A Blocking-Based Approach to Enhance Large-Scale Reference Linking

Analyses and applications based on bibliographic references are of ever increasing importance. However, reference linking methods described in the literature are only able to link around half of the references in papers. To improve the quality of reference linking in large scholarly data sets, we propose a blocking-based reference linking approach that utilizes a rich set of reference fields (title, author, journal, year, etc.) and is independent of a target collection of paper records to be linked to. We evaluate our approach on a corpus of 300,000 references. Relative to the original data, we achieve a 90% increase in papers linked through references, a five-fold increase in bibliographic coupling, and a nine-fold increase in in-text citations covered. The newly established links are of high quality (85% F1)

Which Publications’ Metadata Are in Which Bibliographic Databases? A System for Exploration

The choice of databases containing publications’ metadata (i.e., bibliographic databases) determines the available publication list of any author and, thus, their public appearance and evaluation. Having all publications listed in the various bibliographic databases is therefore important for researchers. However, the average number of publications a researcher publishes per year is steadily rising, making it labor-intensive and time-consuming for authors to investigate whether all their publications are given in all bibliographic databases online. In this paper, we present RefBee, an online system that retrieves the metadata of all publications for a given author from the various bibliographic databases and indicates which publications are missing in which database. Our system is available online at http://refbee.org/ and supports Wikidata, ORCID, Google Scholar, VIAF, DBLP, Dimensions, Microsoft Academic, Semantic Scholar, and DNB/GNB. Our system not only can serve as assistance tool for more than 4.7 million researchers of any discipline and publication’s language, but also incentivizes the usage and population of Wikidata in the scholarly field

The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli

The assignment of the side-chain Nh IR resonances and the determination of the three-dimensional solution structure of the C10S mutant of enzyme IIBcellobiose (IIBcel) of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli are presented. The side-chain resonances were assigned nearly completely using a variety of mostly heteronuclear NMR experiments, including HCCH-TOCSY, HCCH-COSY, and COCCH-TOCSY experiments as well as CBCACOHA, CBCA(CO)NH, and HBHA(CBCA)(CO)NH experiments.In order to obtain the three-dimensional structure, NOE data were collected from N-15-NOESY-HSQC, C-13-HSQC-NOESY, and 2D NOE experiments. The distance restraints derived from these NOE data were used in distance geometry calculations followed by molecular dynamics and simulated annealing protocols. In an iterative procedure, additional NOE assignments were derived from the calculated structures and new structures were calculated. The final set of structures, calculated with approximately 2000 unambiguous and ambiguous distance restraints, has an rms deviation of 1.1 Angstrom, on C alpha atoms. IIBcel consists of a four stranded parallel beta-sheet, in the order 2134. The sheet is flanked with two and three alpha-helices on either side. Residue 10, a cysteine in the wild-type enzyme, which is phosphorylated during the catalytic cycle, is located at the end of the first beta-strand. A loop that is proposed to be involved in the binding of the phosphoryl-group follows the cysteine. The loop appears to be disordered in the unphosphorylated state.</p