This dataset is related to the manuscript "An empirical meta-analysis of the life sciences linked open data on the web" published at Nature Scientific Data. If you use the dataset, please cite the manuscript as follows:Kamdar, M.R., Musen, M.A. An empirical meta-analysis of the life sciences linked open data on the web. Sci Data 8, 24 (2021). https://doi.org/10.1038/s41597-021-00797-yWe have extracted schemas from more than 80 publicly available biomedical linked data graphs in the Life Sciences Linked Open Data (LSLOD) cloud into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. The dataset published here contains the following files:- The set of Linked Data Graphs from the LSLOD cloud from which schemas are extracted.- Refined Sets of extracted classes, object properties, data properties, and datatypes, shared across the Linked Data Graphs on LSLOD cloud. Where the schema element is reused from a Linked Open Vocabulary or an ontology, it is explicitly indicated.- The LSLOD Schema Graph, which contains all the above extracted schema elements interlinked with each other based on the underlying content. Sample instances and sample assertions are also provided along with broad level characteristics of the modeled content. The LSLOD Schema Graph is saved as a JSON Pickle File. To read the JSON object in this Pickle file use the Python command as follows:with open('LSLOD-Schema-Graph.json.pickle' , 'rb') as infile: x = pickle.load(infile, encoding='iso-8859-1')Check the Referenced Link for more details on this research, raw data files, and code references.

Long-Term ST Database carefully split into training and testing datasets.

Database. Visit https://dataone.org/datasets/sha256%3Ab537c48d68d348f5b7e0a4654258f7857b0037ca01037567b5306efb9c4a4e1a for complete metadata about this dataset.

Presentation slides on the identifiers in biosciences at the Japan Open Science Summit (JOSS) 2018.

BioSharing (http://www.biosharing.org) is a curated, web-based, searchable portal of over 1,300 records describing content standards, databases and data policies in the life sciences, broadly encompassing the biological, natural and biomedical sciences. Among many features, the records can be searched and filtered, or grouped via the ‘Collection’ feature according to field of interest. An example is the Collection curated with the NIH BD2K bioCADDIE project, for various purposes. First, to select and track content standards that have been reviewed during the creation of the metadata model underpinning the Data Discovery Index. Second, as the work progresses and the prototype Index harvests dataset descriptors from different databases, the Collection will be extended to include the descriptions of these databases, including which (if any) standards they implement. This is key to support one of the bioCADDIE project use cases: to allow the searching and filtering of datasets that are compliant to a given community standard. Despite a growing set of standard guidelines and formats for describing their experiments, the barriers to authoring the experimental metadata necessary for sharing and interpreting datasets are tremendously high. Understanding how to comply with these standards takes time and effort and researchers view this as a burden that may benefit other scientists, but not themselves. To tackle this, with and for the NIH BD2K CEDAR project, we will explore methods to serve machine-readable versions of these standards that can inform the creation of metadata templates, rendering standards invisible to the researchers and driving them to strive for easier authoring of the experimental metadata. Lastly, as part of the ELIXIR-UK Node BioSharing is being developed to be the ELIXIR Standards Registry and will be progressively cross-linked to other registries, such as the ELIXIR Tools and Services Registry and the ELIXIR Training e-Support System (TeSS).

Premium B2B leads from life sciences companies actively seeking business solutions. Access qualified prospects from biotechnology firms, research laboratories, genomics companies, and diagnostic organizations.

Databases for three populations studied in above formative research in Stata 13. Final report document also attached with questionnaires as annex. Coding corresponds to question number.

The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.

BackgroundMeasures to ensure research integrity have been widely discussed due to the social, economic and scientific impact of research integrity. In the past few years, financial support for health research in emerging countries has steadily increased, resulting in a growing number of scientific publications. These achievements, however, have been accompanied by a rise in retracted publications followed by concerns about the quality and reliability of such publications.ObjectiveThis systematic review aimed to investigate the profile of medical and life sciences research retractions from authors affiliated with Brazilian academic institutions. The chronological trend between publication and retraction date, reasons for the retraction, citation of the article after the retraction, study design, and the number of retracted publications by author and affiliation were assessed. Additionally, the quality, availability and accessibility of data regarding retracted papers from the publishers are described.MethodsTwo independent reviewers searched for articles that had been retracted since 2004 via PubMed, Web of Science, Biblioteca Virtual em Saúde (BVS) and Google Scholar databases. Indexed keywords from Medical Subject Headings (MeSH) and Descritores em Ciências da Saúde (DeCS) in Portuguese, English or Spanish were used. Data were also collected from the Retraction Watch website (www.retractionwatch.com). This study was registered with the PROSPERO systematic review database (CRD42017071647).ResultsA final sample of 65 articles was retrieved from 55 different journals with reported impact factors ranging from 0 to 32.86, with a median value of 4.40 and a mean of 4.69. The types of documents found were erratum (1), retracted articles (3), retracted articles with a retraction notice (5), retraction notices with erratum (3), and retraction notices (45). The assessment of the Retraction Watch website added 8 articles that were not identified by the search strategy using the bibliographic databases. The retracted publications covered a wide range of study designs. Experimental studies (40) and literature reviews (15) accounted for 84.6% of the retracted articles. Within the field of health and life sciences, medical science was the field with the largest number of retractions (34), followed by biological sciences (17). Some articles were retracted for at least two distinct reasons (13). Among the retrieved articles, plagiarism was the main reason for retraction (60%). Missing data were found in 57% of the retraction notices, which was a limitation to this review. In addition, 63% of the articles were cited after their retraction.ConclusionPublications are not retracted solely for research misconduct but also for honest error. Nevertheless, considering authors affiliated with Brazilian institutions, this review concluded that most of the retracted health and life sciences publications were retracted due to research misconduct. Because the number of publications is the most valued indicator of scientific productivity for funding and career progression purposes, a systematic effort from the national research councils, funding agencies, universities and scientific journals is needed to avoid an escalating trend of research misconduct. More investigations are needed to comprehend the underlying factors of research misconduct and its increasing manifestation.

Location of sampling sites, databases (species-with-data files in RDS format) and scripts associated with the paper. Two R scripts for Maximum Likelihood Population Effects models are provided: 1. script_MLPE: R script used to fit maximum likelihood population effects models, considering the entire study area; 2. script_MLPE_sub_areas: R script used to fit maximum likelihood population effects models, considering two sub-areas separately. Three files with coordinates of sampled individuals are provided: 1. WP_coord_N: sampling sites coordinates for all individuals captured in the northern sub-area (EPSG:3035 - ETRS89 / LAEA Europe); 2. WP_coord_S: sampling sites coordinates for all individuals captured in the southern sub-area (EPSG:3035 - ETRS89 / LAEA Europe); 3. WP_coordinates: sampling sites coordinates for all individuals (EPSG:3035 - ETRS89 / LAEA Europe). Two files in RDS format (R software, package SDMtune) with testing and training locations, as well as background points, for building Species Distribution Models (EPSG:3035 - ETRS89 / LAEA Europe).

The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.

Users can search for sample policies, practices, and articles addressing health issues affecting schools and students. Topics include: asthma, school health programs, food safety, STIs, healthy eating, physical activity, sexual orientation, and teen pregnancy, among others. Background The School Health Database is maintained by the National School Boards Association (NSBA) and is supported by the Robert Woods Johnson Foundation and the Centers for Disease Control and Prevention (CDC). The School Health Database provides abstracts for policies and practices addressing health issues affecting schools and students. This database is useful for school policymakers. Topics include: asthma; communities of color; coordinated school health programs; food sa fety/food allergies; sexually transmitted infections; healthy eating; parent, family and community environment; physical activity; sexual orientation; gender identity; sun safety; teen pregnancy; t obacco use; and wellness. User Functionality Users can search approximately 2,000 abstracts. Users can search the database by: keyword, year, and target audience. Users can request more information or free materials by completing a Request Form on the website. Data Notes This database includes nearly 2,000 abstracts regarding programs and policies affecting the school health programs across the United States.

The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan.

The DOI list of the documents retrieved from the WOS Medline database in the research area of Life Sciences & Biomedicine from 2014-2016.

Données ayant servi au projet "Développement d’outils de bio-indication «phytobenthos» et «macro-invertébrés benthiques» pour les eaux de surface continentales de Mayotte". Ce projet a été financé par l'AFB, Agence Française pour la Biodiversité Les correspondants AFB: Olivier MONNIER et Yorick REYJOL (chargés de mission)

The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences.

Desirable characteristics for database identifiers in the life sciences.

This database contains data on the amount of grit particles and arthropods ingested by six hummingbird species sampled in a seasonal ecosystem in western Mexico. Data were collected from the stomach content analysis of the sampled hummingbirds over a one-year period. Data presented are: 1) the total number of grit particles per stomach, 2) the biomass of arthropods ingested (g dry weight/stomach), 3) the Orders of arthropods ingested, and 4) the average chitin content of arthropods ingested (percentage dry weight).

Functional Annotation of Variants - Online Resource (FAVOR, https://favor.genohub.org) is a comprehensive whole-genome variant annotation database and a variant browser, providing hundreds of functional annotation scores from a variety of aspects of variant biological function. This FAVOR Essential Database is comprised of a collection of essential annotation scores for all possible SNVs (8,812,917,339) and observed indels (79,997,898) in Build GRCh38/hg38, including variant info, chromosome, position, reference allele, alternative allele, aPC-Conservation, aPC-Epigenetics, aPC-Epigenetics-Active, aPC-Epigenetics-Repressed, aPC-Epigenetics-Transcription, aPC-Local-Nucleotide-Diversity, aPC-Mappability, aPC-Mutation-Density, aPC-Protein-Function, aPC-Proximity-To-TSSTES, aPC-Transcription-Factor, CAGE promoter, CAGE, MetaSVM, rsID, FATHMM-XF, Gencode Comprehensive Category, Gencode Comprehensive Info, Gencode Comprehensive Exonic Category, Gencode Comprehensive Exonic Info, GeneHancer, LINSIGHT, CADD, rDHS. These annotation scores can be integrated into FAVORannotator (https://github.com/zhouhufeng/FAVORannotator) to create an annotated GDS (aGDS) file by storing the genotype data and their functional annotation data in an all-in-one file. The aGDS file can then facilitate a wide range of functionally-informed downstream analyses.

Earlier this year, Dr. Hoffman and Dr. Fafard published a book chapter on the efficacy and legality of border closures enacted by governments in response to changing COVID-19 conditions. The authors concluded border closures are at best, regarded as powerful symbolic acts taken by governments to show they are acting forcefully, even if the actions lack an epidemiological impact and breach international law. This COVID-19 travel restriction project was developed out of a necessity and desire to further examine the empirical implications of border closures. The current dataset contains bilateral travel restriction information on the status of 179 countries between 1 January 2020 and 8 June 2020. The data was extracted from the ‘international controls’ column from the Oxford COVID-19 Government Response Tracker (OxCGRT). The data in the ‘international controls’ column outlined a country’s change in border control status, as a response to COVID-19 conditions. Accompanying source links were further verified through random selection and comparison with external news sources. Greater weight is given to official national government sources, then to provincial and municipal news-affiliated agencies. The database is presented in matrix form for each country-pair and date. Subsequently, each cell is represented by datum Xdmn and indicates the border closure status on date d by country m on country n. The coding is as follows: no border closure (code = 0), targeted border closure (= 1), and a total border closure (= 99). The dataset provides further details in the ‘notes’ column if the type of closure is a modified form of a targeted closure, either as a land or port closure, flight or visa suspension, or a re-opening of borders to select countries. Visa suspensions and closure of land borders were coded separately as de facto border closures and analyzed as targeted border closures in quantitative analyses. The file titled ‘BTR Supplementary Information’ covers a multitude of supplemental details to the database. The various tabs cover the following: 1) Codebook: variable name, format, source links, and description; 2) Sources, Access dates: dates of access for the individual source links with additional notes; 3) Country groups: breakdown of EEA, EU, SADC, Schengen groups with source links; 4) Newly added sources: for missing countries with a population greater than 1 million (meeting the inclusion criteria), relevant news sources were added for analysis; 5) Corrections: external news sources correcting for errors in the coding of international controls retrieved from the OxCGRT dataset. At the time of our study inception, there was no existing dataset which recorded the bilateral decisions of travel restrictions between countries. We hope this dataset will be useful in the study of the impact of border closures in the COVID-19 pandemic and widen the capabilities of studying border closures on a global scale, due to its interconnected nature and impact, rather than being limited in analysis to a single country or region only. Statement of contributions: Data entry and verification was performed mainly by GL, with assistance from MJP and RN. MP and IW provided further data verification on the nine countries purposively selected for the exploratory analysis of political decision-making.