Smart Harvesting with OXPath

Im DFG-geförderten Projekt Smart Harvesting II werden softwarebasierte Lösungen zur Erfassung und Aufbereitung von semistrukturierten Webdaten, z.B. die Inhaltsverzeichnisse von wissenschaftlichen Zeitschriften oder Konferenzbänden für Literaturdatenbanken wie dblp oder sowiport , entwickelt. Durch die vorherrschende Heterogenität solcher Rohdaten ist diese Arbeit im Falle der manuellen Erfassung sehr personal- und zeitintensiv. In Fällen, in denen bereits auf technische Unterstützung gesetzt wird, werden hierfür spezialisierte Programme, sogenannte Wrapper, eingesetzt, die von fachkundigen Softwareentwicklern erstellt und gewartet werden müssen. Ein Teil unseres Projektes ist es daher, wartungsarme Wrapper zu entwickeln, die auch von Nicht-Informatikern, z.B. Bibliothekaren oder Dokumentaren, einfach bedient und auf häufig neugestaltete, dynamische Webapplikationen angepasst werden können. Hierfür setzen wir auf die quelloffene Abfragesprache OXPath – eine Erweiterung von XPath, die eine deklarative Nachahmung der Interaktion mit einer Website erlaubt und in diesem Zuge Daten gezielt extrahieren kann. Erste Erfahrungen in einem Workshop mit Bibliothekaren und in Übungsgruppen mit Studierenden haben gezeigt, dass bereits Grundkenntnisse in XML und XPath ausreichen, um in den Prozess der Erstellung, Wartung und Pflege von OXPath-Wrappern einzusteigen. Die gewonnenen Daten können vielseitig eingesetzt werden. In Smart Harvesting II werden zusätzliche Internetquellen z.B. in das Datenbankmonitoring integriert oder zur Bereinigung und Aufbereitung der Datenbestände verwendet, z.B. indem weitere Felder wie Kurzbiografien mit Named Entity Recognition nach möglichst vollständigen Autorennamen durchsucht werden, um die Autorendisambiguierung zu verbessern. Im ersten Teil bietet dieser Vortrag neben dem Gesamtüberblick über das Projekt einen Kurzeinstieg und Erfahrungsberichte zu OXPath. Außerdem werden Einsatzbeispiele von OXPath aus dem Arbeitsalltag der Projektteilnehmer dblp computer science bibliography , GESIS und TH Köln demonstriert. Bei Interesse findet zum Abschluss ein praktischer Teil mit dem gemeinsamen Entwickeln eines OXPath-Ausdrucks statt

Spartan Daily, May 9, 2018

Volume 150, Issue 42https://scholarworks.sjsu.edu/spartan_daily_2018/1041/thumbnail.jp

Ukraine’s Exports as a Global Challenge for Its Future

Exports are critical for the highly open Ukrainian economy which is characterized by the large trade deficit. Since independence the major consumers of the Ukrainian products have been the CIS and the EU. Conflict with Russia led to the significant decline of the volume of Ukraine’s export commodities. The export analysis, based on the data provided by the State Statistics Service of Ukraine for the period of 2010-2018 allowed to identify the problems and to come up with possible solutions focusing primarily on the role of the Government of Ukraine in strengthening cooperation with the EU. Firstly, it is suggested to take the institutional steps aimed at expanding and deepening the integration towards the common economic space with the EU, especially the common customs space. Secondly, to explore the opportunities of exporting goods to the countries, with which the EU has signed regional trade agreements. The third step is related to the changing role of Ukraine in the global model of the transformation of the world economy and requires the combination of close cooperation with the EU, on the one hand, and the powerful economies, on the other, thereby contributing to the formation of non-confrontational relations between East and West

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories

Using a knowledge exchange event to assess study participants' attitudes to research in a rapidly evolving research context [version 1; peer review: 3 approved]

BACKGROUND: The UK hosts some of the world’s longest-running longitudinal cohort studies, who make repeated observations of their participants and use these data to explore health outcomes. An alternative method for data collection is record linkage; the linking together of electronic health and administrative records. Applied nationally, this could provide unrivalled opportunities to follow a large number of people in perpetuity. However, public attitudes to the use of data in research are currently unclear. Here we report on an event where we collected attitudes towards recent opportunities and controversies within health data science. METHODS: The event was attended by ~250 individuals (cohort members and their guests), who had been invited through the offices of their participating cohort studies. There were a series of presentations describing key research results and the audience participated in 15 multiple-choice questions using interactive voting pads. RESULTS: Our participants showed a high level of trust in researchers (87% scoring them 4/5 or 5/5) and doctors (81%); but less trust in commercial companies (35%). They supported the idea of researchers using information from both neonatal blood spots (Guthrie spots) (97% yes) and from electronic health records (95% yes). Our respondents were willing to wear devices like a ’Fit-bit’ (78% agreed) or take a brain scan that might predict later mental illness (73%). However, they were less willing to take a new drug for research purposes (45%). They were keen to encourage others to take part in research; whether that be offering the opportunity to pregnant mothers (97% agreed) or extending invitations to their own children and grandchildren (98%). CONCLUSIONS: Our participants were broadly supportive of research access to data, albeit less supportive when commercial interests were involved. Public engagement events that facilitate two-way interactions can influence and support future research and public engagement efforts

Eighth National Conference of Institute of Scientometrics on “Scholarly Communication and Scientometrics”

Conference Repor