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At least 55 records · Page 3Linked to original sources
PubMedDate not supplied

Chemical machine vision: automated extraction of chemical metadata from raster images.

We present a novel application of machine vision methods for the identification of chemical composition diagrams from two-dimensional digital raster images. The method is based on the use of Gabor wavelets and an energy function to derive feature vectors from digital images. These are used for training and classification purposes using a Kohonen network for classification with the Euclidean distance norm. We compare this method with previous approaches to transforming such images to a molecular connection table, which are designed to achieve complete atom connection table fidelity but at the expense of requiring human interaction. The present texture-based approach is complementary in attempting to recognize higher order features such as the presence of a chemical representation in the original raster image. This information can be used for providing chemical metadata descriptors of the original image as part of a robot-based Internet resource discovery tool.

Data Display↗
PubMedDate not supplied

Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators.

Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.

Journal Article↗
PubMedDate not supplied

A searching and reporting system for relational databases using a graph-based metadata representation.

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

Computer Simulation↗
PubMed2002

Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences.

The Olfactory Receptor Database (ORDB; http://senselab.med.yale.edu/senselab/ordb) is a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. To deal with the very large OR gene family, we have constructed an algorithm that automatically downloads sequences from web sources such as GenBank and SWISS-PROT into the database. The algorithm uses hypertext markup language (HTML) parsing techniques that extract information relevant to ORDB. The information is then correlated with the metadata in the ORDB knowledge base to encode the unstructured text extracted into the structured format compliant with the database architecture, entity attribute value with classes and relationship (EAV/CR), which supports the SenseLab project as a whole. Three population methods: batch, automatic and semi-automatic population are discussed. The data is imported into the database using extensible markup language (XML).

Algorithms↗
PubMed2004

An integrated content and metadata based retrieval system for art.

A new approach to image retrieval is presented in the domain of museum and gallery image collections. Specialist algorithms, developed to address specific retrieval tasks, are combined with more conventional content and metadata retrieval approaches, and implemented within a distributed architecture to provide cross-collection searching and navigation in a seamless way. External systems can access the different collections using interoperability protocols and open standards, which were extended to accommodate content based as well as text based retrieval paradigms. After a brief overview of the complete system, we describe the novel design and evaluation of some of the specialist image analysis algorithms including a method for image retrieval based on sub-image queries, retrievals based on very low quality images and retrieval using canvas crack patterns. We show how effective retrieval results can be achieved by real end-users consisting of major museums and galleries, accessing the distributed but integrated digital collections.

Abstracting and Indexing↗
PubMedDate not supplied

Metadata-driven ad hoc query of patient data: meeting the needs of clinical studies.

Clinical study data management systems (CSDMSs) have many similarities to clinical patient record systems (CPRSs) in their focus on recording clinical parameters. Requirements for ad hoc query interfaces for both systems would therefore appear to be highly similar. However, a clinical study is concerned primarily with collective responses of groups of subjects to standardized therapeutic interventions for the same underlying clinical condition. The parameters that are recorded in CSDMSs tend to be more diverse than those required for patient management in non-research settings, because of the greater emphasis on questionnaires for which responses to each question are recorded separately. The differences between CSDMSs and CPRSs are reflected in the metadata that support the respective systems' operation, and need to be reflected in the query interfaces. The authors describe major revisions of their previously described CSDMS ad hoc query interface to meet CSDMS needs more fully, as well as its porting to a Web-based platform.

Computer Security↗
PubMedDate not supplied

Quality management, certification and rating of health information on the Net with MedCERTAIN: using a medPICS/RDF/XML metadata structure for implementing eHealth ethics and creating trust globally.

MedCERTAIN (MedPICS Certification and Rating of Trustworthy Health Information on the Net, http://www.medcertain.org/) is a recently launched international project funded under the European Union's (EU) "Action Plan for safer use of the Internet". It provides a technical infrastructure and a conceptual basis for an international system of "quality seals", ratings and self-labelling of Internet health information, with the final aim to establish a global "trustmark" for networked health information. Digital "quality seals" are evaluative metadata (using standards such as PICS=Platform for Internet Content Selection, now being replaced by RDF/XML) assigned by trusted third-party raters. The project also enables and encourages self-labelling with descriptive metainformation by web authors. Together these measures will help consumers as well as professionals to identify high-quality information on the Internet. MedCERTAIN establishes a fully functional demonstrator for a self- and third-party rating system enabling consumers and professionals to filter harmful health information and to positively identify and select high quality information. We aim to provide a trustmark system which allows citizens to place greater confidence in networked information, to encourage health information providers to follow best practices guidelines such as the Washington eHealth Code of Ethics, to provide effective feedback and law enforcement channels to handle user complaints, and to stimulate medical societies to develop standard for patient information. The project further proposes and identifies standards for interoperability of rating and description services (such as libraries or national health portals) and fosters a worldwide collaboration to guide consumers to high-quality information on the web.

Certification↗
PubMed2001

A metadata framework for interoperating heterogeneous genome data using XML.

The rapid advances in the Human Genome Project and genomic technologies have produced massive amounts of data populated in a large number of network-accessible databases. These technological advances and the associated data can have a great impact on biomedicine and healthcare. To answer many of the biologically or medically important questions, researchers often need to integrate data from a number of independent but related genome databases. One common practice is to download data sets (text files) from various genome Web sites and process them by some local programs. One main problem with this approach is that these programs are written on a case-by-case basis because the data sets involved are heterogeneous in structure. To address this problem, we define metadata that maps these heterogeneously structured files into a common eXtensible Markup Language (XML) structure to facilitate data interoperation. We illustrate this approach by interoperating two sets of essential yeast genes that are stored in two yeast genome databases (MIPS and YPD).

Databases, Genetic↗
PubMedDate not supplied

Data and metadata reporting standards for the U.S. Environmental Protection Agency's PM Supersites Research Program.

The EPA Supersites Research Program needs consistency of metadata and data structures to facilitate information sharing among investigators, analysts, and ultimately secondary data users. Under the auspices of NARSTO a successful mechanism was created to develop and implement reporting standards. The development effort included working closely with Supersites data coordinators, investigators, and technical experts, and also leveraging from existing data standards and practices. Overall, the standards are getting good acceptance from the atmospheric research community.

Cities↗
PubMed2005

Metadata driven generation of reports for clinical studies.

We have developed a reporting engine to dynamically create Web-based reports for multiple types of clinical studies in a large-scale clinical study data management system (CSDMS), TrialDB. The engine, currently in production use, generates reports based on metadata that is defined through a GUI, thus eliminating the need to write code for every report.

Clinical Trials as Topic↗
PubMed2006

On-the-fly form generation and on-line metadata configuration--a clinical data management Web infrastructure in Java.

In this paper we describe the approach to build a web-based clinical data management infrastructure on top of an entity-attribute-value (EAV) database which provides for flexible definition and extension of clinical data sets as well as efficient data handling and high performance query execution. A "mixed" EAV implementation provides a flexible and configurable data repository and at the same time utilizes the performance advantages of conventional database tables for rarely changing data structures. A dynamically configurable data dictionary contains further information for data validation. The online user interface can also be assembled dynamically. A data transfer object which encapsulates data together with all required metadata is populated by the backend and directly used to dynamically render frontend forms and handle incoming data. The "mixed" EAV model enables flexible definition and modification of clinical data sets while reducing performance drawbacks of pure EAV implementations to a minimum. The system currently is in use in an electronic patient record with focus on flexibility and a quality management application (www.healthgate.at) with high performance requirements.

Austria↗
PubMed1998

MCM generator: a Java-based tool for generating medical metadata.

In a previous paper we introduced the need to implement a mechanism to facilitate the discovery of relevant Web medical documents. We maintained that the use of META tags, specifically ones that define the medical subject and resource type of a document, help towards this goal. We have now developed a tool to facilitate the generation of these tags for the authors of medical documents. Written entirely in Java, this tool makes use of the SAPHIRE server, and helps the author identify the Medical Subject Heading terms that most appropriately describe the subject of the document. Furthermore, it allows the author to generate metadata tags for the 15 elements that the Dublin Core considers as core elements in the description of a document. This paper describes the use of this tool in the cataloguing of Web and non-Web medical documents, such as images, movie, and sound files.

Cataloging↗
PubMed2001

Using metadata to create navigation paths in the HealthInsite Internet gateway.

The objective of this study was to evaluate the HealthInsite topic query technique, which uses a dynamic database search to assign resources to a topic. It is an alternative to the explicit classification technique, which relies on the classification of each resource using a predefined classification scheme. We performed a recall-precision analysis on all topics within the broad topic area of Child Health. Recall and precision errors were checked to determine which part of the information retrieval process was at fault. We then compared the topic query technique with the explicit classification technique. The results show errors or problems at every stage of the information retrieval process. This has initiated a review of all the tools used in the process, from indexing guidelines to the search engine. While many errors could be corrected, there were still features of the explicit classification technique that could not be achieved by the topic query technique. In conclusion, the topic query technique has the advantage of flexibility, but close co-operation between the different information retrieval specialists is needed to get the best results. The HealthInsite topic navigation structure should be regarded as an organized set of predefined searches rather than a full classified listing.

Abstracting and Indexing↗
PubMedDate not supplied

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

Databases as Topic↗
PubMed2006

MetaBasis: a web-based database containing metadata on software tools and databases in the field of bioinformatics.

UNLABELLED: We have developed an integrated web-based relational database information system, which offers an extensive search functionality of validated entries containing available bioinformatics computing resources. This system, called MetaBasis, aims to provide the bioinformatics community, and especially newcomers to the field, with easy access to reliable bioinformatics databases and tools. MetaBasis is focused on non-commercial and open-source software tools. AVAILABILITY: http://metabasis.bioacademy.gr/

Computational Biology↗