| 1. |
- Hatos, Andras, et al.
(författare)
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DisProt : intrinsic protein disorder annotation in 2020
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:D1, s. D269-D276
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Protein Disorder (DisProt, URL:https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.
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| 2. |
- Lerink, Bas J. W., et al.
(författare)
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How much wood can we expect from European forests in the near future?
- 2023
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Ingår i: Forestry (London). - : Oxford University Press. - 0015-752X .- 1464-3626. ; 96:4, s. 434-447
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Tidskriftsartikel (refereegranskat)abstract
- The demand for wood in Europe is expected to increase in the coming decades. However, any theoretical maximum supply will be affected by sustainability constraints, the motivations of forest owners and regional factors, such as incentives, species and assortments. However, the influence of these factors on supply is changeable. In this study, we quantify what might be realistically available as additional wood supply from currently existing European forests, based on a combination of results of the forest resource model EFISCEN-Space and a literature review of national supply projections. Wood mobilization scenarios for 10 representative Model Regions in Europe that assume forest owners and managers in the simulated regions will adapt their behaviour to alternative behaviour as recorded from other regions were projected with the EFISCEN-Space model. The realistic additional potential based on the literature review is 90 million m(3) yr(-1). This potential should be attainable within 10-20 years. However, the simulations in the Model Regions found potentials to be lower in 7 out of 10 cases as compared with the country they are located in. On average, the model regions reached less than half of the potential as compared with the literature review. This suggests that the realistic additional potential at the European scale may well be lower if all mobilization barriers are taken into account in more detail, but also highlights the uncertainty surrounding these estimates. We conclude from the analyses that although there are large differences in potential between regions and the analysis method employed, there are no 'hotspots' where a large pool of accessible wood can be quickly mobilized using existing infrastructure for nearby industries. An increase in harvest would therefore only be possible with a large effort that spans the whole chain, from forest owners' behaviour to capacity building, financial incentives and matching resources to harvesting capacity. The additionally available wood can most likely only be mobilized against higher marginal costs and will thus only become available in times of higher stumpage prices. The largest potential lies in privately owned forests which often have a fragmented ownership but will most likely be able to supply more wood, though mostly from deciduous species. In the long term (more than 20 years), additional wood, compared with the amounts we found for short term, can only be made available through investments in afforestation, forest restoration, improved forest management and more efficient use of raw material and recycled material.
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| 3. |
- Teodoro, Douglas, et al.
(författare)
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ORBDA: An &ITopen&ITEHR benchmark dataset for performance assessment of electronic health record servers
- 2018
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- The openEHR specifications are designed to support implementation of flexible and interoperable Electronic Health Record (EHR) systems. Despite the increasing number of solutions based on the openEHR specifications, it is difficult to find publicly available healthcare datasets in the openEHR format that can be used to test, compare and validate different data persistence mechanisms for openEHR. To foster research on openEHR servers, we present the openEHR Benchmark Dataset, ORBDA, a very large healthcare benchmark dataset encoded using the openEHR formalism. To construct ORBDA, we extracted and cleaned a de-identified dataset from the Brazilian National Healthcare System (SUS) containing hospitalisation and high complexity procedures information and formalised it using a set of openEHR archetypes and templates. Then, we implemented a tool to enrich the raw relational data and convert it into the openEHR model using the openEHR Java reference model library. The ORBDA dataset is available in composition, versioned composition and EHR openEHR representations in XML and JSON formats. In total, the dataset contains more than 150 million composition records. We describe the dataset and provide means to access it. Additionally, we demonstrate the usage of ORBDA for evaluating inserting throughput and query latency performances of some NoSQL database management systems. We believe that ORBDA is a valuable asset for assessing storage models for openEHR-based information systems during the software engineering process. It may also be a suitable component in future standardised benchmarking of available openEHR storage platforms.
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