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arXiv2007

OA@MPS - a colourful view

The open access agenda of the Max Planck Society, initiator of the Berlin Declaration, envisions the support of both the green way and the golden way to open access. For the implementation of the green way the Max Planck Society through its newly established unit (Max Planck Digital Library) follows the idea of providing a centralized technical platform for publications and a local support for editorial issues. With regard to the golden way, the Max Planck Society fosters the development of open access publication models and experiments new publishing concepts like the Living Reviews journals.

cs.DL↗
arXiv2007

Reconstruction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates

The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. In this study, we have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalization-specialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting protein-protein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. Our study had also demonstrated the flexibility of the two-layered generalization-specialization paradigm by using the same generalization layer for two specialized information extraction tasks.

cs.IR↗
arXiv2007

When are recommender systems useful?

Recommender systems are crucial tools to overcome the information overload brought about by the Internet. Rigorous tests are needed to establish to what extent sophisticated methods can improve the quality of the predictions. Here we analyse a refined correlation-based collaborative filtering algorithm and compare it with a novel spectral method for recommending. We test them on two databases that bear different statistical properties (MovieLens and Jester) without filtering out the less active users and ordering the opinions in time, whenever possible. We find that, when the distribution of user-user correlations is narrow, simple averages work nearly as well as advanced methods. Recommender systems can, on the other hand, exploit a great deal of additional information in systems where external influence is negligible and peoples' tastes emerge entirely. These findings are validated by simulations with artificially generated data.

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arXiv2008

Content Reuse and Interest Sharing in Tagging Communities

Tagging communities represent a subclass of a broader class of user-generated content-sharing online communities. In such communities users introduce and tag content for later use. Although recent studies advocate and attempt to harness social knowledge in this context by exploiting collaboration among users, little research has been done to quantify the current level of user collaboration in these communities. This paper introduces two metrics to quantify the level of collaboration: content reuse and shared interest. Using these two metrics, this paper shows that the current level of collaboration in CiteULike and Connotea is consistently low, which significantly limits the potential of harnessing the social knowledge in communities. This study also discusses implications of these findings in the context of recommendation and reputation systems.

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arXiv2007

Simrank++: Query rewriting through link analysis of the click graph

We focus on the problem of query rewriting for sponsored search. We base rewrites on a historical click graph that records the ads that have been clicked on in response to past user queries. Given a query q, we first consider Simrank as a way to identify queries similar to q, i.e., queries whose ads a user may be interested in. We argue that Simrank fails to properly identify query similarities in our application, and we present two enhanced version of Simrank: one that exploits weights on click graph edges and another that exploits ``evidence.'' We experimentally evaluate our new schemes against Simrank, using actual click graphs and queries form Yahoo!, and using a variety of metrics. Our results show that the enhanced methods can yield more and better query rewrites.

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arXiv2008

Knowledge management by wikis

Wikis provide a new way of collaboration and knowledge sharing. Wikis are software that allows users to work collectively on a web-based knowledge base. Wikis are characterised by a sense of anarchism, collaboration, connectivity, organic development and self-healing, and they rely on trust. We list several concerns about applying wikis in professional organisation. After these concerns are met, wikis can provide a progessive, new knowledge sharing and collaboration tool.

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arXiv2008

NCore: Architecture and Implementation of a Flexible, Collaborative Digital Library

NCore is an open source architecture and software platform for creating flexible, collaborative digital libraries. NCore was developed by the National Science Digital Library (NSDL) project, and it serves as the central technical infrastructure for NSDL. NCore consists of a central Fedora-based digital repository, a specific data model, an API, and a set of backend services and frontend tools that create a new model for collaborative, contributory digital libraries. This paper describes NCore, presents and analyzes its architecture, tools and services; and reports on the experience of NSDL in building and operating a major digital library on it over the past year and the experience of the Digital Library for Earth Systems Education in porting their existing digital library and tools to the NCore platform.

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arXiv2008

The aDORe Federation Architecture

The need to federate repositories emerges in two distinctive scenarios. In one scenario, scalability-related problems in the operation of a repository reach a point beyond which continued service requires parallelization and hence federation of the repository infrastructure. In the other scenario, multiple distributed repositories manage collections of interest to certain communities or applications, and federation is an approach to present a unified perspective across these repositories. The high-level, 3-Tier aDORe federation architecture can be used as a guideline to federate repositories in both cases. This paper describes the architecture, consisting of core interfaces for federated repositories in Tier-1, two shared infrastructure components in Tier-2, and a single-point of access to the federation in Tier-3. The paper also illustrates two large-scale deployments of the aDORe federation architecture: the aDORe Archive repository (over 100,000,000 digital objects) at the Los Alamos National Laboratory and the Ghent University Image Repository federation (multiple terabytes of image files).

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arXiv2008

Object Re-Use & Exchange: A Resource-Centric Approach

The OAI Object Reuse and Exchange (OAI-ORE) framework recasts the repository-centric notion of digital object to a bounded aggregation of Web resources. In this manner, digital library content is more integrated with the Web architecture, and thereby more accessible to Web applications and clients. This generalized notion of an aggregation that is independent of repository containment conforms more closely with notions in eScience and eScholarship, where content is distributed across multiple services and databases. We provide a motivation for the OAI-ORE project, review previous interoperability efforts, describe draft ORE specifications and report on promising results from early experimentation that illustrate improved interoperability and reuse of digital objects.

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arXiv2008

Towards Usage-based Impact Metrics: - First Results from the MESUR Project

Scholarly usage data holds the potential to be used as a tool to study the dynamics of scholarship in real time, and to form the basis for the definition of novel metrics of scholarly impact. However, the formal groundwork to reliably and validly exploit usage data is lacking, and the exact nature, meaning and applicability of usage-based metrics is poorly understood. The MESUR project funded by the Andrew W. Mellon Foundation constitutes a systematic effort to define, validate and cross-validate a range of usage-based metrics of scholarly impact. MESUR has collected nearly 1 billion usage events as well as all associated bibliographic and citation data from significant publishers, aggregators and institutional consortia to construct a large-scale usage data reference set. This paper describes some major challenges related to aggregating and processing usage data, and discusses preliminary results obtained from analyzing the MESUR reference data set. The results confirm the intrinsic value of scholarly usage data, and support the feasibility of reliable and valid usage-based metrics of scholarly impact.

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arXiv2008

Specification of an extensible and portable file format for electronic structure and crystallographic data

In order to allow different software applications, in constant evolution, to interact and exchange data, flexible file formats are needed. A file format specification for different types of content has been elaborated to allow communication of data for the software developed within the European Network of Excellence "NANOQUANTA", focusing on first-principles calculations of materials and nanosystems. It might be used by other software as well, and is described here in detail. The format relies on the NetCDF binary input/output library, already used in many different scientific communities, that provides flexibility as well as portability accross languages and platforms. Thanks to NetCDF, the content can be accessed by keywords, ensuring the file format is extensible and backward compatible.

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arXiv2008

Clustering of scientific citations in Wikipedia

The instances of templates in Wikipedia form an interesting data set of structured information. Here I focus on the cite journal template that is primarily used for citation to articles in scientific journals. These citations can be extracted and analyzed: Non-negative matrix factorization is performed on a (article x journal) matrix resulting in a soft clustering of Wikipedia articles and scientific journals, each cluster more or less representing a scientific topic.

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arXiv2008

Semantic Analysis of Tag Similarity Measures in Collaborative Tagging Systems

Social bookmarking systems allow users to organise collections of resources on the Web in a collaborative fashion. The increasing popularity of these systems as well as first insights into their emergent semantics have made them relevant to disciplines like knowledge extraction and ontology learning. The problem of devising methods to measure the semantic relatedness between tags and characterizing it semantically is still largely open. Here we analyze three measures of tag relatedness: tag co-occurrence, cosine similarity of co-occurrence distributions, and FolkRank, an adaptation of the PageRank algorithm to folksonomies. Each measure is computed on tags from a large-scale dataset crawled from the social bookmarking system del.icio.us. To provide a semantic grounding of our findings, a connection to WordNet (a semantic lexicon for the English language) is established by mapping tags into synonym sets of WordNet, and applying there well-known metrics of semantic similarity. Our results clearly expose different characteristics of the selected measures of relatedness, making them applicable to different subtasks of knowledge extraction such as synonym detection or discovery of concept hierarchies.

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arXiv2008

ICT, Community Memory and Technological Appropriation

The core mission of universities and higher education institutions is to make public the results of their work and to preserve the collective memory of the institution. This includes the effective use of information and communication technologies (ICT) to systematically compile academic and research achievements as well as disseminate effectively this accumulated knowledge to society at large. Current efforts in Latin America and Venezuela in particular, are limited but provide some valuable insights to pave the road to this important goal. The institutional repository of Universidad de Los Andes (ULA) in Venezuela (www.saber.ula.ve) is such an example of ICT usage to store, manage and disseminate digital material produced by our University. In this paper we elaborate on the overall process of promoting a culture of content creation, publishing and preservation within ULA.

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arXiv2008

Cross-concordances: terminology mapping and its effectiveness for information retrieval

The German Federal Ministry for Education and Research funded a major terminology mapping initiative, which found its conclusion in 2007. The task of this terminology mapping initiative was to organize, create and manage 'cross-concordances' between controlled vocabularies (thesauri, classification systems, subject heading lists) centred around the social sciences but quickly extending to other subject areas. 64 crosswalks with more than 500,000 relations were established. In the final phase of the project, a major evaluation effort to test and measure the effectiveness of the vocabulary mappings in an information system environment was conducted. The paper reports on the cross-concordance work and evaluation results.

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