21,432 research outputs found
Mapping Large Scale Research Metadata to Linked Data: A Performance Comparison of HBase, CSV and XML
OpenAIRE, the Open Access Infrastructure for Research in Europe, comprises a
database of all EC FP7 and H2020 funded research projects, including metadata
of their results (publications and datasets). These data are stored in an HBase
NoSQL database, post-processed, and exposed as HTML for human consumption, and
as XML through a web service interface. As an intermediate format to facilitate
statistical computations, CSV is generated internally. To interlink the
OpenAIRE data with related data on the Web, we aim at exporting them as Linked
Open Data (LOD). The LOD export is required to integrate into the overall data
processing workflow, where derived data are regenerated from the base data
every day. We thus faced the challenge of identifying the best-performing
conversion approach.We evaluated the performances of creating LOD by a
MapReduce job on top of HBase, by mapping the intermediate CSV files, and by
mapping the XML output.Comment: Accepted in 0th Metadata and Semantics Research Conferenc
Searching for superspreaders of information in real-world social media
A number of predictors have been suggested to detect the most influential
spreaders of information in online social media across various domains such as
Twitter or Facebook. In particular, degree, PageRank, k-core and other
centralities have been adopted to rank the spreading capability of users in
information dissemination media. So far, validation of the proposed predictors
has been done by simulating the spreading dynamics rather than following real
information flow in social networks. Consequently, only model-dependent
contradictory results have been achieved so far for the best predictor. Here,
we address this issue directly. We search for influential spreaders by
following the real spreading dynamics in a wide range of networks. We find that
the widely-used degree and PageRank fail in ranking users' influence. We find
that the best spreaders are consistently located in the k-core across
dissimilar social platforms such as Twitter, Facebook, Livejournal and
scientific publishing in the American Physical Society. Furthermore, when the
complete global network structure is unavailable, we find that the sum of the
nearest neighbors' degree is a reliable local proxy for user's influence. Our
analysis provides practical instructions for optimal design of strategies for
"viral" information dissemination in relevant applications.Comment: 12 pages, 7 figure
PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens.
Large-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise. To make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots. PinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions and test datasets
Improving average ranking precision in user searches for biomedical research datasets
Availability of research datasets is keystone for health and life science
study reproducibility and scientific progress. Due to the heterogeneity and
complexity of these data, a main challenge to be overcome by research data
management systems is to provide users with the best answers for their search
queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we
investigate a novel ranking pipeline to improve the search of datasets used in
biomedical experiments. Our system comprises a query expansion model based on
word embeddings, a similarity measure algorithm that takes into consideration
the relevance of the query terms, and a dataset categorisation method that
boosts the rank of datasets matching query constraints. The system was
evaluated using a corpus with 800k datasets and 21 annotated user queries. Our
system provides competitive results when compared to the other challenge
participants. In the official run, it achieved the highest infAP among the
participants, being +22.3% higher than the median infAP of the participant's
best submissions. Overall, it is ranked at top 2 if an aggregated metric using
the best official measures per participant is considered. The query expansion
method showed positive impact on the system's performance increasing our
baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively.
Our similarity measure algorithm seems to be robust, in particular compared to
Divergence From Randomness framework, having smaller performance variations
under different training conditions. Finally, the result categorization did not
have significant impact on the system's performance. We believe that our
solution could be used to enhance biomedical dataset management systems. In
particular, the use of data driven query expansion methods could be an
alternative to the complexity of biomedical terminologies
Representing Dataset Quality Metadata using Multi-Dimensional Views
Data quality is commonly defined as fitness for use. The problem of
identifying quality of data is faced by many data consumers. Data publishers
often do not have the means to identify quality problems in their data. To make
the task for both stakeholders easier, we have developed the Dataset Quality
Ontology (daQ). daQ is a core vocabulary for representing the results of
quality benchmarking of a linked dataset. It represents quality metadata as
multi-dimensional and statistical observations using the Data Cube vocabulary.
Quality metadata are organised as a self-contained graph, which can, e.g., be
embedded into linked open datasets. We discuss the design considerations, give
examples for extending daQ by custom quality metrics, and present use cases
such as analysing data versions, browsing datasets by quality, and link
identification. We finally discuss how data cube visualisation tools enable
data publishers and consumers to analyse better the quality of their data.Comment: Preprint of a paper submitted to the forthcoming SEMANTiCS 2014, 4-5
September 2014, Leipzig, German
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