ElVisML: an open data format for the exchange and storage of electrophysiological data in ophthalmology

2017 ◽  
Vol 136 (1) ◽  
pp. 75-92
Author(s):  
Torsten Strasser ◽  
Tobias Peters ◽  
Herbert Jägle ◽  
Eberhart Zrenner
Keyword(s):  
Open Data ◽  
Data Format ◽  
Electrophysiological Data ◽  
And Storage

scholarly journals Assessing Large-Scale, Cross-Domain Knowledge Bases for Semantic Search

2020 ◽  
Vol 39 (3) ◽  
pp. 595-602
Author(s):  
Aatif Ahmad Khan ◽  
Sanjay Kumar Malik
Keyword(s):  
Domain Knowledge ◽  
Large Scale ◽  
Open Data ◽  
Knowledge Bases ◽  
Semantic Search ◽  
Semantic Web Technologies ◽  
Data Format ◽  
Web Technologies ◽  
Cross Domain ◽  
Description Framework

Semantic Search refers to set of approaches dealing with usage of Semantic Web technologies for information retrieval in order to make the process machine understandable and fetch precise results. Knowledge Bases (KB) act as the backbone for semantic search approaches to provide machine interpretable information for query processing and retrieval of results. These KB include Resource Description Framework (RDF) datasets and populated ontologies. In this paper, an assessment of the largest cross-domain KB is presented that are exploited in large scale semantic search and are freely available on Linked Open Data Cloud. Analysis of these datasets is a prerequisite for modeling effective semantic search approaches because of their suitability for particular applications. Only the large scale, cross-domain datasets are considered, which are having sizes more than 10 million RDF triples. Survey of sizes of the datasets in triples count has been depicted along with triples data format(s) supported by them, which is quite significant to develop effective semantic search models.

scholarly journals mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements

2020 ◽  
Vol 20 (1) ◽  
pp. 172-183
Author(s):  
Ranjeet S. Bhamber ◽  
Andris Jankevics ◽  
Eric W. Deutsch ◽  
Andrew R. Jones ◽  
Andrew W. Dowsey
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Data Format ◽  
And Storage

IFC for Infrastructure

2017 ◽  
Vol 6 (3) ◽  
pp. 44-56 ◽  
Author(s):  
Pierre Benning
Keyword(s):  
Data Model ◽  
System Approach ◽  
Open Data ◽  
Coordinate Systems ◽  
Data Format ◽  
International Standard ◽  
Industry Foundation Classes ◽  
Development Phases

The industry foundation classes (IFCs) data model is a neutral and open data format defined by an international standard (ISO 16739), which allows the description of a construction as a collection of standard objects. These objects are quite well defined for describing a building, but their use is still far from being adapted (and then adopted) for infrastructure. The article presents a new methodology to enrich the IFC model for an infrastructure, in particular, for the scope of bridges, based on a system approach. The first step is to identify all the absent concepts and classes in the current IFC definition, procedural geometry, coordinate systems, etc., and then proposes “bridge oriented” new entities in order to enrich the current IFC model. The next IFC development phases, dedicated to other infrastructure domains, will be based on this experienced methodology.

scholarly journals mzMLb: a future-proof raw mass spectrometry data format based on standards-compliant mzML and optimized for speed and storage requirements

2020 ◽  
Author(s):  
Ranjeet S. Bhamber ◽  
Andris Jankevics ◽  
Eric W Deutsch ◽  
Andrew R Jones ◽  
Andrew W Dowsey
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
File Size ◽  
Data Format ◽  
File Access ◽  
Data Interchange ◽  
File Formats ◽  
Reference Implementation ◽  
And Storage ◽  
Access Efficiency

AbstractWith ever-increasing amounts of data produced by mass spectrometry (MS) proteomics and metabolomics, and the sheer volume of samples now analyzed, the need for a common open format possessing both file size efficiency and faster read/write speeds has become paramount to drive the next generation of data analysis pipelines. The Proteomics Standards Initiative (PSI) has established a clear and precise XML representation for data interchange, mzML, receiving substantial uptake; nevertheless, storage and file access efficiency has not been the main focus. We propose an HDF5 file format ‘mzMLb’ that is optimised for both read/write speed and storage of the raw mass spectrometry data. We provide extensive validation of write speed, random read speed and storage size, demonstrating a flexible format that with or without compression is faster than all existing approaches in virtually all cases, while with compression, is comparable in size to proprietary vendor file formats. Since our approach uniquely preserves the XML encoding of the metadata, the format implicitly supports future versions of mzML and is straightforward to implement: mzMLb’s design adheres to both HDF5 and NetCDF4 standard implementations, which allows it to be easily utilised by third parties due to their widespread programming language support. A reference implementation within the established ProteoWizard toolkit is provided.

Building Future “Smart Energy Cities”

2017 ◽  
pp. 125-147
Keyword(s):  
Energy Use ◽  
Prediction Models ◽  
Smart Cities ◽  
Open Data ◽  
Web Based ◽  
Related Data ◽  
Iot Platform ◽  
Information And Communication ◽  
The City ◽  
And Storage

In the process of building the future cities, Information and Communication Technology (ICT) and Internet of Things (IoT) solutions are the key enablers. Although there are plenty of energy related data available in the cities, there are no established methodologies and validated tools to collect, integrate and analyse them so that they can support energy use optimization. In this context, the aim of this chapter is to present the Smart Cities IoT Platform. A “wireless telemetry cloud” over the city can be created, which facilitates the transferring of open data from the distributed sources (weather station, installed equipment, etc.). The proposed IoT Platform is composed of prediction models, scenarios and rules, as well as a database to store the data and results. With the Smart Cities IoT Platform, web-based applications can be created, customised to the specific characteristics and needs of end-users, including the fields of buildings, infrastructure, transport, generation and storage.

scholarly journals A Study on the Provision of National R&D Information in LOD (Linked Open Data) Format

2016 ◽  
Vol 9 (44) ◽  
Author(s):  
Nam Gyu Kang ◽  
Kyung Tae Lim ◽  
Woo Seung Jo ◽  
Jeong Oh Kim ◽  
Tae Hyun Kim ◽  
...  
Keyword(s):  
Open Data ◽  
Linked Open Data ◽  
Data Format

scholarly journals Geothematic open data in Umbria region

2016 ◽  
Author(s):  
Andrea Motti ◽  
Norman Natali
Keyword(s):  
Open Data ◽  
Weighted Average ◽  
Geological Survey ◽  
Geological Model ◽  
Data Format ◽  
Characteristic Index ◽  
Geological Maps ◽  
Umbria Region ◽  
Key Word ◽  
Data Portal

Detailed information about geology, hydrogeology and seismic hazard issues for Umbria region are contained in a spatial database available as open data format (shapefile or KMZ) and distributed under the regional open data portal called Open Data Umbria (http://dati.umbria.it) where 297 datasets have been produced by Umbria Region until now and most of them are made by Geological Survey. Geological Survey of Regione Umbria carried out a 20 years program to produce 276 geological maps at 1:10.000 reference scale with an accurate geological model of the regional surface and providing millions of geological data. The key word is the characteristic index of the single geologic unit. Characteristic index , shown in percentage, calculates the ratio between the surface of the geologic units compared to their thickness. Thickness value for each geologic unit is intended to be based on rank level and calculated as weighted average of the thickness for each geologic unit.

scholarly journals Collection, Processing and Storage of Bibliographic Records using Semantic Web Technologies

2015 ◽  
pp. 37-42 ◽  
Author(s):  
O. N. Shorin
Keyword(s):  
High Performance ◽  
Open Data ◽  
Semantic Integration ◽  
Semantic Web Technologies ◽  
Web Technologies ◽  
Bibliographic Records ◽  
Storage Solutions ◽  
Processing And Storage ◽  
And Storage ◽  
Different Sources

Implementation of the project on semantic integration of bibliographic records has allowed to solve urgent problems: there is developed domain ontology and created modules of interaction with a variety of automated library information systems; bibliographic records converted from different formats into RDF, enriched using the information obtained from different sources, and released in accordance with the principles of Linked Open Data. Hand-ling one of the world’s largest arrays of bibliographic records required utilization of highly specialized protocols of access to information, high-performance processing algorithms and scalable storage solutions.

scholarly journals Mars, a molecule archive suite for reproducible analysis and reporting of single molecule properties from bioimages

2021 ◽  
Author(s):  
Nadia M Huisjes ◽  
Thomas M Retzer ◽  
Matthias J Scherr ◽  
Rohit Agarwal ◽  
Barbara Safaric ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rapid Development ◽  
Open Data ◽  
Data Format ◽  
Quantitative Classification ◽  
Biological Phenomena ◽  
Derived Properties ◽  
Reproducible Analysis ◽  
Single Molecule Analysis

The rapid development of new imaging approaches is generating larger and more complex datasets revealing the time evolution of individual cells and biomolecules. Single-molecule techniques, in particular, provide access to rare intermediates in complex, multistage molecular pathways, but few standards exist for processing these information-rich datasets, posing challenges for wider dissemination. Here, we present Mars, an open-source platform for storage and processing of image-derived properties of biomolecules. Mars provides Fiji/ImageJ2 commands written in Java for common single-molecule analysis tasks using a Molecule Archive architecture that is easily adapted to complex, multistep analysis workflows. Three diverse workflows involving molecule tracking, multichannel fluorescence imaging, and force spectroscopy, demonstrate the range of analysis applications. A comprehensive graphical user interface written in JavaFX enhances biomolecule feature exploration by providing charting, tagging, region highlighting, scriptable dashboards, and interactive image views. The interoperability of ImageJ2 ensures Molecule Archives can easily be opened in multiple environments, including those written in Python using PyImageJ, for interactive scripting and visualization. Mars provides a flexible solution for reproducible analysis of image-derived properties facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible to everyone.

scholarly journals Photon-HDF5: open data format and computational tools for timestamp-based single-molecule experiments

2016 ◽  
Author(s):  
Antonino Ingargiola ◽  
Ted Laurence ◽  
Robert Boutelle ◽  
Shimon Weiss ◽  
Xavier Michalet
Keyword(s):  
Single Molecule ◽  
Open Data ◽  
Data Format ◽  
Computational Tools
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