Detailed Metadata Research Articles

Technical note: An anomaly in pH data in South Africa’s national water quality monitoring database – implications for future use

The South African national water quality database (Water Management System) houses data records from several environmental monitoring programmes, including the National Chemical Monitoring Programme (NCMP). The NCMP comprises an extensive surface water quality monitoring programme, managed by the Department of Water and Sanitation (DWS). The purpose of this technical note is to alert users to a systematic anomaly recently observed in the pH dataset of the NCMP, reflected in an abrupt increase between pre- and post-1990 data records. Although the cause of the anomaly in pH could not be confirmed with high confidence, an inappropriate acid rinse procedure in pre-1990 analytical methods was identified as the most likely cause, based on available evidence. This was supported by the variation in relative sensitivity when comparing the effect on waters with different buffering capacities, i.e., water with low buffering capacity (represented by total alkalinity < 10 mg/L, as CaCO3) showing the largest anomaly, compared with waters of higher buffering capacity (represented by total alkalinity > 30 mg/L, as CaCO3) showing the smallest anomaly. Historical pH data records in the NCMP (i.e. pre-1990), therefore should be used with caution, especially in more weakly buffered systems. The possibility of reconstructing data using a correction factor derived from detailed statistical analyses of the post-1990 pH characteristics at selected sites is a possible solution that could be investigated in future. A key lesson learnt is the need to be diligent in capturing detailed meta-data on sampling procedures and analytical methods in datasets spanning several generations. Availability of such information is critical in order to provide users with a means of evaluating the suitability and comparability of data records in long-term datasets. The DWS includes such meta-data in the current version of the database, dating from about 1995 onwards.

Global distribution data for cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in 2010

Global data sets on the geographic distribution of livestock are essential for diverse applications in agricultural socio-economics, food security, environmental impact assessment and epidemiology. We present a new version of the Gridded Livestock of the World (GLW 3) database, reflecting the most recently compiled and harmonized subnational livestock distribution data for 2010. GLW 3 provides global population densities of cattle, buffaloes, horses, sheep, goats, pigs, chickens and ducks in each land pixel at a spatial resolution of 0.083333 decimal degrees (approximately 10 km at the equator). They are accompanied by detailed metadata on the year, spatial resolution and source of the input census data. Two versions of each species distribution are produced. In the first version, livestock numbers are disaggregated within census polygons according to weights established by statistical models using high resolution spatial covariates (dasymetric weighting). In the second version, animal numbers are distributed homogeneously with equal densities within their census polygons (areal weighting) to provide spatial data layers free of any assumptions linking them to other spatial variables.

GeneLab: Omics database for spaceflight experiments.

To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated 'omics' (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search across several public bioinformatics repositories. Archived datasets can be queried using full-text search (e.g. keywords, Boolean and wildcards) and results can be sorted in multifactorial manner using assistive filters. GLDS also provides a collaborative platform built on GenomeSpace for sharing files and analyses with collaborators. It currently houses 172 datasets and supports standard guidelines for submission of datasets, MIAME (for microarray), ENCODE Consortium Guidelines (for RNA-seq) and MIAPE Guidelines (for proteomics). https://genelab.nasa.gov/.

Documenting provenance in noncomputational workflows: Research process models based on geobiology fieldwork in Yellowstone National Park

A comprehensive record of research data provenance is essential for the successful curation, management, and reuse of data over time. However, creating such detailed metadata can be onerous, and there are few structured methods for doing so. In this case study of data curation in support of geobiology research conducted at Yellowstone National Park, we describe a method of “Research Process Modeling” for documenting noncomputational data provenance in a structured yet flexible way. The method combines systems analysis techniques to model research activities, the World Wide Web Consortium Provenance (PROV) ontology to illustrate relationships between data products, and simple inventory methods to account for research processes and data products. It also supports collaborative data curation between information professionals and researchers, and is therefore a significant step toward producing more useable and interpretable research data. We demonstrate how this method describes data provenance more robustly than “flat” metadata alone and fills a critical gap in the documentation of provenance for field‐based and noncomputational workflows. We discuss potential applications of this approach to other research domains.

XPSSurfA: An open collaborative XPS data repository using the CMSShub platform

X‐ray photoelectron spectroscopy (XPS) is a widely used surface analysis technique employed in fundamental research, applied research, service laboratories, and industry. Good‐quality analytical outcomes depend critically on spectral references. Many examples of XPS reference databases exist, including print editions, sets of spectral peak positions drawn from the literature, and digital archives and libraries. We report the development of a new digital XPS database comprising survey spectra and region spectra for a range of materials types, collected under a common set of analytical conditions. Each material is described using spectra collected at multiple pass energies with all photoelectron and X‐ray induced Auger transitions represented. Detailed metadata are provided for each material and each spectrum, presented using a schema that incorporates the ISO 16243 and 14976 standards and extensions developed in this work. Spectra are shared under a Creative Commons International (4.0) attribution, non‐commercial licence (CC BY‐NC) in Kratos (.dset), VAMAS (.vms), and XML (.xml) formats. It is intended that reference spectra be imported directly into XPS data analysis software packages for reference and comparison purposes, matching either the peak or transition of interest and the instrument pass energy. The database is flexible and scalable in structure and has the potential to become a core XPS reference resource.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and micro-epidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population and ultimately the whole metapopulation, is efficiently simulated using C++ objects and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g. large-scale simulations and likelihood-free inference. Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license. Supplementary data are available at Bioinformatics online.

LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse.

Long non-coding RNAs (lncRNAs) constitute an important layer of chromatin regulation that contributes to various biological processes and diseases. By interacting with chromatin, many lncRNAs can regulate that state of chromatin by recruiting chromatin-modifying complexes and thus control large-scale gene expression programs. However, the available information on interactions between lncRNAs and chromatin is hidden in a large amount of dispersed literature and has not been extensively collected. We established the LnChrom database, a manually curated resource of experimentally validated lncRNA–chromatin interactions. The current release of LnChrom includes 382 743 interactions in human and mouse. We also manually collected detailed metadata for each interaction pair, including those of chromatin modifying factors, epigenetic marks and disease associations. LnChrom provides a user-friendly interface to facilitate browsing, searching and retrieving of lncRNA–chromatin interaction data. Additionally, a large amount of multi-omics data was integrated into LnChrom to aid in characterizing the effects of lncRNA–chromatin interactions on epigenetic modifications and transcriptional expression. We believe that LnChrom is a timely and valuable resource that can greatly motivate mechanistic research into lncRNAs.Database URL: http://biocc.hrbmu.edu.cn/LnChrom/

Crossroads Corpus creation: Design and case study

Abstract This paper illustrates a methodological approach to the design of an annotated corpus using a case study of phonetic convergences and divergences by multilingual speakers in southwestern Senegal’s Casamance region. The newly compiled corpus contains approximately 183,000 annotations of multilingual, spoken data, gathered by eight researchers over a ten year span using methods ranging from structured lexical elicitation in controlled contexts to naturally occurring, multilingual conversations. The area from which the data were collected consists of three villages and their primary languages, and yet many more contribute to the linguistic landscape. Detailed metadata inform analyses of variation, the context in which a speech act took place and between whom, the speakers’ linguistic repertoires, trajectories, and social networks, as well as the larger language context. A potential path for convergence or divergence that emerged during data collection and in building and searching the corpus is the crossroads in the phonetic production of word-initial velar plosives. Word-initial [k] emerges in one language where only [ɡ] is present in the other; the third utilizes both. The corpus design makes it feasible, not only to identify areas of accommodation, but to grasp the context, enabling a sociolinguistically informed analysis of the speakers’ linguistic behavior.

AgroPortal: A vocabulary and ontology repository for agronomy

Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain’s semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences. We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web. The AgroPortal specifically satisfies requirements of the agronomy community in terms of ontology formats (e.g., SKOS vocabularies and trait dictionaries) and supported features (offering detailed metadata and advanced annotation capabilities). In this paper, we present our platform’s content and features, including the additions to the original technology, as well as preliminary outputs of five driving agronomic use cases that participated in the design and orientation of the project to anchor it in the community. By building on the experience and existing technology acquired from the biomedical domain, we can present in AgroPortal a robust and feature-rich repository of great value for the agronomic domain.

User-Friendly InSAR Data Products: Fast and Simple Timeseries Processing

Interferometric synthetic aperture radar (InSAR) methods provide high-resolution maps of surface deformation applicable to many scientific, engineering, and management studies. Despite its utility, the specialized skills and computer resources required for InSAR analysis remain as barriers for truly widespread use of the technique. Reduction of radar scenes to maps of temporal deformation evolution requires not only detailed metadata describing the exact radar and surface acquisition geometries, but also a software package that can combine these for the specific scenes of interest. Furthermore, the range-Doppler reference frame and radar coordinate system itself are confusing, so that many users find it hard to incorporate even useful products in their customary analyses. Finally, the sheer data volume needed for interferogram time series makes InSAR analysis challenging for many analysis systems. We show here that it is possible to deliver radar data products to users that address all of these difficulties, so that the data acquired by large, modern satellite systems are ready to use in more natural coordinates, without requiring further processing, and in as small volume as possible.

Mesonets: Mesoscale Weather and Climate Observations for the United States

Abstract Mesoscale in situ meteorological observations are essential for better understanding and forecasting the weather and climate and to aid in decision-making by a myriad of stakeholder communities. They include, for example, state environmental and emergency management agencies, the commercial sector, media, agriculture, and the general public. Over the last three decades, a number of mesoscale weather and climate observation networks have become operational. These networks are known as mesonets. Most are operated by universities and receive different levels of funding. It is important to communicate the current status and critical roles the mesonets play. Most mesonets collect standard meteorological data and in many cases ancillary near-surface data within both soil and water bodies. Observations are made by a relatively spatially dense array of stations, mostly at subhourly time scales. Data are relayed via various means of communication to mesonet offices, with derived products typically distributed in tabular, graph, and map formats in near–real time via the World Wide Web. Observed data and detailed metadata are also carefully archived. To ensure the highest-quality data, mesonets conduct regular testing and calibration of instruments and field technicians make site visits based on “maintenance tickets” and prescheduled frequencies. Most mesonets have developed close partnerships with a variety of local, state, and federal-level entities. The overall goal is to continue to maintain these networks for high-quality meteorological and climatological data collection, distribution, and decision-support tool development for the public good, education, and research.

Zircon U–Pb age and Hf isotope evidence for an Eoarchaean crustal remnant and episodic crustal reworking in response to supercontinent cycles in NW India

Scattered T DM2 (3.8–3.2 Ga) for 3.28–2.99 Ga zircons from the Proterozoic Delhi Supergroup in northwestern India provide evidence for generation of juvenile crust and reworking of older crust. Depleted mantle-like ε Hf( t ) values (+7.2 to +5.6) for 2.86–2.71 Ga zircons indicate that generation of juvenile crust occurred during this period and ceased at 2.71 Ga. Extensive magmatism at 2.66–2.34, 2.11–2.01 and 1.60–1.37 Ga was dominated by reworking of pre-existing crust with variable ages, and the last two periods were accompanied by formation of juvenile crust. An Eoarchaean age of 3671 ± 15 Ma represents the oldest age found in NW India. Zircons formed during supercontinent assembly have positive to negative ε Hf( t ) values, suggesting involvement of juvenile and ancient crust, whereas largely positive ε Hf( t ) values for zircons crystallized subsequent to supercontinent amalgamation suggest involvement of predominantly juvenile crust. Correlation of detrital age patterns and tectonomagmatic events indicates a conjugate position for northern Indian and the Cathaysia Block of South China during the assembly of Nuna. The South China Block remained juxtaposed to India until its separation from Pangaea in the late Palaeozoic. Supplementary material: Supplementary data, including detailed metadata related to laboratory and sample preparation methods, U-Pb and Lu-Hf isotopic compositions of the analyzed samples and standards are available at https://doi.org/10.6084/m9.figshare.c.3711847

Homogenization of Sea Surface Temperature at Xiao Changshan marine station in the east of the Bohai Sea using the PMT method

Using the PMTred algorithm (penalized maximum T test) and the detailed metadata archive, the monthly mean sea surface temperature (SST) datasets from 1960 to 2011 have been detected and adjusted. Results show that the SST time series has serious problems of inhomogeneity. The changes in observation instruments and observation system are the main causes of the discontinuity. For the monthly SST time series, the negative adjustments have the high proportion, which may be greatly due to the SST decreasing after automation. It is found that the annual mean SST trends have changed obviously before and after adjusted. The increasing trend of annual mean SST after adjustment is higher than before, by up to 0.252 °C/10 yr.

Developing an Integrated Image Bank and Metadata for Large-scale Research in Cerebrovascular Disease: Our Experience from the Stroke Image Bank Project

A framework for building an infrastructure that semantically integrates, archives and reuses data for various research purposes in human brain imaging remains critical. In particular, problems of aligning technical, clinical and professional systems in order to facilitate data sharing are a recurring issue in brain imaging. However, large samples of well characterised images with detailed metadata are increasingly needed. This paper outlines the experience of the NeuroGrid Stroke Exemplar and further work in the Brain Research Imaging Centre and Stroke Trials Unit in developing an infrastructure that facilitates the linkage, archiving and reuse of imaging data from stroke patients for large scale clinical and epidemiological studies. We examined data from 12 past stroke projects carried out over the past two decades in our centre and two large trials with 329 centres. We assessed previously published schemas and those developed specifically for large multicentre ischaemic and haemorrhagic stroke treatment trials. We then developed our own harmonised and integrated schema and database with a web-based interface system, aiming to be flexible and adaptable to future trials and observational studies. We then linked image and meta-data from 3079 patients acquired in stroke research in one centre in a 14 year period (1996 – 2010) with prospective central hospital health statistics to obtain long term follow-up. Our integrated database includes 3079 subjects and over 550 federated and searchable data items including imaging details, medical history and examination, stroke and laboratory details, which maps to large multicentre stroke trials with imaging data from over 10,000 patients from 30 countries. The central linkage identified 879 of 3079 patients had died, 525 had recurrent strokes and 291 developed dementia during up to a 19 year period (range=0 -19; median=9.04; IQR=12.17) of follow-up, demonstrating its utility. The core metadata schema, has benefited from extensive development in large clinical trials. Further trials’ data can now be added. It provides an opportunity to crosslink and reuse data for a range of large scale stroke brain imaging clinical and research purposes including developing data analytics models for research into common brain diseases and their consequences.

Marine geology data accessibility in the European Framework: The I.G.M.E. participation in the GEO-SEAS project.

During more than 30 years of activity and participation in numerous research projects, the Institute of Geology and Mineral Exploration of Greece has carried out extensive work in marine geology and a vast amount of data has been collected. In order for those data to be available and used by the international scientific community, a need for standardization and harmonization was imminent. Towards this scope IGME, along with 25 other marine geological and geophysical data centres, located in 17 European maritime countries, participated in the GEO-SEAS project: the implementation of an e-infrastructure. The aim of the project was to enable users to identify, locate and access pan-European, harmonised and federated marine geological and geophysical datasets and derived data products held by the data centres through a single common data portal. All available data have been harmonized according to the GEO-SEAS guidelines and standards. Detailed metadata files were created, accompanied by the corresponding data and additional information files. The standardization, harmonization and provision of data and metadata, carried out through the GEO-SEAS project, are aligned with European directives and recent large-scale framework programs on global and European scales.

The mouse Gene Expression Database (GXD): 2017 update.

The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.

Redefining Gold Standard Testing for Diagnosing Leptospirosis: Further Evidence from a Well-Characterized, Flood-Related Outbreak in Sri Lanka.

A gap in the leptospirosis field remains the lack of well-characterized sample collections that allow for comparison of new methods to standard ones. In the context of a flood-related outbreak of leptospirosis evaluated in Anuradhapura, Sri Lanka, a specimen bank was obtained with detailed metadata accompanied by gold standard diagnostic test results. Blood samples collected on admission and 14 days later from suspected cases of leptospirosis were tested using microscopic agglutination test (MAT) (17 serovars), an in-house enzyme-linked immunosorbent assay (ELISA) using a locally obtained strain of Leptospira kirschneri as sonicated antigen, a commercially available ELISA based on sonicated Leptospira biflexa, and a quantitative polymerase chain reaction (qPCR) assay targeting the pathogenic Leptospira-specific 16S rRNA gene. Of 62 patients presenting within the first 2 days of illness, 31 had confirmed leptospirosis based either on paired-sample MAT or qPCR. During the acute phase, qPCR was most sensitive, detecting 74% of definitively diagnosed cases; immunoglobulin G (IgG) ELISA (in-house), IgG ELISA (commercial), and MAT had sensitivities of 35.5%, 12.0%, and 22.6%, respectively, in detecting definitively diagnosed cases using acute phase serum. Of 40 patients with paired sera, 10 were qPCR positive. Of these, five samples were negative by paired-sample MAT. Of the 11 MAT-positive samples, only five were detected using qPCR confirming that both tests are needed for maximal sensitivity. Regional leptospiral serovar-specific IgG ELISA was superior to MAT. Knowing the regionally dominant serovars improves serological sensitivity in the analysis of acute specimens by ELISA, but qPCR was most sensitive in this patient population.

Serials Data in the Data Age: Project CERES Data for Digitization and Print Preservation

The report summarizes a presentation given at the 2015 NASIG conference. It outlines metadata used by Project CERES, a print preservation and digitization project supported by a partnership between the United States Agriculture Information Network and the Center for Research Libraries. It also outlines metadata guidelines used to disclose print holdings committed for preservation and provides tips on creating efficiencies in gathering the detailed issue level data and providing quality assurance for digitization. Gathering detailed metadata to support the preservation of print is an investment in the preservation of essential scholarly resources. Project CERES can be used as a model for other programs coupling preservation and digitization.

Concept indexing and expansion for social multimedia websites based on semantic processing and graph analysis

ABSTRACTThis study presents a human-centric technique for social video expansion based on semantic processing and graph analysis. The objective is to increase metadata of an online video and to explore related information, thereby facilitating user browsing activities. To analyze the semantic meaning of a video, shots and scenes are firstly extracted from the video on the server side. Subsequently, this study uses annotations along with ConceptNet to establish the underlying framework. Detailed metadata, including visual objects and audio events among the predefined categories, are indexed by using the proposed method. Furthermore, relevant online media associated with each category are also analyzed to enrich the existing content. With the above-mentioned information, users can easily browse and search the content according to the link analysis and its complementary knowledge. Experiments on a video dataset are conducted for evaluation. The results show that our system can achieve satisfactory performance, thereby demonstrating the feasibility of the proposed idea.

Study of Archaeological Sites with Imagery: A Case on Narsingdi Region, Bangladesh

Ancient historical illustrations are the main introduction of any area which develops the civilization, cultural importance of the region. Wari is the most important archaeological illustration which enriches the history, culture of the surroundings of Bangladesh. As a riverine country continuous cyclone, river bank erosion, flood, landslide and other natural disasters have altered our ancient civilization since the beginning. For this reason many enriched ancient civilization and culture have engraved by rivers and our ancient arts, culture and civilization are ruined. Currently the major problem of archaeological sites is that there is no geo-spatial database prepared so far. This study therefore, is attempted to prepare a geo-spatial database on archaeological sites like Wari Bateshwar region to develop metadata, relevant information and geo-tagged photos having spatial references to fulfill the purpose of exploring and surveying archaeological sites as well as to develop a methodological framework which documents physical and cultural aspects. Primary data have been used for this study was collected through mainly field observation, interviewing and GPS survey according to predesigned information collection sheet. In this study, total 52 archaeological sites have been identified where only two are recognized by government and rests of them are unrecognized. Satellite navigation data and remote sensing imagery were also integrating with the information collection sheet. Detailed metadata and geo-tagged photos on the each archaeological site contains spatial references has been developed which will help understanding further work on archaeological sites. The govt., academic departments and the NGOs should come forward to fulfill the recommendations in the study.