PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease

The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value < 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers.Database URL: www.peptickddb.com

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

OpenTED Browser: Insights into European Public Spendings

We present the OpenTED browser, a Web application allowing to interactively browse public spending data related to public procurements in the European Union. The application relies on Open Data recently published by the European Commission and the Publications Office of the European Union, from which we imported a curated dataset of 4.2 million contract award notices spanning the period 2006-2015. The application is designed to easily filter notices and visualise relationships between public contracting authorities and private contractors. The simple design allows for example to quickly find information about who the biggest suppliers of local governments are, and the nature of the contracted goods and services. We believe the tool, which we make Open Source, is a valuable source of information for journalists, NGOs, analysts and citizens for getting information on public procurement data, from large scale trends to local municipal developments.Comment: ECML, PKDD, SoGood workshop 201

Overview of the personalized and collaborative information retrieval (PIR) track at FIRE-2011

The Personalized and collaborative Information Retrieval (PIR) track at FIRE 2011 was organized with an aim to extend standard information retrieval (IR) ad-hoc test collection design to facilitate research on personalized and collaborative IR by collecting additional meta-information during the topic (query) development process. A controlled query generation process through task-based activities with activity logging was used for each topic developer to construct the final list of topics. The standard ad-hoc collection is thus accompanied by a new set of thematically related topics and the associated log information. We believe this can better simulate a real-world search scenario and encourage mining user information from the logs to improve IR effectiveness. A set of 25 TREC formatted topics and the associated metadata of activity logs were released for the participants to use. In this paper we illustrate the data construction phase in detail and also outline two simple ways of using the additional information from the logs to improve retrieval effectiveness

The Archives Unleashed Project: Technology, Process, and Community to Improve Scholarly Access to Web Archives

The Archives Unleashed project aims to improve scholarly access to web archives through a multi-pronged strategy involving tool creation, process modeling, and community building -- all proceeding concurrently in mutually --reinforcing efforts. As we near the end of our initially-conceived three-year project, we report on our progress and share lessons learned along the way. The main contribution articulated in this paper is a process model that decomposes scholarly inquiries into four main activities: filter, extract, aggregate, and visualize. Based on the insight that these activities can be disaggregated across time, space, and tools, it is possible to generate "derivative products", using our Archives Unleashed Toolkit, that serve as useful starting points for scholarly inquiry. Scholars can download these products from the Archives Unleashed Cloud and manipulate them just like any other dataset, thus providing access to web archives without requiring any specialized knowledge. Over the past few years, our platform has processed over a thousand different collections from over two hundred users, totaling around 300 terabytes of web archives.This research was supported by the Andrew W. Mellon Foundation, the Social Sciences and Humanities Research Council of Canada, as well as Start Smart Labs, Compute Canada, the University of Waterloo, and York University. We’d like to thank Jeremy Wiebe, Ryan Deschamps, and Gursimran Singh for their contributions