Factual Databases Research Articles

Formation of Automated Interactive Informational Resources of Agricultural Machinery and Equipment, Foreign Experience of Their use and Maintenance

The author presents the results of research on the formation of a digital environment on the basis of factual databases intended for system analysis of information on machinery and equipment for agricultural production, as well as the use of innovative technologies in the field of technical service for the effective maintenance of foreign agricultural machines.

New approaches to bibliographing factual information in local studies

The author examines the possibility for overcoming formal approaches to de-visu bibliographing factual information in local studies. She proposes a technology for bibliographing published local facts in the circumstances of digitalization. The sample abstracts supplementing bibliographic descriptions in local e-catalogs and factual local databases like “calendar of memorable dates” or “local chronicles” are provided. These databases should become the quality full-text bibliographic and factual resources, reliable and relevant, high quality and meeting user demands. The «de-facto» approach to bibliographing will facilitate the 5-fold increase in the number of hits of property digital resources of cultural institutions by the year 2024, which is envisaged by the “Culture” national project. It would also enable to accumulate reliable information on facts and events in local/regional history, interesting and unique facts, and famous local countrymen. This only technology will enable the libraries to remain irreplaceable. The author provides examples of bibliographing factual information on local studies.

"Normalization paradox" research in factual relational databases on ORACLE platform

Subject of Research.The paper presents the results of experimental assessment of relationship force between database normalization degree and database response formation time on a query. The research aim lies in the search of objective assessment of correlation force between database normalization degree and the run time of the enclosed inquiries to it depending on the required depth of the recursion realized in the inquiry ("normalization paradox" model). Method. The applied method is based on implementation of the correlation analysis according to the results of a numerical experiment for "normalization paradox" identification. Main Results. It is established that correlation between the recursion depth caused by achievement of a certain normal form of tables and inquiry performance time is rather weak in databases on the ORACLE platform. Interrelation between the database volume determined by the number of considered objects and delivery formation time is also weak. The valid conclusion is formulated about the absence of grounds for carrying out the database denormalization or not achievement of high normal forms for the good of the increase in its speed when performing requests for selection of records. All significant conclusions are drawn on the relation of factual databases on the ORACLE platform. Transposition of results on the other up-to-date database systems was not performed. Practical Relevance. The practical relevance of work consists in objective justification of the need (but not sufficiency) for reductions of the relations of the relational database under control of ORACLE Database 11g R2 to the highest normal forms for ensuring its integrity. The research result novelty is caused by experimental confirmation of the hypothesis validity about selection time dependence of tuples on database normalization degree at the recursive selection procedure and formulation of "normalization paradox" model for databases on the ORACLE platform

THE SOLANUM TUBEROSUM KNOWLEDGE BASE: THE SECTION ON MOLECULAR-GENETIC REGULATION OF METABOLIC PATHWAYS

Rapid development of high-performance genomic, transcriptomic, proteomic and metabolic technologies led to an information explosion in the field of plant biology and agrobiology. To date, the number of scientific publications on only one of the most important agricultural crops of Solanum tuberosum L. (potato) has exceeded 1.5 million. Effective access to knowledge distributed over such a multitude of non-formalized natural language textual sources requires the use of special computer-assisted intelligent methods of data mining (text-mining). However, in the literature, there is no data on the application of intellectual methods of automatic knowledge extraction from publications on agricultural crops, such as potato. Previously we have developed a pilot version of the SOLANUM TUBEROSUM knowledge base. SOLANUM TUBEROSUM is a computer platform for complex intellectual processing of large data bodies, including (1) automatic analysis of scientific publications and databases for extraction of information on genetics, markers, breeding, diagnostics, protection and storage technologies for potato, (2) formalized representation of extracted information in the knowledge base, (3) user access to these data, (4) analysis and visualization of query results. The ontology of the SOLANUM TUBEROSUM knowledge base contains dictionaries of molecular genetic objects (proteins, genes, metabolites, microRNAs, biomarkers); phenotypic characteristics of potato varieties; potato diseases and pests; biotic/abiotic environmental factors; potato agrobiotechnologies. This article describes the current version of the SOLANUM TUBEROSUM knowledge base developed from an extensive analysis of scientific publications on the moleculargenetic regulation of metabolic pathways in potatoes, as well as model plant organisms (maize, rice, Arabidopsis thaliana). In total, about 9,000 full-text articles and more than 130,000 abstracts of PubMed were analyzed. With the help of automatic analysis of scientific publications, more than 59,000 facts on molecular genetic interactions and genetic regulation were identified, and the analysis of factual databases revealed more than 380,000 such interactions in the examined organisms. It turned out that about 3 % of extracted facts about molecular genetic interactions and genetic regulation were related to Solanum tuberosum L. Thus, the inclusion of information on well-studied model species during the extraction of information on the molecular-genetic regulation of metabolic processes is important. It allows prediction of orthologous genes in potato and their further identification and analysis based on homology. An associative network of genetic regulation of starch biosynthesis in potatoes, including 33 metabolites, 36 proteins, 6 metabolic pathways and 132 interactions between them, 86 of which describe catalytic reactions, and the rest – regulatory events, was reconstructed. The reconstructed network is the basis for the search for target genes for directed mutagenesis and marker-oriented selection of potato varieties with specified starch properties. The trial version of the SOLANUM TUBEROSUM knowledge base is available at http://www-bionet.sysbio.cytogen.ru/and/ plant/.

Interactome of the hepatitis C virus: Literature mining with ANDSystem

A study of the molecular genetics mechanisms of host–pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV–host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 ‘new' proteins were found not previously referred to in any external databases of protein–protein interactions for HCV–host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV–host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein–protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein–protein interactions and microRNA-regulation did not depend on how well the proteins were studied, while protein–disease interactions appeared to be dependent on the level of study. In particular, the mean number of diseases linked to well-studied proteins (proteins were considered well-studied if they were mentioned in 50 or more PubMed publications) from the HCV interactome was 20.8, significantly exceeding the mean number of associations with diseases (10.1) for the total set of well-studied human proteins present in ANDSystem. For proteins not highly poorly-studied investigated, proteins from the HCV interactome (each protein was referred to in less than 50 publications) distribution of the number of diseases associated with them had no statistically significant differences from the distribution of the number of diseases associated with poorly-studied proteins based on the total set of human proteins stored in ANDSystem. With this, the average number of associations with diseases for the HCV interactome and the total set of human proteins were 0.3 and 0.2, respectively. Thus, ANDSystem, extended with the HCV interactome, can be helpful in a wide range of issues related to analyzing HCV–host interactions in the search for anti-HCV drug targets. The demo version of the extended ANDSystem covered here containing only interactions between human proteins, genes, metabolites, diseases, miRNAs and molecular–genetic pathways, as well as interactions between human proteins/genes and HCV proteins, is freely available at the following web address: http://www-bionet.sscc.ru/psd/andhcv/.

The need for a multidisciplinary team approach to life science workflows*†

Information retrieval for life science research (a broad rubric encompassing many traditional disciplines such as biochemistry, botany, cell biology, and molecular biology [1]) often involves the use of combinations of multiple information resources. Such combinations have been called “workflows” [2, 3] and may include factual databases such as Genbank [4], literature databases such as Entrez-PubMed [5], and analysis tools such as the Basic Local Alignment Search Tool (BLAST) [6]. Information resources can be combined in different ways toward the same goal; varying combinations may produce different results for the same research question. Combinations that produce different results may appear equivalent to a scientifically sophisticated user who lacks knowledge of metadata about the resources that may indicate the possibility of varying results. In addition, a user who pursues only a single combination of resources may not even realize that another combination might produce different results. This study's objective was to compare the results of three intuitively plausible and seemingly similar workflows for retrieving gene function information, with the goal of illustrating the importance of library science in bioinformatics and the need for a multidisciplinary team approach to authoring, vetting, and using life science workflows.

Material Database Syndication with RSS

Every material database on the Internet has a different data schema. There are some trial attempts to define unified schema for material databases, but since the structure of scientific data is very complicated and changes dynamically, defining a complete data schema is an impossible task. There are two major approaches for material data standards: one is MatDB, an attempt to define precise and detailed metadata, and the other is MatML, which only defines a framework. However, there is a third way: loose syndication, such as blogs with RSS. RSS, RDF Site Summary, or Really Simple Syndication, was developed to summarize document pages, but it can be extended to describe metadata of factual databases. In this presentation, an RSS extension for material database summaries is discussed.

The National Library of Medicine and Drug Information. Part 2: An Evolving Future

The National Library of Medicine (NLM) began in 1836 as a small collection of books in the office of the Army Surgeon General. Today, the NLM is the world’s largest medical library, providing access to its vast collection of seven million items onsite and through the World Wide Web. Historical interest in drug information dates to 1967, when Congress provided funds for a Drug Literature Program at the NLM. Drug information is now dispersed among a number of NLM bibliographic and factual databases that offer an array of clinical, research, and toxicological drug data. Target audiences for drug information include consumers, patients, healthcare practitioners, clinical researchers, and scientists. Drug development and medical publishing have both accelerated to such an extent that it is virtually impossible for healthcare practitioners and researchers to keep apprised of current information. Due to wide utilization for posting medically-related data, the Internet is discussed in terms of its impact on medical library responsibilities, drug information and efforts to evaluate Web-based health information, and how resultant imperatives indicate a need to create new drug-related databases including an Internet portal to drug information.

The National Library of Medicine and Drug Information. Part 1: Present Resources

The National Library of Medicine began in 1836 as a small collection of books in the office of the Army Surgeon General. Today, the National Library of Medicine is the world's largest medical library, providing access to its vast collection of seven million items onsite and through the World Wide Web. Historical interest in drug information dates to 1967, when Congress provided funds for a Drug Literature Program at the National Library of Medicine. Drug information is now dispersed among a number of National Library of Medicine bibliographic and factual databases that offer an array of clinical, research, and toxicological drug data. Target audiences for drug information include consumers, patients, healthcare practitioners, clinical researchers, and scientists. Drug development and medical publishing have both accelerated to such an extent that it is virtually impossible for healthcare practitioners and researchers to keep apprised of current information. Due to wide utilization for posting medically-re...

Copyright as a Rule of Evidence

This Article endeavors to offer a unified explanation for a wide variety of copyright doctrines, including the fixation requirement, the merger doctrine and the requirement that eligible works demonstrate at least a modicum of creativity. That explanation: these doctrines mitigate what would otherwise be difficult problems of proof. More specifically, each of these doctrines serves to deny protection in cases particularly prone to evidentiary complexity. The implicit logic is that, in these cases, the social cost of further litigation would likely outweigh the social benefit derived from offering copyright protection in the first place. Understanding these doctrines in this light offers a number of insights into their appropriate scope and application. For instance, the evidentiary theory resolves a long-standing debate over whether factual databases should be eligible for copyright protection (they should), and it also makes clear significant weaknesses in the current legal treatment of both derivative and jointly authored works.

Comparison of 35 electronic databases for environmental risk assessment.

The objective of this work is to classify and evaluate the major factual electronic databases that could be efficiently questioned for environmental risk assessment of various chemicals. A series of 35 databases available on commercial CD-ROMs and/or freely accessible on the Internet were listed and compared for the presence or absence of information for 27 environmental criteria. A factorial correspondence analysis indicated that most of the 35 databases are specialized in physicochemical, toxicological or ecotoxicological data but a few of them are nonspecialized databases able to answer simultaneously in various areas. We then evaluated these 35 databases by querying them for 14 selected test chemicals. It appeared that the percentage of chemicals being listed in the databases was very unequal and none of the 35 databases obtained 14 positive responses. The quality of the responses was determined by calculating the number of criteria being documented for the previously listed chemicals in each database. It suggested that HSDB, DOSE, TOMES, IPCS are the most efficient databases to be used for an urgent search of environmental data.

Searching fee and non-fee toxicology information resources: an overview of selected databases

Toxicology profiles organize information by broad subjects, the first of which affirms identity of the agent studied. Studies here show two non-fee databases (ChemFinder and ChemIDplus) verify the identity of compounds with high efficiency (63% and 73% respectively) with the fee-based Chemical Abstracts Registry file serving well to fill data gaps (100%). Continued searching proceeds using knowledge of structure, scope and content to select databases. Valuable sources for information are factual databases that collect data and facts in special subject areas organized in formats available for analysis or use. Some sources representative of factual files are RTECS, CCRIS, HSDB, GENE-TOX and IRIS. Numerous factual databases offer a wealth of reliable information; however, exhaustive searches probe information published in journal articles and/or technical reports with records residing in bibliographic databases such as BIOSIS, EMBASE, MEDLINE, TOXLINE and Web of Science. Listed with descriptions are numerous factual and bibliographic databases supplied by 11 producers. Given the multitude of options and resources, it is often necessary to seek service desk assistance. Questions were posed by telephone and e-mail to service desks at DIALOG, ISI, MEDLARS, Micromedex and STN International. Results of the survey are reported.

Construction and Application of Materials Database for Non-Equilibrium and Metastable Phases

The Institute for Materials Research, Tohoku University (IMR) is a collaborative research institute and open to scientists all over the world. Research subjects of IMR covers most advanced materials of non-equilibrium and/or metastable phases. In order to contribute an original materials database on these research subjects, a comprehensive project was started in 1987. As a result of 11 years of continuous effort, an integrated database system consisting of both literature and numerical factual databases has been constructed and become one of the largest systems in Japanese universities. This paper introduces the details of the management systems, utilization interfaces and contents of the database system, as well as the future IMR database projects.

A PC program to standardize the description of measurement results of thermophysical properties of solids

One of the most serious problems of factual databases is the data input, especially when the relation between the properties of interest and the material or experimental parameters is complex. In order to enable data input in the field of thermophysical properties, a new special PC program has been developed, which facilitates the data input by means of a windows technique. In these windows, the user is presented with input fields where alphanumerical values or integers can be inserted corresponding to a given list of descriptors. In principle, this list can be extended by each user. The problem, however, is then to keep all other users informed about the updated list of descriptors. It is intended to establish a community of users of this programme for the purposes of standardization of data input and acceleration of information exchange about measurement results.

Trends in Advanced Materials Data: Regularities and Predictions

Recently, there have been a number of reports identifying technologies of strategic importance. These technologies, which reflect the full range of national critical technology needs, are: materials, manufacturing, informatics and computing, biotechnology/life sciences, aeronautics/surface transport and energy/environment. In support of these technologies there has been much discussion on their research infrastructure, e.g., instrumentation, telecommunication networks, and supercomputing facilities. With the exception of biotechnology/life sciences, however, there has been little discussion on the uses of evaluated numeric and factual databases at the research level. The uses of databases are more advanced in biotechnology and life science research than in other fields, and this has been driven by the needs of genetic research, protein engineering, and drug design, where researchers need data and models for the design of new products. The needs of databases and their manipulation tools in materials science research are also essential in developing an intelligent research infrastructure. Given the present financial constraints, there is a need to use existing funds more efficiently and effectively. One way to achieve this is to use all available experimental data from various intersecting disciplines and bind them together with knowledge which will aid in the design of new materials.

A stereochemically accurate chemical substance database based on the systematic names of organic compounds. 1. Low molecular weight organic compounds

A chemical substance database, containing chemical structures generated automatically from their IUPAC systematic names, is described. The structure generation program can convert the names of natural products, peptides, and stereochemically complex names into stereochemically correct connection tables. More than 300,000 commonly encountered compounds are stored in the database and are publicly accessible through the JOIS-F online system, which also offers mass spectral, thermochemical, and other factual databases.

Recent trends in legal bibliographical documentation

We discuss the development of factual and bibliographical databases and database systems, including management systems and information retrieval systems. Special reference is made to the International Bibliography on Computers and Law, with respect to both the current situation and future plans.

Biomolecular data: a resource in transition

Part 1 The emergence of biomolecular data management: data proliferation - a challenge for science and for CODATA, A.E.Busard how much sequence data the databanks will be processing in the near future, C.Burks CODATA helps the development of sequence databases, B.Keil the structure of nucleotide sequence databases, G.N.Cameron hte National Library of Medicine, D.A.B.Lindberg a method for the rapid and accurate deposition of nucleic acid data in an acceptably annotated form, R.T.Walker. Part 2 Managing biomolecular data: compilation of tRNA sequences and sequences of tRNA genes, M.Sprinzl problems in maintaining a protein sequence database, Y.Seto et al collection and standardization of crystal structure data by the protein data bank, T.F.Koetzle et al quality control for a rapidly changing database, W.C.Barker et al the database crisis - problems and solutions, efforts of an emerging Japanese database, A.Tsugita the human gene mapping library, R.L.Miller factual databases in basic research, R.J.Roberts the Berlin RNA database - problems and solutions, J.Wolters and V.Erdmann. Part 3 Using biochemical data: the problem with GENBANK, E.A.Kabat some perspective of a database user, R.M.Stephens why industrial scientists are interested in the future development of sequence databases, J.L.Modelevsky availability of nucleic acid sequences data in Poland, J.Augustyniack international protein and peptide database, B.Wittman-Liebold IRIS - integrated RNA information for systematics, H.Hori and Y.Saton expert system simulations as active learning environments, D.L.Brutlag integrated access to sequence and structural data - principles of design of comprehensive databases for molecular biology, A.Lesk searching for codes in the sequences, E.N.Trifonov semantic and syntactic patterns in the genetic language, T.F.Smith databases - what's there and what's needed, M.Kanehisa. Part 4 Future trends in the management of biomolecular data: toward global data interfacing, D.R.Masys linking sequence databases to the current scientific literature, D.A.Benson global interfacing of people, places, data and knowledge - calm seas and prosperous voyage?, M.I.Krichevsky global data exchange on compact disk read-only memory, F.R.Blattner BIONET - an NIH computer resource for molecular biology, D.L.Brutlag and D.Kristofferson the database as a communication medium, J.W.Fickett some ideas towards an electronic information centre for biotechnology, A.Fletcher computer education in biochemistry, chemistry and molecular biology, V.Erdmann et al sources of data in the GENBANK database, C.Burks to publish or not to publish DNA sequences, R.D.Wells to publish or not to publish, P.Kahn and L.Philipson.

Factual databases for materials design and manufacturing.

The present status of scientific and technological factual databases is reviewed. The number of source information which should be entered into a materials database is very large, therefore the databases must be optimally structured in records and files. As an example, the structure of JICST TH (the Japan Information Center of Science and Technology Thermophysical and Thermochemical Property Database) is presented. Discussion is made on characteristics of data items, validation of materials databases, the present status and future aspect of delivery and database systems.

Computerized representation of data and knowledge on high-temperature corrosion and corrosion control

Databases and knowledge bases are tools for the transfer of information from the source to the user of the information, and they are becoming increasingly computerized because both their source and user environments are being computerized. Thus, in the field of corrosion, the challenge is to represent the results of quantitative measurement, metallurgical evaluation and field experience in computer-logical form. The task is not only to computerize, i.e. to make machine-readable a spectrum of information comprising factual data and knowledge ranging from precise mathematical to heuristic categories, but also to generate data documentation for different types of users and applications, i.e. to permit the prediction, analysis, diagnostics and control of corrosion. Contrary to the situation for systems involving mechanical properties, corrosion and corrosion control cannot be structured in factual databases or databanks alone but require an approach combining databanks, knowledge bases and expert systems. The required scope and logics of corrosion metadata to be documented is reviewed in this paper in relation to the organization of corrosion databanks and knowledge bases. Testing and data reporting standards are rather scarce, but some international activities supporting their development are under way. The importance of an international standard terminology is emphasized as an enabling function for database networks.