Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs

AT-GIS: highly parallel spatial query processing with associative transducers

Users in many domains, including urban planning, transportation, and environmental science want to execute analytical queries over continuously updated spatial datasets. Current solutions for largescale spatial query processing either rely on extensions to RDBMS, which entails expensive loading and indexing phases when the data changes, or distributed map/reduce frameworks, running on resource-hungry compute clusters. Both solutions struggle with the sequential bottleneck of parsing complex, hierarchical spatial data formats, which frequently dominates query execution time. Our goal is to fully exploit the parallelism offered by modern multicore CPUs for parsing and query execution, thus providing the performance of a cluster with the resources of a single machine. We describe AT-GIS, a highly-parallel spatial query processing system that scales linearly to a large number of CPU cores. ATGIS integrates the parsing and querying of spatial data using a new computational abstraction called associative transducers(ATs). ATs can form a single data-parallel pipeline for computation without requiring the spatial input data to be split into logically independent blocks. Using ATs, AT-GIS can execute, in parallel, spatial query operators on the raw input data in multiple formats, without any pre-processing. On a single 64-core machine, AT-GIS provides 3× the performance of an 8-node Hadoop cluster with 192 cores for containment queries, and 10× for aggregation queries

FAIRness and Usability for Open-access Omics Data Systems

Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the FAIRness of NASAs GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

Development and application of computer software techniques to human factors task data handling problems Final report, 21 Jun. 1965 - 21 Jun. 1966

Computer software techniques applied to human factors task data handling problem