Map Files Research Articles

Digital preservation of knowledge in the public sector: a pre-ingest tool

This paper describes the need for coordinating pre-ingest activities in digital preservation of archival records. As a result of the wide use of electronic records management systems (ERMS) in agencies, the focus is on several issues relating to the interaction of the agency’s ERMS and public repositories. This paper indicates the importance of using digital recordkeeping metadata to meet more precisely and at the same time semi-automatically the criteria set by memory institutions. The paper provides an overview of one prospective solution and describes the Estonian National Archives’ universal archiving module (UAM). A case study reports the use of the UAM in preserving the digital records of the Estonian Minister for Population and Ethnic Affairs. In this project, the preparation and transfer of archival records was divided into ten phases, starting from the description of the archival creator and ending with controlled transfer. The case study raises questions about how much recordkeeping metadata can be used in archival description and how the interaction of the agency’s ERMS and ingest by the archives could be more automated. The main issues (e.g. classification, metadata elements variations, mapping, and computer files conversions) encountered during that project are discussed. Findings show that the Open Archival Information System functional model’s ingest part should be reconceptualised to take into account preparatory work. Adding detailed metadata about the structure, context and relationships in the right place at the right time could get one step closer to digital codified knowledge archiving by creating synergies with various other digital repositories.

Compression Algorithm for all Specified bases in Nucleic Acid Sequences

rganizations such as IT industry, colleges and Scientists regularly encounter problems to handle large data sets for their different purpose in many areas as for example biological research. These limitations also affect internet search to fetch data, business for analysis etc. So it is simply needed generalized but special types of compression algorithm for dissimilar data to get utmost saving percentage. In this article Compression of biological data that is single and double strand DNA and single strand RNA have been considered. Since biological data are less random compare to any text data that means redundancy within the sequences are more but they have some special property as for example different types of repeat one of such repeat is called dinucleotide repeat .This type of repeat are more in any sequence. Here the two proposed algorithm are based on this repeat using static fixed length LUT for input file and output file mapping.

The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study, and mitigating tools

ObjectiveApplying the science of networks to quantify the discriminatory impact of the ICD-9-CM to ICD-10-CM transition between clinical specialties.Materials and MethodsDatasets were the Center for Medicaid and Medicare Services ICD-9-CM to ICD-10-CM mapping files, general equivalence mappings, and statewide Medicaid emergency department billing. Diagnoses were represented as nodes and their mappings as directional relationships. The complex network was synthesized as an aggregate of simpler motifs and tabulation per clinical specialty.ResultsWe identified five mapping motif categories: identity, class-to-subclass, subclass-to-class, convoluted, and no mapping. Convoluted mappings indicate that multiple ICD-9-CM and ICD-10-CM codes share complex, entangled, and non-reciprocal mappings. The proportions of convoluted diagnoses mappings (36% overall) range from 5% (hematology) to 60% (obstetrics and injuries). In a case study of 24 008 patient visits in 217 emergency departments, 27% of the costs are associated with convoluted diagnoses, with ‘abdominal pain’ and ‘gastroenteritis’ accounting for approximately 3.5%.DiscussionPrevious qualitative studies report that administrators and clinicians are likely to be challenged in understanding and managing their practice because of the ICD-10-CM transition. We substantiate the complexity of this transition with a thorough quantitative summary per clinical specialty, a case study, and the tools to apply this methodology easily to any clinical practice in the form of a web portal and analytic tables.ConclusionsPost-transition, successful management of frequent diseases with convoluted mapping network patterns is critical. The http://lussierlab.org/transition-to-ICD10CM web portal provides insight in linking onerous diseases to the ICD-10 transition.

스토리지 클래스 메모리에서의 파일 접근 설계

Storage Class Memory(SCM), such as PRAM, FRAM and MRAM, are expected to be comparable to DRAM in terms of access speed and to Flash memory in terms of capacity in a near future. In this paper, assuming that not only the secondary storage (HDD or Flash memory) but also the primary memory (DRAM) will be replaced by SCM in the future computer systems, we propose an efficient file access framework for the SCM based computer systems. The proposed framework do not assign exclusive area in the SCM to the file system and uses various memory-related techniques, such as unified data access path, zero-copy data read using file mapping, copy-on-write, and multiple page pre-faulting for file management. Based on the preliminary experimental results, we could conclude that the proposed framework can be an efficient baseline for designing a new operating system for the SCM based computer systems.

Extending MapMan Ontology to Tobacco for Visualization of Gene Expression

Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30,000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom made NimbleGen oligoarray, that contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated data set will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

LabVIEW 2010 Computer Vision Platform Based Virtual Instrument and Its Application for Pitting Corrosion Study

A virtual instrumentation (VI) system called VI localized corrosion image analyzer (LCIA) based on LabVIEW 2010 was developed allowing rapid automatic and subjective error-free determination of the pits number on large sized corroded specimens. The VI LCIA controls synchronously the digital microscope image taking and its analysis, finally resulting in a map file containing the coordinates of the detected probable pits containing zones on the investigated specimen. The pits area, traverse length, and density are also determined by the VI using binary large objects (blobs) analysis. The resulting map file can be used further by a scanning vibrating electrode technique (SVET) system for rapid (one pass) “true/false” SVET check of the probable zones only passing through the pit's centers avoiding thus the entire specimen scan. A complete SVET scan over the already proved “true” zones could determine the corrosion rate in any of the zones.

RDB2RDF: A relational to RDF plug‐in for Eclipse

SUMMARYThe process of transforming data stored in relational databases (RDBs) into sets of Resource Description Framework (RDF) triples is known as triplification or RDB2RDF. It consists of two consecutive operations, schema extraction and data conversion. Schema extraction is a process similar to creating an external schema, and contains a collection of database views. The data conversion is divided into two steps. The first step consists of deciding how to represent database schema concepts in terms of RDF classes and properties, defining an RDB2RDF mapping. The second step consists of the actual conversion of relational data to RDF data instances, based on the mapping previously defined. Although the schema extraction is very well understood, the data conversion operation is still murky. Indeed, the World Wide Web Consortium RDB2RDF Working Group has been working to define a standard language, called R2RML, to describe RDB2RDF mapping files. The definition of the R2RML, however, is still undergoing changes. In this paper, we introduce an Eclipse plug‐in that supports the entire conversion process. Its architecture takes into consideration the specificities of the triplification process by providing a modular structure that encapsulates the stable and well‐understood components separately from the volatile, change‐prone mapping strategies. The latter are accessible via a well‐defined interface to promote information hiding and separation of concerns and to facilitate evolution. Copyright © 2012 John Wiley & Sons, Ltd.

THE IRANIAN NATIONAL GEODATA REVISION STRATEGY AND REALIZATION BASED ON GEODATABASE

Abstract. In recent years, using of spatial database for storing and managing spatial data has become a hot topic in the field of GIS. Accordingly National Cartographic Center of Iran (NCC) produces – from time to time – some spatial data which is usually included in some databases. One of the NCC major projects was designing National Topographic Database (NTDB). NCC decided to create National Topographic Database of the entire country-based on 1:25000 coverage maps. The standard of NTDB was published in 1994 and its database was created at the same time. In NTDB geometric data was stored in MicroStation design format (DGN) which each feature has a link to its attribute data (stored in Microsoft Access file). Also NTDB file was produced in a sheet-wise mode and then stored in a file-based style. Besides map compilation, revision of existing maps has already been started. Key problems of NCC are revision strategy, NTDB file-based style storage and operator challenges (NCC operators are almost preferred to edit and revise geometry data in CAD environments). A GeoDatabase solution for national Geodata, based on NTDB map files and operators' revision preferences, is introduced and released herein. The proposed solution extends the traditional methods to have a seamless spatial database which it can be revised in CAD and GIS environment, simultaneously. The proposed system is the common data framework to create a central data repository for spatial data storage and management.

ARVO-CL: The OpenCL version of the ARVO package — An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Introduction of Graphical Processing Units (GPUs) and computing using GPUs in recent years opened possibilities for simple parallelization of programs. In this update, we present the modernized version of program ARVO [J. Busa, J. Dzurina, E. Hayryan, S. Hayryan, C.-K. Hu, J. Plavka, I. Pokorný, J. Skivanek, M.-C. Wu, Comput. Phys. Comm. 165 (2005) 59]. The whole package has been rewritten in the C language andparallelized usingOpenCL. Somenew tricks have been added to the algorithm in order to savememory much needed for efficient usage of graphical cards. A new tool called ‘input_structure’ was added for conversion of pdb files into files suitable for work with the C and OpenCL version of ARVO. New version program summary Program title: ARVO-CL Catalog identifier: ADUL_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUL_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 11834 No. of bytes in distributed program, including test data, etc.: 182528 Distribution format: tar.gz Programming language: C, OpenCL. Computer: PC Pentium; SPP’2000. Operating system: All OpenCL capable systems. Has the code been vectorized or parallelized?: Parallelized using GPUs. A serial version (non GPU) is also included in the package.

The mouse-human anatomy ontology mapping project

The overall objective of the Mouse–Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered.Database URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit

Test of a building vulnerability model for L’Aquila earthquake

During 2002, as part of a collaboration between the National Civil Protection Department and the University of L'Aquila, a methodology for assessing the vulnerability of an urban center was developed. The methodology considered the urban territory as well as the complex of physical and functional relationships of the urbanized territory and not a simple summation of elements, in order to analyze simultaneously the multiple factors necessary to determine the vulnerability of the whole center. This methodology was applied to the city of L'Aquila and two other smaller towns, and in previous studies, some maps representing the possible vulnerability of buildings were prepared for the centre of the city of l’Aquila. These maps graduate the possible vulnerability in four different classes and have a maximum resolution of 25 m. After the earthquake in April 2009, it is possible to assess the accuracy of the model comparing predicted vulnerability with the map of fitness for human habitation realized after the earthquake. The vulnerability map considered the buildings situated on the emergency routes, therefore, the comparison was carried out only for these areas. After the seismic event, the map of fitness for human habitation and the actual post-earthquake damage were available: these results were archived in an Access database and also mapped on a 1:2,000 city map. To assure the consistency of these data, Access databases were geocoded and so cross checked with the results reported in the map files. The maps so obtained and verified were compared with the maps of the predicted vulnerability, rasterizing the information reported on the two maps at the same resolution. Thus, it has obtained a raster file containing differences between the vulnerability predicted and observed damages, evidencing that the biggest differences are limited to some small areas. Observing the localization of these areas, it seems that there may exist a correlation between biggest mismatch and some geophysical characteristics of the terrain that can cause local attenuation or amplification of the seismic waves. However, further investigations have to be carried on to confirm these initial results. The main elaborations were performed in open-source packages: GRASS, Q-GIS, and gvSIG.

Design of Intelligent Electrode Design System

Lots of information including vary raw materials components and mechanical properties should be involved in the electrode design process. It was very difficult to manage them. In this article, an effective solution by simulating the artificial design process of electrode was presented in the design of intelligent electrode design system (IEDS). That successfully realized series functions such as electrode formula management, electrode intelligent design. Shared file, named pipe, and file mapping were proposed to solve the communication problem between design module and prediction module which were developed by using different languages and platforms.

AtIPD: A Curated Database of Arabidopsis Isoprenoid Pathway Models and Genes for Isoprenoid Network Analysis

Isoprenoid biosynthesis is one of the essential metabolic pathways in plants and other organisms. Despite the importance of isoprenoids for plant functions, not much is known about the regulation of isoprenoid synthesis. Quantitative technologies and systems approaches are now increasingly used to investigate the regulation of metabolic pathways and networks. Prerequisite for systems approaches is the knowledge of network elements and topologies. Information that can be extracted from the public metabolic pathway databases such as AraCyc and KEGG is often not sufficiently comprehensive and current. Therefore we have built a database of manually curated isoprenoid pathway models and genes, the Arabidopsis thaliana Isoprenoid Pathway Database (AtIPD; http://www.atipd.ethz.ch). The database was compiled using information on pathways and pathway genes from BioPathAt (Lange and Ghassemian, 2003, 2005), KEGG (http://www.genome.jp/kegg), AraCyc (http://www.arabidopsis.org/biocyc), SUBA (http://suba.plantenergy.uwa.edu.au), and from the literature. AtIPD can be searched or browsed to extract data and external links related to isoprenoid pathway models, enzyme activities or subcellular enzyme localizations. To display quantitative gene-related data on curated pathway models, we created image annotation and mapping files for integrated use with the MapMan tool (http://mapman.gabipd.org/web/guest/mapman). Additionally, we built SBML XML files of the isoprenoid pathway images using the Cell DesignerTM tool (http://www.celldesigner.org). Users can download all image and annotation files for customization, e.g., adding pathway structural and regulatory network elements or modifying pathway images to visualize other quantitative protein or metabolite data. AtIPD therefore represents a valuable resource for isoprenoid network analysis.

A Software to Convert ESRI Shapefile to Flash SWF Format and its Extended Application

A shapefile to SWF conversion software was mainly introduced. By converting the traditional GIS files such as ESRI Shapefile to the Shock Wave Flash (SWF) file format, the GIS data was highly compressed and suitable for the Internet publication. The generation of SWF files provided a complement for the current WebGIS technology and by using the converted SWF map files, an extended example of flash-based application in multi-level analysis to the socio-economic data was constructed. The example demenstrated its easy configuration and powerful potential ablities. More powerful applications based on SWF will be continued in the future work.

The influence of pickup protons, from interstellar neutral hydrogen, on the propagation of interplanetary shocks from the Halloween 2003 solar events to ACE and Ulysses: A 3-D MHD modeling study

We describe our 3-D, time ]dependent, MHD solar wind model that we recently modified to include the physics of pickup protons from interstellar neutral hydrogen. The model has a time-dependent lower boundary condition, at 0.1 AU, that is driven by source surface map files through an empirical interface module. We describe the empirical interface and its parameter tuning to maximize model agreement with background (quiet) solar wind observations at ACE. We then give results of a simulation study of the famous Halloween 2003 series of solar events. We began with shock inputs from the Fearless Forecast real ]time shock arrival prediction study, and then we iteratively adjusted input shock speeds to obtain agreement between observed and simulated shock arrival times at ACE. We then extended the model grid to 5.5 AU and compared those simulation results with Ulysses observations at 5.2 AU. Next we undertook the more difficult tuning of shock speeds and locations to get matching shock arrival times at both ACE and Ulysses. Then we ran this last case again with neutral hydrogen density set to zero, to identify the effect of pickup ions. We show that the speed of interplanetary shocks propagating from the Sun to Ulysses is reduced by the effects of pickup protons. We plan to make further improvements to the model as we continue our benchmarking process to 10 AU, comparing our results with Cassini observations, and eventually on to 100 AU, comparing our results with Voyager 1 and 2 observations.

Integrating whole transcriptome sequence data and public databases for analysis of somatic mutations in tumors

The annotation of pathologically relevant somatic variations has gained importance with the wide use of next-generation sequencing in biomedical studies. At present, this evaluation is performed using public tools such as SAMtools and ANNOVAR by comparing predicted mutations and small nucleotide variations (SNVs) with databases such as 1000 Genomes and dbSNP, as well as with paired normal data if available. However, these analytical methods lack the ability to integrate information from the different analyses into a single output. Additionally, many approaches are filter based and remove data that does not match specific criteria, thus leading to the removal of variations that would otherwise be reconsidered later. To this end, we have developed a Perl wrapper script that utilizes standard next-generation sequencing output files along with SAMtools and ANNOVAR to produce an annotated tumor variant file with sequence calls from related tumor and matched normal samples. We performed SOLiD paired-end sequencing of the whole transcriptome of one lung adenocarcinoma and seven normal lung samples (including one matched normal). BioScope 1.3 was used to map the reads, and the SNVs were identified by the diBayes package. The map files in binary-sequence alignment format (BAM) and SNV files in generic feature format (GFF) were used to annotate the tumor SNVs with matched normal sequence information at each position (diBayes and SAMtools), as well as other normal samples (both position and gene based). Furthermore, SNVs were annotated with positional information, including whether intronic, exonic, or synonymous versus nonsynonymous, as well as with data from the 1000 Genomes Project (allele frequency), the dbSNP database (rs identifiers) and the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Of the 1,804 SNVs initially identified in the tumor sample, 138 SNVs were found in non-coding RNA, and 75 did not appear in the normal samples according to diBayes or in the specific matched normal sample according to SAMtools. Because the capacity to sequence the whole transcriptome is subject to the expression level, the possibility of failure to detect variations in normal lung samples cannot be ignored. To address this concern, we analyzed 1000 Genomes data and found that only 23 of the 75 potential tumor-specific SNVs exhibited allele frequencies <1%, and 6 of these exist in dbSNP. All of these steps can be rapidly performed by a researcher, and modifying the approach to identify other types of SNVs is easily achievable. The use of a single script that tracks input file names and locations is expected to improve data handling and reporting. Notably, all variant data are present in a single file, allowing straightforward modification of criteria and instant hypothesis testing and therefore reducing the need for an informed end user to re-engage a bioinformatician to address another biological question.

Design and Implementation of ZIP Compressed File Mapping Relational Storage Structure

Design and Implementation of ZIP Compressed File Mapping Relational Storage Structure

A Focal Epilepsy and Intellectual Disability Syndrome Is Due to a Mutation in TBC1D24

We characterized an autosomal-recessive syndrome of focal epilepsy, dysarthria, and mild to moderate intellectual disability in a consanguineous Arab-Israeli family associated with subtle cortical thickening. We used multipoint linkage analysis to map the causative mutation to a 3.2 Mb interval within 16p13.3 with a LOD score of 3.86. The linked interval contained 160 genes, many of which were considered to be plausible candidates to harbor the disease-causing mutation. To interrogate the interval in an efficient and unbiased manner, we used targeted sequence enrichment and massively parallel sequencing. By prioritizing unique variants that affected protein translation, a pathogenic mutation was identified in TBC1D24 (p.F251L), a gene of unknown function. It is a member of a large gene family encoding TBC domain proteins with predicted function as Rab GTPase activators. We show that TBC1D24 is expressed early in mouse brain and that TBC1D24 protein is a potent modulator of primary axonal arborization and specification in neuronal cells, consistent with the phenotypic abnormality described.

An Efficient Lossless Compression Algorithm for Vector Maps

This paper suggested a new efficient lossless compression algorithm for vector maps in view of the graphical characteristics. First, we adopt the differential lossless transformation for the graphic data in the vector map files, to make the original data which should have been represented by double model or float model be represented by long model. Then, based on the abbreviated compression, the prediction coding based on the irregular coefficients is used. Namely, it is to dynamically distribute proper byte storage to the transformed coefficients which have been differentiated according to the numerical values, and compressed further combined with a dictionary coding method. Finally, we do an experimental contrast for the compression effect.