6,368 research outputs found
Do peers see more in a paper than its authors?
Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances
Nanoinformatics: developing new computing applications for nanomedicine
Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others
Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models
Background: In this paper we present the approaches and methods employed in
order to deal with a large scale multi-label semantic indexing task of
biomedical papers. This work was mainly implemented within the context of the
BioASQ challenge of 2014. Methods: The main contribution of this work is a
multi-label ensemble method that incorporates a McNemar statistical
significance test in order to validate the combination of the constituent
machine learning algorithms. Some secondary contributions include a study on
the temporal aspects of the BioASQ corpus (observations apply also to the
BioASQ's super-set, the PubMed articles collection) and the proper adaptation
of the algorithms used to deal with this challenging classification task.
Results: The ensemble method we developed is compared to other approaches in
experimental scenarios with subsets of the BioASQ corpus giving positive
results. During the BioASQ 2014 challenge we obtained the first place during
the first batch and the third in the two following batches. Our success in the
BioASQ challenge proved that a fully automated machine-learning approach, which
does not implement any heuristics and rule-based approaches, can be highly
competitive and outperform other approaches in similar challenging contexts
Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review
Since the Simple Knowledge Organization System (SKOS) specification and its
SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a
significant number of conventional knowledge organization systems (KOS)
(including thesauri, classification schemes, name authorities, and lists of
codes and terms, produced before the arrival of the ontology-wave) have made
their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS"
as an umbrella term to refer to all of the value vocabularies and lightweight
ontologies within the Semantic Web framework. The paper provides an overview of
what the LOD KOS movement has brought to various communities and users. These
are not limited to the colonies of the value vocabulary constructors and
providers, nor the catalogers and indexers who have a long history of applying
the vocabularies to their products. The LOD dataset producers and LOD service
providers, the information architects and interface designers, and researchers
in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper
examines a set of the collected cases (experimental or in real applications)
and aims to find the usages of LOD KOS in order to share the practices and
ideas among communities and users. Through the viewpoints of a number of
different user groups, the functions of LOD KOS are examined from multiple
dimensions. This paper focuses on the LOD dataset producers, vocabulary
producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on
Digital Librarie
Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence Community
We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts
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