ORCID Profile
0000-0002-3374-2962
Current Organisations
HES-SO Genève
,
Swiss Institute of Bioinformatics
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Publisher: F1000 Research Ltd
Date: 15-10-2019
DOI: 10.12688/F1000RESEARCH.20136.1
Abstract: Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination integration of IDP data into the ELIXIR Core Data Resources and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
Publisher: Pensoft Publishers
Date: 24-08-2023
Abstract: The Bio ersity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of bio ersity data, services and knowledge. It serves the entire bio ersity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated bio ersity knowledge graph and an emerging new community of users. The BKH is aimed at bio ersity researchers in the widest sense, research infrastructures and publishers (Fig. 1). The BKH is the key product of the EU-funded Bio ersity Community Integrated Knowledge Library (BiCIKL) project (Penev et al. 2022). The four goals of BiCIKL and the BKH are: Improved access to open and FAIR bio ersity data Establishing of bi-directional data linkages between infrastructures Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, s les, sequences, taxonomic names, taxonomic treatments, figures, tables) Testing and implementation of services through use cases and open call projects for researchers outside the project. Improved access to open and FAIR bio ersity data Establishing of bi-directional data linkages between infrastructures Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, s les, sequences, taxonomic names, taxonomic treatments, figures, tables) Testing and implementation of services through use cases and open call projects for researchers outside the project. The BKH consists of several modules, such as the Home page that presents the main user groups and the benefits that the BKH provides to them. It has guidelines and protocols, such as various documents on the policies, functions, and recommendations for the users. And it has relevant projects, that use linked FAIR bio ersity data. In the core of the BKH is the FAIR Data Place (FDP), which presents novel services and tools developed over the course of BiCIKL. In the future, the FDP will also accept services for linked data provided by new contributors. The FDP consists of three sub-modules: Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of bio ersity data they aggregate and serve: specimens, sequences, taxon names and literature. Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Ex les of such services are: ChecklistBank, LifeBlock, OpenBio , TreatmentBank, SIBiLS “Bio ersityPMC”, eBioDiv, SynoSpecies, PlutoF Curation Tool and others. Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of bio ersity data they aggregate and serve: specimens, sequences, taxon names and literature. Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Ex les of such services are: ChecklistBank, LifeBlock, OpenBio , TreatmentBank, SIBiLS “Bio ersityPMC”, eBioDiv, SynoSpecies, PlutoF Curation Tool and others. Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. The BKH serves as a navigation system in a universe of interconnected bio ersity research infrastructures and is open to new contributors and collaborators in accessing open data and knowledge by anybody, anywhere, at any time.
No related grants have been discovered for Patrick Ruch.