Uniform Resource Identifiers Research Articles

Moby and Moby 2: Creatures of the Deep (Web)

Facile and meaningful integration of data from disparate resources is the 'holy grail' of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized 'semantic warehouses' that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the 'Deep Web'-that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine 'The State of the Union' for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.

Hogrefe OpenMind License

Hogrefe OpenMind License

Identity of Resources and Entities on the Web

One of the main strengths of the Web is that it allows any party of its global community to share information with any other party. This goal has been achieved by making use of a unique and uniform mechanism of identification, the uniform resource identifiers (URI). Although URIs succeed when used for retrieving resources on the Web, their suitability for identifying any kind of thing, for example, resources that are not on the Web, is not guaranteed. In this article we investigate the meaning of the identity of a Web resource, and how the current situation, as well as existing and possible future improvements, can be modeled and implemented on the Web. In particular, we propose an ontology, IRE, that provides a formal way to model both the problem and the solution spaces. IRE describes the concept of resource from the viewpoint of the Web, by reusing an ontology of information objects, built on top of DOLCE+ and its extensions. In particular, we formalize the concept of Web resource, as distinguished from the concept of a generic entity, and how those and other concepts are related, for example, by different proxy for relations. Based on the analysis formalized in IRE, we propose a formal pattern for modeling and comparing different solutions to the problems of the identity of resources.

Open Horizons: Archiving Perspectives for Services and Frameworks

Sooner or later archives storing electronic data will most likely face the task how to archive resources from the internet. These will usually come in as an URI (Uniform Resource Identifier, pointing at a webpage or some other resource in the internet.References to external documents are not something fundamentally new to archives. Traditionally these references point at a document kept safely in another archive like a National Library. In contrast, information in the internet underlies a continual process of change, pages will be updated, merged or they disappear suddenly, whole domains will raise and fall without leaving a useful trace for reference.The obvious way of treating these resources is to download the concerning page. Despite the copyright issues, what if there are other links on the page? Instead of downloading whole sites or starting to archive the internet, it is advisable to treat these dynamic resources as an information type at its own. At first, it is necessary to examine the structure of this kind of resource.

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

BackgroundThe Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) is a set of guidelines for the annotation and curation processes of computational models, in order to facilitate their exchange and reuse. An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs.ResultsMIRIAM Resources are a set of on-line services created to catalogue data types, their URIs and the corresponding physical URLs (or resources), whether data types are controlled vocabularies or primary data resources. MIRIAM Resources are composed of several components: MIRIAM Database stores the information, MIRIAM Web Services allows to programmatically access the database, MIRIAM Library provides an access to the Web Services and MIRIAM Web Application is a way to access the data (human browsing) and also to edit or add entries.ConclusionsThe project MIRIAM Resources allows an easy access to MIRIAM URIs and the associated information and is therefore crucial to foster a general use of MIRIAM annotations in computational models of biological processes.

REGAP: A Tool for Unicode-Based Web Identity Fraud Detection

ABSTRACT We anticipate the widespread usage of an internationalized resource identifier (IRI) 1 or internationalized domain name (IDN) 2 on the web as complement to universal resource identifier (URI). IRI/IDN is composed of characters in a subset of Unicode, such that a Unicode attack 3 to IRI/IDN could happen. Hence, visually or semantically, certain phishing IRI/IDNs may show high similarity to the real ones. The potential phishing attacks based on this strategy are very likely to happen in the near future with the boosting utilization of IRI/IDN. We invented a method to detect such phishing attack. We constructed a unicode character similarity list (UC-SimList) based on char-char visual and semantic similarities and use a nondeterministic finite automaton (NFA) 4 to identify the potential IRI/IDN-based phishing patterns. We implemented a phishing IRI/IDN pattern generation tool, REGAP, by which phishing IRI/IDN patterns can be generated into regular expressions (RE) for phishing IRI/IDN detection. We ...

URI 서버에 기반한 국가 R&D 기반정보 온톨로지 설계 및 구현

The development of Semantic Web basically requires knowledge which is induced by the formalization and semantization of information, and thus ontology should be introduced as a knowledgization tool. URI(Uniform Resource Identifier) is an indispensible scheme to uniquely indicate individuals on ontology. However, it is difficult to find the use cases of identifiers or URIs in real data sets including science & technology publications. This paper describes the method to construct, manage, and serve reference information based on URI which is a crucial component on establishing national R&D reference information ontology. We expect the reference information which was acquired from about 7,000 proceeding papers would be adopted to Semantic Web applications such as researcher network analysis and outcome statistics.

Bringing Chemical Data onto the Semantic Web

Present chemical data storage methodologies place many restrictions on the use of the stored data. The absence of sufficient high-quality metadata prevents intelligent computer access to the data without human intervention. This creates barriers to the automation of data mining in activities such as quantitative structure-activity relationship modelling. The application of Semantic Web technologies to chemical data is shown to reduce these limitations. The use of unique identifiers and relationships (represented as uniform resource identifiers, URIs, and resource description framework, RDF) held in a triplestore provides for greater detail and flexibility in the sharing and storage of molecular structures and properties.

Modelling fuzzy universal resource identifiers: A first approach

A universal resource identifier (or URI) is a compact string of characters for identifying an abstract or physical resource, providing a simple and extensible means for identifying that resource [1] in the world wide web. In this paper, we present a new modelling approach of extending this identifier to encompass paths of a type of directed labelled fuzzy trees.

Abstract interdomain security assertions: A basis for extra-grid virtual organizations

One significant challenge in building grids between organizations with heterogeneous security systems is the need to express and enforce security policies that specify the users in one organization (the source domain) who are allowed to access the resources in another organization (the target domain). This requires linking the syntax and semantics of security assertions referring to users and their attributes in the source domain to those referring to resources in the target domain. This paper suggests some basic requirements for solving this problem, in particular, an abstract form of interdomain security assertion (IDSA) relying, for instance, on globally meaningful URIs (Uniform Resource Identifiers) to refer to users, resources, and their attributes. This canonical abstract form of IDSA is, however, used strictly for assertion mapping purposes. It may—but need not—be visible in any concrete security assertion syntax in any domain. The paper further suggests different scenarios in which URIs for users, resources, and attributes defined in one domain can be mapped to semantically meaningful references—with varying degrees of granularity and accountability—in another domain where they would otherwise be meaningless.

Standards - Metadata standards for educational resources

In the 1990s, recognition of the potential economies of reusing educational materials spawned the development of metadata standards for sharing and storing learning objects. Metadata is data that describes a physical or electronic resource and can be used to manage collections of documents, images, and other information in a repository such as an archive or museum. Some metadata elements, such as title, description, subject, and keywords, are similar to those that libraries use to catalog their holdings. Other elements, such as the uniform resource identifier (URI), are specific to a digital, Web-based environment. Metadata can be stored in a digital library or repository that provides services to search or browse for educational materials. The Dublin Core Metadata Element Set and IEEE Learning Object Metadata are two popular metadata standards that facilitate cataloging, searching, and reuse of such resources.

Metadata: A Fundamental Component of the Semantic Web

Metadata: A Fundamental Component of the Semantic Web

Principled design of the modern Web architecture

The World Wide Web has succeeded in large part because its software architecture has been designed to meet the needs of an Internet-scale distributed hypermedia application. The modern Web architecture emphasizes scalability of component interactions, generality of interfaces, independent deployment of components, and intermediary components to reduce interaction latency, enforce security, and encapsulate legacy systems. In this article we introduce the Representational State Transfer (REST) architectural style, developed as an abstract model of the Web architecture and used to guide our redesign and definition of the Hypertext Transfer Protocol and Uniform Resource Identifiers. We describe the software engineering principles guiding REST and the interaction constraints chosen to retain those principles, contrasting them to the constraints of other architectural styles. We then compare the abstract model to the currently deployed Web architecture in order to elicit mismatches between the existing protocols and the applications they are intended to support.

Remedies for common user-agent problems

User agents---that is browsers and other programs that deal with the Web---can fail the user in many ways. This article, by three people deeply involved with the development of the Web, documents some typical common user agent problems, and suggests correct ways of working.<BR><BR>The authors use several Web-specific technical terms, so let me list the important ones here:<BR><BR>• Fragment identifier: the part of a URI Web address after a `#' character, typically identifying a sub-part of a document (e.g. http://www.example.com/index.html#contact).<BR>• HTTP: hypertext transfer protocol - the protocol used for transferring documents between a server and a client.<BR>• Media type (also known as MIME type): an identifying string like "text/html" or "image/gif" used by servers and clients for identifying the type of a document.<BR>• PNG: a bitmapped image format, like GIF and JPEG, but with better user experience properties<BR>• RFC: `Request for comments' - the name given to Internet standards published by the IETF (Internet Engineering Task Force)<BR>• SVG: structured vector graphics: a non-bitmapped image format that scales better than bitmapped formats like PNG, GIF and JPEG.<BR>• URI: (Universal resource identifier) a `Web address', such as http://www.acm.org<BR>• URI scheme: the part of a URI before the colon, such as http: and ftp:<BR><BR>---Steven Pemberton

The PURL Project

A PURL is a Persistent Uniform Resource Locator. Functionally, a PURL is a URL (Uniform Resource Locator). However, instead of pointing directly to the location of an Internet resource, a PURL points to an intermediate resolution service. The PURL project is a result of OCLC participation in the Internet Engineering Task Force (IETF) Uniform Resource Identifier working groups. PURLs satisfy many of the requirements of Uniform Resource Names (URNs). They use current technologies and can be transitioned smoothly into a URN architecture once it is in place.

Scalable human-friendly resource names

To fill the gap between what uniform resource names (URNs) provide and what humans need, we propose a new kind of uniform resource identifier (URI) called human-friendly names (HFNs). In this article, we present the design for a scalable HFN-to-URL (uniform resource locator) resolution mechanism that makes use of the Domain Name System (DNS) and the Globe location service to name and locate resources. This new URI proposes to improve both scalability and usability in naming replicated resources on the Web.

Version augmented URIs for reference permanencevia an apache module design

The World Wide Web is perhaps the most convenient library resource ever to exist. Yet it also suffers from a critical flaw: WWW document citations existing as clickable links and as standard references in printed documents are quite unreliable. This arises from the ease with which these documents may be altered. Alteration of cited WWW documents may lead to the citations themselves becoming invalid or inaccurate. Printed documents are less prone to such problems due to the greater difficulty in altering or eradicating them. As a consequence of the alterability of WWW documents, the whole traditional system of new work building upon an archive of unchangeable previous work ceases to be valid. For the first time in history, documents are being built upon a shifting foundation to an extent of ever increasing and serious proportions. This work investigates a system aimed at encouraging the stability of WWW documents. In doing so it helps to preserve the accuracy of citations over time. The system presented extends a document's URI (Universal Resource Identifier) to include date or revision information thus allowing document providers to permit users to refer accurately to a particular document version. This paper both describes the system and demonstrates its use. The system is implemented as an Apache WWW server module. The module processes and retrieves documents referenced with extended URIs. It provides a model public domain system for alleviating the problem of content stable WWW documents.

Uniform Resource Identifiers and Online Serials

Summary The widespread acceptance of the World Wide Web makes it the method of choice for publishing online serials. However, concerns ranging from rights management to the long-term integrity of citations are just two of the issues which continue to impede the widespread adoption of such a mode of publication. This paper discusses the history and purposes of Uniform Resource Identifiers (URIs) as well as the role identifiers will play in the deployment of online serials. Particular attention is paid to development of Uniform Resource Names (URNs), one of the goals of which is to use existing identifier systems, such as ISBNs, ISSNs, and SICIs. The paper describes URN syntax and resolution, then presents some illustrations of how WWW-based publication of online serials might use different forms of URIs.

The Digital Library on Campus: A Perspective from a UK Academic Environment

Whichever definition you wish to employ, the age of the digital library is upon us. There is much theoretical discussion about the nature of the digital library, but whatever form it comes to assume in the future, its foundations are surely being laid now. It is often remarked that there will be no place in it for librarians who will be displaced from the world of information to become merely curators of book museums. But this is not the experience of this librarian who i s hearing more loudly now than ever before, demands from our users for information in digital form and an insistence that libraries should be exploiting IT on their behalf. To the academic community, we have been traditionally the gatekeepers to the world of information. They now see us as being effectively the purse-holders for information, and they are looking first to us to provide the information services they need for teaching and research.The Follett Report published in 1993, has had a tremendous influence in the UK in this respect. Its recommendations have led directly to the release of funds specifically for libraries which has provided a window of opportunity for institutions wishing to collaborate in digitization projects. The author discusses briefly some of those in which Oxford is closely involved.Many forces have contributed to the new expectations of the library profession, but of perhaps most significance has been the accelerating growth of high bandwidth networks and internet connectivity. At last it is becoming feasible for libraries to consider tackling the problems of the information explosion and shrinking budgets, by moving truly from 'holdings to 'access' policies. There is also the demand that our information services should reach beyond library buildings to the users' desktops on campus and at home. As a practicing digital librarian who has had to grapple with the technicalities of providing integrated and ubiquitous information systems in the real virtual world, certain difficulties have become apparent which are common to most UK academic establishments and, I suspect, to those in Europe, the US and India too.With respect to accessing quality CD-ROM and magnetic databases, mounted logicaly or remotely, the SilverPlatter ERL system has provided us with a powerful mechanism, especially with the development of WebSPIRS, which allows access to databases from standard WWW browsers, and provides support for Z39.50, which will allow access from Z39.50 clients.The WWW has achieved a high integration of internet sources and we are using it for many applications. But it has inherent limitations, in particular, the 'stateless' nature of the http protocol and the semantic poverty of HTML. We shall examine these issues in the light of new ,standards and technologies that are emerging, in particular, the IETF's work on Uniform Resource Identifiers, the Text Encoding Initiative and Sun's JAVA programming language. http://dx.doi.org/10.14429/dbit.17.6.3241

Uniform Resource Identifiers and the Effort to Bring "Bibliographic Control" to the Web: An Overview of Current Progress

Unlike the Online Catalog, the Web does not offer an infrastructure for bibliographic control. In 1992, to deal with these inadequacies, the Internet Engineering Task Force (IETF) chartered the Uniform Resource Identifiers (URI) Working Group to discuss and develop standards for naming, describing and addressing Internet resources