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At least 757 records · Page 42Linked to original sources
PubMed2005

A comprehensive pathway map of epidermal growth factor receptor signaling.

The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. A map of molecular interactions of the EGFR signaling system is a valuable resource for research in this area. In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways. The map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML).

Animals↗
PubMed1998

Bidirectional sticker systems.

We introduce two-sided sticker systems, the two-sided variant of a computability model introduced as an abstraction of Adleman's style of DNA computing and of the matching of the so-called Watson-Crick complements. Several types of sticker systems are shown to have the same power as regular grammars, one variant is found to represent the linear languages, and another one is proved to be able to represent any recursively enumerable language. From this result we infer that any recursively enumerable language can be represented as the projection of the intersection of two minimal linear languages.

Base Composition↗
PubMed2000

XML: a lingua franca for science?

XML is a new language designed to solve one of the biggest problems of the World Wide Web: its main language, HTML, is not extensible. In this article, the authors discuss the current successes and limitations of the World Wide Web, briefly explain the basics of XML and present the benefits of using XML as a data-exchange language. Finally, they discuss real-life applications that have been developed using XML, with a focus on biology.

Internet↗
PubMedDate not supplied

Requirements for medical modeling languages.

OBJECTIVE: The development of tailor-made domain-specific modeling languages is sometimes desirable in medical informatics. Naturally, the development of such languages should be guided. The purpose of this article is to introduce a set of requirements for such languages and show their application in analyzing and comparing existing modeling languages. DESIGN: The requirements arise from the practical experience of the authors and others in the development of modeling languages in both general informatics and medical informatics. The requirements initially emerged from the analysis of information modeling techniques. The requirements are designed to be orthogonal, i.e., one requirement can be violated without violation of the others. RESULTS: The proposed requirements for any modeling language are that it be "formal" with regard to syntax and semantics, "conceptual," "expressive," "comprehensible," "suitable," and "executable." The requirements are illustrated using both the medical logic modules of the Arden Syntax as a running example and selected examples from other modeling languages. CONCLUSION: Activity diagrams of the Unified Modeling Language, task structures for work flows, and Petri nets are discussed with regard to the list of requirements, and various tradeoffs are thus made explicit. It is concluded that this set of requirements has the potential to play a vital role in both the evaluation of existing domain-specific languages and the development of new ones.

Medical Informatics↗
PubMed1994

Rationale for the Arden Syntax.

The Arden Syntax, a language designed for writing and sharing task-specific knowledge for Medical Logic Modules (MLMs), has been recently accepted as a standard by the ASTM. The syntax is concerned with the critical task of sharing medical knowledge bases across many institutions. Because of the relative lack of agreement on vocabularies and data standards and because of the many other obstacles, the developers of the Arden Syntax took a pragmatic, straightforward approach that has borne fruit in a very short period of time. The syntax provides a vehicle for the health care community to begin sharing, so that we can see what works and what does not work, and we can begin to address the critical obstacles. In designing a language like the Arden Syntax, the authors make many decisions--but the final document gives only the result of these decisions without any explanation. By writing down the rationale behind the design of the syntax, we hope to aid users of the language, implementors of the language, and future designers of new languages.

Artificial Intelligence↗
PubMedDate not supplied

Genomic messaging system language including command extensions for clinical data categories.

This paper, in the area of clinical bioinformatics, highlights relatively efficient means of storing, exchanging, protecting, and searching human and other genomic data, so as to make the data securely accessible to researchers while respecting patient privacy. One important idea is that the GMSL language can be considered as an extension of the way DNA and protein sequences are written so as to carry with them the wishes of the patient in regard to fine-grained consent (as well as retaining the medical experts' cautions, instructions for use, and annotation), and this is carried, whatever environment (e.g., XML) that the data is from or whatever it is going to. At the deepest level, a stream of data expressed in GMSL resembles highly compressed stream of self-checking machine code. For the reader less familiar with the computational aspects, some simple examples illustrate how the raw language looks and works as a raw stream of (interpreted) bytes. The bioinformatics applications are not confined to the clinical domain. This paper completes the initial specification of the language as previously presented and reports on some important extensions including clinical data categories.

Base Sequence↗
PubMed2006

Cross-lingual alignment of biomedical acronyms and their expansions.

We propose a method that aligns biomedical acronyms and their definitions across different languages. The approach is based upon a freely available tool for the extraction of abbreviations together with their expansions, and the subsequent normalization of language-specific variants, synonyms, and translations of the extracted acronym definitions. In this step, acronym expansions are mapped onto a language-independent concept-layer on which intra- as well as interlingual comparisons are drawn.

Germany↗
PubMed1982

Service-conditional medical student aid programs: The experience of the states.

Medical student aid programs tied to a service commitment are in operation in 31 states. The programs provide various options for students to pay back the financial support given by the state, the most popular form being cancellation of the financial obligation to the the state if a service commitment is fulfilled. Although the statutory language and program literature claim a major objective of the programs to be the provision of manpower to underserved areas, lenient "buy-out" provisions and small awards relative to the total tuition have caused these programs to be used as sources of low-interest loans. Moreover, states do not provide subsidies to promote service in unattractive areas; thus, there is little reason for physician graduates to locate in low-income areas. State cooperation with the federal National Health Service Corps Scholarship Program, which does provide subsidies to physicians practicing in underserved areas, may provide the states a strategy for meeting their legislative objectives of providing physicians for the underserved.

Medically Underserved Area↗
PubMed2002

An XML Gateway to Patient Data for Medical Research Applications.

As the medical environment becomes increasingly electronic, clinical databases are continually growing, accruing masses of patient information. This wealth of data is an invaluable source of information to researchers, serving as a testbed for the development of new information technologies and as a repository of real-world data for data mining and population-based studies. However, the true utility of this information is not fulfilled, in part because of issues pertaining to security and patient confidentiality, but also due to the lack of an effective infrastructure to access the data. This paper describes a system, DataServer, that permits researchers to query and retrieve data from multiple clinical data sources, automatically deidentifying patient data so that it can be used for research purposes. DataServer functions as an application framework, enabling extensible markup language (XML)-based querying of existing medical databases. Key aspects of DataServer include ready inclusion of new information resources, minimal processing impact on existing clinical systems via a distributed cache, and flexible output representation via XSL (eXtensible Style Language) transforms.

Databases, Factual↗
PubMed1994

Generalizing spontaneous language in developmentally delayed children via a visual cue procedure using caregivers as therapists.

Developmentally delayed children are recognized by deficits in language, motor skills, and social interaction. The importance of this topic is demonstrated by the fact that many studies have focused on increasing different aspects of this population's language. New training elements for this population were used here (e.g., the visual cue method was used in home settings). Caregivers were trained as therapists to teach children spontaneous speech by targeting two behaviors. The visual cue method was effective for increasing spontaneous speech in developmentally delayed children in the home. This finding is significant in that home training with caregivers promoted generalization of language by programming common stimuli. Implication of these data for future research is discussed.

Caregivers↗
PubMed2006

Web-based viewer for systematic combination of anatomy and nomenclature.

Integrating anatomic nomenclature with geometric anatomic data via a web interface and providing illustration and visualization tools presents numerous challenges. We have developed a library of anatomic models and methods for navigating anatomic nomenclature. Based on the library and tools, we have developed a simple, yet powerful, open web-based tool that uses tree navigation and selection for assembling and downloading self-documenting anatomic scenes in Virtual Reality Modeling Language.

Computer Simulation↗
PubMed1996

An intention-based language for representing clinical guidelines.

Automated support for guideline-based care would be enhanced considerably by a standard representation of clinical guidelines. To faciliate use and reuse, we suggest a representation that includes the explicit intentions of the guideline's author. These intentions include the desirable actions of the care provider and the patient states to be achieved before, during, and after the administration of the guideline. Intentions are temporal patterns of provider actions or patient states to be maintained, achieved, or avoided. We view automated support as a collaborative effort of the health-care provider and an automated assistant and involves several different tasks. We defined the syntax and, the semantics of a text-based language (ASBRU) for representation and annotation of clinical guidelines. The language supports maintenance of the automated assistant's knowledge base and could improve the quality and flexibility of the automated assistant's recommendations. In the ASGAARD project, we are developing reasoning mechanisms that use the ASBRU language for execution and critiquing tasks in conjunction with online electronic patient medical records.

Expert Systems↗
PubMed1992

Acquisition, generalization, and spontaneous use of color adjectives: a comparison of incidental teaching and traditional discrete-trial procedures for children with autism.

Incidental teaching and traditional discrete-trial procedures were used to teach two children with autism the expressive use of two color adjectives to describe preferred toys and food items. The two teaching procedures were performed in a classroom setting, and generalization and spontaneous usage were assessed at home with parents. The results demonstrated that traditional discrete-trial teaching was more efficient and produced faster acquisition and, initially, greater generalization. However, by follow-up, the incidental teaching methods resulted in equal retention, greater generalization, and equal or greater spontaneous usage. The findings indicate that although it takes a longer time for children with autism to learn with incidental teaching procedures, once they have acquired an ability, it may be more permanent. It is recommended that incidental teaching procedures be included in future language development programs for children with autism.

Autistic Disorder↗
PubMed2003

Designing XML schemas for bioinformatics.

Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

Biotechnology↗
PubMed1998

Advanced query mechanisms for biological databases.

Existing query interfaces for biological databases are either based on fixed forms or textual query languages. Users of a fixed form-based query interface are limited to performing some pre-defined queries providing a fixed view of the underlying database, while users of a free text query language-based interface have to understand the underlying data models, specific query languages and application schemas in order to formulate queries. Further, operations on application-specific complex data (e.g., DNA sequences, proteins), which are usually provided by a variety of software packages with their own format requirements and peculiarities, are not available as part of, nor integrated with biological query interfaces. In this paper, we describe generic tools that provide powerful and flexible support for interactively exploring biological databases in a uniform and consistent way, that is via common data models, formats, and notations, in the framework of the Object-Protocol Model (OPM). These tools include (i) a Java graphical query construction tool with support for automatic generation of Web query forms that can be either used for further specifying conditions, or can be saved and customized; (ii) query processors for interpreting and executing queries that may involve complex application-specific objects, and that could span multiple heterogeneous databases and file systems; and (iii) utilities for automatic generation of HTML pages containing query results, that can be browsed using a Web browser. These tools avoid the restrictions imposed by traditional fixed-form query interfaces, while providing users with simple and intuitive facilities for formulating ad-hoc queries across heterogeneous databases, without the need to understand the underlying data models and query languages.

Animals↗
PubMed1992

A BASIC algorithm for calculating the postmortem interval from arthropod successional data.

A computer algorithm, implemented in the BASIC language, is presented for calculating the postmortem interval (PMI) from arthropod successional data. Entomology-assisted determination of the PMI promises to be a reliable technique in cases of homicide, suicide, accidental death, and unattended death due to natural causes. The program requires, as input, the identity of arthropod taxa recovered from human remains in a death scene investigation and machine-readable data on carrion-associated arthropod taxa and their known successional patterns of activity for the same geographical area. The program performs rapid comparisons of these lists and, on output, calculates an upper and lower estimate of the PMI, identifies the definitive taxa for these limits, and determines if the remaining corpse taxa have known successional patterns that are consistent for this estimate. An alternate output is provided if one or more corpse taxa do not overlap all the others at any single time in the succession. In that event, the user is prompted to recheck the identity of the non-overlapping taxon or taxa or reevaluate the environmental circumstances surrounding the case in question. Results of the analysis are saved to an ASCII file for output to a printer for making paper copies useful for the entomologist's Case Study Final Report. This program may make possible wider use of this technique in law enforcement and medical investigator offices that utilize both forensic entomologist expertise and IBM PCs (or compatible computers).

Accidents↗
PubMed1996

An object-oriented class library for medical software development.

The objective of this research is the development of a Medical Object Library (MOL) consisting of reusable, inheritable, portable, extendable C++ classes that facilitate rapid development of medical software at reduced cost and increased functionality. The result of this research is a library of class objects that range in function from string and hierarchical file handling entities to high level, procedural agents that perform increasingly complex, integrated tasks. A system built upon these classes is compatible with any other system similarly constructed with respect to data definitions, semantics, data organization and storage. As new objects are built, they can be added to the class library for subsequent use. The MOL is a toolkit of software objects intended to support a common file access methodology, a unified medical record structure, consistent message processing, standard graphical display facilities and uniform data collection procedures. This work emphasizes the relationship that potentially exists between the structure of a hierarchical medical record and procedural language components by means of a hierarchical class library and tree structured file access facility. In doing so, it attempts to establish interest in and demonstrate the practicality of the hierarchical medical record model in the modern context of object oriented programming.

Humans↗
PubMed1999

The Biopolymer Markup Language.

SUMMARY: An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed. AVAILABILITY: The language definition is available in HTML form at http://www.proteometrics.com/BIOML/. The BioML browser is available on request from the author.

Biopolymers↗