517 research outputs found
Citation recommendation: approaches and datasets
Citation recommendation describes the task of recommending citations for a given text. Due to the overload of published scientific works in recent years on the one hand, and the need to cite the most appropriate publications when writing scientific texts on the other hand, citation recommendation has emerged as an important research topic. In recent years, several approaches and evaluation data sets have been presented. However, to the best of our knowledge, no literature survey has been conducted explicitly on citation recommendation. In this article, we give a thorough introduction to automatic citation recommendation research. We then present an overview of the approaches and data sets for citation recommendation and identify differences and commonalities using various dimensions. Last but not least, we shed light on the evaluation methods and outline general challenges in the evaluation and how to meet them. We restrict ourselves to citation recommendation for scientific publications, as this document type has been studied the most in this area. However, many of the observations and discussions included in this survey are also applicable to other types of text, such as news articles and encyclopedic articles
Scientific names of organisms : attribution, rights, and licensing
© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.As biological disciplines extend into the âbig dataâ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A âblue listâ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed
Scientific names of organisms: attribution, rights, and licensing
abstract: Background
As biological disciplines extend into the âbig dataâ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world.
Findings
The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts.
Conclusions
A âblue listâ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.The electronic version of this article is the complete one and can be found online at: http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-7
Socioanalysis: a communicational research device for social intervention
"This paper presents a socio-communicative device for research, diagnosis and intervention in communities and organizations. It submits theoretical propositions and categories of analysis for ongoing research and diagnosis of organizational and community issues and problems, as well as the development of programs for intervention in institutions, community development, information programs, educational and health projects, conflict solving, governance and social participation, communications and promotion of social capital. The authors consider the indispensable realization of interdisciplinary research associating social practices to communication processes and vice versa. Communication processes are also the fundamental interaction devices through which human practices reproduce social relations, promoting and reorganizing the self-reproduction of a social system. In order to help collectives such as communities, institutions, social and economic organizations to build better environments, better working and living conditions, social research needs to integrate communication and information processes to the diagnosis and design of social programs." (author's abstract
Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)
This report records and discusses the Third Workshop on Sustainable Software
for Science: Practice and Experiences (WSSSPE3). The report includes a
description of the keynote presentation of the workshop, which served as an
overview of sustainable scientific software. It also summarizes a set of
lightning talks in which speakers highlighted to-the-point lessons and
challenges pertaining to sustaining scientific software. The final and main
contribution of the report is a summary of the discussions, future steps, and
future organization for a set of self-organized working groups on topics
including developing pathways to funding scientific software; constructing
useful common metrics for crediting software stakeholders; identifying
principles for sustainable software engineering design; reaching out to
research software organizations around the world; and building communities for
software sustainability. For each group, we include a point of contact and a
landing page that can be used by those who want to join that group's future
activities. The main challenge left by the workshop is to see if the groups
will execute these activities that they have scheduled, and how the WSSSPE
community can encourage this to happen
\u3cem\u3ePlasmodium falciparum\u3c/em\u3e SSB Tetramer Wraps Single-Stranded DNA with Similar Topology but Opposite Polarity to \u3cem\u3eE. coli\u3c/em\u3e SSB
Single-stranded DNA binding (SSB) proteins play central roles in genome maintenance in all organisms. Plasmodium falciparum, the causative agent of malaria, encodes an SSB protein that localizes to the apicoplast and likely functions in the replication and maintenance of its genome. P. falciparum SSB (Pf-SSB) shares a high degree of sequence homology with bacterial SSB proteins but differs in the composition of its C-terminus, which interacts with more than a dozen other proteins in Escherichia coli SSB (Ec-SSB). Using sedimentation methods, we show that Pf-SSB forms a stable homo-tetramer alone and when bound to single-stranded DNA (ssDNA). We also present a crystal structure at 2.1 Ă
resolution of the Pf-SSB tetramer bound to two (dT)35 molecules. The Pf-SSB tetramer is structurally similar to the Ec-SSB tetramer, and ssDNA wraps completely around the tetramer with a âbaseball seamâ topology that is similar to Ec-SSB in its â65 binding modeâ. However, the polarity of the ssDNA wrapping around Pf-SSB is opposite to that observed for Ec-SSB. The interactions between the bases in the DNA and the amino acid side chains also differ from those observed in the Ec-SSBâDNA structure, suggesting that other differences may exist in the DNA binding properties of these structurally similar proteins
Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications
The Micropublications semantic model for scientific claims, evidence,
argumentation and annotation in biomedical publications, is a metadata model of
scientific argumentation, designed to support several key requirements for
exchange and value-addition of semantic metadata across the biomedical
publications ecosystem.
Micropublications allow formalizing the argument structure of scientific
publications so that (a) their internal structure is semantically clear and
computable; (b) citation networks can be easily constructed across large
corpora; (c) statements can be formalized in multiple useful abstraction
models; (d) statements in one work may cite statements in another,
individually; (e) support, similarity and challenge of assertions can be
modelled across corpora; (f) scientific assertions, particularly in review
articles, may be transitively closed to supporting evidence and methods.
The model supports natural language statements; data; methods and materials
specifications; discussion and commentary; as well as challenge and
disagreement. A detailed analysis of nine use cases is provided, along with an
implementation in OWL 2 and SWRL, with several example instantiations in RDF.Comment: Version 4. Minor revision
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