Database Information Retrieval Research Articles

CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics

Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in both sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable the generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, concomitant progress has not been observed to the same extent in data analysis and post-processing steps, arguably constituting the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide-level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate the applicability of our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0.

INFORMATION SUPPORT OF OCCUPATIONAL SAFETY CONSULTING ON THE BASIS OF THE MONITORING SYSTEM

The article identifies the need to improve the information support of occupational safety consulting by creating a monitoring system. This is due to changes in the regulatory framework of labor protection, as well as changes in the structure of State Labour Service of Ukraine. The development of a monitoring system is due to the need for comprehensive modernization of information and analytical support in the field of labor protection. The lack of a subsystem of analytical data processing complicates the implementation of queries and prevents effective multicriteria information retrieval in databases, creating integrated reports, complicates or prevents the use of mathematical modeling techniques to predict occupational safety and occupational risk assessment. The basic principles on which the system of state monitoring of labor protection should be based are determined (the principle of purposefulness, the principle of planning, the scientific principle, the principle of objectivity, etc.). The main functions of the monitoring system for information support of occupational safety consulting are: accounting and analysis of indicators of labor protection; labor protection planning; organization and control of work on the implementation of labor protection measures; evaluation of the results of the planned activities. The implementation of the proposed principles and approaches to the development of a monitoring system becomes possible in the active development of information technology, as a result of which computer and communication technology and software have become widespread in all industrial and scientific fields. For the functioning of the monitoring system it is necessary to develop a set of methods, techniques and algorithms that establish the procedure for collecting, processing, analyzing and using data in the process of management activities in the field of labor protection. The use of the results of the monitoring system will increase the level of awareness of managers and specialists who carry out management in the field of labor protection, as well as ensure the scientific validity of management decisions.

Uso de las tecnologías de la información y comunicación como herramienta de apoyo en el aprendizaje de los estudiantes de medicina

El uso de medios electrónicos como herramienta educativa es algo muy frecuente en la sociedad global del conocimiento, favorecido por el avance tecnológico. Se emplean nuevas alternativas en la práctica docente y en los procesos educativos, y las instituciones dedicadas a la educación médica no son la excepción. El objetivo de este trabajo fue establecer el uso de las tecnologías de la información y la comunicación (TIC) para el aprendizaje en estudiantes de medicina de la Universidad Autónoma de Tamaulipas, campus sur. Se siguió un estudio descriptivo, observacional y transversal. Los datos se recabaron a través de un cuestionario aplicado a 109 estudiantes. Del total de participantes, el 90.83 % contaba con computadora portátil, el 94.50 % con internet, ya sea en computadora o celular. El tiempo empleado diariamente usando las TIC para actividades educativas era entre 2 h y 4 h y el Google académico fue la base de datos más empleada para búsqueda de información. Por otro lado, se encontró que entre el 50 % y el 75 % de los encuestados tienen comprensión y dominio del idioma inglés. El uso de las TIC es de gran apoyo para los estudiantes, ya que les permite facilitar las búsquedas de información científica y médica, además de desarrollar competencias en el procesamiento y manejo de la información, para intercambiar información científica actualizada y continuar con su educación médica.

Discovering seminal works with marker papers

Bibliometric information retrieval in databases can employ different strategies. Commonly, queries are performed by searching in title, abstract and/or author keywords (author vocabulary). More advanced queries employ database keywords to search in a controlled vocabulary. Queries based on search terms can be augmented with their citing papers if a research field cannot be curtailed by the search query alone. Here, we present another strategy to discover the most important papers of a research field. A marker paper is used to reveal the most important works for the relevant community. All papers co-cited with the marker paper are analyzed using reference publication year spectroscopy (RPYS). For demonstration of the marker paper approach, density functional theory is used as a research field. Comparisons between a prior RPYS on a publication set compiled using a keyword-based search in a controlled vocabulary and three different co-citation RPYS analyses show very similar results. Similarities and differences are discussed.

Research on We—Media Information Retrieval Technology of Knowledge Map

As the development direction of information retrieval technology gradually evolves toward the relationship of search entities, traditional relational databases are difficult to satisfy, and graph databases are specifically created to handle the relationships between data. This article explains the basic concept of graph database, and takes the example of domain-specific database information retrieval as an example, analyzes its advantages and disadvantages, and analyzes the challenges faced by the graph database in full-text information retrieval.

Automated Self-learning Chatbot Initially Build as a FAQs Database Information Retrieval System: Multi-level and Intelligent Universal Virtual Front-office Implementing Neural Network

In this paper we propose a novel approach of an automatic creation of a chatbot exploiting only a questions-answers archive. The described model is not bound to a particular context or language, and it allows to initially retrieve information from a FAQs database using natural language, by allowing successively the automation of customer support services for the optimization of human resources thus implementing a self-learning chatbot system. We also propose a solution based on dynamical information system capable of exploiting the potential of the proposed model in a universal virtual front-office, including the statistics and tests necessary to validate the solution, and a comparison between neural network and AIML results.

Classification and Applicability of Technological Mandrels

В данной статье рассмотрен вопрос разнообразия технологических оправок, применяемых на операциях механической обработки в цехах промышленных предприятий. Для условий современного производства была представлена классификация технологических оправок по их технологическим признакам, которая раскрывает тип оправок в зависимости от вида установочной поверхности, вида базовой поверхности и типа посадки обрабатываемой детали с установочной поверхностью оправки. Далее в статье приведена логическая таблица выбора оправок в зависимости от параметров применяемости: вид обработки, точность базового отверстия обрабатываемой детали, соотношение длины к диаметру, радиальное и торцевое биение заготовки и вид применяемой оправки. Затем представлен подход создания информационно-поисковой базы данных технологических оправок на основе применения булевых функций. Использование такой базы данных на промышленных предприятиях позволит подбирать тип необходимой технологической оправки на основе синтеза производственных параметров. Так, в статье представлены булевы функции шлицевой оправки с жидким наполнителем и переналаживаемой оправки с полиуретаном, используемые на операции токарной обработки. В завершение представлены булевы функции основных конструкций технологических оправок, выведенные на основе логической таблицы.

A Trend Analysis of Information Retrieval Models

: Information retrieval technologies behind web search engines in the field of computer science were bought up in the year of 1950s. It is a process of retrieving the relevant documents based on the queries raised by the user. It deals with the representation, storage and access of information items. In this system, the generated outputs are ranked according to their relevance. The information retrieval (IR) uses data models that make a retrieval process easier when compared to the traditional IR database model. In this work, we analyse the most popular information retrieval models such as boolean, vector space, probabilistic and latent semantic analysis and evaluate the performance of the models by using the underlying parameters like concept, representation, word occurrence, information type, output, pros and cons of the models. This study aims to determine the appropriate model for different situations and additionally describes the indexing methods for decrementing search space and different probing (searching) techniques to retrieve the information.

INFLUENCE OF SPEED, TIME OF HOMOGENIZATION, TYPE OF SURFACE ACTIVE SUBSTANCE ON THE SIZE OF PENTOXYPHILLINE NANOPARTICLES BASED ON POLY-DL-LAKTIDE-CO-GLICOLIDE

Nanopharmacology is a set of methods and techniques used in the creation, study, production and use of nanostructures (size about 1–700 nm) with new chemical, physical, and biological properties. For a long time pharmacologists have been working on molecular, and sometimes even on a submolecular level for synthesizing new drugs and explaining their mechanism of action. Thanks to this, the interest of pharmacology in nanotechnology is connected with new ways of obtaining and using medicines. One way of obtaining new forms of drugs is the synthesis of nanoparticles, since they allow the active substance to overcome the protective barriers of the body such as, for example, the immune system. Due to the fact that the surface of nanoparticles (nanocapsules) is multilayered, their resistance to the action of the protective mechanisms of the body increases, which allows the drug to retain the activity of the pharmacological action, as well as its structure for a longer time. The possibility of penetration through biological barriers, tissue-specificity, rate of drug release depends largely on the size and surface properties of nanoparticles. The aim of our study was to study the influence of such important factors as time, homogenization rate and the type of surface active substance, on the size of the obtained nanoparticles of pentoxifylline based on poly-DL-lactide-co-glycolide (PLGA). Materials and methods . The research was carried out using the information retrieval database (PubMed), as well as the results of our own research. Results and discussion . It has been found that the dispersion phase of the sample, in which polyvinyl alcohol was used as the surfactant, had the smallest size, particularly, the average hydrodynamic radius of the particles amounted to 175.4 nm. The influence of the speed and time of homogenization on the size of nano particles of pentoxifylline based on PLGA was experimentally proved. Also, microphotographs of nanoparticles of pentoxifylline based on poly-DL-lactide-coglycolide (PLGA) are presented. Conclusion .Our studies prove the effect of the speed and time of homogenization, as well as the type of surfactant, on the size of nanoparticles of pentoxifylline based on poly-DL-lactide-co-glycolide. As a result of the studies, the procedure for obtaining nanoparticles of pentoxifylline was adjusted.

Furthering benefit/risk ratio and cost effectiveness of anticancer drugs.

In Russia, the incidence of melanoma is increasing steadily. The approved standard of specialized medical care for melanoma of the skin defined the range of drugs, recommended for the provision of quality health care. However, it appears that the most effective innovative and safe medicines are at the same time the most expensive drugs. The most important is the assessment of drug use, taking into account their relative efficacy, safety (risk/benefit) and cost (economic efficiency), which may help to create the conditions for controlling their use. Based on this analysis, it is necessary to introduce drugs on the lists of drugs within the framework of the provision of state guarantees of free medical care to citizens (patients). To analyze the drug use according to the standard of specialized medical care for melanoma of the skin, to perform information retrieval in specialized libraries and databases Cochrane, Pubmed, Medline, as well as in the database of the state register of medicines (GRLS) of Russian Ministry of Health. The nomenclature of drugs was determined according to the standards of specialized medical care for 2006 and 2012, to the data of GRLS; information searches were performed in specialized libraries and databases Cochrane, Pubmed, Medline. Analysis of anticancer drugs for melanoma of the skin consisted of determining of nomenclature of drugs, included in the standard of specialized medicine care. The standard of specialized medicine care for patients with malignant melanoma of the skin (with specialized assistance) (Order dated December 6, 2006 № 828) includes the following anticancer drugs: dacarbazine (alkylating agents), vinblastine (antineoplastic agent - an alkaloid), cisplatin (platinum), lomustine (nitrosoureas), bleomycin (antitumor agent, an antibiotic) [1]. The standard of specialized medical care in melanoma skin generalization or recurrent disease (chemotherapy) (Order of November 7, 2012 № 604n) includes the following anticancer drugs: lomustine and fotemustine (nitrosoureas), dacarbazine and temozolomide (alkylating agents), cisplatin (platinum) [2]. So, the standard of specialized medical care for for melanoma of the skin by 2012 compared with the standard of care by 2006 includes temozolomide and fotomustin and excludes vinblastine and bleomycin. Based on the database GRLS of Russian Ministry of Health Care [3], as well as information retrieval in databases of Cochrane, Pubmed, Medline the efficacy and safety of melanoma of the skin have proven innovative products, in particular, such as vemurafenib (Zelboraf) dobrafenib (Tafinlar) and trametinib (Mekinist) that are already registered in Russia. At the stage of the clinical study are targeted drugs, such as GSK1120212, AMG 678, pembrolizumab, ipilimumab, tremilimumab, nivolumab and etc. The inclusion or exclusion of data from the restrictive drug lists, such as lists of "Vital and essential medicines", "Drugs for certain categories of citizens", the "Minimum range", according to the Russian Government Decree №871 of 28.08.2014 [4] is carried out after the risk/benefit ratio and cost effectiveness assessment to increase their availability. The availability of high-quality, effective and safe drugs for medical use within the reduced budget, taking into account the formation of a rational and balanced system of health care is the main task of the strategy of the drug provision of the population of Russia for the period till 2025 [5]. The most rational use of limited resources and cost containment within the framework of state regulation refers to modern trends in the health care of the Russian Federation. There is a need to develop targets aimed at all subjects of the pharmaceutical market, to increase the availability of innovative drugs for melanoma of the skin treatment. This strategy should be based on evidence and assessments of the efficacy, safety and economic viability of anticancer drugs.

Information Retrieval in Telemedicine: a Comparative Study on Bibliographic Databases.

Background and Aims:The first step in each systematic review is selection of the most valid database that can provide the highest number of relevant references. This study was carried out to determine the most suitable database for information retrieval in telemedicine field.Methods:Cinhal, PubMed, Web of Science and Scopus databases were searched for telemedicine matched with Education, cost benefit and patient satisfaction. After analysis of the obtained results, the accuracy coefficient, sensitivity, uniqueness and overlap of databases were calculated.Results:The studied databases differed in the number of retrieved articles. PubMed was identified as the most suitable database for retrieving information on the selected topics with the accuracy and sensitivity ratios of 50.7% and 61.4% respectively. The uniqueness percent of retrieved articles ranged from 38% for Pubmed to 3.0% for Cinhal. The highest overlap rate (18.6%) was found between PubMed and Web of Science. Less than 1% of articles have been indexed in all searched databases.Conclusion:PubMed is suggested as the most suitable database for starting search in telemedicine and after PubMed, Scopus and Web of Science can retrieve about 90% of the relevant articles.

Simulation of Fast Retrieval Method for Large-Scale Image Database

The traditional database information retrieval method is achieved by retrieving simple corresponding association of the attributes, which has the necessary requirement that image only have a single characteristic, with increasing complexity of image, it is difficult to process further feature extraction for the image, resulting in great increase of time consumed by large-scale image database retrieval. A fast retrieval method for large-scale image databases is proposed. Texture features are extracted in the database to support retrieval in database. Constraints matching method is introduced, in large-scale image database, referring to the texture features of image in the database to complete the target retrieval. The experimental results show that the proposed algorithm applied in the large-scale image database retrieval, augments retrieval speed, thereby improves the performance of large-scale image database.

FmMDb: A Versatile Database of Foxtail Millet Markers for Millets and Bioenergy Grasses Research

The prominent attributes of foxtail millet (Setaria italica L.) including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html), a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.

El grupo de trabajo sobre consultas en bases de datos del CAICYT: un antecedente argentino en la pre-historia de las búsquedas de información científica y tecnológica en Internet. Parte 1: contexto original y conformación del grupo

This article refers to the initial stage of a project generated in the early 1980s in CAICYT (Argentine Centre for Scientific and Technological Information); the project was dedicated to bibliographic information retrieval in databases through terminals connected to remote computers. The project led to the formation of a workgroup composed by representatives from various institutions that pioneered interactive access to foreign science and technology databases from Argentina. It addresses the technological, institutional and disciplinary context of the project, the works undertaken to provide the infrastructure and equipment that were necessary, the profile and initial training of the professionals involved, and dissemination activities that were performed. The second part will deal with the development, activities and legacy of the group.

Multimedia visualization and interactive systems

PurposeThis paper aims to present the schematic for building a multimedia information visualization system and digital archive which takes advantage of a wider spectrum of media elements (images, sound, datasets) and interactivity with regards to research level historical body of knowledge.Design/methodology/approachThe methodology for this interactive multimedia visualized system was based on create a digital environment to explore larger bodies of research that expand on simple text‐based Information Retrieval Database systems. Through photos, videos, interactive maps, digital audio interviews, primary documents and narrative structures the system presents new methodologies for building digital libraries. The “educational” objective of this project was to present a stylistically elegant yet intellectually robust interactive multimedia information system for academic libraries.FindingsBuilding new online digital libraries must involve robust interactivity to take advantage of the computer's intrinsic specificity and the wider set of choices open to the human perceptual apparatus. Instead of text‐based navigation systems, a more creative set of visual “tools” should be explored for digital libraries including interactivity and cognitive cartographies. Key here are the terms “visual metaphor” and innovatively structuring visually intuitive “narratives” into non‐linear dynamic but humanly usable information systems.Research limitations/implicationsIn expanding the range of “allowable” “historical archival media” (audio, video, images, datasets, databases) in digital libraries and keeping research level academic integrity, future questions regard what this means for historiography, information construction, and questions surrounding epistemology and “archives” of the future.Practical implicationsTechnically, the successes in building this digital library information system solve the question of how to present a large robust amount of information indifferent rich media formats in an interesting and engaging manner. The project points to methodologies to present a research spectrum depth structure of textual material that can seamlessly be incorporated through wider spectrum of media elements: images, video, audio, music, datasets and interactivity.Originality/valueThis paper provides a methodology for marrying a textual body of academic research with a wider spectrum of media elements (sound, images, datasets, music) and incorporating them into a digital library through an innovative methodology. It will be valuable to anyone needing guidelines and specific algorithmic recipes and suggestions for building new millennia digital libraries which take advantage of a wider spectrum of media elements.

Information Retrieval Design: Principles and Options for Information Description, Organization, Display, and Access in Information Retrieval Databases, Digital Libraries, Catalogs, and Indexes20054James D. Anderson and José Pérez‐Carballo. Information Retrieval Design: Principles and Options for Information Description, Organization, Display, and Access in Information Retrieval Databases, Digital Libraries, Catalogs, and Indexes. St Petersburg, FL: Ometeca Institute 2005. 617 pp. US$60.00 (soft cover),

Information Retrieval Design: Principles and Options for Information Description, Organization, Display, and Access in Information Retrieval Databases, Digital Libraries, Catalogs, and Indexes20054James D. Anderson and José Pérez‐Carballo. <i>Information Retrieval Design: Principles and Options for Information Description, Organization, Display, and Access in Information Retrieval Databases, Digital Libraries, Catalogs, and Indexes</i>. St Petersburg, FL: Ometeca Institute 2005. 617 pp. US$60.00 (soft cover),

Summary of article appearing in “In This Issue,” JASIST, 55(4), 281–282 (2004): An Information Processing Model of Undergraduate Electronic Database Information Retrieval

Journal of the American Society for Information Science and TechnologyVolume 55, Issue 14 p. 1306-1306 Letter to the Editor Summary of article appearing in “In This Issue,” JASIST, 55(4), 281–282 (2004): An Information Processing Model of Undergraduate Electronic Database Information Retrieval Karen Macpherson, Corresponding Author Karen Macpherson [email protected] School of Information Management and Tourism, University of CanberraSchool of Information Management and Tourism, University of Canberra, ACT 2601, AustraliaSearch for more papers by this author Karen Macpherson, Corresponding Author Karen Macpherson [email protected] School of Information Management and Tourism, University of CanberraSchool of Information Management and Tourism, University of Canberra, ACT 2601, AustraliaSearch for more papers by this author First published: 17 August 2004 https://doi.org/10.1002/asi.20094Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume55, Issue14December 2004Pages 1306-1306 RelatedInformation

An information processing model of undergraduate electronic database information retrieval

AbstractIn this paper, it is suggested that a number of theoretical and practical perspectives on information literacy can be obtained through the examination of tenets of cognitive psychology. One aspect of cognitive psychology—information processing theory—is applied to the development of a two‐stage model of the information retrieval process. This model of information retrieval has utility along two dimensions: firstly, in the conceptualization of the information retrieval process; and secondly, in the development of teaching strategies informed by such a model. The efficacy of this model was tested in a large two‐phase experimental study at the University of Canberra, Australia. Statistically significant results support the effectiveness of the concept‐based teaching of information retrieval and the utility of the model as an explanation of the cognitive underpinnings of information retrieval.

Musical Works and Information Retrieval

Music bibliographers and librarians are accustomed to an essential dichotomy that presents itself in the ordering of musical documents for retrieval. The documents themselves (scores and recordings, mostly) must be represented in retrieval systems according to their physical characteristics (that is, according to formatted physical descriptions) for the purposes of general bibliographic control; but the musical works that are contained in and conveyed by these documents require representation according to their intellectual origins and musical characteristics (that is, author and uniform title headings). Collections of musical documents are unique among collections of documents (in libraries, bibliographies, etc.) in that the influence of repertory is such that a given collection will have many instantiations of the same musical work--one Tchaikovsky Fifth Symphony (a musical work), but a dozen scores of different sizes and formats, and dozens of recordings, not to mention excerpts and arrangements. Thus the intellectual control of musical works assumes tremendous importance in the work of music librarians and bibliographers. At the beginning of this new century we find a rapidly evolving domain for research and very pragmatic implementation known as Music Information Retrieval (MIR). Music Information Retrieval is basically the activity of automating the retrieval of musical works, or parts of musical works. MIR embraces everything from query-by-humming systems that allow a searcher to hum a tune for which the database returns an audio output, to the design of metadata structures and standard name-title-subject querying of bibliographic databases. The field encompasses various system-Engineering components, such as audioinformation retrieval (AIR), and it also encompasses musicological engineering problems such as recognition of parts of musical works. A major component is the creation of digital music libraries--electronic repositories of musical works. We will look more closely at the components of MIR later, but for now it is important to comprehend the evolution of this new domain for music librarianship and bibliography. In information retrieval in general, as well as in music information retrieval, the objects or that will be mapped into databases for retrieval must be well-defined. An entity is simply a thing--it might be a physical characteristic or it might be a concept. Entities occupy prominent positions in the structure of information retrieval databases. Consider an online catalog: therein things such as tides, composers' names, tide-page transcriptions, etc., could all be considered entities. Entities have attributes (inherent characteristics that can be defined) that are used to structure their representations in information retrieval systems. In music information retrieval, as we will see below, there are many potential entities at play. But universal to the retrieval of music information--whether it be bibliographic or audiographic using surrogates or real-time sound--is the concept of the musical work. Musical works, then, as opposed to musical documents such as scores or recordings of musical works, form a key entity for music information retrieval. Ultimately, searches for a given musical work rely on the hope of subsequent selection of instantiation in one of several documentary formats. Musical works have been variously and industriously described by musicologists and music bibliographers. Yet, in the information retrieval domain, the work as opposed to the document has only recently received focused attention. (1) Efforts to define works as information retrieval entities and to document their occurrence empirically are quite recent. In fact, systems for bibliographic information retrieval, and more recently for information storage and retrieval, have been designed with the document as the key entity, and works have been dismissed as too abstract or difficult to define empirically to take a role in information retrieval. …

Indexing, teaching of See: Information retrieval design

Places the teaching of (about) indexing into the context of the 20 fundamental attributes of all information retrieval databases or systems, ranging from back-of-the-book indexes to physical and digital libraries, indexing and abstracting services, and online or web-based message/document retrieval services.