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The Budapest Open Access Initiative arises from a small but lively meeting convened in Budapest by the Open Society Institute (OSI) on December 1-2, 2001. The purpose of the meeting was to accelerate progress in the international effort to make research articles in all academic fields freely available on the internet. The participants represented many points of view, many academic disciplines, and many nations, and had experience with many of the ongoing initiatives that make up the open access movement. In Budapest they explored how the separate initiatives could work together to achieve broader, deeper, and faster success. They explored the most effective and affordable strategies for serving the interests of research, researchers, and the institutions and societies that support research. Finally, they explored how OSI and other foundations could use their resources most productively to aid the transition to open access and to make open-access publishing economically self-sustaining. The result is the Budapest Open Access Initiative. It is at once a statement of principle, a statement of strategy, and a statement of commitment.

Despite significant growth in the number of research papers available through open access, principally through author self-archiving in institutional archives, it is estimated that only c. 20% of the number of papers published annually are open access. It is up to the authors of papers to change this. Why might open access be of benefit to authors? One universally important factor for all authors is impact, typically measured by the number of times a paper is cited (some older studies have estimated monetary returns to authors from article publication via the role citations play in determining salaries). Recent studies have begun to show that open access increases impact. More studies and more substantial investigations are needed to confirm the effect, although a simple example demonstrates the effect.

"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

Welcome to the National Center for Biomedical Ontology's BioPortal. BioPortal is a Web-based application for accessing and sharing biomedical ontologies. New features in BioPortal 2.0 include: * Full ontology navigation using Flash visualization * Web-service access to BioPortal content and capabilities, which enables developers to use our BioPortal services in their tools. * Ability to add Marginal Notes to classes in BioPortal ontologies, a feature that enables the community to comment on ontologies and to discuss their contents * Ability to create Point to Point Mappings between concepts in different BioPortal ontologies * Bulk export of ontology-to-ontology mappings in RDF format * Navigation of multiple ontologies, which enables users to have several ontologies opened simultaneously in different tabs in the user interface * URIs for all ontology content, which enable developers to access and share BioPortal content from their applications * Improved support through Protégé for ontologies in OWL format

The three most important aspects of an Open Science model are: 1) Open Access to scientific journals; 2) access to the raw material as Open Data; and 3) access to the transparent Open Process of the research methodologies itself.

This article posits a definition and theory for "Library 2.0". It suggests that recent thinking describing the changing Web as "Web 2.0" will have substantial implications for libraries, and recognizes that while these implications keep very close to the history and mission of libraries, they still necessitate a new paradigm for librarianship. The paper applies the theory and definition to the practice of librarianship, specifically addressing how Web 2.0 technologies such as synchronous messaging and streaming media, blogs, wikis, social networks, tagging, RSS feeds, and mashups might intimate changes in how libraries provide access to their collections and user support for that access.

BiOS is a response to inequities in food security, nutrition, health, natural resource management and energy. Our goal is to democratise problem solving to enable diverse solutions through decentralised innovation. Open Source We promote an innovation paradigm that focuses on a distinction between the tools of innovation and the products. We promote licenses that couple rights with responsibilities to foster efficient development, improvement, sharing and use of technology. Open Science We create and share new biological enabling technologies and platforms that can be used to deliver innovations. We develop new licensing and distributive collaboration mechanisms that have resonance with the open source software movement, but are tailored for biological innovation. Open Society We enhance the transparency, accessibility and capability to use all the tools of science, whether patented, open access or public domain.

PLoS Computational Biology is a peer-reviewed, open-access journal featuring works of exceptional significance that further our understanding of living systems at all scales through the application of computational methods. It is the official journal of the International Society for Computational Biology.

The "Open Stack" refers to a set of technologies that work together to make it easier for web developers and users to manage access to user data across the Web.

"This research is grounded in the anthropological understanding that each individual is a unique 'energy source' (Bateson 1972) responsible for acting upon their socially and culturally inflected interpretations in an equally particular way. These indexes capture the actual moments of interaction, of the coming together of individuals in conversational and behavioural exchange (Rapport and Overing 2000). The indexes in this research focus on the socio-cultural field (rather than physical, archaeological or linguistic sub-disciplines), which has been a key element of the discipline since its establishment in the 19th century. Above all, this report highlights how this Cultural Mapping project will offer unparalleled global access into anthropology's own minimal definition: that is, a means to see the Other as Self, and the Self as Other."

Interesting work, based in anthropology

The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge and opportunity. The challenge is to stay afloat in the flood of biological data, keeping it as accessible, up-to-date, and integrated as possible. The opportunity is to cultivate new models of data curation and exchange that take advantage of direct participation by a greater portion of the community.

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our visionis that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that they are semantically interoperable and useful for improving biomedical science and clinical care. Our resources include the Open Biomedical Ontologies (OBO) library, the Open Biomedical Data (OBD) repositories, and tools for accessing and using this information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects to enable outside research and stimulate technology development in the Center. The Center undertakes outreach and educational activities (Biomedical Informatics Program) to train future researchers to use biomedical ontologies and related tools with the goal of enhancing scientific discovery.

The Biomedical Grid Terminology (BiomedGT) is an open, collaboratively developed terminology for translational research. BiomedGT builds on the strengths of the NCI Thesaurus, including concept orientation, description logic, and public accessibility. While the current terminology has been seeded with NCI Thesaurus content, it is being restructured to facilitate open content development. The goal is to evolve BiomedGT into a set of federated sub-terminologies, with content maintained by experts in the relevant research communities.

But I've never seen a service that brings social bookmarking and semantic search together the way AntStorm does. The service works on two major fronts: first, AntStorm allows you to upload your bookmarks, tag them, share them, and access them from any computer you choose, and second, AntStorm uses your tagged bookmarks to power a semantic search engine that will help you find new sites and services that match your interests.

See also: http://lists.w3.org/Archives/Public/semantic-web/2008Apr/0005.html NaturalOWL is an open-source natural language generation engine written in Java. It produces descriptions of individuals (e.g., items for sale, museum exhibits) and classes (e.g., types of exhibits) in English and Greek from OWL DL ontologies. The ontologies must have been annotated in RDF with linguistic and user modeling resources. We demonstrate a plug-in for Protege that can be used to produce these resources and to generate texts by invoking NaturalOWL. We also demonstrate how NaturalOWL can be used by robotic avatars in Second Life to describe the exhibits of virtual museums. NaturalOWL demonstrates the benefits of Natural Language Generation (NLG) on the Semantic Web. Organizations that need to publish information about objects, such as exhibits or products, can publish OWL ontologies instead of texts. NLG engines, embedded in browsers or Web servers, can then render the ontologies in multiple natural languages, whereas computer programs may access the ontologies directly.

Linked Environments for Atmospheric Discovery (LEAD) makes meteorological data, forecast models, and analysis and visualization tools available to anyone who wants to interactively explore the weather as it evolves. The LEAD Portal brings together all the necessary resources at one convenient access point

Triplify is based on the definition of relational database queries for a specific Web application in order to retrieve valuable information and to convert the results of these queries into RDF, JSON and Linked Data. Experiences showed that for most web-applications a relatively small number of queries (mostly between 3-7) is sufficient to extract the important information. After generating such database views the Triplify software can be used to convert the view into an RDF, JSON or Linked Data representation, which can be shared and accessed on the (Semantic) Web.

The NeuroCommons project seeks to make all scientific research materials - research articles, annotations, data, physical materials - as available and as useable as they can be. We do this by both fostering practices that render information in a form that promotes uniform access by computational agents - sometimes called "interoperability". We want knowledge sources to combine meaningfully, enabling semantically precise queries that span multiple information sources. Our work covers general data and knowledge sources used in computational biology as well as sources specific to neuroscience and neuromedicine. The practices that we develop and promote are designed to play well on the Semantic Web. We view our technical work not as creating a new service or content library, although we do both, but rather as helping to promote the growth of semantically linked scientific information.

DIYbio is an organization for the ever expanding community of citizen scientists and DIY biological engineers that value openness & responsibility. DIYbio aims to be an "Institution for the Amateur" -- an umbrella organization that provides some of the same resources afforded by more traditional institutions like academia and industry, such as access to a community of experts, to technical literature and other resources, to responsible oversight for health and safety, and an interface between the community and the public at large.

MarkMail is a free service for searching mailing list archives, with huge advantages over traditional search engines. It is powered by MarkLogic Server: Each email is stored internally as an XML document, and accessed using XQuery. All searches, faceted navigation, analytic calculations, and HTML page renderings are performed by a small MarkLogic Server cluster running against millions of messages.