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PubMed2006

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

BACKGROUND: With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. RESULTS: The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. CONCLUSION: The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.

Database Management Systems↗

PubMed2005

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

OBJECTIVE: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. DESIGN: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. RESULTS: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. CONCLUSION: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

Abstracting and Indexing↗

PubMed1997

Using the GRAIL language for classification management.

This paper describes a novel approach in classification management where a formal model of medical semantics is being used for manipulations on existing classification systems. The paper addresses the issue of semi-automatically making specialist classifications that are compatible with the source classification. The examples in this paper are from a limited domain. At the time of the presentation results will be shown of the present modelling work within the GALEN-In-Use project. The model will then contain several thousands of medical procedures from four different classification centres.

Classification↗

PubMed1998

The role of compositionality in standardized problem list generation.

Compositionality is the ability of a Vocabulary System to record non-atomic strings. In this manuscript we define the types of composition, which can occur. We will then propose methods for both server based and client-based composition. We will differentiate the terms Pre-Coordination, Post-Coordination, and User-Directed Coordination. A simple grammar for the recording of terms with concept level identification will be presented, with examples from the Unified Medical Language System's (UMLS) Metathesaurus. We present an implementation of a Window's NT based client application and a remote Internet Based Vocabulary Server, which makes use of this method of compositionality. Finally we will suggest a research agenda which we believe is necessary to move forward toward a more complete understanding of compositionality. This work has the promise of paving the way toward a robust and complete Problem List Entry Tool.

Humans↗

PubMed1999

Use of the Extensible Stylesheet Language (XSL) for medical data transformation.

Recently, the Extensible Markup Language (XML) has received growing attention as a simple but flexible mechanism to represent medical data. As XML-based markups become more common there will be an increasing need to transform data stored in one XML markup into another markup. The Extensible Stylesheet Language (XSL) is a stylesheet language for XML. Development of a new mammography reporting system created a need to convert XML output from the MEDLee natural language processing system into a format suitable for cross-patient reporting. This paper examines the capability of XSL as a rule specification language that supports the medical XML data transformation. A set of nine relevant transformations was identified: Filtering, Substitution, Specification, Aggregation, Merging, Splitting, Transposition, Push-down and Pull-up. XSL-based methods for implementing these transformations are presented. The strengths and limitations of XSL are discussed in the context of XML medical data transformation.

Database Management Systems↗

PubMed2003

A prototype natural language interface to a large complex knowledge base, the Foundational Model of Anatomy.

We describe a constrained natural language interface to a large knowledge base, the Foundational Model of Anatomy (FMA). The interface, called GAPP, handles simple or nested questions that can be parsed to the form, subject-relation-object, where subject or object is unknown. With the aid of domain-specific dictionaries the parsed sentence is converted to queries in the StruQL graph-searching query language, then sent to a server we developed, called OQAFMA, that queries the FMA and returns output as XML. Preliminary evaluation shows that GAPP has the potential to be used in the evaluation of the FMA by domain experts in anatomy.

Anatomy↗

PubMed2003

Medical problem and document model for natural language understanding.

We are developing tools to help maintain a complete, accurate and timely problem list within a general purpose Electronic Medical Record system. As a part of this project, we have designed a system to automatically retrieve medical problems from free-text documents. Here we describe an information model based on XML (eXtensible Markup Language) and compliant with the CDA (Clinical Document Architecture). This model is used to ease the exchange of clinical data between the Natural Language Understanding application that retrieves potential problems from narrative document, and the problem list management application.

Computer Simulation↗

PubMed2004

CliniViewer: a tool for viewing electronic medical records based on natural language processing and XML.

With the evolving use of computers in healthcare, the electronic medical record (EMR) is becoming more and more popular. A tool is needed that would enable physicians to accurately and efficiently access clinical information in multiple medical records associated with a particular patient. Both natural language processing (NLP) and the eXtensible Markup Language (XML) have been used in the clinical domain for capturing, representing, and utilizing clinical information and both have shown great potential. In this paper, we demonstrate another use of XML and NLP through CliniViewer, a tool that organizes and presents the clinical information in multiple records. We also describe the flexibility and capability provided when combining XML and NLP to summarize, navigate, and conceptualize structured information. The tool has been fully implemented and tested using patients with multiple discharge summaries.

Humans↗

PubMed1997

[Determination of caffeine and sodium benzoate contents in caffeine and sodium benzoate injection by P-matrix method].

The contents of caffeine and sodium benzoate injection may be determined by P-matrix method without separation of its components. BSAIC language is used for programming. The average recovery of caffeine is 100.0% and that of sodium benzoate is 99.95%. The variation coefficient of caffeine is 0.40% and that of sodium benzoate is 0.65%. On the basis of recovery rate and data observed it is concluded that this method is accurate, reliable, simple and rapid as compared with the standard pharmacopoeia regulations.

Caffeine↗

PubMed1994

The component-based architecture of the HELIOS medical software engineering environment.

The constitution of highly integrated health information networks and the growth of multimedia technologies raise new challenges for the development of medical applications. We describe in this paper the general architecture of the HELIOS medical software engineering environment devoted to the development and maintenance of multimedia distributed medical applications. HELIOS is made of a set of software components, federated by a communication channel called the HELIOS Unification Bus. The HELIOS kernel includes three main components, the Analysis-Design and Environment, the Object Information System and the Interface Manager. HELIOS services consist in a collection of toolkits providing the necessary facilities to medical application developers. They include Image Related services, a Natural Language Processor, a Decision Support System and Connection services. The project gives special attention to both object-oriented approaches and software re-usability that are considered crucial steps towards the development of more reliable, coherent and integrated applications.

Computer Communication Networks↗

PubMedDate not supplied

A PC-based workstation for real-time acquisition, processing, and display of electromyogram signals.

A system for real-time acquisition, processing, display, and logging of multiple channels of the EMG waveform has been described. By designing this system around the configuration of a standard PC, custom hardware was avoided. Similarly, software was designed in a higher-level language (C), simplifying the programming burden and minimizing custom software development. Components of the software are available off the shelf. The computational capacity of generic PCs facilitates very high rates of numeric calculation, as required by some advanced EMG amplitude estimation algorithms. Computational capacity is expected to increase, facilitating ever more numerically intensive EMG algorithms that are likely to be developed in the future. The system described here has been used in the development of an adaptive window EMG amplitude-estimation algorithm. The system is extensible and can be altered for many uses related to EMG and biosignal processing.

Algorithms↗

PubMed1998

Hospitexte: towards a document-based hypertextual electronic medical record.

The patient record is a repository for knowledge about a patient. Work in Artificial Intelligence and knowledge representation has evidenced the intrinsic difficulty of formalizing knowledge for computer processing. It is therefore not a surprise that most attempts at computerizing the patient record have only had a limited degree of success or applicability. We claim that this is due to the fact that medicine is an empirical domain, and thus fundamentally resists formalization. Therefore, the only way medical knowledge can be fully expressed is through natural languages which is indeed what clinicians actually use. We proposed and designed an electronic medical record which adheres to this hypothesis and where structured documents play a prominent role.

Artificial Intelligence↗

PubMed1993

A patient education program.

Everyday language used by health care professionals in gastroenterology is often unfamiliar to patients, regardless of their level of education. Consequently, the best efforts to explain diagnoses to patients can result in confusion and anxiety instead of understanding. A patient education program was designed in an attempt to correct this problem. This article describes how the patient education program was developed and implemented.

Documentation↗

PubMed1987

Language training for generalization.

This paper presents a classroom-based language intervention program for preschool children with language delays or deficits. A major goal of the program is to ensure that children acquire missing skills through daily speech therapy and that they actively generalize these skills from therapy times to other classroom activities. This paper presents data collected with two children during daily speech therapy sessions and daily play activities. Instances in which the children generalized new language acquired in therapy to play activities will be discussed as well as instances in which the children failed to generalize new language. In addition, the influence of peer and teacher language usage on children's language production will be discussed. Finally, recommendations to enhance generalization of language skills within and across school settings will be presented.

Child↗

PubMed1993

A hardware-independent data acquisition package incorporating a simulation driver and simulation description language.

Device drivers for commercial data acquisition boards (DASH-16, DT2801) and a device driver for a virtual data acquisition board have been developed and incorporated in a single package for a multiple station anesthesia research laboratory. The package provides a compiler for a simulation description language which is used to program the virtual board. The package, written in C for the IBM PC, was designed to be easily extended with additional drivers. Applications using the package can control all supported devices without the programmer having to learn the details of the hardware.

Computer Simulation↗

PubMed2005

The SIMRI project: a versatile and interactive MRI simulator.

This paper gives an overview of SIMRI, a new 3D MRI simulator based on the Bloch equation. This simulator proposes an efficient management of the T2* effect, and in a unique simulator integrates most of the simulation features that are offered in different simulators. It takes into account the main static field value and enables realistic simulations of the chemical shift artifact, including off-resonance phenomena. It also simulates the artifacts linked to the static field inhomogeneity like those induced by susceptibility variation within an object. It is implemented in the C language and the MRI sequence programming is done using high level C functions with a simple programming interface. To manage large simulations, the magnetization kernel is implemented in a parallelized way that enables simulation on PC grid architecture. Furthermore, this simulator includes a 1D interactive interface for pedagogic purpose illustrating the magnetization vector motion as well as the MRI contrasts.

Algorithms↗

PubMed1978

Maternal speech to normal and Down's syndrome children matched for mean length of utterance.

The study was designed to provide data on the maternal linguistic environments of normal and Down's syndrome children at three levels of language development, as assessed by children's mean length of utterances (MLU). The three MLU levels were 1.00--1.50, 1.75--2.25, and 2.50--3.00, respectively. The subjects were 21 Down's syndrome children and their natural mothers and 21 normal children and their natural mothers. Normal children ranged in chronological age from 20 to 32 months and Down's syndrome children from 3 to 12 years. A one-hour verbal interaction between mother and child was tape recorded at home in a free-play situation. Maternal speech was analyzed using 20 measures related to its output-numerical, lexical, syntactical, semantic-structural, semantic-pragmatic, and language-teaching aspects. Additionally, eight measures of children's speech related to the output-numerical, lexical, syntactical semantic-structural aspects, and to imitativeness of maternal speech were computed as a means of testing the validity of the MLU-matching that forms a basis for this study. Except for the Type-token ratio, which favored Down's syndrome children, normal and Down's syndrome children were not found to differ. In contrast, there were numerous differences between the children in the different aspects of speech considered according to language level. None of the comparisons made of mother's speech to normal and to Down's syndrome children led to differences for any of the three children's language levels studied. It appeared that the maternal linguistic environments of language-learning Down's syndrome and normal children of corresponding MLU were similar in most respects. In contrast, there were numerous differences in mother's speech according to the language level of the children addressed. This confirmed that the expressive language level of the children is a far more powerful factor in influencing maternal speech than whether they are normal or Down's syndrome children. The implications of these findings were related to the delay-difference question in the language development of Down's syndrome children and to various interpretations of the effects of maternal linguistic input for language development and for intervention programs of language enhancement in the Down's syndrome child.

Adult↗

PubMed1980

Receptive and expressive language problems occurring in combination with a seizure disorder: a case report.

The purpose of this case report is to present an example of a child with receptive and expressive language problems occurring in combination with a seizure disorder. For a period of 3 years the seizure disorder appeared to be controlled by medication and the child made substantial improvement in a language remediation program. A sudden disruption of decoding abilities was the only behavioral indication that the treatment program needed to be reassessed. Descriptions of the child's behaviors, subsequent neurological evaluation, and goals of the language habilitation program are presented.

Child↗