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PubMed2005

[Ten critical theses for patient applied telematic applications in health care].

Telematics applications in health care improve patient care in many ways. Especially the improvements through electronic communication, documentation and cooperation between the different providers have high potential for a qualitative and effective health care. Immaterialization of patient records enables their availability as health records across all health care institutions that are involved in the treatment of a patient. However, the realization of a telematic platform in health care raises new questions concerning ethical and technical issues. These questions must be answered in consideration of the interests of citizens, patients, health care providers and insurance companies. Against this background ten critical theses regarding patient-oriented applications in health telematics are presented and discussed. Special attention is paid to the changes in the relationship between patients and physicians and the necessity to establish a new cooperative medical documentation culture, based on controlled vocabularies and where patients and physicians together decide, which information should be added to the central health record, as well as the creation of the necessary trustworthiness and the balance of effective benefit of health telematics and the informational self determination of the patient.

Computer Communication Networks↗

PubMed2002

TAIR: a resource for integrated Arabidopsis data.

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.

Arabidopsis↗

PubMed1989

A poisonous plant file in TOXLINE.

A file has been added to TOXLINE on the subject of the toxicology of poisonous plants. It contains 2508 records, each of which comprises the full reference, key words, Chemical Abstracts Service Registry Number and abstract when available. A controlled vocabulary was constructed for the indexing and can be obtained from the National Technical Information Service. Searches can be made for several different data elements including authors; year; significant textwords of the title or abstract; journal or book; document type such as review or case report; geographic place at the level of continent, nation and state/province; plant species at the level of family, genus and species; plant parts involved; animal species affected including humans; type of harmful effects including major signs and lesions and chemicals.

Information Systems↗

PubMed2004

Information content in Medline record fields.

BACKGROUND: The authors have been conducting text mining analyses (extraction of useful information from text) of Medline records, using Abstracts as the main data source. For literature-based discovery, and other text mining applications as well, all records in a discipline need to be evaluated for determining prior art. Many Medline records do not contain Abstracts, but typically contain Titles and Mesh terms. Substitution of these fields for Abstracts in the non-Abstract records would restore the missing literature to some degree. OBJECTIVES: Determine how well the information content of Title and Mesh fields approximates that of Abstracts in Medline records. APPROACH: Select historical Medline records related to Raynaud's Phenomenon that contain Abstracts. Determine the information content in the Abstract fields through text mining. Then, determine the information content in the Title fields, the Mesh fields, and the combined Title-Mesh fields, and compare with the information content in the Abstracts. RESULTS: Four metrics were used to compare the information content related to Raynaud's Phenomenon in the different fields: total number of phrases; number of unique phrases; content of factors from factor analyses; content of clusters from multi-link clustering. The Abstract field contains almost an order of magnitude more phrases than the other fields, and slightly more than an order of magnitude more unique phrases than the other fields. Each field used a factor matrix with 14 factors, and the combination of all 56 factors for the four fields represented 27 separate, but not unique, themes. These themes could be placed in two major categories, with two sub-categories per major category: Auto-immunity (antibodies, inflammation) and circulation (peripheral vessel circulation, coronary vessel circulation). All four sub-categories included representation from each field. Thus, while the focus of the representation of each field in each sub-category was moderately different, the four sub-category structure could be identified by analyzing the total factors in each field. In the cluster comparison phase of the study, the phrases used to create the clusters were the most important phrases identified for each factor. Thus, the factor matrix served as a filter for words used for clustering. While clusters were generated for all four fields, the Title hierarchy tended to be fragmented due to sparsity of the co-occurrence matrix that underlies the clusters. Therefore, the Title clusters were examined at only the lower levels of aggregation. The Abstract, Mesh, and Mesh + Title fields had the same first level taxonomy categories, auto-immunity and circulation. At the second level, the Abstract, Mesh, and Mesh + Title fields had the autoimmune diseases and antibodies sub-category in common. The Abstract and Mesh fields shared fascia inflammation as the other auto-immunity sub-category, while the other Mesh + Title sub-category focuses on vinyl chloride poisoning from industrial contact, and consequences of antineoplastic agents. However, in both cases, even though the words may be different, inflammation may be the common theme. CONCLUSIONS: For taxonomy generation, especially at the higher levels, each of the four fields has a similar thematic structure. At very detailed levels, the Mesh and Title fields run out of phrases relative to the Abstract field. Therefore, selection of field (s) to be employed for taxonomy generation depends on the objectives of the study, particularly the level of categorization required for the taxonomy. For information retrieval, or literature-based discovery, selection of the appropriate field again depends on the study objectives. If large queries, or large numbers of concepts or themes are desired, then the field with the largest number of technical phrases would be desirable. If queries or concepts represented by the more accepted popular terminology is adequate, then the smaller fields may be sufficient. Because of its established and controlled vocabulary, the Mesh field lags the Title or Abss the Title or Abstract fields in currency. Thus, the Title or Abstract fields would retrieve records with the most explicitly stated current concepts, but the Mesh field would capture a larger swath of fields that contained a concept of interest but perhaps had a wider range of specific terminology in the Abstract or Title text. In addition, this study provides the first validated estimate of the disparity in information retrieved through text mining limited to Titles and Mesh terms relative to entire Abstracts. As much of the older biomedical literature was entered into electronic databases without associated Abstracts, literature-based discovery exercises that search the older medical literature may miss a substantial proportion of relevant information. On the basis of this study, it may be estimated that up to a log order more information may be retrieved when complete Abstracts are searched.

Abstracting and Indexing↗

PubMed2005

Methodology to ease the construction of a terminology of problems.

INTRODUCTION: Problem lists summarize an aspect of the patient's medical history and provide an important way to implement entry points for clinical pathways and guideline-oriented care. However, in order to automate processes based on problem lists, the use of controlled vocabularies is required. We developed a methodology to extract a collection of standardized problem-related terms from medical documents entered in free text by physicians. METHODS: We extracted a corpus of sentences describing problems from a randomized selection of admission notes collected at the University Hospitals of Geneva. Theses sentences underwent manual and automatic normalization processes, and a statistical clustering, in order to build a set of terms. RESULTS: We obtained 17,805 sentences from 5000 admission notes. We refined them into 1546 terms, 88.6% of which could be related to a relevant problem statement. DISCUSSION: A clinically relevant problems terminology was derived from clinical admission notes in free-text using a few methodical steps with a reasonable investment of human resources. Such an approach will ease the development and the use of problem lists better suited to user needs.

Medical Records, Problem-Oriented↗

PubMed2005

Desiderata for domain reference ontologies in biomedicine.

Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy. The purpose of this paper is to explore how two domain reference ontologies--the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data. We analyze those kinds of usages of these two domain reference ontologies and suggest desiderata for reference ontologies in biomedicine. While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes. We suggest five desirable characteristics for reference ontologies: good lexical coverage, good coverage in terms of relations, compatibility with standards, modularity, and ability to represent variation in reality.

Anatomy↗

PubMed2005

Graph theoretic modeling of large-scale semantic networks.

During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998-2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Algorithms↗

PubMed2006

A novel system for environmental monitoring through a cooperative/synergistic scheme between bioindicators and biosensors.

This paper addresses environmental monitoring through a robust dynamic integration between biomonitor and biosensor systems, a strategy that has not been attempted before. The two systems are conceptually interrelated and methodologically correlated to a cooperative/synergistic scheme (CSS) with a view to minimise uncertainty and monitoring costs and increase reliability of pollution control and abatement. The structures and operations of the biosensor component (in terms of sensitivity, device and method versatility, nature-mimicking physicochemical mechanisms, prospects and technological input) are such that they reinforce or promote the structures and operations of the natural component (in terms of bio-surveillance, impact assessment, environmental quality indexing, stress responses, metabolic pathways, etc.) and vice versa. The bioindicator ontology presented herein, including concepts, relations and controlled vocabulary aiming at establishing an integrated methodology for mapping/assessing negative environmental externalities, provides a useful tool for the design/development/implementation of an environmental network for the monitoring of a variety of pollutants over time and space and the assessment of environmental quality; the collection of the available information and its classification into taxonomic and partonomic relations allows the construction of a database that links pollutants with organisms' response, at a phenomenological and in-depth level, considering ecological parameters, relations and geomorphologic characteristics. As a result, a computer program has been designed/developed as a decision support system and has been successfully tested on a representative population of species indigenous to southern Greece. Significantly, a novel system in the form of a rational framework at the conceptual design level has been developed, that actually contributes towards achieving a cost-effective long-term monitoring program, with the flexibility to counter on-course any (anticipated or not) variations/modifications of the surveillance environment. This novel and pioneering approach will further offer a dynamic system utilised in (a) environmental impact studies and risk assessment (positive/analytic approach), (b) decision-making in the short-run (normative/tactic approach), and (c) policy-making in the long-run (normative/strategic approach). The proposed CSS, based on the integration of multiple data sources, can establish a local area network, incorporated into/expanding to a wide area network, thus offering the potential of better predictive ability and greater lead-time warning at alarm conditions than that provided by separate, stand-alone surveillance modalities.

Biosensing Techniques↗

PubMedDate not supplied

Data input module for Birth Defects Systems Manager.

The need for a computational bioinformatics infrastructure to manage the vast digital information from functional genomics and proteomics motivated us to develop Birth Defects Systems Manager (BDSM) as an open resource to facilitate analysis and discovery in developmental biology and developmental toxicity. This report describes the design, development and implementation of the data loading module of BDSM, referred to as LoadBDSM. It includes a shared data directory resource that can be granted various levels of security for different research groups or investigators to manage experimental datasets individually or in groups. LoadBDSM allows the upload of data and experiment details using controlled semantics for developmental exposure (toxicant, dosing scenario, intervention), biological sample (species, tissue, stage) and disease outcome (time, risk, phenotype). It adheres to existing controlled vocabulary plus rules of inference (ontologies) for experiment, data and metadata annotations. LoadBDSM extends the capabilities of BDSM to support the emergence of "embryo-formatics" defined here as the data, information and knowledge from genomic sciences applied to, or derived from, an embryological context. This includes, but is not limited to, delineating pathways and biological regulatory networks for specific chemicals or classes of developmental toxicants, developing novel biomarkers indicative of exposure and/or predictive of adverse effects, and integrating modern computing and information technology with data from molecular biology.

Abnormalities, Drug-Induced↗

PubMed2003

Zea mays ontology--a database of international terms.

Data retrieval, comprehension and sharing within and between plant-based databases are essential to exploit comparative genomic information to elucidate functional aspects of plant biology and to conduct studies of synteny and homology. However, the functionality is often hampered by the variability of terms used to describe comparable objects. The Zea mays Plant Structure Ontology database is designed to overcome this problem via the provision of a controlled vocabulary that facilitates knowledge sharing. It comprises international botanical terms, references, synonyms, and phylogenetic information and is open-source.

Databases, Factual↗

PubMed2006

Interpreting experimental results using gene ontologies.

High-throughput experimental techniques, such as microarrays, produce large amounts of data and knowledge about gene expression levels. However, interpretation of these data and turning it into biologically meaningful knowledge can be challenging. Frequently the output of such an analysis is a list of significant genes or a ranked list of genes. In the case of DNA microarray studies, data analysis often leads to lists of hundreds of differentially expressed genes. Also, clustering of gene expression data may lead to clusters of tens to hundreds of genes. These data are of little use if one is not able to interpret the results in a biological context. The Gene Ontology Consortium provides a controlled vocabulary to annotate the biological knowledge we have or that is predicted for a given gene. The Gene Ontologies (GOs) are organized as a hierarchy of annotation terms that facilitate an analysis and interpretation at different levels. The top-level ontologies are molecular function, biological process, and cellular component. Several annotation databases for genes of different organisms exist. This chapter describes how to use GO in order to help biologically interpret the lists of genes resulting from high-throughput experiments. It describes some statistical methods to find significantly over- or underrepresented GO terms within a list of genes and describes some tools and how to use them in order to do such an analysis. This chapter focuses primarily on the tool GOstat (http://gostat.wehi.edu.au). Other tools exist that enable similar analyses, but are not described in detail here.

Animals↗

PubMed2001

A MeSH based intelligent search intermediary for Consumer Health Information Systems.

GIN Austria (Gesundheitsinformationsnetz Austria) offers patients and consumers reliable medical knowledge about diseases, wellness and disease management in an easy understandable way and enables them to quick and incessant access to informations about the Austrian health system and Austrian health organizations. To achieve full customer (patients, citizens) satisfaction to find relevant information we propose a concept of a vector-model oriented IR-Tool based on the controlled vocabulary of the MeSH Thesaurus (german version). By this approach users who are often not used to scientific terms and expressions are supported to build up their own query with MeSH Main Headings. In a second step broader and narrower Main Headings are added to the query vector by the system. For this calculation an adapted version of the Floyd-Warshall algorithm for directed, azyclic graphs is used. The tool is part of the GIN Search Modul, which will ease gathering health information from different heterogenous internet datasources.

Austria↗

PubMedDate not supplied

Intelligent medical information filtering.

This paper describes an intelligent information filtering system to assist users to be notified of updates to new and relevant medical information. Among the major problems users face is the large volume of medical information that is generated each day, and the need to filter and retrieve relevant information. The Internet has dramatically increased the amount of electronically accessible medical information and reduced the cost and time needed to publish. The opportunity of the Internet for the medical profession and consumers is to have more information to make decisions and this could potentially lead to better medical decisions and outcomes. However, without the assistance from professional medical librarians, retrieving new and relevant information from databases and the Internet remains a challenge. Many physicians do not have access to the services of a medical librarian. Most physicians indicate on surveys that they do not prefer to retrieve the literature themselves, or visit libraries because of the lack of recent materials, poor organisation and indexing of materials, lack of appropriate and available material, and lack of time. The information filtering system described in this paper records the online web browsing behaviour of each user and creates a user profile of the index terms found on the web pages visited by the user. A relevance-ranking algorithm then matches the user profiles to the index terms of new health care web pages that are added each day. The system creates customised summaries of new information for each user. A user can then connect to the web site to read the new information. Relevance feedback buttons on each page ask the user to rate the usefulness of the page to their immediate information needs. Errors in relevance ranking are reduced in this system by having both the user profile and medical information represented in the same representation language using a controlled vocabulary. This system also updates the user profiles, automatically relieving this burden from the user, but also allowing the user to explicitly state preferences. An initial evaluation of this system was done with health consumers using a web site on consumer health. It was found that users often modified their criteria for what they considered relevant not only between browsing sessions but also during a session. A user's criteria for what is relevant is constantly changing as they interact with the information. New revised metrics of recall and precision are needed to account for the partially relevant judgements and the dynamically changing criteria of users. Future research, development, and evaluation of interactive information retrieval systems will need to take into account the users' dynamically changing criteria of relevance.

Artificial Intelligence↗

PubMed1991

Reactive chemical hedges: a search tool for comprehensive retrieval of chemical safety data.

A step-by-step procedure has been developed for compiling search hedges and has been applied to the topic of reactive chemicals. Special problems encountered in compiling the reactive chemical hedges are presented, including improvements in processing efficiency and recall performance achieved by trimming the hedge with a controlled vocabulary. A reactive chemical value index has been developed and used to rank six chemical databases according to their safety content. From these rankings, new on-line sources have been identified for reactive chemical information.

Chemical Phenomena↗

PubMed1998

Integration of haemodynamic and electrocardiographic waveform data with DICOM images.

The cardiac catheterization procedure involves acquisition of haemodynamic and electrocardiographic waveforms, as well as X-ray angiographic images. The DICOM standards is being extended to address robust interchange of this waveform data together with the image data, so as to present an integrated data set for the procedure. The proposed waveform information object definition is one of the new generation of DICOM extensions, and uses controlled vocabularies and coded entry sequences to represent clinically significant aspects of the data acquisition. This enables a generic waveform object to be specialized for disparate uses, e.g., haemodynamics, electrocardiograms, phonocardiograms, and electrophysiological data.

Cardiac Catheterization↗

PubMed2002

Association of genes to genetically inherited diseases using data mining.

Although approximately one-quarter of the roughly 4,000 genetically inherited diseases currently recorded in respective databases (LocusLink, OMIM) are already linked to a region of the human genome, about 450 have no known associated gene. Finding disease-related genes requires laborious examination of hundreds of possible candidate genes (sometimes, these are not even annotated; see, for example, refs 3,4). The public availability of the human genome draft sequence has fostered new strategies to map molecular functional features of gene products to complex phenotypic descriptions, such as those of genetically inherited diseases. Owing to recent progress in the systematic annotation of genes using controlled vocabularies, we have developed a scoring system for the possible functional relationships of human genes to 455 genetically inherited diseases that have been mapped to chromosomal regions without assignment of a particular gene. In a benchmark of the system with 100 known disease-associated genes, the disease-associated gene was among the 8 best-scoring genes with a 25% chance, and among the best 30 genes with a 50% chance, showing that there is a relationship between the score of a gene and its likelihood of being associated with a particular disease. The scoring also indicates that for some diseases, the chance of identifying the underlying gene is higher.

Chromosome Mapping↗

PubMed2000

[The electronic patient recrod: an essential part of using telematics in health care].

The DIADOQ CPR supports the explicit representation of the medical acts, facts and main inferences underlying the process of health care delivery. A controlled vocabulary is maintained by a frame-based concept system. This representation is the foundation for a consistent and comparable recording of patient data and for the flexible adaptation of screen forms to clinical contexts. The explicit and structured representation of the process of health care delivery enables the tight integration of knowledge-based decision support in the CPR system.

Artificial Intelligence↗

PubMed1992

[Development and organization of a knowledge-based documentation system for ophthalmologic video documentation].

We introduce a system for documentation of ophthalmological video tapes. This system can be implemented without regarding the German data security law (Bundesdatenschutzgesetz), because the documentation of the patient identification and the video tape identification number is done manually and separated from the EDP-supported documentation of the video tape identification number and the contents of the tape. But the use of a controlled vocabulary framework for diagnosis and surgery can be considered as the main advantage of this system. This enables a complete and fast retrieval to all records containing the terms searched for. Our system provides additional space for non-standardized text-documentation, e.g. comments etc... The implemented search-editor allows a fast retrieval to all records by input of strings, which can be connected by boolean expressions.

Computer Security↗