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NG4J - 'Named Graphs API for Jena' is an extension to the Jena Semantic Web framework for parsing, manipulating and serializing sets of Named Graphs. For details about Named Graphs see http://www.w3.org/2004/03/trix/

"URIs, a universal identification scheme, are different from human names insofar as they can provide the ability to reliably access the thing identified. URIs also can function to reference a non-accessible thing in a similar manner to how names function in natural language. There are two distinctly different relationships between names and things: access and reference. To confuse the two relations leads to underlying problems with Web architecture. Reference is by nature ambiguous in any language. So any attempts by Web architecture to make reference completely unambiguous will fail on the Web. Despite popular belief otherwise, making further ontological distinctions often leads to more ambiguity, not less. Contrary to appeals to Kripke for some sort of eternal and unique identification, reference on the Web uses descriptions and therefore there is no unambiguous resolution of reference. On the Web, what is needed is not just a simple redirection, but a uniform and logically consistent manner of associating descriptions with URIs that can be done in a number of practical ways that should be made consistent. "

A great review of the challenges that follow from using URIs for both access and reference

Named Graphs is the idea that having multiple RDF graphs in a single document/repository and naming them with URIs provides useful additional functionality built on top of the RDF Recommendations.

The Semantic Web isn't just about putting data on the web. It is about making links, so that a person or machine can explore the web of data. With linked data, when you have some of it, you can find other, related, data. Like the web of hypertext, the web of data is constructed with documents on the web. However, unlike the web of hypertext, where links are relationships anchors in hypertext documents written in HTML, for data they links between arbitrary things described by RDF,. The URIs identify any kind of object or concept. But for HTML or RDF, the same expectations apply to make the web grow: 1. Use URIs as names for things 2. Use HTTP URIs so that people can look up those names. 3. When someone looks up a URI, provide useful information. 4. Include links to other URIs. so that they can discover more things.

Giving unique and meaningful names to every human gene

OpenSocial's API reference describes a number of classes ('Person', 'Name', 'Email', 'Phone', 'Url', 'Organization', 'Address', 'Message', 'Activity', 'MediaItem', 'Activity', …), each of which has various properties whose values are either strings, references to instances of other classes, or enumerations. I'd like to make them usable beyond the confines of OpenSocial, so I'm making an RDF/OWL version. OpenSocial's schema is an attempt to provide an overarching model for much of present-day mainstream 'social networking' functionality, including dating, jobs etc. Such a broad effort is inevitably somewhat open-ended, and so may benefit from being linked to data from other complementary sources.

Faviki is a social bookmarking tool which allows you to tag webpages you want to remember with Wikipedia terms. This means that everybody uses the same names for tags from the world's largest collection of knowledge. Thanks to DBpedia, which extracts structured information from Wikipedia and represents it in a flexible data model, these tags are reference to objects which are categorized automatically, keeping your and your friend's bookmarks and interests well organized.

Unstructured Information Management applications are software systems that analyze large volumes of unstructured information in order to discover knowledge that is relevant to an end user. UIMA is a framework and SDK for developing such applications. An example UIM application might ingest plain text and identify entities, such as persons, places, organizations; or relations, such as works-for or located-at. UIMA enables such an application to be decomposed into components, for example "language identification" -> "language specific segmentation" -> "sentence boundary detection" -> "entity detection (person/place names etc.)". Each component must implement interfaces defined by the framework and must provide self-describing metadata via XML descriptor files. The framework manages these components and the data flow between them. Components are written in Java or C++; the data that flows between components is designed for efficient mapping between these languages. UIMA additionally provides capabilities to wrap components as network services, and can scale to very large volumes by replicating processing pipelines over a cluster of networked nodes.

This is the homepage for an ongoing research and development project named PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition. Within this project so far, among others, an ontology has been defined; a pathway database (which integrates and interfaces with several public pathway databases) has been constructed; and some software tools have been developed for effective integration, querying, analysis, and manipulation of pathway data.

KML is a file format used to display geographic data in an earth browser, such as Google Earth, Google Maps, and Google Maps for mobile. A KML file is processed in much the same way that HTML (and XML) files are processed by web browsers. Like HTML, KML has a tag-based structure with names and attributes used for specific display purposes. Thus, Google Earth and Maps act as browsers for KML files.

iLeonardo is an impressive site for those interested in research. It's a social utility that connects people and their notebooks which are collections of information from the Web. iLeonardo combines search methodologies, social bookmarks and social networks to produce relevant search results and ranking determined by people - not bots or publishers.The name of the service is obviously an homage to the legendary renaissance man, Leonardo Da Vinci, who was famous for his notebook collection of research information, thoughts and ideas. ILeonardo and its notebook collection technology strives to help the Leonardo's of the digital age. see: http://mashable.com/2008/09/01/research-tools/

The OKKAM project aims at enabling the Web of Entities, namely a virtual space where any collection of data and information about any type of entities (e.g. people, locations, organizations, events, products, ...) published on the Web can be integrated into a single virtual, decentralized, open knowledge base

Trends in programming language development and adoption point to Python as the high-level systems integration language of choice. Python leverages a vast developer-base external to the Neuroscience community, and promises leaps in simulation complexity and maintainability to any neural simulator which adopts it. As more and more simulators support Python, model development times can be drastically reduced by promoting code sharing and reuse across simulator communities. As a result, modellers can devote their software development time to innovating new simulation tools such as network topology databases, stimulus programming, analysis and visualisation tools, and simulation accounting, to name a few.

In 2000, Nicola Guarino and Chris Welty published a series of papers on what came to be named OntoClean, a methodology for ontology-driven conceptual analysis. The methodology has been receiveing increasing levels of attention in various communities, and on this page we hope to provide a central repository for information regarding OntoClean, to help keep the community in touch with how the methodology is being implemented, supported, used, extended, and referenced.

Theory Garden™ MindDraw™ is the brainchild of Professor Richard J. Boland, Jr. and Dr. Tanvir Y. Goraya, Ph.D.It grows form reserach funded from 1991 to 1994 by the National Science Foundation Porgram on coordination Theory and Collaborative Technology. That award was supplemented by a grant form Digital Equipment Corporation (DEC) and included development of a software tool named Spider. Publications describing the Spider project are listed below.

How do chess players make decisions? How do they avoid the combinatorial explosion? How do we go from rooks and knights to abstract thought? What is abstract thought like? These are some of the questions involving the Capyblanca project. The name, of course, is a blend between José Raoul Capablanca, and Hofstadter's original Copycat Project implemented by Melanie Mitchell, which brought us so many ideas. Well, after almost 5 years, we have a proof-of-concept in the form of a running program, and we are GPL'ing the code, so interested readers might take it to new directions which we cannot foresee.

Faviki is a tool that brings together social bookmarking and Wikipedia. It lets you bookmark web pages using Wikipedia's terms. In Faviki, everybody uses the same names for tags from the world's largest collection of knowledge!

Theory Garden™ Seed™ is the brainchild of Professor Richard J. Boland, Jr. and Dr. Tanvir Y. Goraya. It grows from research funded from by the National Science Foundation Program on Coordination Theory and Collaborative Technology. That award was supplemented by a grant from Digital Equipment Corporation and resulted in the development of a software tool named Spider. Publications describing the Spider project are listed below.

ZooKeeper is a high-performance coordination service for distributed applications. It exposes common services - such as naming, configuration management, synchronization, and group services - in a simple interface so you don't have to write them from scratch. You can use it off-the-shelf to implement consensus, group management, leader election, and presence protocols. And you can build on it for your own, specific needs.

Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. This site provides free access to all the data and software from the Ensembl project. Click on a species name to browse the data.