Related Metadata Research Articles

FVD: The fish-associated virus database

With the expanding of marine and freshwater aquaculture, the outbreaks of aquatic animal diseases have increasingly become the major threats to the healthy development of aquaculture industries. Notably, viral infections lead to massive fish deaths and result in great economic loss every year across the world. Hence, it is meaningful to clarify the biodiversity, geographical distribution and host specificity of fish-associated viruses. In this study, viral sequences detected in fish samples were manually collected from public resources, along with the related metadata, such as sampling time, location, specimen type and fish species. Moreover, the information regarding the host fish, including aliases, diet type and geographic distribution were also integrated into a database (FVD). To date, FVD covers the information of 4860 fish-associated viruses belonging to 15 viral families, which were detected from 306 fish species in 57 countries. Meanwhile, sequence alignment, live data statistics and download function are available. Through the user-friendly interface, FVD provides a practical platform that would not only benefit virologists who want to disclose the spread of fish-associated viruses, but also zoologists who focus on the health of domestic and wild animals. Furthermore, it may facilitate the surveillance and prevention of fish viral diseases.Database URL: http://bioinfo.ihb.ac.cn/fvd

Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics

IntroductionAvailability of large cohorts of samples with related metadata provides scientists with extensive material for studies. At the same time, recent development of modern high-throughput ‘omics’ technologies, including metabolomics, has resulted in the potential for analysis of large sample sizes. Representative subset selection becomes critical for selection of samples from bigger cohorts and their division into analytical batches. This especially holds true when relative quantification of compound levels is used.ObjectivesWe present a multivariate strategy for representative sample selection and integration of results from multi-batch experiments in metabolomics.MethodsMultivariate characterization was applied for design of experiment based sample selection and subsequent subdivision into four analytical batches which were analyzed on different days by metabolomics profiling using gas-chromatography time-of-flight mass spectrometry (GC–TOF–MS). For each batch OPLS-DA® was used and its p(corr) vectors were averaged to obtain combined metabolic profile. Jackknifed standard errors were used to calculate confidence intervals for each metabolite in the average p(corr) profile.ResultsA combined, representative metabolic profile describing differences between systemic lupus erythematosus (SLE) patients and controls was obtained and used for elucidation of metabolic pathways that could be disturbed in SLE.ConclusionDesign of experiment based representative sample selection ensured diversity and minimized bias that could be introduced at this step. Combined metabolic profile enabled unified analysis and interpretation.

The CENDARI infrastructure in GIS-based historical research

PurposeThe purpose of this paper is to propose a way of using already existing archival resources in the geographic information system (GIS).Design/methodology/approachThe essence of the methodology used was to identify semantic relations of archival documents with geographical space and develop their metadata into spatially related metadata, ready to use in GIS and to join geographical names occurring in these metadata with exact places to which they were related to. Research was based on two digital collections from the Library of Contemporary History in Stuttgart on-line service. These collections were related to the First World War and they included metadata prepared in MAB standard.FindingsAs the results of the research, two sample metadata sets related to posters and ration coupons were developed. Thesauruses of coordinates of places and regions mentioned in documents metadata in different semantic context were also created. To complete the methodology, the assumptions of the GIS structure and concept of applying metadata in them, have been proposed.Research limitations/implicationsThe research also presents limitations in effective implementation of the proposed solutions, which lie mainly in lack of rules and consequences in recording geographical names in metadata.Originality/valueThe value of the proposed solution is easy way of using already existing data in GIS and possibilities of gathering, managing, presenting and analyzing archives with one parameter more than in traditional databases – with spatial information. The added value and an effective use of already collected data lies in the strong recommendation of defining and implementation of rules for recording geographical names in archival documents metadata. This will help in a wide use of collected data in any spatial-based solutions as well as in automation of process of joining archives with geographical space, and finally in dissemination of collected resources.

UHCSDB: UltraHigh Carbon Steel Micrograph DataBase

We present a new microstructure dataset consisting of ultrahigh carbon steel (UHCS) micrographs taken over a range of length scales under systematically varied heat treatments. Using the UHCS dataset as a case study, we develop a set of visualization tools for interacting with and exploring large microstructure and metadata datasets. Based on generic microstructure representations adapted from the field of computer vision, these tools enable image-based microstructure retrieval, as well as spatial maps of both microstructure and related metadata, such as processing conditions or properties measurements. We provide the microstructure image data, processing metadata, and source code for these microstructure exploration tools. The UHCS dataset is intended as a community resource for development and evaluation of microstructure data science techniques and for creation of microstructure data science teaching modules.

Pilot implementation of the US EPA interoperable watershed network

BackgroundThe mission of the United States Environmental Protection Agency (EPA) is to protect human health and the environment, including air, water and land. Understanding the extent of pollution in waters and identifying waters for protection has been based in part on water quality monitoring data collected and shared by parties (federal, state, tribal, and local) throughout the U.S. To date, this monitoring data has been largely represented by data collected as a water quality sample (data collected by a technician in the field or analyzed in a lab). EPA’s “STORage and RETrieval” (STORET) and the Water Quality Exchange (WQX) have served as the repository for all this sampling data. However, these tools and systems were not designed to handle today’s continuous water quality sensors. EPA has therefore embarked on the Interoperable Watersheds Network (IWN) project, which is focused on identifying a common set of formats and standards for data, and on testing and validating these standards as well as new ways of sharing data and metadata. The completed IWN will greatly expand the sharing of data and its use, thereby streamlining the assessment, restoration, and protection of surface water quality at all levels of government.MethodsStakeholder workgroups were engaged to assist with developing requirements for the three major project components: required attributes and query capability for a centralized metadata catalog, technological and data requirements for data providers, and desired functionality for a web-based discovery tool that provides access to the catalog services and provider data.ResultsThe pilot implementation of IWN uses the Open Geospatial Consortium (OGC) Sensor Observation Service (SOS) 2.0 and WaterML2 standards as the foundation for a distributed sensor data sharing network. Data owners in locations across the United States have worked with EPA to publish their continuous sensor data and related metadata either through “data appliances” running the open-source 52° North implementation of SOS or using commercial software like Kisters’ KiWIS product.Metadata are harvested into a centralized catalog that provides a REST Service API for sensor discovery. Users can discover data by querying for specific parameters, or using spatial boundaries such as HUC, county, a buffered point, or a user defined polygon. The sensor results are returned as GeoJSON, which can be used to create maps. The API also provides the service endpoints for the sensors, which can be used to access the continuous data to create charts or download the data for other analysis.ConclusionThe pilot IWN demonstrates that standards-based interoperability can provide a sound basis for a national-scale clearinghouse for continuous sensor data, though scalability of the approach will need further testing. Selected technical detail, lessons learned, and future plans for the IWN are included in the discussion.

The GRASS GIS temporal framework

ABSTRACTThe availability of continental and global-scale spatio-temporal geographical data sets and the requirement to efficiently process, analyse and manage them led to the development of the temporally enabled Geographic Resources Analysis Support System (GRASS GIS). We present the temporal framework that extends GRASS GIS with spatio-temporal capabilities. The framework provides comprehensive functionality to implement a full-featured temporal geographic information system (GIS) based on a combined field and object-based approach. A significantly improved snapshot approach is used to manage spatial fields of raster, three-dimensional raster and vector type in time. The resulting timestamped spatial fields are organised in spatio-temporal fields referred to as space-time data sets. Both types of fields are handled as objects in our framework. The spatio-temporal extent of the objects and related metadata is stored in relational databases, thus providing additional functionalities to perform SQL-based analysis. We present our combined field and object-based approach in detail and show the management, analysis and processing of spatio-temporal data sets with complex spatio-temporal topologies. A key feature is the hierarchical processing of spatio-temporal data ranging from topological analysis of spatio-temporal fields over boolean operations on spatio-temporal extents, to single pixel, voxel and vector feature access. The linear scalability of our approach is demonstrated by handling up to 1,000,000 raster layers in a single space-time data set. We provide several code examples to show the capabilities of the GRASS GIS Temporal Framework and present the spatio-temporal intersection of trajectory data which demonstrates the object-based ability of our framework.

ASTROLABE: A Rigorous, Geodetic-Oriented Data Model for Trajectory Determination Systems

The constant irruption of new sensors is a challenge for software systems that do not rely on generic data models able to manage change or innovation. Several data modeling standards exist. Some of these address the problem from a generic perspective but are far too complex for the kind of applications targeted by this work, while others focus strictly on specific kinds of sensors. These approaches pose a problem for the maintainability of software systems dealing with sensor data. This work presents ASTROLABE, a generic and extensible data model specifically devised for trajectory determination systems working with sensors whose error distributions may be fully modeled using means and covariance matrices. A data model relying on four fundamental entities (observation, state, instrument, mathematical model) and related metadata is described; two compliant specifications (for file storage and network communications) are presented; a portable C++ library implementing these specifications is also briefly introduced. STROLABE, integrated in CTTC’s trajectory determination system NAVEGA, has been extensively used since 2009 in research and production (real-life) projects, coping successfully with a significant variety of sensors. Such experience helped to improve the data model and validate its suitability for the target problem. The authors are considering putting ASTROLABE in the public domain.

Megathrust and accretionary wedge properties and behaviour in the Makran subduction zone

This work forms part of the NERC- and ESRC-funded project ‘Earthquakes without Frontiers’ and was partially supported by the NERC large grant ‘Looking inside the Continents from Space’. CP is funded by an NERC studentship. The facilities of IRIS Data Services, and specifically the IRIS Data Management Center, were used for access to waveforms, related metadata, and/or derived products used in this study. IRIS Data Services are funded through the Seismological Facilities for the Advancement of Geoscience and EarthScope (SAGE) Proposal of the National Science Foundation under Cooperative Agreement EAR-1261681.

Chile Strong Ground Motion Flatfile

The Nazca-South American plate boundary produces large-magnitude events (Mw> 8) every 20 years on the coast of Chile. This work describes a public ground motion database that contains 3,572 records from 477 earthquakes and 181 seismic stations, which includes the recent 2015 Mw8.3 Illapel earthquake. The data set is controlled by subduction interface and inslab events. The oldest event included is Valparaiso (1985), and the magnitude span is 4.6–8.8 Mw. The source-to-site distance metrics reported are the closest distance to the rupture plane ( Rrup), epicentral ( Repi) and hypocentral ( Rhyp) distances, with a range for Rrupfrom 20 to 650 km. Site characterization is based on VS30, ranging from 110 to 1,951 m/s. Intensity measures included are peak ground acceleration, spectral acceleration values from 0.01 to 10 s, Arias intensity, and peak ground velocity. Each record was uniformly processed component by component. A flatfile with the related metadata and the spectral accelerations from processed ground motions is available at NEEShub ( http://doi.org/10.17603/DS2N30J ; Bastías and Montalva 2015 ).

The Debsources Dataset: two decades of free and open source software

We present the Debsources Dataset: source code and related metadata spanning two decades of Free and Open Source Software (FOSS) history, seen through the lens of the Debian distribution. The dataset spans more than 3 billion lines of source code as well as metadata about them such as: size metrics (lines of code, disk usage), developer-defined symbols (ctags), file-level checksums (SHA1, SHA256, TLSH), file media types (MIME), release information (which version of which package containing which source code files has been released when), and license information (GPL, BSD, etc). The Debsources Dataset comes as a set of tarballs containing deduplicated unique source code files organized by their SHA1 checksums (the source code), plus a portable PostgreSQL database dump (the metadata). A case study is run to show how the Debsources Dataset can be used to easily and efficiently instrument very long-term analyses of the evolution of Debian from various angles (size, granularity, licensing, etc.), getting a grasp of major FOSS trends of the past two decades. The Debsources Dataset is Open Data, released under the terms of the CC BY-SA 4.0 license, and available for download from Zenodo with DOI reference 10.5281/zenodo.61089.

Cy-TEST - A new platform for training and testing in cytopathology

Introduction/ Background Clinical training at the European level requires flexible ways to provide education across borders with the goal of a unified way to teach and assess quality. The Cy-TEST project focuses on Cytological Training at European Standard through Telepathology. The project (2014-1-IT01-KA202-002607) has been approved and funded in 2014 by EU within the ERASMUS+ Program. The project consortium is composed of 4 leading university Institutions (COREP and University of Turin, University of Padua, Imperial College of London, IPATIMUP/University of Porto and University of Graz) with technological development and support provided by CRS4. In addition, it benefits from the collaboration of International Organizations (EFCS, Eurocytology, OME) and is open to contributions from additional groups and Societies. Aims Our aim was the establishment of a platform for the sharing of digital pathology images and of an auxiliary system that will use the latter platform for the distribution of cytologist training courses with an integrated virtual microscopy capability. Methods The Cy-TEST platform is based on the integration between Moodle, an e-learning platform designed to create personalized learning environments, and OME OMERO, a well-known open source software for visualization, management and analysis of biological microscope images. The former is used to provide access to a database of questions produced by specialized trainers and the latter provides access to digital pathology images and related metadata. We chose to base our infrastructure upon Moodle because it is one of the top leading platform for online education with a large community of users across both academic and enterprise level, highly customizable and modular. OMERO was chosen because of its compatibility with a large number of image formats for digital pathology images, its handling of image metadata (i.e., TAGs and Regions of Interest) and its easily extensible web platform. Results The web platform can be used with a wide range of devices, it is compatible with most of the image formats produced by digital slides scanners and it can scale to a wide student body. Teachers can create courses, populate the Question Bank and aggregate questions in quizzes, while students can take classes and tests. When creating questions, teachers can choose images previously loaded and annotated. We provide two new types of questions: multiple choice, focused on an image and its ROIs, and interactive, where students identify areas on the image by markers that will be automatically compared to instructor’s specified ROIs. The currently deployed system holds already a set of several hundreds of images classified by categories (e.g., tissue type and diseases) with associated ROIs identified by pathologists. The Cy-TEST platform provides a full technological solution for a more homogeneous training and testing of cytotechnicians and cytopathologists with uniform quality level assurance mechanism. The system could be easily extended to support the teaching of histopathological diagnosis. Moreover, the Cy-TEST platform paves the way to an e-QUATE test, thus providing an efficient and economical way to replicate the test at European scale (see Branca et al., 2000). The sustainability of the platform and the supported educational material (images, questions and evaluation algorithms) will be guaranteed by its integration in EFCS activities. We expect to distribute the Cy-TEST System for validation by October 2016, for further information contact infocytest@corep.it.

BSHAP project strong ground motion database and selection of suitable ground motion models for the Western Balkan Region

The Harmonization of Seismic Hazard Maps in the Western Balkan Countries Project (BSHAP) was funded for 7 years by NATO Science for Peace and Security Program to support the preparation of new seismic hazard maps of the Western Balkan Region. In the framework of BSHAP, the regional free field strong motion network capacity was significantly increased by deployed recorders (Gulerce et al. in Final report of improvements in the Harmonized Seismic Hazard Maps for the Western Balkan Countries (BSHAP-2) Project, NATO SfP-984374. http://wbalkanseismicmaps.org/ , 2015) and the BSHAP strong motion database that includes both pre-BSHAP (mostly analogue) and post-BSHAP (all digital) recordings was compiled. The BSHAP strong motion database includes uniformly processed strong motions along with the related earthquake metadata and station information; therefore, it provides a solid base for the ground motion characterization studies in the region. The established database is used for selection of the ground motion prediction equations (GMPEs) to be employed in the probabilistic seismic hazard assessment by comparing the compiled strong ground motions with the predictions of candidate global and Euro-Mediterranean GMPEs in a systematic manner. Details of the selection strategy including the analysis of model predictions for ground motion scaling, data testing to evaluate the model performance, and ranking is provided here along with the GMPE logic tree used in the proposed seismic hazard maps by Kuka et al. (Bull Earthq Eng, under review).

FemSMA Corpus Workbench. Ein Werkzeug zur Unterstützung der qualitativen und quantitativen Analyse von textuellen Daten

In various areas of (linguistic) research, there is a need to analyse larger amounts of textual data. Digitisation and the availability of computational linguistics tools offer substantial support in qualitatively and quantitatively analysing those data sets. Keeping, maintaining and presenting data and their metadata within one system facilitate data inspection and browsing. Quick assessment of data sets for the presence or absence of specific textual characteristics is supported by the possibility to manually annotate segments of text with theory-driven meta-information in combination with automatic analysis employing computational linguistics tools and computerized search. In the present contribution, the FemSMA Corpus Workbench CWB is introduced. CWB is a computational linguistics tool for manual and automatic annotation and analysis of text documents. CWB supports storage and maintenance of, and annotation and search in textual data and related metadata. CWB is a client-server application with a web interface as frontend for data inspection and manual annotation. Data storage and automatic processing is done at server side. Automatically annotated are word-level features such as parts of speech; general word features such as capitalisation, character reduplication, abbreviation; swear words and emotion words. Due to its modular system architecture, CWB can be flexibly extended, which, however, requires the involvement of computational linguists to adapt and extend CWB’s automatic analysis and search functionalities, and represent the new functionality in the web interface.

J-TEXT WebScope: An efficient data access and visualization system for long pulse fusion experiment

Fusion research is an international collaboration work. To enable researchers across the world to visualize and analyze the experiment data, a web based data access and visualization tool is quite important [1]. Now, a new WebScope based on RIA (Rich Internet Application) is designed and implemented to meet these requirements.On the browser side, a fluent and intuitive interface is provided for researchers at J-TEXT laboratory and collaborators from all over the world to view experiment data and related metadata. The fusion experiments will feature long pulse and high sampling rate in the future. The data access and visualization system in this work has adopted segment and scale concept. Large data samples are re-sampled in different scales and then split into segments for instant response. It allows users to view extremely large data on the web browser efficiently, without worrying about the limitation on the size of the data. The HTML5 and JavaScript based web front-end can provide intuitive and fluent user experience. On the server side, a RESTful (Representational State Transfer) web API, which is based on ASP.NET MVC (Model View Controller), allows users to access the data and its metadata through HTTP (HyperText Transfer Protocol). An interface to the database has been designed to decouple the data access and visualization system from the data storage. It can be applied upon any data storage system like MDSplus or JTEXTDB, and this system is very easy to deploy as well.A WebScope with data provider both for MDSplus and JTEXTDB is implemented and deployed. The WebScope has been integrated into J-TEXT LogBook, an experimental recording system for J-TEXT. It is now serving J-TEXT daily experiment. In the future more databases as the data source will be supported and it will support visualization of more data types besides waveform.

Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.

The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif-small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif-small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif-small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.

A Novel Adaptation Method for HTTP Streaming of VBR Videos over Mobile Networks

Recently, HTTP streaming has become very popular for delivering videos over the Internet. For adaptivity, a provider should generate multiple versions of a video as well as the related metadata. Various adaptation methods have been proposed to support a streaming client in coping with strong bandwidth variations. However, most of existing methods target at constant bitrate (CBR) videos only. In this paper, we present a new method for quality adaptation in on-demand streaming of variable bitrate (VBR) videos. To cope with strong variations of VBR bitrate, we use a local average bitrate as the representative bitrate of a version. A buffer-based algorithm is then proposed to conservatively adapt video quality. Through experiments in the mobile streaming context, we show that our method can provide quality stability as well as buffer stability even under very strong variations of bandwidth and video bitrates.

Large geospatial images discovery: metadata model and technological framework

The advancements in geospatial web technology triggered efforts for disclosure of valuable resources of historical collections. This paper focuses on the role of spatial data infrastructures (SDI) in such efforts. The work describes the interplay between SDI technologies and potential use cases in libraries such as cartographic heritage. The metadata model is introduced to link up the sources from these two distinct fields. To enhance the data search capabilities, the work focuses on the representation of the content-based metadata of raster images, which is the crucial prerequisite to target the search in a more effective way. The architecture of the prototype system for automatic raster data processing, storage, analysis and distribution is introduced. The architecture responds to the characteristics of input datasets, namely to the continuous flow of very large raster data and related metadata. Proposed solutions are illustrated on the case study of cartometric analysis of digitised early maps and related metadata encoding.

Life Cycle Management Considerations of Remotely Sensed Geospatial Data and Documentation for Long Term Preservation

As geospatial missions age, one of the challenges for the usability of data is the availability of relevant and updated metadata with sufficient documentation that can be used by future generations of users to gain knowledge from the original data. Given that remote sensing data undergo many intermediate processing steps, for example, an understanding of the exact algorithms employed and the quality of that data produced could be key considerations for these users. As interest in global climate data is increasing, documentation about older data, their origins, and their provenance are valuable to first-time users attempting to perform historical climate research or comparative analysis of global change. Incomplete or missing documentation could be what stands in the way of a new researcher attempting to use the data. Therefore, preservation of documentation and related metadata is sometimes just as critical as the preservation of the original observational data. The Goddard Earth Sciences–Data and Information Service Center (GES DISC), a NASA Earth science Distributed Active Archive Center (DAAC) that falls under the management structure of the Earth Science Data and Information System (ESDIS), is actively pursuing the preservation of all necessary artifacts needed by future users.In this article, we will detail the data custodial planning and the data lifecycle process developed for content preservation, and our implementation of a Preservation System to safeguard documents and associated artifacts from legacy (older) missions, as well as detail lessons learned regarding access rights and confidentiality of information issues. We also elaborate on key points that made our preservation effort successful; the primary points being drafting of a governing baseline for historical data preservation from satellite missions and using the historical baseline as a guide to content filtering of what documents to preserve. The Preservation System currently archives documentation content for High Resolution Dynamics Limb Sounder (HIRDLS), Upper Atmosphere Research Satellite (UARS), Total Ozone Mapping Spectrometer (TOMS) mission data, and the 1960s era Nimbus mission. Documentation from other missions like the Tropical Rainfall Measuring Mission (TRMM), the Ozone Monitoring Instrument (OMI), and the Atmospheric Infra-Red Sounder (AIRS) are also slated to be added to this repository, as well as other mission datasets to be preserved at the GES DISC.

An Effective User Profiling Data Structure for Dynamic License

In this work, we defined and constructed an effective user profiling data structure for the dynamic license of digital contents. The user profiling data structure can be deduced from the analysis on existing digital music license purchase pattern included in the user profiling data. It is designed to trace the user's license purchase pattern and can be used to analyze and trace the user's license access pattern with the history based aged-MRU algorithm. Since dynamic license has more complicate features on describing license actions and relations with other persons than static license, the user profiling data structure also should have more member items in metadata. By comparing the difference of static license features with dynamic license features, we can validate the user profiling data structure for dynamic license and can get the effectiveness of the data structure on license purchase prediction of the dynamic license as like the static license. In order to construct the user profiling data structure for the dynamic license, several metadata items should be added to the user profiling data structure for the static license. In this work, we proposed a kind of simple user profiling data structure for dynamic license and evaluated its effectiveness of the next user license purchase prediction with the aged-MRU algorithm. The evaluation results show that the proposed user profiling data structure for the dynamic license can present the related metadata to the license purchase and can predict the next license purchase activity in dynamic license environment.

Sustainable and Accessible Integrated Heritage Science Datasets

A current challenge in the scientific, humanities and cultural heritage realm is the storage of and access to the increasing volume of digital datasets, paramount to advancing knowledge and assuring the future of research. The European Union has established a number of research infrastructures focused on addressing access and sustainability of digital data, while initiatives in the Unites States appear less integrated. The establishment of standardized digital protocols for storing and accessing scientific cultural heritage data is critical to ensuring interoperability between heritage institutions, and the preservation of international culture in libraries archives, and museums. The Preservation Research and Testing Division of the Library of Congress has moved forward with an initiative to standardize and make accessible, data from a range of scientific instrumentation, including related metadata files and assuring open access file formats.