize a subset of the data, from within any subregion of the model, satisfying a given declarative constraint. In past work, membership in these subsets had been determined solely by the electrical quantities at the vertices of the tetrahedral elements within the model along with an arbitrary choice made by the user. However, this study expands upon previous work to utilize an alternative means of classification, calculating the centroid of each tetrahedron and assigning electrical properties to these centroids based on the distances of each centroid to the four corners of the tetrahedron. After the modifications, it is expected that the extracted subsets of the model will represent the data in a more realistic and conservative manner and provide more insight into the process of defibrillation than previous methods of data extraction and visualization.

Algorithms↗
PubMed2005

A Java application for tissue section image analysis.

The medical industry has taken advantage of Java and Java technologies over the past few years, in large part due to the language's platform-independence and object-oriented structure. As such, Java provides powerful and effective tools for developing tissue section analysis software. The background and execution of this development are discussed in this publication. Object-oriented structure allows for the creation of "Slide", "Unit", and "Cell" objects to simulate the corresponding real-world objects. Different functions may then be created to perform various tasks on these objects, thus facilitating the development of the software package as a whole. At the current time, substantial parts of the initially planned functionality have been implemented. Getafics 1.0 is fully operational and currently supports a variety of research projects; however, there are certain features of the software that currently introduce unnecessary complexity and inefficiency. In the future, we hope to include features that obviate these problems.

Cytological Techniques↗
PubMed2005

Competitive hybridization kinetics reveals unexpected behavior patterns.

Although the kinetics of hybridization between a soluble polynucleotide and an immobilized complementary sequence have been studied by others, it is almost universally assumed that the interaction between each probe/target pair can be treated as a separate event. This simplifies the mathematics considerably, but it can give a false picture of the extent of hybridization that one achieves at equilibrium as well as the relative quantities of each hybridized pair during the approach to equilibrium. Here we solve the relevant kinetics equations simultaneously using Mathematica as a simulation language. Among the interesting results of this study are that, for certain circumstances, the relative ratio of incorrect to correct hybrids can change dramatically with time; that the relative abundances of two pairs are not what one would expect based on their equilibrium dissociation constants; that the volume of a wash solution after hybridization can have a large effect on results; and the fact that a short wash is typically better than a long one. We show that an optimum wash time exists for a given set of conditions. In addition, the ratio of soluble to insoluble (spotted) molecules can influence results substantially. Finally, the true levels of rare transcripts can be masked by the presence of highly abundant ones. Code is supplied to enable others to study conditions beyond those presented in this article.

Base Composition↗
PubMed2002

Generic data modelling and use of XML standard for home telemonitoring of chronically ill patients.

In recent years, internet-based home telemonitoring systems that allow transmission of patient data to a central database and offer immediate access to the data by the care providers have become available. The adoption of Extensible Mark-up Language (XML) as a W3C standard has generated a lot of interest in the potential value of this language in health informatics. However the telemonitoring systems often work with only one or a few types of medical devices and thus are limited in the types of diseases they can monitor. This is because different medical devices produce different types of data and the existing telemonitoring systems are generally built around a proprietary data schema specific for the device used. In this paper, we describe a generic data schema for a telemonitoring system that is applicable to different types of medical devices and different diseases, and then we present an architecture for the exchange of clinical information as data, signals of telemonitoring and clinical reports in the XML standard, up-to-date information in each electronic patient record and integration in real time with the information collected during the telemonitoring activities in the XML schema, between all the structures involved in the health care process of the patient.

Chronic Disease↗
PubMed2002

DataServer: an infrastructure to support evidence-based radiology.

Following a requirements analysis for development of an information infrastructure supporting evidence-based radiology, the objective of this study was the development of a data gateway to support flexible access to the totality of a patient's electronic medical records through a single, uniform representation, regardless of the underlying data sources (eg, hospital information systems [HIS], radiology information systems [RIS], picture archiving and communication systems [PACS]). XML-based (eXtensible Markup Language) technologies were employed to create an application framework permitting querying of different clinical databases. The contents of different data sources were represented by using XML. On the basis of these representations, users can specify queries. The system transforms the XML queries into a query format understood by the specific databases, processes the query, and transforms the results back into an XML format. XML results can then be transformed in accordance to different data-formatting standards. Access to several different data sources, including HIS, RIS, and PACS, has been accomplished with this framework. The extensible nature of the XML data gateway enables data sources to be readily added. The framework also provides a means by which data can be systematically de-identified to protect patient confidentiality, thus supporting research endeavors.

Evidence-Based Medicine↗
PubMedDate not supplied

Common data model for neuroscience data and data model exchange.

OBJECTIVE: Generalizing the data models underlying two prototype neurophysiology databases, the authors describe and propose the Common Data Model (CDM) as a framework for federating a broad spectrum of disparate neuroscience information resources. DESIGN: Each component of the CDM derives from one of five superclasses-data, site, method, model, and reference-or from relations defined between them. A hierarchic attribute-value scheme for metadata enables interoperability with variable tree depth to serve specific intra- or broad inter-domain queries. To mediate data exchange between disparate systems, the authors propose a set of XML-derived schema for describing not only data sets but data models. These include biophysical description markup language (BDML), which mediates interoperability between data resources by providing a meta-description for the CDM. RESULTS: The set of superclasses potentially spans data needs of contemporary neuroscience. Data elements abstracted from neurophysiology time series and histogram data represent data sets that differ in dimension and concordance. Site elements transcend neurons to describe subcellular compartments, circuits, regions, or slices; non-neuroanatomic sites include sequences to patients. Methods and models are highly domain-dependent. CONCLUSIONS: True federation of data resources requires explicit public description, in a metalanguage, of the contents, query methods, data formats, and data models of each data resource. Any data model that can be derived from the defined superclasses is potentially conformant and interoperability can be enabled by recognition of BDML-described compatibilities. Such metadescriptions can buffer technologic changes.

Animals↗
PubMed1995

A comparison of the temporal expressiveness of three database query methods.

Time is a multifaceted phenomenon that developers of clinical decision-support systems can model at various levels of complexity. An unresolved issue for the design of clinical databases is whether the underlying data model should support interval semantics. In this paper, we examine whether interval-based operations are required for querying protocol-based conditions. We report on an analysis of a set of 256 eligibility criteria that the T-HELPER system uses to screen patients for enrollment in eight clinical-trial protocols for HIV disease. We consider three data-manipulation methods for temporal querying: the consensus query representation Arden Syntax, the commercial standard query language SQL, and the temporal query language TimeLineSQL (TLSQL). We compare the ability of these three query methods to express the eligibility criteria. Seventy nine percent of the 256 criteria require operations on time stamps. These temporal conditions comprise four distinct patterns, two of which use interval-based data. Our analysis indicates that the Arden Syntax can query the two non-interval patterns, which represent 54% of the temporal conditions. Timepoint comparisons formulated in SQL can instantiate the two non-interval patterns and one interval pattern, which encompass 96% of the temporal conditions. TLSQL, which supports an interval-based model of time, can express all four types of temporal patterns. Our results demonstrate that the T-HELPER system requires simple temporal operations for most protocol-based queries. Of the three approaches tested, TLSQL is the only query method that is sufficiently expressive for the temporal conditions in this system.

Decision Making, Computer-Assisted↗
PubMed2003

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Database Management Systems↗
PubMed2002

DIABCARD CCMIS--a portable and scalable CPR for diabetes care.

The aim of this paper is to introduce the main software module of the DIABCARD Chip Card Medical Information System (DIABCARD CCMIS) that provides an online, portable diabetes medical record information system based on a high performance object-oriented rapid application development language such as Borland Delphi. A chip card based medical information system was developed as a good possibility to create a portable electronic patient record. In particular the patient data card makes the up-to-date patient's record available whenever needed. The developed DIABCARD Core System, described in this paper, includes a patient record management system that has the ability to handle topics such as administrative and medical data, medical anamnesis, and physical examination data. Issues tackled were simplicity, data security and reporting, customization, and internationalization. Especially for the two last issues (customization and internationalization) a novel approach based on using native initialization table files is presented. Proper care has been addressed during the development of the software modules for matters of security, data integrity and confidentiality.

Database Management Systems↗
PubMed2006

Proof-of-concept design and development of an EN13606-based electronic health care record service.

OBJECTIVE: The authors present an Electronic Healthcare Record (EHR) server, designed and developed as a proof of concept of the revised prEN13606:2005 European standard concerning EHR communications. METHODS: The development of the server includes five modules: the libraries for the management of the standard reference model, for the demographic package and for the data types; the permanent storage module, built on a relational database; two communication interfaces through which the clients can send information or make queries; the XML (eXtensible Markup Language) process module; and the tools for the validation of the extracts managed, implemented on a defined XML-Schema. RESULTS: The server was subjected to four phases of trials, the first three with ad hoc test data and processes to ensure that each of the modules complied with its specifications and that the interaction between them provided the expected functionalities. The fourth used real extracts generated by other research groups for the additional purpose of testing the validity of the standard in real-world scenarios. CONCLUSION: The acceptable performance of the server has made it possible to include it as a middleware service in a platform for the out-of-hospital follow-up and monitoring of patients with chronic heart disease which, at the present time, supports pilot projects and clinical trials for the evaluation of eHealth services.

Computer Systems↗
PubMed1998

Web based 3-D medical image visualization on the PC.

With the recent advance of Web and its associated technologies, information sharing on distribute computing environments has gained a great amount of attention from many researchers in many application areas, such as medicine, engineering, and business. One basic requirement of distributed medical consultation systems is that geographically dispersed, disparate participants are allowed to exchange information readily with each other. Such software also needs to be supported on a broad range of computer platforms to increase the softwares accessibility. In this paper, the development of world-wide-web based medical consultation system for radiology imaging is addressed to provide platform independence and greater accessibility. The system supports sharing of 3-dimensional objects. We use VRML (Virtual Reality Modeling Language), which is the defacto standard in 3-D modeling on the Web. 3-D objects are reconstructed from CT or MRI volume data using a VRML format, which can be viewed and manipulated easily in Web-browsers with a VRML plug-in. A Marching cubes method is used in the transformation of scanned volume data sets to polygonal surfaces of VRML. A decimation algorithm is adopted to reduce the number of meshes in the resulting VRML file. 3-D volume data are often very large in size, hence loading the data on PC level computers requires a significant reduction of the size of the data, while minimizing the loss of the original shape information. This is also important to decrease network delays. A prototype system has been implemented (http://cybernet5.snu.ac.kr/-cyber/mrivrml .html), and several sessions of experiments are carried out.

Algorithms↗
PubMed2025

AutoPM3: enhancing variant interpretation via LLM-driven PM3 evidence extraction from scientific literature.

MOTIVATION: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has become cost-effective, interpreting these variants-particularly collecting literature-based evidence like ACMG/AMP PM3-remains complex and time-consuming. RESULTS: We present AutoPM3, a method that automates PM3 evidence extraction from literatures using open-source large language models (LLMs). AutoPM3 combines a Text2SQL-based variant extractor and a retrieval-augmented generation (RAG) module, enhanced by a variant-specific retriever and fine-tuned LLM, to separately process tables and text. We curated PM3-Bench, a dataset of 1027 variant-publication evidence pairs from ClinGen. On openly accessible pairs, AutoPM3 achieved 86.1% accuracy for variant hits and 72.5% recall for in trans variants-outperforming other methods, including those using larger models. We uncovered the effectiveness of AutoPM3's key modules, especially for variant-specific retriever and Text2SQL, through the sequential ablation study. AutoPM3 located evidence in 76 s, demonstrating that open-source LLMs can offer an efficient, cost-effective solution for rare disease diagnosis. AVAILABILITY AND IMPLEMENTATION: AutoPM3 is implemented and freely available under the MIT license at https://github.com/HKU-BAL/AutoPM3.

Genetic Variation↗
PubMed2002

Design and implementation of microarray gene expression markup language (MAGE-ML).

BACKGROUND: Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies. RESULTS: To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. CONCLUSIONS: MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.

Computer Simulation↗
PubMed1998

Patient information exchange guideline MERIT-9 using medical markup language MML.

To realize clinical data exchange between healthcare providers, there must be many standards in many layers. Terms and codes should be standardized, syntax to wrap the data must be mutually parsable, then transfer protocol or exchange media should be agreed. Among many standards for the syntax, HL7 and DICOM are most successful. However, everything could not be handled by HL7 solely. DICOM is good for radiology images, but, other clinical images are already handled by other "lighter" data formats like JPEG, TIFF. So, it is not realistic to use only one standard for every area of clinical information. For description of medical records, especially for narrative information, we created SGML DTD for medical information, called MML (Medical Markup Language). It is already implemented in more than 10 healthcare providers in Japan. As it is a hierarchical description of information, it is easily used as a basis of object request brokering. It is again not realistic to use MML solely for clinical information in various level of detail. Therefore, we proposed a guide-line for use of available medical standards to facilitate clinical information exchange between healthcare providers. It is called MERIT-9 (MEdical Records, Images, Texts,--Information eXchange). A typical use is HL7 files, DICOM files, referred from an MML file in a patient record, as external entities. Both MML and MERIT-9 are research projects of Japanese Ministry of Health and Welfare, and the purpose is to facilitate clinical data exchanges. They are becoming to be used in technical specifications for new hospital information systems in Japan.

Hospital Information Systems↗