Cross-reference Information Research Articles

Encoding Near-Synonym Relations in Monolingual English Learner's Dictionaries: The Case of Germanic and Latinate "Equivalents"

ABSTRACT: This article examines the semantic relations between pairs of Germanic and Latinate near-synonyms in contemporary English, such as hug/embrace, isle/island , and brave/courageous , which dictionaries traditionally treat as equivalent in meaning, regardless of context-independent differences between them. These word pairs are challenging for learners of English as a Foreign Language, especially when their L1 is a Romance language. Monolingual English learner's dictionaries (MELDs) do not, in general, clearly or systematically disambiguate near-synonyms of different origin. An improvement in dictionary treatment of near-synonyms is thus called for. After outlining the main types and subtypes of meaning relations identified through the analysis of a sample of Germanic and Latinate word pairs, synonymy in the "Big Five" MELDs is examined. Proposals are then made to better encode synonym similarities and differences with cross-reference information in the form of tags, labels, and usage notes.

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data

More than 61,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. SIFTS incorporates residue-level annotations from many other biological resources. SIFTS data is available in various formats like XML, CSV and TSV format or also accessible via the PDBe REST API but always maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. Here, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProtKB, Pfam, SCOP2, and CATH residue-level annotations directly into the PDBx/mmCIF files from the PDB archive. With the integrated UniProtKB annotations, these files now provide consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended dictionary yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at the residue level resulting in better data interoperability, supporting improved data analysis and visualisation.

Text Mining of Biomedical Articles Using the Konstanz Information Miner (KNIME) Platform: Hemolytic Uremic Syndrome as a Case Study.

ObjectivesAutomated systems for information extraction are becoming very useful due to the enormous scale of the existing literature and the increasing number of scientific articles published worldwide in the field of medicine. We aimed to develop an accessible method using the open-source platform KNIME to perform text mining (TM) on indexed publications. Material from scientific publications in the field of life sciences was obtained and integrated by mining information on hemolytic uremic syndrome (HUS) as a case study.MethodsText retrieved from Europe PubMed Central (PMC) was processed using specific KNIME nodes. The results were presented in the form of tables or graphical representations. Data could also be compared with those from other sources.ResultsBy applying TM to the scientific literature on HUS as a case study, and by selecting various fields from scientific articles, it was possible to obtain a list of individual authors of publications, build bags of words and study their frequency and temporal use, discriminate topics (HUS vs. atypical HUS) in an unsupervised manner, and cross-reference information with a list of FDA-approved drugs.ConclusionsFollowing the instructions in the tutorial, researchers without programming skills can successfully perform TM on the indexed scientific literature. This methodology, using KNIME, could become a useful tool for performing statistics, analyzing behaviors, following trends, and making forecast related to medical issues. The advantages of TM using KNIME include enabling the integration of scientific information, helping to carry out reviews, and optimizing the management of resources dedicated to basic and clinical research.

Military History from the Street

In Ireland and the Great War, the late Keith Jeffery argued that the 1914–18 conflict was an essential context for the Irish independence struggle, and that the Easter Rising (1916), the War of Independence (1919–21) and Civil War (1922–3) were integral parts of the same story.1 This is also the starting point of Dublin’s Great Wars, a ‘new military history’ and prosopography of British soldiers and Irish republicans who resided in Ireland’s capital city during these years. There is much to commend ‘military history from the street’, Grayson’s methodology of using ‘every source possible to draw in the military service of everyone from a given area’. Online sources have transformed the speed and ease with which researchers can search for and cross-reference information. The author’s approach is predicated largely on the vast word-searchable collections of primary-source records relating to the First World War that have become available online in recent years.2 Some marvellous material has been unearthed in British military pension and service records, diaries, newspapers, personal testimony and journals.

De-identified linkage of data across separate registers: a proposal for improved protection of personal information in registry-based clinical research

Over the last decades the advent of digital documentation has provided research communities with valuable resources of information for clinical research. To utilize the potential of information about patients, their health care, and its outcome that is already available in different registers, the possibility to cross-reference information from different registers is inevitably required. When performing linkage, we are currently forced to disclose information of participating subjects either to the administration of the other register(s) or to the researcher. Considering the increased concern of issues around personal integrity, this is a limitation that affects the ethical implications of proposed research and that might in the end affect the willingness of subjects to participate in registers. For this reason we propose a different methodology for performing cross-referencing, one that effectively prevents information leakage between the different organizations participating in linking the data. We believe that it is possible to use commonly adopted technologies within the area of data security and encryption to perform linkage without disclosing any sensitive information between different participants. In this paper we demonstrate how common techniques of encryption could be implemented to achieve that and furthermore significantly simplify discovery and feasibility surveying ahead of studies.

Maps of Daesh: The Cartographic Warfare Surrounding Insurgent Statehood

The ongoing Syrian civil war raises new cartographic challenges, including the ethical question of how the self-proclaimed Islamic State should be represented. Based on a comparative study, this article investigates the visual languages of IS sanctuary maps as published by news agencies, intelligence agencies, or circulated by the insurgents themselves. I argue that the statehood of territory held by the IS is symbolically contested through cartographic choices that reflect the diverging interests of the map makers. Beyond official representations, the article also considers the maps created by amateur conflict mappers and visual forensics experts, who extract and cross-reference information from social media including posted cell phone and drone footage, georeferenced tweets, and satellite images. I argue that the novel visual strategies developed by these practitioners for presenting visual evidence emphasize nonrepresentational aspects of cartography and represent a countermodel to established cartographic languages that follows an indexical rather than iconic or symbolic paradigm.

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.

Expert System for Monitoring Pollution of Rivers and Lakes

This research presents the state of the art of expert systems applied to one solution for monitoring and control of pollution of Brazilian rivers and lakes, because of the many cases of indiscriminate pollution of its rivers and lakes and it comes to affect people's lives and biodiversity as a whole. This application generates reports and supports traceability creation and cross-reference information to search for possible causes and appropriate solutions to the problem raised. Its main contribution is supporting the government and its human specialists how to deal with this great environmental problem using computers as specialists and help them choosing what decisions to make.

Inequality in the distribution of rheumatologists in Brazil: Correlation with local of medical residency, Gross Domestic Product and Human Development Index

ObjectiveTo assess the distribution of rheumatologists in Brazil and their correlation with Medical Residency specialization offer, Gross Domestic Product (Gdp) And Municipal Human Development Index (HDI-M) of units of the federation (UFs). MethodsQuery to various official databases, data summarization by techniques for descriptive statistics and cross-referenced information. For correlation analysis, we used the Spearman correlation coefficient (r). ResultsThere were 1229 rheumatologists regularly registered in the country. The Northern region had only 3.6% of the total (n = 44), while the Southeast had 42.2% (n = 519). The State capitals, added to the five largest municipalities in each UF, concentrated 75.8% of these specialists (n = 931). In total, 49.9% of rheumatologists offered treatment at SUS. A general ratio of 157,809 inhabitants per rheumatologist in Brazil was determined, but with wide variation among UFs with respect to this ratio. In the years 2000-2012, there were 593 Rheumatology Residency graduated physicians in Brazil. We observed a positive correlation among number of rheumatologists compared with GDP (r = 0.94), HDI-M of the State capitals (r = 0.77) and number of Rheumatology Residency graduated physicians (r = 0.79) in UFs. ConclusionsWe noted a strong concentration of rheumatologists in State capitals and larger municipalities, with noticeable inequalities also between UFs and country regions. The distribution of these professionals accompanied GDP, HDI-M of the State capital and number of Rheumatology Residency graduated physicians, suggesting that factors related to income opportunities and human development and the place of speciality training may influence the geographical fixation of rheumatologists.

Plant and Cell Physiology 2014 Online Database Issue

We are proud to present the fourth Database Issue of Plant and Cell Physiology (PCP) (available online at http://pcp.oxfordjour nals.org/). As we have introduced in previous years (Matsuoka and Yano 2010, Obayashi and Yano 2013), the ultimate goal of PCP’s annual Database Issue is to provide a useful online resource and forum for discussion of bioinformatics research, and in particular the development and maintenance of the infrastructure of web databases for plant science. Recently, largescale biological data sets, such as those for DNA polymorphisms and gene expression, have been obtained using next-generation sequencing technology. In addition, website and database construction has also become easier due to the many commercial and non-commercial types of software that have been recently released and widely distributed. This has resulted in the creation of many diverse web-based tools and databases that house and/or analyze large-scale data. However, it is not always easy for researchers to extract data efficiently from such databases, since their concept, contents and/or functions may sometimes be unclear. Therefore, to promote discussion and develop bioinformatics approaches and omics/knowledge information specifically for the plant sciences, databases ought to be designed with particular specifications in mind, for instance to include user-friendly interfaces, search functions and manuals. To ensure that a common consensus is reached in this and future Database Issues, PCP has updated its Instructions for Authors and implemented standard key features and descriptions of databases and online tools (see http://www.oxfordjournals.org/our_journals/pcp/pcp_2013_ call_for_paper.html), which will aid researchers in extracting relevant data. This year’s collection of Database articles promises to provide useful omics data to plant researchers, and comprise descriptions of nine sophisticated web databases. On pages 1–9 (e3), Kiefer et al. (2014) report on a new Brassica database—BrassiBase (http://brassibase.cos.uni-heidelberg.de/). The authors aim to develop an online database system of cross-referenced information and resources on Brassicaceae taxonomy, systematics, evolution, traits and germplasm resources. Biological material and resources, either collected directly in the wild or held in germplasm collections, are often taxonomically misidentified and are very rarely further characterized and documented. BrassiBase will close these various gaps and provide the full potential of research focusing on the adaptive characters and character trait evolution in the Brassicaceae. MEGANTE (https://megante.dna.affrc.go.jp/) is a web-based annotation system that makes plant genome annotation easy for non-bioinformaticians (Numa and Itoh 2014; see pp. 1–8 (e2)). Users can submit a sequence of up to 10 Mb in length and save up to 100 sequences on the server. The annotation is visualized with a genome browser and the results can be downloaded in a Microsoft Excel format. Yonemaru et al. (2014; see pp. 1–12 (e9)) introduce the HapRice database, which provides information about single nucleotide polymorphisms (SNPs) in different rice genomes. The SNP haplotypes were determined by the allele frequencies in two populations consisting of 3,334 SNPs within 76 world accessions and 3,252 SNPs within 177 Japanese accessions, and will aid marker-assisted breeding and provide useful additional markers for geneticists. The SNP information is available from the HapRice database (http://qtaro.abr.affrc.go.jp/). To allow a comprehensive understanding of the interactions between an organism’s metabolites and the chemical-level contribution of metabolites to human health, Nakamura et al. (2014; see pp. 1–9 (e7)) constructed a metabolite activity database known as the KNApSAcK Metabolite Activity DB (http://kanaya.naist.jp/MetaboliteActivity/top. jsp). The KNApSAcK Metabolite Activity DB is integrated within the KNApSAcK Family DBs (Afendi et al. 2012, Nakamura et al. 2013) to facilitate further systematized research in various omics fields, especially metabolomics, nutrigenomics and foodomics. The KNApSAcK Metabolite Activity DB could also be utilized for developing novel drugs and materials, as well as for identifying viable drug resources and other useful compounds. On pages 1–9 (e5), Fukami-Kobayashi et al. (2014) also describe the integration of omics information and resources in plant science. The original SABRE (Systematic consolidation of Arabidopsis and other Botanical Resources) database (Yamazaki et al. 2010), retrieved TAIR (The Arabidopsis Information Resource) gene models and their annotations, together with homologous gene clones from various species, and

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.

A WebGIS system for relating genetic soil classification of China to soil taxonomy

Soil classification is the basis for the exchange of soil science research results and the foundation for the application of modern soil resource management methods. A WebGIS-based system designed to relate genetic soil classification of China (GSCC) to soil taxonomy (ST) was developed to enhance global cooperation and to support communication between China and the other countries on important agricultural and environmental issues. The system has a Browse Server (B/S) structure and exploits the 1:1,000,000 soil databases of China using WebGIS functionality. This paper describes the application of the WebGIS system for easily accessing cross-reference information between GSCC to ST. First, we describe the three-level B/S structure of the system. The cross-reference methodologies, referenceability and maximum referenceability, are then explained and applied at three geographic scales (i.e. nation, region and pedon). Finally, three sub-modules based on the supported scales are described and illustrated with application scenarios to familiarize users with the inquiry system and its usage. The main advantage of the system is that it considers statistical similarity in the spatial distributions between the two different classification systems. Users with limited knowledge are able to obtain soil cross-reference information using an intuitive interface, which supports query, visualization and analysis via a web browser at the most detailed level. The inquiry system benefits the development of soil classification science and international academic exchange.

Fast human detection using a novel boosted cascading structure with meta stages.

We propose a method that can detect humans in a single image based on a novel cascaded structure. In our approach, both intensity-based rectangle features and gradient-based 1-D features are employed in the feature pool for weak-learner selection. The Real AdaBoost algorithm is used to select critical features from a combined feature set and learn the classifiers from the training images for each stage of the cascaded structure. Instead of using the standard boosted cascade, the proposed method employs a novel cascaded structure that exploits both the stage-wise classification information and the interstage cross-reference information. We introduce meta-stages to enhance the detection performance of a boosted cascade. Experiment results show that the proposed approach achieves high detection accuracy and efficiency.

Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells

Although a huge amount of mammalian genomic data does become publicly available, there are still hurdles for biologists to overcome before such data can be fully exploited. One of the challenges for gaining biological insight from genomic data has been the inability to cross-reference transcriptomic and proteomic data using a single informational platform. To address this, we constructed an open-access database that enabled us to cross-reference transcriptomic and proteomic data obtained from immune cells. The database, named RefDIC (Reference genomics Database of Immune Cells), currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells. RefDIC is the first open-access database for immunogenomics and serves as an important information-sharing platform, enabling a focused genomic approach in immunology. All raw data and information can be accessed from http://refdic.rcai.riken.jp/. The microarray data is also available at http://cibex.nig.ac.jp/ under CIBEX accession no. CBX19, and http://www.ebi.ac.uk/pride/ under PRIDE accession numbers 2354-2378 and 2414.

The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere

Bioinformatics, the application of computational tools to the management and analysis of biological data, has stimulated rapid research advances in genomics through the development of data archives such as GenBank, and similar progress is just beginning within ecology. One reason for the belated adoption of informatics approaches in ecology is the breadth of ecologically pertinent data (from genes to the biosphere) and its highly heterogeneous nature. The variety of formats, logical structures, and sampling methods in ecology create significant challenges. Cultural barriers further impede progress, especially for the creation and adoption of data standards. Here we describe informatics frameworks for ecology, from subject-specific data warehouses, to generic data collections that use detailed metadata descriptions and formal ontologies to catalog and cross-reference information. Combining these approaches with automated data integration techniques and scientific workflow systems will maximize the value of data and open new frontiers for research in ecology.

Focus on vacuum and cryogenics

Focus on vacuum and cryogenics

Name Authority Work for OCLC Copy Cataloging: Is It Worth the Effort?

ABSTRACT In 1996, a study was undertaken at the University of Arkansas Libraries to evaluate the practice of front-end authority work for monographs copy cataloging. A sample of 283 name headings originating from Library of Congress, OCLC “Enhance” member, and general member copy was examined, and analysis revealed that 47.3 percent of headings correctly matched authority records already present in the library's local file. Another 41.3 percent exactly matched records in the OCLC authority file. These findings prompted the library to cease checking name headings at the point of cataloging. However, the level of inaccuracies present, combined with the value of authority records for cross-reference and note information, ensured that the Database Maintenance Unit would continue to review local headings reports and perform needed authority work.

Science fiction magazine story index, 1926-1995

Since the appearance of the first science fiction magazine in 1926, thousands of short stories have been published in periodicals devoted to the genre. This reference tool provides assistance in the daunting task of locating short stories published in science fiction publications, providing indexes to magazines, authors and titles, allowing a variety of options for research on 34,000 stories appearing in nearly 5000 issues of 133 genre magazines. Stories from all major American publications, as well as from several minor periodicals, are indexed. Also included is an appendix of bibliographies for the best-known and most prolific contributors to short science fiction, placing their periodical work within the context of their careers and providing cross reference information. A user's guide provides further assistance for research.

The AC 2000: The Astrographic Catalogue on the System Defined by the [ITAL]Hipparcos[/ITAL] Catalogue

The AC 2000 is a positional catalog of 4,621,836 stars covering the entire sky. The average epoch of position is 1907. The data are from the images measured and published as part of the Astrographic Catalogue (AC). The positions are on the system defined by the Hipparcos Catalogue, having originally been reduced plate-by-plate using the Astrographic Catalog Reference Stars. In addition to the astrometric data, magnitudes (on the Tycho B system) and cross-referencing information are included. These positions are valuable for the computation of proper motions, and were combined with the positions from the recently released Tycho Catalogue to improve proper motions of almost 1 million stars. The resulting catalog is known as the ACT Reference Catalog (the name ACT is from AC 2000 and Tycho). Both the AC 2000 and ACT are now available on CD-ROM and can be obtained by contacting the first author above. A World Wide Web site describing various aspects of the reductions is also maintained by the Astrometry Department, US Naval Observatory.

LIGAND: chemical database for enzyme reactions.

The existing molecular biology databases focus on the sequence and structural aspects of biological macromolecules, i.e. DNAs, RNAs and proteins. However, in order to understand the functional aspects, it is essential to computerize the interaction of these molecules. Furthermore, living cells contain additional molecules, such as metabolic compounds and metal ions, that may also be considered as parts of the basic building blocks of life, but are not well organized in public databases. LIGAND chemical database is our attempt to solve these problems, at least for enzymatic reactions. LIGAND consists of two sections: ENZYME and COMPOUND. The ENZYME section is an extension of previous studies (Suyama et al. , Comput. Applic. Biosci., 9, 9-15, 1993), and it is a flat-file representation of 3303 enzymes and 2976 enzymatic reactions in the chemical equation format that can be parsed by machine. The COMPOUND section has been newly constructed for information on the nomenclature and chemical structures of compounds. It contains 5383 chemical compounds. Both ENZYME and COMPOUND entries contain rich cross-reference information, most of which is automatically generated by the DBGET/LinkDB system, thus providing the linkage between chemical and biological databases. LIGAND is updated daily, tightly coupled with the KEGG metabolic pathway database, and forms the basis for reconstruction and computation of pathways. LIGAND can be accessed through the DBGET/LinkDB and KEGG systems in the Japanese GenomeNet database service via http://www.genome.ad.jp/. The flat-file format of the LIGAND database can be downloaded by anonymous FTP via ftp://kegg. genome.adjp/molecules/ligand/. goto@kuicr.kyoto-u.ac.jp; nishioka@scl.kyoto-u.ac.jp; kanehisa@kuicr.kyoto-u.ac.jp