Exploring Large Document Repositories with RDF Technology: The DOPE Project (original) (raw)
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2004
The DOPE project (Drug Ontology Project for Elsevier) is driven by the need to access multiple information sources through a single interface. In this paper, we describe how DOPE allows thesaurus-driven access to heterogeneous and distributed data, based on the RDF data model. The architecture allows for the easy addition of thesauri and data sources, and can facilitate explorations in ontology mapping and data integration. ยง Corresponding
International Journal of Intelligent Systems and Applications, 2012
For more relevant informational retrieval and matching of user request with metadata about biomedical informational recourses it is necessary to formulize the user knowledge about this subject domain. We propose to use the ontologies and associated with them thesauri of the appropriate subject domains for representation of biomedicine knowledge. The algorithms of formation and normalization of the multilinguistic thesauruses, and also methods of their comparison are given in this work.
The instantiation of OmniPaper RDF prototype in the context of scientific publications
The Electronic Library, 2009
The purpose of this paper is to present an instance of the system developed in the OmniPaper project, regarding the mechanisms of distributed information retrieval. These mechanisms were developed for newspapers' articles and they were then instantiated in the context of the scientific publication. Another goal concerns the use of a central metadatabase developed to accomplish the syndication of contents, through the RSS approach. Design/methodology/approach One of the steps of the system's development was the definition of the metadata layer that supports the research and the navigation functionalities as well as the contents' syndication. Several tasks were performed for the definition of the metadata layer, namely: (1) analysis of several metadata standard vocabularies; (2) Selection of the metadata elements; (3) Definition of an application profile and the RSS template; (4) Development of a metadatabase, through the use of a native RDF database management system to store the RSS descriptions of the scientific publications; (5) Implementation of the search and navigation processes developed in the prototype through the use of the RDFS version of the WordNet and the RDFS version of classification system of Association for Computing Machinery Computing Classification System (ACM CCS); finally (5) Tests and validation of all developed functionalities.
LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies
The Lexical Grid (LexGrid) project is an on-going community-driven initiative coordinated by the Mayo Clinic Division of Biomedical Statistics and Informatics (BSI). It provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. While successfully used and adopted in the biomedical and clinical community, an important requirement is to align the existing LexGrid model with emerging Semantic Web standards and specifications. This paper introduces the LexRDF model, which maps the LexGrid model elements to corresponding constructs in W3C specifications such as RDF, OWL, and SKOS. Our mapping specification successfully used W3C standards to represent most of the existing LexGrid components, and those that did not map point out issues in the existing specifications that the W3C may want to consider in future work. With LexRDF, the terminological information represented in LexGrid can be tra...
Knowledge management in biomedical libraries: A semantic web approach
Information Systems Frontiers, 2009
In recent years, technological advances in highthroughput techniques and efficient data gathering methods, coupled with a world-wide effort in computational biology, have resulted in an enormous amount of life science data available in repositories devoted to biomedical literature. These repositories lack the ability to attain an effective and accurate search. Using semantic technologies as the key for interoperation enables searching and processing of biomedical literature in a more efficient way. However, emerging semantic applications take for granted specific knowledge that biomedical researchers may not have. This paper presents design principles for easy-to-use biomedical semantic applications by means of ontology-based annotations and faceted search. The proposed approach is backed with a usable prototype that shows the breakthroughs of adding these principles to a biomedical digital library where identifying and searching information are critical aspects for non-semantic Web experts.
NBDC RDF portal: a comprehensive repository for semantic data in life sciences
Database
In the life sciences, researchers increasingly want to access multiple databases in an integrated way. However, different databases currently use different formats and vocabularies, hindering the proper integration of heterogeneous life science data. Adopting the Resource Description Framework (RDF) has the potential to address such issues by improving database interoperability, leading to advances in automatic data processing. Based on this idea, we have advised many Japanese database development groups to expose their databases in RDF. To further promote such activities, we have developed an RDF-based life science dataset repository called the National Bioscience Database Center (NBDC) RDF portal. All the datasets in this repository have been reviewed by the NBDC to ensure interoperability and queryability. As of July 2018, the service includes 21 RDF datasets, comprising over 45.5 billion triples. It provides SPARQL endpoints for all datasets, useful metadata and the ability to download RDF files. The NBDC RDF portal can be accessed at https://integbio.jp/rdf/.
Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches
2000
We describe Semantic MEDLINE, a Web application that manages the results of PubMed searches by summarizing and visu- alizing semantic predications extracted from MEDLINE citations and linking them to several structured resources to provide an integrated environment. To demonstrate its utility, we present a scenario in which we use Semantic MEDLINE to gain insights into relaxin, a hormone whose function
Semantic MEDLINE: a web application to manage the results of PubMed searches
We describe Semantic MEDLINE, a Web application that manages the results of PubMed searches by summarizing and visu-alizing semantic predications extracted from MEDLINE citations and linking them to several structured resources to provide an integrated environment. To demonstrate its utility, we present a scenario in which we use Semantic MEDLINE to gain insights into relaxin, a hormone whose function in humans has not been fully elucidated. We propose Semantic MEDLINE as an enabling information resource and exploration tool for biomedical scientists, health care profes-sionals, and consumers. (For access, send e-mail to trindflesch@mail.nih.gov).
Theorie, Semantik und Organisation von Wissen, 2017
Currently, the conventional channel for reporting scientific results is the Web electronic publishing. Despite the advances in electronic publishing scientific articles are still published in paper print formats such as PDFs. The emergence of the Semantic Web and Linked Data environment provides new opportunities for communicating, sharing, and integrating scientific knowledge in digital formats that can overcome the limitations of the current print format, suitable only for reading by people. This paper explores the possibilities of this new environment proposing a semantic model of scholarly electronic articles in biomedical sciences. Thereby the results of scientific research can be published electronically, shared in structured, interlinked formats, enabling their crawling by software agents, facilitating semantic retrieval, knowledge reuse, validation of scientific results, identification of traces of scientific discoveries, new scientific insights, and identification of knowledge contradictions or inconsistencies.
The Semantic Portal for Supporting Research Community: a Review
International Journal on Advanced Science, Engineering and Information Technology, 2011
Current state of the art of typical search engines like Google, Yahoo and others are delivering references in terms of web URL or links to the related website. As such the results did not deliver the right answers required to the users needs. In addition to that as soon as the users require a collection of the information obtained, these search engines failed to do so resulting in the human intervention in-combining the information from several sources. Due ot the advancement and the vast number of sites and information on the web, demands in providing higher precision results are required to aid users in obtaining the most relevant result to the search process. One of the promising areas of the Semantic Web is enhancing the query capabilities for information. Small vertical vocabularies and ontologies have emerged, and the community of people using these and generating data is growing daily. However queries or search mechanisms that utilizea the vasrt amount of vocabularies, ontologies and data in digital libraries is still very much lacking. Therefore searching over heteregoneous records, data in digital library community or the Web has become a well known problem to the mass public. As such a solution is needed for a federated search across multiple resources available. However it remains unclear on how Semantic Web or its technology is used in constructing a digital library system or aid in enhancing the quality of the search results performed. This leads to the current work proposed, as work will be conducted to provide possible components that will construct the semantic web portal. The work performed is essential to facilitate semantic searches for research community in large-scale distributed digital library system. The subject research community is chosen particularly to aid in ensuring hat result obtained are accordingly to the users relevant needs. The expected outcomes of the research are an architecture that utilizes the semantic technology that will promote semantic web portal in the digital library and a semantic search mechanism that will provide better results and a combination of useful results relevant to the users.