Ten simple rules for making a vocabulary FAIR Cox, Simon J. D; Gonzalez-Beltran, Alejandra N; Magagna, Barbara ...
PLoS computational biology,
06/2021, Letnik:
17, Številka:
6
Journal Article
Recenzirano
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We present ten simple rules that support converting a legacy vocabulary—a list of terms available in a print-based glossary or in a table not accessible using web standards—into a FAIR vocabulary. ...Various pathways may be followed to publish the FAIR vocabulary, but we emphasise particularly the goal of providing a globally unique resolvable identifier for each term or concept. A standard representation of the concept should be returned when the individual web identifier is resolved, using SKOS or OWL serialised in an RDF-based representation for machine-interchange and in a web-page for human consumption. Guidelines for vocabulary and term metadata are provided, as well as development and maintenance considerations. The rules are arranged as a stepwise recipe for creating a FAIR vocabulary based on the legacy vocabulary. By following these rules you can achieve the outcome of converting a legacy vocabulary into a standalone FAIR vocabulary, which can be used for unambiguous data annotation. In turn, this increases data interoperability and enables data integration.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The joint W3C (World Wide Web Consortium) and OGC (Open Geospatial Consortium) Spatial Data on the Web (SDW) Working Group developed a set of ontologies to describe sensors, actuators, samplers as ...well as their observations, actuation, and sampling activities. The ontologies have been published both as a W3C recommendation and as an OGC implementation standard. The set includes a lightweight core module called SOSA (Sensor, Observation, Sampler, and Actuator) available at: http://www.w3.org/ns/sosa/, and a more expressive extension module called SSN (Semantic Sensor Network) available at: http://www.w3.org/ns/ssn/. Together they describe systems of sensors and actuators, observations, the used procedures, the subjects and their properties being observed or acted upon, samples and the process of sampling, and so forth. The set of ontologies adopts a modular architecture with SOSA as a self-contained core that is extended by SSN and other modules to add expressivity and breadth. The SOSA/SSN ontologies are able to support a wide range of applications and use cases, including satellite imagery, large-scale scientific monitoring, industrial and household infrastructures, social sensing, citizen science, observation-driven ontology engineering, and the Internet of Things. In this paper we give an overview of the ontologies and discuss the rationale behind key design decisions, reporting on the differences between the new SSN ontology presented here and its predecessor Web Semantics: Science, Services and Agents on the World Wide Web 17 (2012), 25–32 developed by the W3C Semantic Sensor Network Incubator group (the SSN-XG). We present usage examples and describe alignment modules that foster interoperability with other ontologies.
Cardiac involvement predicts outcome in systemic AL amyloidosis and influences therapeutic options. Current methods of cardiac assessment do not quantify myocardial amyloid burden. We used ...equilibrium contrast cardiovascular magnetic resonance (EQ-CMR) to quantify the cardiac interstitial compartment, measured as myocardial extracellular volume (ECV) fraction, hypothesizing it would reflect amyloid burden.
Sixty patients with systemic AL amyloidosis (65% men, median age 65 years) underwent conventional clinical cardiovascular magnetic resonance, including late enhancement, equilibrium contrast cardiovascular magnetic resonance, and clinical cardiac evaluation, including ECG, echocardiography, assays of N-terminal pro-brain natriuretic peptide and Troponin T, and functional assessment comprising the 6-minute walk test in ambulant individuals. Cardiac involvement in the amyloidosis patients was categorized as definite, probable, or none, suspected by conventional criteria. Findings were compared with 82 healthy controls. Mean ECV was significantly greater in patients than healthy controls (0.25 versus 0.40, P<0.001) and correlated with conventional criteria for characterizing the presence of cardiac involvement, the categories of none, probable, definite corresponding to ECV of 0.276 versus 0.342 versus 0.488, respectively (P<0.001). ECV was correlated with cardiac parameters by echocardiography (eg, Tissue Doppler Imaging TDI S-wave R=0.52, P<0.001) and conventional cardiovascular magnetic resonance (eg, indexed left ventricular mass R=0.56, P<0.001). There were also significant correlations with N-terminal pro-brain natriuretic peptide (R=0.69, P<0.001) and Troponin T (R=0.53, P=0.006). ECV was associated with smaller QRS voltages (R=0.57, P<0.001) and correlated with poorer performance in the 6-minute walk test (R=0.36, P=0.03).
Myocardial ECV measurement has potential to become the first noninvasive test to quantify cardiac amyloid burden.
This paper presents a metadata model for physical samples, developed by CSIRO for its role as an allocating agent. The model is essential for connecting various samples to the Web in a systematic ...manner. It serves as a basis for registering and publishing samples from researchers and laboratories in CSIRO with the International Geo Sample Number (IGSN). The model is simple, extensible and publicly available. We specify how existing controlled vocabularies are incorporated into the model development, and discuss their relevance and limitations. We also describe the mappings between the developed model and existing standards. This is necessary to extend the model's adoption across various science domains. The model has been implemented and tested in the context of two large sample repositories in CSIRO. The results demonstrate the effectiveness of the metadata model while maintaining its flexibility to adapt to various sample types.
•A metadata model for physical samples and sample collections is presented.•The model was developed by CSIRO for its role as an allocating agent.•It is generic, extensible and publicly available.•It has been applied to register samples and publish their metadata on the Web.•The results demonstrate that the model works in practice.
We introduce new OWL ontologies for observations and sampling features, based on the O&M conceptual model from OGC and ISO 19156. Previous efforts, (a) through the W3C SSN project, and (b) following ...ISO rules for conversion from UML, had dependencies on elaborate pre-existing ontologies and frameworks. The new ontologies, known as om-lite and sam-lite, remove such dependencies, and can therefore be used with minimal ontological commitment beyond the O&M conceptual model. Time and space concepts, for which there are multiple existing solutions, are implemented as stub-classes, and patterns for linking to the existing ontologies are described. PROV is used to support certain requirements for the description of specimens. A more general alignment of both observation and sampling feature ontologies with PROV is described, as well as mappings to some other observation models and ontologies.
The prognostic importance of renal insufficiency (RI) in patients undergoing primary percutaneous coronary intervention (PCI) for acute myocardial infarction (AMI) has not been well characterized.
...PCI was performed in 2082 AMI patients without shock presenting within 12 hours of symptom onset in a prospective, multicenter randomized trial. RI was defined as a calculated (Cockroft-Gault) creatinine clearance (CrCl) < or =60 mL/min. RI at baseline was present in 18% of patients. Compared with patients without RI, patients with RI were older and were more likely to be female; to have hypertension, peripheral vascular disease, or cerebrovascular disease; and to present in heart failure. Mortality was markedly increased in patients with versus without baseline RI both at 30 days (7.5% versus 0.8%, P<0.0001) and at 1 year (12.7% versus 2.4%, P<0.0001). Mortality rates increased incrementally for every 10-mL/min decrease in baseline CrCl. By multivariate analysis, reduced baseline CrCl was a powerful independent predictor of 30-day mortality (hazard ratio, 5.77; P<0.0001) and remained associated with reduced survival at 1 year (hazard ratio, 1.98; P=0.08). Hemorrhagic complications and transfusion requirements were also increased more than 2-fold in patients with RI, as were severe restenosis (diameter stenosis > or =70%; 20.6% versus 11.8%, P=0.024) and infarct artery reocclusion (14.7% versus 7.3%, P=0.02).
Baseline RI in patients with AMI undergoing primary PCI is associated with a markedly increased risk of mortality, as well as bleeding and restenosis. Novel approaches are needed to improve the otherwise poor prognosis of patients with RI and AMI.
The Sensor, Observation, Sample, and Actuator (SOSA) ontology provides a formal but lightweight general-purpose specification for modellingthe interaction between the entities involved in the acts of ...observation, actuation, and sampling. SOSA is the result of rethinking the W3C-XG Semantic Sensor Network (SSN) ontology based on changes in scope and target audience, technical developments, and lessons learned over the past years. SOSA also acts as a replacement of SSN’s Stimulus Sensor Observation (SSO) core. It has been developed by the first joint working group of the Open Geospatial Consortium (OGC) and the World Wide Web Consortium (W3C) on Spatial Data on the Web. In this work, we motivate the need for SOSA, provide an overview of the main classes and properties, and briefly discuss its integration with the new release of the SSN ontology as well as various other alignments to specifications such as OGC’s Observations and Measurements (O&M), Dolce-Ultralite (DUL), and other prominent ontologies. We will also touch upon common modelling problems and application areas related to publishing and searching observation, sampling, and actuation data on the Web. The SOSA ontology and standard can be accessed at https://www.w3.org/TR/vocab-ssn/.
The public health and economic consequences of Plasmodium falciparum malaria are once again regarded as priorities for global development. There has been much speculation on whether anthropogenic ...climate change is exacerbating the malaria problem, especially in areas of high altitude where P. falciparum transmission is limited by low temperature. The International Panel on Climate Change has concluded that there is likely to be a net extension in the distribution of malaria and an increase in incidence within this range. We investigated long-term meteorological trends in four high-altitude sites in East Africa, where increases in malaria have been reported in the past two decades. Here we show that temperature, rainfall, vapour pressure and the number of months suitable for P. falciparum transmission have not changed significantly during the past century or during the period of reported malaria resurgence. A high degree of temporal and spatial variation in the climate of East Africa suggests further that claimed associations between local malaria resurgences and regional changes in climate are overly simplistic.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The New Zealand Active Faults Database Langridge, RM; Ries, WF; Litchfield, NJ ...
New Zealand journal of geology and geophysics,
01/2016, Letnik:
59, Številka:
1
Journal Article
Recenzirano
The New Zealand Active Faults Database (NZAFD) is a national geospatial database of active faults - including their locations, names and degrees of activity - that have deformed the ground surface of ...New Zealand within the last 125,000 years. The NZAFD is used for geological research, hazard modelling and infrastructure planning and is an underlying dataset for other nationally significant hazard applications such as the National Seismic Hazard Model. Recent refinements to the data structure have improved the accuracy of active fault locations and characteristics. A subset of active fault information from the NZAFD, generalised for portrayal and use at a scale of 1:250,000 (and referred to as NZAFD250), is freely available online and can be downloaded in several different formats to suit the needs of a range of users including scientists, governmental authorities and the general public. To achieve a uniform spatial scale of 1:250,000 a simplification of detailed fault locational data was required in some areas, while in other areas new mapping was necessary to provide a consistent level of coverage. Future improvements to the NZAFD will include the incorporation of data on active folds and offshore active faults.
We have developed an OWL ontology for the geologic timescale, derived from a Unified Modeling Language (UML) model that formalized the practice of the International Commission for Stratigraphy (ICS) ...(Cox and Richard
2005
). The UML model followed the ISO/TC 211 modeling conventions, and was the basis for an XML implementation that was integrated into GeoSciML 3.0. The OWL ontology is derived using rules for generating OWL ontologies from ISO-conformant UML models, as provided in a (draft) standard from ISO/TC 211. The basic ontology is also aligned with SKOS to allow multilingual labels, and to enable delivery through a standard vocabulary interface. All versions of the International Stratigraphic Chart from 2004 to 2014 have been encoded using the ontology. Following ICS practice, the elements of the timescale retain the same identifiers across the multiple versions, though the information describing each geochronologic unit evolves with the versions of the timescale. The timescales are published through multiple web interfaces and APIs.
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