Shared Data Resource
Dotaz
Zobrazit nápovědu
Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.
- Klíčová slova
- antivenom, drug discovery, genomics, machine learning, peptidomics, proteomics, toxin databases, transcriptomics, venom resources,
- MeSH
- big data * MeSH
- databáze faktografické MeSH
- internet * MeSH
- výpočetní biologie * metody MeSH
- živočišné jedy * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- živočišné jedy * MeSH
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and launched various projects and initiatives to ensure good data management practices for scientific excellence. These projects have resulted in a rich set of tools and resources highly valuable for FAIR data management. However, these resources remain scattered across projects and ELIXIR structures, making their dissemination and application challenging. Therefore, it becomes imminent to coordinate these efforts for sustainable and harmonised RDM practices with dedicated forums for RDM professionals to exchange knowledge and share resources. The proposed ELIXIR RDM Community will bring together RDM experts to develop ELIXIR's vision and coordinate its activities, taking advantage of the available assets. It aims to coordinate RDM best practices and illustrate how to use the existing ELIXIR RDM services. The Community will be built around three integral pillars, namely, a network of RDM professionals, RDM knowledge management and RDM training expertise and resources. It will also engage with external stakeholders to leverage benefits and provide a forum to RDM professionals for regular knowledge exchange, capacity building and development of harmonised RDM practices, keeping in line with the overall scope of the RDM Community. In the short term, the Community aims to build upon the existing resources and ensure that the content of these remain up to date and fit for purpose. In the long run, the Community will aim to strengthen the skills and knowledge of its RDM professionals to support the emerging needs of the scientific community. The Community will also devise an effective strategy to engage with other ELIXIR structures and international stakeholders to influence and align with developments and solutions in the RDM field.
- Klíčová slova
- Common best practices, Data management, Data management plans, Data management training, Data stewardship, FAIR principles, Research data life cycle, community standards,
- MeSH
- data management * metody MeSH
- lidé MeSH
- výzkum MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Financial development and geopolitical risks can significantly affect sustainable development. However, the roles of these factors in sustainable development are rarely investigated. Thus, this study takes into account the role of geopolitical risk while exploring the effects of financial development, natural resource rents, and eco-innovation on sustainable development in the Organization for Economic Co-operation and Development (OECD) countries. To this end, yearly data from 1990 to 2019 is analyzed using advanced econometric tests. The Common Correlated Effects Mean Group (CCEMG) results indicate that financial development and eco-innovation are significantly and positively related to sustainable development. Natural resource rents have a detrimental impact on sustainable development which confirms the presence of the resource curse hypothesis in OECD countries. Furthermore, the results revealed that controlling geopolitical risk is useful in fostering sustainable development. Lastly, the panel Granger causality test unveiled one-way causality from financial development, eco-innovation, natural resource rents, and geopolitical risk to sustainable development. Moreover, causalities are found from geopolitical risk to financial development, eco-innovation and natural resources. These findings suggest that OECD countries should prioritize financial development and eco-innovation policies for sustainable development while mitigating the negative effects of natural resource rents. The geopolitical risk can harm sustainable development, so policymakers should promote international cooperation and risk-sharing.
- Klíčová slova
- Financial development, Geopolitical risk, Green innovation, Resource richness, Sustainable development,
- MeSH
- ekonomický rozvoj MeSH
- oxid uhličitý MeSH
- přírodní zdroje * MeSH
- trvale udržitelný rozvoj * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- oxid uhličitý MeSH
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
Myositis International Health and Research Collaborative Alliance (MIHRA) is a newly formed purpose-built non-profit charitable research organization dedicated to accelerating international clinical trial readiness, global professional and lay education, career development and rare disease advocacy in IIM-related disorders. In its long form, the name expresses the community's scope of engagement and intent. In its abbreviation, MIHRA, conveys linguistic roots across many languages, that reflects the IIM community's spirit with meanings such as kindness, community, goodness, and peace. MIHRA unites the global multi-disciplinary community of adult and pediatric healthcare professionals, researchers, patient advisors and networks focused on conducting research in and providing care for pediatric and adult IIM-related disorders to ultimately find a cure. MIHRA serves as a resourced platform for collaborative efforts in investigator-initiated projects, consensus guidelines for IIM assessment and treatment, and IIM-specific career development through connecting research networks.MIHRA's infrastructure, mission, programming and operations are designed to address challenges unique to rare disease communities and aspires to contribute toward transformative models of rare disease research such as global expansion and inclusivity, utilization of community resources, streamlining ethics and data-sharing policies to facilitate collaborative research. Herein, summarises MIHRA operational cores, missions, vision, programming and provision of community resources to sustain, accelerate and grow global collaborative research in myositis-related disorders.
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
- Klíčová slova
- bioinformatics, community driven, curation, database, registry, software,
- MeSH
- lidé MeSH
- software * MeSH
- systémy řízení databází MeSH
- účast komunity * MeSH
- výpočetní biologie metody normy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
- MeSH
- anotace sekvence MeSH
- databáze jako téma MeSH
- databáze proteinů * MeSH
- internet MeSH
- konformace proteinů, alfa-helix MeSH
- konformace proteinů, beta-řetězec MeSH
- lidé MeSH
- molekulární modely MeSH
- počítačová grafika MeSH
- proteiny chemie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční analýza proteinů metody MeSH
- šíření informací MeSH
- uživatelské rozhraní počítače * MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Názvy látek
- proteiny MeSH
The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes, including 2,850 novel null, 2,987 novel conditional- ready, and 4,433 novel reporter alleles.
- MeSH
- delece genu * MeSH
- fenotyp MeSH
- genetické asociační studie * MeSH
- genom * MeSH
- genotyp * MeSH
- internet MeSH
- mezinárodní spolupráce MeSH
- mutageneze MeSH
- myší embryonální kmenové buňky cytologie metabolismus MeSH
- myši knockoutované MeSH
- myši MeSH
- šíření informací MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
The known challenge of underutilization of data and biological material from biorepositories as potential resources for medical research has been the focus of discussion for over a decade. Recently developed guidelines for improved data availability and reusability-entitled FAIR Principles (Findability, Accessibility, Interoperability, and Reusability)-are likely to address only parts of the problem. In this article, we argue that biological material and data should be viewed as a unified resource. This approach would facilitate access to complete provenance information, which is a prerequisite for reproducibility and meaningful integration of the data. A unified view also allows for optimization of long-term storage strategies, as demonstrated in the case of biobanks. We propose an extension of the FAIR Principles to include the following additional components: (1) quality aspects related to research reproducibility and meaningful reuse of the data, (2) incentives to stimulate effective enrichment of data sets and biological material collections and its reuse on all levels, and (3) privacy-respecting approaches for working with the human material and data. These FAIR-Health principles should then be applied to both the biological material and data. We also propose the development of common guidelines for cloud architectures, due to the unprecedented growth of volume and breadth of medical data generation, as well as the associated need to process the data efficiently.
- Klíčová slova
- FAIR (Findable, Accessible, Interoperable, and Reusable) principles, incentives, open science, privacy protection, provenance information management, quality,
- MeSH
- banky biologického materiálu * organizace a řízení normy MeSH
- databáze faktografické normy MeSH
- důvěrnost informací normy MeSH
- lidé MeSH
- šíření informací metody MeSH
- směrnice jako téma MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
