Group items tagged

# The primary intention of creating aTags is not the categorization of the document, but the representation of the key facts inside the document. Key facts in the biomedical domain might be, for example, "Protein A interacts with protein B" or "Overexpression of protein A in tissue B is the cause of disease C". # An aTag is comprised of a set of associated entities. The size of the set is arbitrary, but will typically lie between 2 and 5 entities. For example, the fact "Protein A binds to protein B" can be represented with an aTag comprising of the three entities "Protein A", "Molecular interaction" and "Protein B". Similarly, the fact "Overexpression of protein A in tissue B is the cause of disease C" can be represented with an aTag comprising of the four entities "Overexpression", "Protein A", "Tissue B" and "Disease C". # Each document or database entry can be described with an arbitrary number of such aTags. Each aTag can be associated with the relevant portions of text or data in a fine granularity. # The entities in an aTag are not simple strings, but resources that are part of ontologies and RDF/OWL-enabled databases. For example, "Protein A" and "Protein B" are resources that are defined in the UniProt database, whereas "Molecular Interaction" is a class in the branch of biological processes of the Gene Ontology. They are identified with their URIs.

The Lemur Toolkit is a open-source toolkit designed to facilitate research in language modeling and information retrieval. Lemur supports a wide range of industrial and research language applications such as ad-hoc retrieval, site-search, and text mining. The toolkit supports indexing of large-scale text databases, the construction of simple language models for documents, queries, or subcollections, and the implementation of retrieval systems based on language models as well as a variety of other retrieval models. The system is written in the C and C++ languages, and is designed as a research system to run under Unix operating systems, although it can also run under Windows.

The Lemur Toolkit is a open-source toolkit designed to facilitate research in language modeling and information retrieval. Lemur supports a wide range of industrial and research language applications such as ad-hoc retrieval, site-search, and text mining. The toolkit supports indexing of large-scale text databases, the construction of simple language models for documents, queries, or subcollections, and the implementation of retrieval systems based on language models as well as a variety of other retrieval models. The system is written in the C and C++ languages, and is designed as a research system to run under Unix operating systems, although it can also run under Windows.

This paper is based on a study of personal experience narratives told by witnesses of the September 11th attacks in calls to C-SPAN. Drawing on research on narratives of ordinary and extraordinary experiences and witnessing, the author offers a framework for analyzing the structure and function of eyewitness accounts. Analysis focuses on methods callers use to show and tell the audience where they were, what they were doing, and what they were thinking at the time of the attacks. Verbal, visual, and structural features of these narratives are highlighted, with particular attention given to orientation and ideation components of the narratives. The design of these components and their location within the callers' stories are shown to construct the narratives as eyewitness accounts, position the callers and audience members as witnesses, and engage all in a therapeutic sensemaking process.

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 ontology supports the development of Protégé ontologies using the OntoClean methodology (PDF). This methodology for ontological analysis was developed by N. Guarino and C. Welty. The OntoClean methodology applies the notions used for ontological analysis in philosophy to analyzing conceptual modeling in information systems. If you include this Protégé ontology in your ontology, you can annotate your classes with meta-properties of identity, unity, essence, and dependence. The OntoClean ontology in Protégé also contains constraints in the Protégé Axiom Language (PAL) enabling you to verify whether the ontology is "clean"---does not violate any of the constraints based on these properties.

This blog is a place for readers to discuss the beta version of our new book, "Evolving Collective Intelligence" by Douglas C. Engelbart, Valerie Landau, and Eileen Clegg. After reading the beta version, Do you have a quote to contribute? Clarifications on the content? An idea for another essay? Feedback will be input for our improved first edition, in keeping with Doug's philosophy of continuous improvement and collaboration. Please go to the "about" page.

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.

The Future of the Internet - a federating theme for activities on future networks, software and service architectures, networked media systems and the Internet of Things. Over the last 20 years society, economy and technology evolved in many directions and into new areas. Many of these evolutions have created opportunities which must be taken into account when crafting future Networks.

Alchemy is a software package providing a series of algorithms for statistical relational learning and probabilistic logic inference, based on the Markov logic representation. Alchemy allows you to easily develop a wide range of AI applications, including: * Collective classification * Link prediction * Entity resolution * Social network modeling * Information extraction

PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.

Argumentative allows you to express an argument's structure in a visual form which is simpler to understand. Reads RE3 & RTNL

This project is a collaborative effort by computer scientists and engineers from Texas A&M and UC Berkeley consulting with natural scientists and documentary filmmakers. The goal is to advance the fundamental understanding of automated and collaborative systems that combine sensors, actuators, and human input to observe and record detailed natural behavior in remote settings.