SEARCH · PubMed Health

Results for “Programming Languages”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 595 records · Page 33Linked to original sources

PubMed2002

Communication in science.

Science must have a common language. For centuries, Latin language carried out this job, but the progress in computer technology and internet world through the last 20 years, began to produce a new language with the new century; the computer language. The information masses, which need data language standardization, are the followings; Digital libraries and medical education systems, Consumer health informatics, Medical education systems, World Wide Web Applications, Database systems, Medical language processing, Automatic indexing systems, Image processing units, Telemedicine, New Generation Internet (NGI).

Communication↗

PubMed2003

A vocabulary development and visualization tool based on natural language processing and the mining of textual patient reports.

Medical terminologies are critical for automated healthcare systems. Some terminologies, such as the UMLS and SNOMED are comprehensive, whereas others specialize in limited domains (i.e., BIRADS) or are developed for specific applications. An important feature of a terminology is comprehensive coverage of relevant clinical terms and ease of use by users, which include computerized applications. We have developed a method for facilitating vocabulary development and maintenance that is based on utilization of natural language processing to mine large collections of clinical reports in order to obtain information on terminology as expressed by physicians. Once the reports are processed and the terms structured and collected into an XML representational schema, it is possible to determine information about terms, such as frequency of occurrence, compositionality, relations to other terms (such as modifiers), and correspondence to a controlled vocabulary. This paper describes the method and discusses how it can be used as a tool to help vocabulary builders navigate through the terms physicians use, visualize their relations to other terms via a flexible viewer, and determine their correspondence to a controlled vocabulary.

Algorithms↗

PubMed2006

Terminology model discovery using natural language processing and visualization techniques.

Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.

Automation↗

PubMed2006

Enrichment of OBO ontologies.

This paper describes a frame-based integration of the three GO subontologies, the Chemical Entities of Biological Interest ontology, and the Cell Type Ontology in which relationships are modeled in a way that better captures the semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions by identifying patterns in GO terms, mapping these patterns to new, specific relationships, and matching term substrings to concepts. Using this methodology, a predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid, resulting in an initial set of over 4000 assertions. Furthermore, this methodology programmatically integrates assertions into an ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels.

Computational Biology↗

PubMed1997

Computer assisted medical diagnosis using the Web.

The ADM (Aide au diagnostic Medical) project was started 15 years ago and was the first telematic project for physicians in France using the MINITEL terminal. The knowledge base contains information on more than 10000 diseases from all pathological fields, using more than 100000 signs or symptoms. The ADM system has two main functionalities for physicians: consultation of diseases descriptions and list of diseases containing one or more symptoms. The ADM knowledge base is supported by a relational database management system (DBMS ORACLE) and we developed a Web interface using the Perl language to produce HTML pages for the web server. We will describe our experience on redesigning a large existing medical knowledge base for diffusion on the web Internet.

Artificial Intelligence↗

PubMedDate not supplied

Design and development of chemical ontologies for reaction representation.

This paper describes the development of chemical ontologies applied to the representation of organic chemical reactions. The ontologies are built using the methodology known as methontology. The hierarchically structured set of terms describing the subdomains, namely, organic reactions, organic compounds, and reagents, are constructed into individual ontologies. The ontologies consist of about 200 concepts and around 125 individuals. A set of binary relations is defined in order to integrate the ontologies with applications. The ontologies are implemented as an XML application with a set of vocabulary describing the domain knowledge. This paper also features an easy-to-use chemical ontological support system (COSS) intended to represent organic chemical reactions automatically. As a model application, the automatic representation of aliphatic nucleophilic substitution reactions is demonstrated using COSS. The paper also describes a keyword-based search system whose functionality is backed with COSS.

Algorithms↗

PubMed1985

A fast DNA sequence handling program for Apple II computer in BASIC and 6502 assembler.

A fast general purpose DNA handling program has been developed in BASIC and machine language. The program runs on the Apple II plus or on the Apple IIe microcomputer, without additional hardware except for disk drives and printer. The program allows file insertion and editing, translation into protein sequence, reverse translation, search for small strings and restriction enzyme sites. The homology may be shown either as a comparison of two sequences or through a matrix on screen. Two additional features are: (i) drawing restriction site maps on the printer; and (ii) simulating a gel electrophoresis of restriction fragments both on screen and on paper. All the operations are very fast. The more common tasks are carried out almost instantly; only more complex routines, like finding homology between large sequences or searching and sorting all the restriction sites in a long sequence require longer, but still quite acceptable, times (generally under 30 s).

Base Sequence↗

PubMed2003

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO. RESULTS: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.

Artificial Intelligence↗

PubMed2004

Pedro: a configurable data entry tool for XML.

UNLABELLED: Pedro is a Java application that dynamically generates data entry forms for data models expressed in XML Schema, producing XML data files that validate against this schema. The software uses an intuitive tree-based navigation system, can supply context-sensitive help to users and features a sophisticated interface for populating data fields with terms from controlled vocabularies. The software also has the ability to import records from tab delimited text files and features various validation routines. AVAILABILITY: The application, source code, example models from several domains and tutorials can be downloaded from http://pedro.man.ac.uk/.

Computer Graphics↗

PubMed2004

PIML: the Pathogen Information Markup Language.

MOTIVATION: A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data. RESULTS: The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents. AVAILABILITY: All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

Bacteria↗

PubMed2005

METIS: multiple extraction techniques for informative sentences.

SUMMARY: METIS is a web-based integrated annotation tool. From single query sequences, the PRECIS component allows users to generate structured protein family reports from sets of related Swiss-Prot entries. These reports may then be augmented with pertinent sentences extracted from online biomedical literature via support vector machine and rule-based sentence classification systems. AVAILABILITY: http://umber.sbs.man.ac.uk/dbbrowser/metis/

Algorithms↗

PubMed2005

Intelligent client for integrating bioinformatics services.

MOTIVATION: In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem. RESULTS: In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Automation↗

PubMed2003

A rapid speech synthesizing software on a PDA for Japanese with speech impairments.

We developed a Japanese-language, rapid synthesizing software application for use on a personal digital assistant. It has an unrestricted vocabulary and can synthesize words and sentences within 3 s. Eight hundred common sentences and words are preregistered. By touching the first character at the head of a preregistered sentence or word from an on-screen Kana (Japanese alphabet) chart, the user can select the sentence or word to be spoken. Characters on the Kana chart can also be input sequentially. Two Japanese subjects with speech impairments rated the device highly for its portability and quick response. Whereas communication previously had to be done by writing or sign language, it was easy for listeners with or without specialized training in communication with persons with speech impairments to understand the output from this device, making conversation easier which, in turn, improved the quality of life and social activity of these persons with speech impairments.

Asian People↗

PubMedDate not supplied

A novel visualization model for web search results.

This paper presents an interactive visualization system, named WebSearchViz, for visualizing the Web search results and acilitating users' navigation and exploration. The metaphor in our model is the solar system with its planets and asteroids revolving around the sun. Location, color, movement, and spatial distance of objects in the visual space are used to represent the semantic relationships between a query and relevant Web pages. Especially, the movement of objects and their speeds add a new dimension to the visual space, illustrating the degree of relevance among a query and Web search results in the context of users' subjects of interest. By interacting with the visual space, users are able to observe the semantic relevance between a query and a resulting Web page with respect to their subjects of interest, context information, or concern. Users' subjects of interest can be dynamically changed, redefined, added, or deleted from the visual space.

Algorithms↗

PubMedDate not supplied

FacetMap: A scalable search and browse visualization.

The dominant paradigm for searching and browsing large data stores is text-based: presenting a scrollable list of search results in response to textual search term input. While this works well for the Web, there is opportunity for improvement in the domain of personal information stores, which tend to have more heterogeneous data and richer metadata. In this paper, we introduce FacetMap, an interactive, query-driven visualization, generalizable to a wide range of metadata-rich data stores. FacetMap uses a visual metaphor for both input (selection of metadata facets as filters) and output. Results of a user study provide insight into tradeoffs between FacetMap's graphical approach and the traditional text-oriented approach.

Algorithms↗

PubMedDate not supplied

Representing information in patient reports using natural language processing and the extensible markup language.

OBJECTIVE: To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. METHODS: A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. RESULTS: The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. CONCLUSIONS: Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available.

Humans↗

PubMed2005

Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

BACKGROUND: The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest. RESULTS: This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a set of easily implemented rules. Applying these techniques to 12,300 abstracts, a precision of 0.61 and a recall of 0.97 were obtained, (f = 0.74) and when allowing for two-hop and three-hop relations discovered by graphical analysis, the precision was 0.74 (f = 0.83). CONCLUSION: This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches.

Artificial Intelligence↗

PubMed2005

Columba: an integrated database of proteins, structures, and annotations.

BACKGROUND: Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. DESCRIPTION: COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. CONCLUSION: The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

Base Sequence↗