ORCID Profile
0000-0003-2263-2108
Current Organisations
Naturalis Biodiversity Center
,
University of Sydney
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Pensoft Publishers
Date: 10-09-2021
DOI: 10.3897/BISS.5.74233
Abstract: The Horizon 2020 project Bi o ersity C ommunity I ntegrated K nowledge L ibrary (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in bio ersity and life sciences. Together, the BiCIKL 14 partners will solidify open science practices by providing access to data, tools and services at each stage of, and along the entire bio ersity research and data life cycle (specimens, sequences, taxon names, analytics, publications, bio ersity knowledge graph) (Fig. 1, see also the BiCIKL kick-off presentation through Suppl. material 1), in compliance with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. The existing services provided by the participating infrastructures will expand through development and adoption of shared, common or interoperable domain standards, resulting in liberated and enhanced flows of data and knowledge across these domains. BiCIKL puts a special focus on the bio ersity literature. Over the span of the project, BiCIKL will develop new methods and workflows for semantic publishing and integrated access to harvesting, liberating, linking, and re-using sub-article-level data extracted from literature (i.e., specimens, material citations, sequences, taxonomic names, taxonomic treatments, figures, tables). Data linkages may be realised with different technologies (e.g., data warehousing, linking between FAIR Data Objects, Linked Open Data) and can be bi-lateral (between two data infrastructures) or multi-lateral (among multiple data infrastructures). The main challenge of BiCIKL is to design, develop and implement a FAIR Data Place (FDP), a central tool for search, discovery and management of interlinked FAIR data across different domains. The key final output of BiCIKL will the future Bio ersity Knowledge Hub (BKH), a one-stop portal, providing access to the BiCIKL services, tools and workflows, beyond the lifetime of the project.
Publisher: Informa UK Limited
Date: 04-03-2023
Publisher: Pensoft Publishers
Date: 16-09-2022
Abstract: The landscape of bio ersity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional bio ersity informatics space, while others operate across a broad front, but differ from others by data type(s) handled, their geographic scope and the life cycle phase(s) of the data they support. In an effort to characterise the various dimensions of the bio ersity informatics landscape, we developed a framework and dataset to survey these dimensions for ten organisations (DiSSCo, GBIF, iBOL, Catalogue of Life, iNaturalist, Bio ersity Heritage Library, GeoCASe, LifeWatch, eLTER ELIXIR), relative to both their current activities and long-term strategic ambitions. The survey assessed the contact between the infrastructure organisations by capturing the breadth of activities for each infrastructure across five categories (data, standards, software, hardware and policy), for nine types of data (specimens, collection descriptions, opportunistic observations, systematic observations, taxonomies, traits, geological data, molecular data and literature) and for seven phases of activity (creation, aggregation, access, annotation, interlinkage, analysis and synthesis). This generated a dataset of 6,300 verified observations, which have been scored and validated by leading members of each infrastructure organisation. The resulting data allow high-level questions about the overall bio ersity informatics landscape to be addressed, including the greatest gaps and contact between organisations.
Publisher: Pensoft Publishers
Date: 09-09-2019
DOI: 10.3897/RIO.5.E46404
Abstract: European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – creating a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2004 SYNTHESYS has been an essential instrument supporting this community, underpinning new ways to access and exploit collections, harmonising policy and providing significant new insights for thousands of researchers, while fostering the development of new approaches to face urgent societal challenges. SYNTHESYS+ is a fourth iteration of this programme, and represents a step change in the evolution of this community. For the first time SYNTHESYS+ brings together the European branches of the global natural science organisations (GBIF www.gbif.org/, TDWG www.tdwg.org/, GGBN gbn_portal/ and CETAF cetaf.org/) with an unprecedented number of collections, to integrate, innovate and internationalise our efforts within the global scientific collections community. Major new developments addressed by SYNTHESYS+ include the delivery of a new virtual access programme, providing digitisation on demand services to a significantly expanded user community the construction of a European Loans and Visits System (ELViS) providing, for the first time, a unified gateway to accessing digital, physical and molecular collections and a new data processing platform (the Specimen Data Refinery), applying cutting edge artificial intelligence to dramatically speed up the digital mobilisation of natural history collections. The activities of SYNTHESYS+ form a critical dependency for DiSSCo - the Distributed System of Scientific Collections (dissco.eu/), which is the European Research Infrastructure for natural science collections, under the ESFRI umbrella. DiSSCo will undertake the maintenance and sustainability of SYNTHESYS+ products at the end of the programme.
Publisher: Informa UK Limited
Date: 04-05-2023
Publisher: Pensoft Publishers
Date: 26-01-2022
DOI: 10.3897/RIO.8.E81136
Abstract: BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of bio ersity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, s les, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens & sequences & species & analytics & publications & bio ersity knowledge graph & re-use.
Publisher: Elsevier BV
Date: 06-2023
Publisher: Wiley
Date: 20-03-2023
DOI: 10.5694/MJA2.51888
Publisher: Informa UK Limited
Date: 25-05-2021
DOI: 10.1080/15563650.2021.1921186
Abstract: There is growing evidence in the literature that patients' age is associated with increased risk of death in acute pesticide poisoning. However, few studies have investigated whether the age effect differs between males and females. We aimed to examine the association between age-sex and risk of death in acute pesticide self-poisoning. A prospective cohort of deliberate pesticide-poisoned patients admitted to ten rural Sri Lankan hospitals between March 2002 and December 2019. The pesticide ingested was identified based on identification of container or history. A mixed effects logistic regression was fitted to investigate the effect of age-sex on death in acute pesticide self-poisoning adjusting for clinical symptoms on admission, measured by Glasgow Coma Scale and Poison Severity Score, and controlling for clustering among hospital sites. In total, 201 different pesticides were ingested by patients. 6,643 patients ingested an unknown pesticide. A single pesticide was co-ingested with alcohol by 4,603 patients. Of the 28,303 patients enrolled, 2,028 patients died, resulting in case fatality of 7.2% (95% CI 6.9-7.5). The effect of age on case fatality was stronger for males after 21 years of age. The odds of dying for each 5 years increase in age was 1.26 (95% CI 1.23-1.28) times higher for males versus 1.14 (95% CI 1.10-1.19) times higher for females. Missing data were handled by multiple imputation. Patient's age-sex are important risk factors for death in acute pesticide self-poisoning even after controlling for clinical effects. The age effect on the odds of dying was significantly different for males and females, with this effect being stronger for males. Given that patient's age and sex are very easy to collect on admission, our study highlights the need for incorporating these risk factors in policy and clinical decisions.
Publisher: Pensoft Publishers
Date: 07-03-2022
DOI: 10.3897/ARPHAPREPRINTS.E82955
Abstract: The landscape of bio ersity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional bio ersity informatics space, while others operate across a broad front but differ from others by data type(s) handled, their geographic scope and the life cycle phase(s) of the data they support. In an effort to characterise the various dimensions of the bio ersity informatics landscape, we developed a framework and dataset to survey these dimensions for ten organisations (DiSSCo, GBIF, iBOL, Catalogue of Life, iNaturalist, Bio ersity Heritage Library, GeoCASe, LifeWatch, eLTER, ELIXIR), relative to both their current activities and long-term strategic ambitions. The survey assessed the contact between the infrastructure organisations by capturing the breadth of activities for each infrastructure across five categories (data, standards, software, hardware and policy), for nine types of data (specimens, collection descriptions, opportunistic observations, systematic observations, taxonomies, traits, geological data, molecular data, and literature), and for seven phases of activity (creation, aggregation, access, annotation, interlinkage, analysis, and synthesis). This generated a dataset of 6,300 verified observations, which have been scored and validated by leading members of each infrastructure organisation. The resulting data allows high-level questions about the overall bio ersity informatics landscape to be addressed, including the greatest gaps and contact between organisations.
Publisher: Springer Science and Business Media LLC
Date: 18-03-2020
Publisher: Wiley
Date: 24-02-2021
DOI: 10.1002/SIM.8915
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.
Publisher: Elsevier BV
Date: 11-2020
No related grants have been discovered for Firouzeh Noghrehchi.