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SUMMARY: The Sequencing Read Archive is one of the largest and fastest-growing repositories of sequencing data, containing tens of petabytes of sequenced reads. Its data is used by a wide scientific community, often beyond the primary study that generated them. Such analyses rely on accurate metadata concerning the type of experiment and library, as well as the organism from which the sequenced reads were derived. These metadata are typically entered manually by contributors in an error-prone process, and are frequently incomplete. In addition, easy-to-use computational tools that verify the consistency and completeness of metadata describing the libraries to facilitate data reuse, are largely unavailable. Here, we introduce HTSinfer, a Python-based tool to infer metadata directly and solely from bulk RNA-sequencing data generated on Illumina platforms. HTSinfer leverages genome sequence information and diagnostic genes to rapidly and accurately infer the library source and library type, as well as the relative read orientation, 3' adapter sequence and read length statistics. HTSinfer is written in a modular manner, published under a permissible free and open-source license and encourages contributions by the community, enabling easy addition of new functionalities, e.g. for the inference of additional metrics, or the support of different experiment types or sequencing platforms. AVAILABILITY AND IMPLEMENTATION: HTSinfer is released under the Apache License 2.0. Latest code is available via GitHub at https://github.com/zavolanlab/htsinfer, while releases are published on Bioconda. A snapshot of the HTSinfer version described in this article was deposited at Zenodo at 10.5281/zenodo.13985958.
Artificial intelligence (AI) methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new algorithms, but access to such data is often hindered by the lack of standards for sharing datasets. We discuss the barriers to sharing annotated image datasets and suggest specific guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are sure that the Metadata, Incentives, Formats and Accessibility (MIFA) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high-quality training and benchmarking data.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The complexities of non-target effects of registered pesticides on biocontrol agents (BCAs) hinder the optimization of integrated pest management programs in agriculture. The wealth of literature on BCA-pesticide compatibility allows for the investigation of factors influencing BCA susceptibility and the generalized impacts of different pesticides. We conducted a meta-analysis using 2088 observations from 122 published articles to assess non-target effects on two phytoseiid species (Neoseiulus californicus and Phytoseiulus persimilis), a parasitoid (Encarsia formosa), and two microbial BCAs (Trichoderma harzianum and Metarhizium anisopliae). We explored the contributions of bioassay factors (exposure duration, temperature, test methods, mode of actions (MOA), and type of pesticide), and simulated effects of compatibility on target pests. MOA groups 21 and 6 were the most harmful to predatory mites and E. formosa, increasing mortality during pesticide-BCA compatibility. Exposure duration, temperature, and test methods were identified as the most influential factors increasing mortality in phytoseiids during pesticide exposure. Insecticides and fungicides were the most represented and harmful groups to BCAs. Although most bioassays were conducted at room temperature, temperatures between 21 and 22 °C were the most harmful to phytoseiids and E. formosa during toxicity assays. Exposure durations of 1-3 days (54-85 %) for predators/parasitoids and 1-5 days (>50 %) for microbial BCAs highlight the lack of data on long-term impacts. In assessing pesticide impacts on target pests, pesticides with compatible concentrations above mean LC50 values were more effective. This study not only identified compatibility trends but also highlighted factors responsible for discrepancies in results and knowledge gaps that need to be addressed.
- Klíčová slova
- Biocontrol agents, Compatibility, Neoseiulus californicus, Pesticides, Phytoseiulus persimilis, Trichoderma,
- MeSH
- biologická kontrola škůdců metody MeSH
- biologická ochrana farmakologie MeSH
- insekticidy farmakologie MeSH
- Metarhizium účinky léků MeSH
- pesticidy * farmakologie toxicita MeSH
- roztoči účinky léků MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- metaanalýza MeSH
- přehledy MeSH
- Názvy látek
- biologická ochrana MeSH
- insekticidy MeSH
- pesticidy * MeSH
SUMMARY: ShinySOM offers a user-friendly interface for reproducible, high-throughput analysis of high-dimensional flow and mass cytometry data guided by self-organizing maps. The software implements a FlowSOM-style workflow, with improvements in performance, visualizations and data dissection possibilities. The outputs of the analysis include precise statistical information about the dissected samples, and R-compatible metadata useful for the batch processing of large sample volumes. AVAILABILITY AND IMPLEMENTATION: ShinySOM is free and open-source, available online at gitlab.com/exaexa/ShinySOM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- algoritmy * MeSH
- metadata MeSH
- průběh práce MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.
We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.
The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
- Klíčová slova
- FAIR data, birds, data standards, database, long-term studies, meta-data standards, research network,
- MeSH
- databáze faktografické MeSH
- metadata * MeSH
- ptáci * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.
- Klíčová slova
- Education, FAIR Principles, Open Access, Open Data, Open Science, Quality Management, Standardisation,
- MeSH
- biologické vědy * MeSH
- důvěra * MeSH
- kvalita života MeSH
- metadata MeSH
- mezinárodní spolupráce MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Background: Our previous study analyzed the age trajectory of mortality (ATM) in 14 European countries, while this study aimed at investigating ATM in other continents and in countries with a higher level of mortality. Data from 11 Non-European countries were used. Methods: The number of deaths was extracted from the WHO mortality database. The Halley method was used to calculate the mortality rates in all possible calendar years and all countries combined. This method enables us to combine more countries and more calendar years in one hypothetical population. Results: The age trajectory of total mortality (ATTM) and also ATM due to specific groups of diseases were very similar in the 11 non-European countries and in the 14 European countries. The level of mortality did not affect the main results found in European countries. The inverse proportion was valid for ATTM in non-European countries with two exceptions. Slower or no mortality decrease with age was detected in the first year of life, while the inverse proportion model was valid for the age range (1, 10) years in most of the main chapters of ICD10. Conclusions: The decrease in child mortality with age may be explained as the result of the depletion of individuals with congenital impairment. The majority of deaths up to the age of 10 years were related to congenital impairments, and the decrease in child mortality rate with age was a demonstration of population heterogeneity. The congenital impairments were latent and may cause death even if no congenital impairment was detected.
- Klíčová slova
- WHO database, age, childhood, congenital anomalies, mortality rate,
- Publikační typ
- časopisecké články MeSH
Background: Mortality rate rapidly decreases with age after birth, and, simultaneously, the spectrum of death causes show remarkable changes with age. This study analyzed age-associated decreases in mortality rate from diseases of all main chapters of the 10th revision of the International Classification of Diseases. Methods: The number of deaths was extracted from the mortality database of the World Health Organization. As zero cases could be ascertained for a specific age category, the Halley method was used to calculate the mortality rates in all possible calendar years and in all countries combined. Results: All causes mortality from the 1st day of life to the age of 10 years can be represented by an inverse proportion model with a single parameter. High coefficients of determination were observed for total mortality in all populations (arithmetic mean = 0.9942 and standard deviation = 0.0039). Slower or no mortality decrease with age was detected in the 1st year of life, while the inverse proportion method was valid for the age range [1, 10) years in most of all main chapters with three exceptions. The decrease was faster for the chapter "Certain conditions originating in the perinatal period" (XVI).The inverse proportion was valid already from the 1st day for the chapter "Congenital malformations, deformations and chromosomal abnormalities" (XVII).The shape of the mortality decrease was very different for the chapter "Neoplasms" (II) and the rates of mortality from neoplasms were age-independent in the age range [1, 10) years in all populations. Conclusion: The theory of congenital individual risks of death is presented and can explain the results. If it is valid, latent congenital impairments may be present among all cases of death that are not related to congenital impairments. All results are based on published data, and the data are presented as a supplement.
- Klíčová slova
- WHO database, age, childhood, congenital anomalies, mortality rate,
- Publikační typ
- časopisecké články MeSH
