Online assessment of protein interaction information extraction systems

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 01-03-201

Data Publications Correlate with Citation Impact

Neuroscience and molecular biology have been generating large datasets over the past years that are reshaping how research is being conducted. In their wake, open data sharing has been singled out as a major challenge for the future of research. We conducted a comparative study of citations of data publications in both fields, showing that the average publication tagged with a data-related term by the NCBI MeSH (Medical Subject Headings) curators achieves a significantly larger citation impact than the average in either field. We introduce a new metric, the data article citation index (DAC-index), to identify the most prolific authors among those data-related publications. The study is fully reproducible from an executable Rmd (R Markdown) script together with all the citation datasets. We hope these results can encourage authors to more openly publish their data

Overview of the protein-protein interaction annotation extraction task of BioCreative II

© 2008 Krallinger et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution Licens

Der Georgszyklus in der Filialkirche hl. Georg bei Rottenmann

Der Bestand der mittelalterlichen Wandmalereien in Österreich, besonders jener der Steiermark, weist durch den „Freilegungsboom“ des letzten Drittels des 20. Jahrhunderts eine beachtenswerte Anzahl auf. Diese Maßnahme stellt sich aber als zweischneidiges Schwert heraus, da eine Vielzahl von Objekten nach wie vor in keiner ausführlichen kunsthistorischen Arbeit behandelt worden sind und die freigelegten Wandmalereien mangels eines Monitoringplans zur Erhaltung dem Verfall frei gegeben sind. Das primäre Ziel dieser Arbeit stellt daher eine Beschreibung und Erfassung der Wandmalereien des Langhauses der Filialkirche hl. Georg bei Rottenmann dar. Der dargestellte Georgszyklus wird als zentrales Thema behandelt und wird einer Analyse hinsichtlich der textlichen Grundlagen unterzogen. Durch diesen Arbeitschritt wird gezeigt, dass eine Vielzahl von Szenen des Georgszyklus in der Filialkirche die ältesten erhaltenen Wandmalereibeispiele des Georgsmartyriums darstellen. Mit Hilfe von Vergleichsbeispielen, wird die Einzigartigkeit sichtbar gemacht. Der Darstellung eines Kampfes zwischen zwei Reitern wird ein größerer Teil dieser Arbeit gewidmet. Es wird darin überprüft ob ein Zusammenhang mit den Plastiken der Regensburger Dollingergruppe besteht, da diese eine ähnliche Darstellungsart aufweisen. Bezug genommen wird dabei auf das Dollingerlied und-sage wodurch weitere Zusammenhänge zwischen dem Rottenmanner und Regensburger Darstellungen beleuchtet werden. In weiterer Folge wird das Spektrum der Reiterkampfszene auf den alpinen und voralpinen Raum ausgeweitet. Auf diese Weise wird ersichtlich, dass eine beachtenswerte Anzahl an Reiterkampfszenen aus dem 13. und 14. Jahrhundert erhalten ist. Anhand von betrachtenden Vergleichen können Gemeinsamkeiten, aber auch Unterschiede der Darstellungen erkannt werden. Diese Arbeit liefert somit einen Beitrag zur Entschlüsselung des Wandmalereiprogrammes des Langhauses der Filialkirche hl. Georg bei Rottenmann und zeigt, dass die Darstellungen nicht als isolierte Beispiele zu sehen sind, sondern im Zusammenhang mit weiteren mitteleuropäischen Objekten zu sehen sind

QuantUM: Quantitative Safety Analysis of UML Models

When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day work. This is mainly due to the lack of methods that can be directly applied to architecture level models, for instance given as UML diagrams. Also, it is necessary that the description methods used do not require a profound knowledge of formal methods. Our approach bridges this gap and improves the integration of quantitative safety analysis methods into the development process. All inputs of the analysis are specified at the level of a UML model. This model is then automatically translated into the analysis model, and the results of the analysis are consequently represented on the level of the UML model. Thus the analysis model and the formal methods used during the analysis are hidden from the user. We illustrate the usefulness of our approach using an industrial strength case study.Comment: In Proceedings QAPL 2011, arXiv:1107.074

ExTRI: Extraction of transcription regulation interactions from literature

The regulation of gene transcription by transcription factors is a fundamental biological process, yet the relations between transcription factors (TF) and their target genes (TG) are still only sparsely covered in databases. Text-mining tools can offer broad and complementary solutions to help locate and extract mentions of these biological relationships in articles. We have generated ExTRI, a knowledge graph of TF-TG relationships, by applying a high recall text-mining pipeline to MedLine abstracts identifying over 100,000 candidate sentences with TF-TG relations. Validation procedures indicated that about half of the candidate sentences contain true TF-TG relationships. Post-processing identified 53,000 high confidence sentences containing TF-TG relationships, with a cross-validation F1-score close to 75%. The resulting collection of TF-TG relationships covers 80% of the relations annotated in existing databases. It adds 11,000 other potential interactions, including relationships for ~100 TFs currently not in public TF-TG relation databases. The high confidence abstract sentences contribute 25,000 literature references not available from other resources and offer a wealth of direct pointers to functional aspects of the TF-TG interactions. Our compiled resource encompassing ExTRI together with publicly available resources delivers literature-derived TF-TG interactions for more than 900 of the 1500–1600 proteins considered to function as specific DNA binding TFs. The obtained result can be used by curators, for network analysis and modelling, for causal reasoning or knowledge graph mining approaches, or serve to benchmark text mining strategies.We thank the participants of the COST Action GREEKC (CA15205) for fruitful discussions during workshops supported by COST (European Cooperation in Science and Technology).Peer ReviewedPostprint (published version

Fatigue Assessment of Wire and Arc Additively Manufactured Ti-6Al-4V

Wire and arc additively manufactured (WAAM) parts and structures often present internal defects, such as gas pores, and cause irregularities in the manufacturing process. In order to describe and assess the effect of internal defects in fatigue design, this research study investigates the fatigue strength of wire arc additive manufactured structures covering the influence of imperfections, particularly gas pores. Single pass WAAM structures are manufactured using titanium alloy Ti-6Al-4V and round fatigue, tensile specimen are extracted. Tensile tests and uniaxial fatigue tests with a load stress ratio of R = 0.1 were carried out, whereby fatigue test results are used for further assessments. An extensive fractographic and metallographic fracture surface analysis is utilized to characterize and measure crack-initiating defects. As surface pores as well as bulk pores are detected, a stress intensity equivalent ∆Keqv transformation approach is presented in this study. Thereby, the defect size of the surface pore is transformed to an increased defect size, which is equivalent to a bulk pore. Subsequently, the fatigue strength assessment method by Tiryakioğlu, commonly used for casting processes, is applied. For this method, a cumulative Gumbel extreme value distribution is utilized to statistically describe the defect size. The fitted distribution with modified data reveals a better agreement with the experimental data than unmodified. Additionally, the validation of the model shows that the usage of the ∆K modified data demonstrates better results, with a slight underestimation of up to about −7%, compared to unmodified data, with an overestimation of up to about 14%, comparing the number of load cycles until failure. Hence, the presented approach applying a stress intensity equivalent transformation of surface to bulk pores facilitates a sound fatigue strength assessment of WAAM Ti-6Al-4V structures

Data publications correlate with citation impact

Neuroscience and molecular biology have been generating large atasets over the past years that are reshaping how research is being conducted.In their wake, open data sharing has been singled out as a major challenge for the future of research. We conducted a comparative study of citations of data publications in both fields, showing that the average publication tagged with a data-related term by the NCBI MeSH(MedicalSubjectHeadings) curators achieves a significantly larger citation impact than the average in either field. We introduce a new metric, the data article citation index(DAC-index), to identify the most prolific authors among those data-related publications.The study is fully reproducible from an executable Rmd(RMarkdown)script to gether with all the citation datasets. We hope these results can encourage authors to more openly publish their data