1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

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

Medical Image Data and Datasets in the Era of Machine Learning-Whitepaper from the 2016 C-MIMI Meeting Dataset Session.

At the first annual Conference on Machine Intelligence in Medical Imaging (C-MIMI), held in September 2016, a conference session on medical image data and datasets for machine learning identified multiple issues. The common theme from attendees was that everyone participating in medical image evaluation with machine learning is data starved. There is an urgent need to find better ways to collect, annotate, and reuse medical imaging data. Unique domain issues with medical image datasets require further study, development, and dissemination of best practices and standards, and a coordinated effort among medical imaging domain experts, medical imaging informaticists, government and industry data scientists, and interested commercial, academic, and government entities. High-level attributes of reusable medical image datasets suitable to train, test, validate, verify, and regulate ML products should be better described. NIH and other government agencies should promote and, where applicable, enforce, access to medical image datasets. We should improve communication among medical imaging domain experts, medical imaging informaticists, academic clinical and basic science researchers, government and industry data scientists, and interested commercial entities

Rayman: Interoperability use of Meteorological Observation

The observation of atmospheric phenomena enables generating of knowledge about the weather and meteors occurrence in a region. When this information is georeferenced it becomes useful for a great number of professional and public activities in the field of e.g. building, infrastructures, aeronautics, biota, tourism, agriculture and energy. At the present time access to that information is limited. Few meteorological agencies apply geo-Standards, hindering the development of GIS tools for monitoring, threshold alerts and decision support helping. This work describes how public agencies publish meteorological data and the solution developed at the Spanish Electrical Network (REE) to store the information provided by the Spanish Meteorological Agency (AEMET). The implemented solution enables the access to the weather observations collected by the meteorological agency and the rays captured by the detection network in a interoperable way and the exploitation, by as well a desktop GIS capable of connecting with Oracle-Spatial database as through the interfaces of the OGC standardized services (WMS, WFS and SOS)

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Italian center for Astronomical Archives publishing solution: modular and distributed

The Italian center for Astronomical Archives tries to provide astronomical data resources as interoperable services based on IVOA standards. Its VO expertise and knowledge comes from active participation within IVOA and VO at European and international level, with a double-fold goal: learn from the collaboration and provide inputs to the community. The first solution to build an easy to configure and maintain resource publisher conformant to VO standards proved to be too optimistic. For this reason it has been necessary to re-think the architecture with a modular system built around the messaging concept, where each modular component speaks to the other interested parties through a system of broker-managed queues. The first implemented protocol, the Simple Cone Search, shows the messaging task architecture connecting the parametric HTTP interface to the database backend access module, the logging module, and allows multiple cone search resources to be managed together through a configuration manager module. Even if relatively young, it already proved the flexibility required by the overall system when the database backend changed from MySQL to PostgreSQL+PgSphere. Another implementation test has been made to leverage task distribution over multiple servers to serve simultaneously: FITS cubes direct linking, cubes cutout and cubes positional merging. Currently the implementation of the SIA-2.0 standard protocol is ongoing while for TAP we will be adapting the TAPlib library. Alongside these tools a first administration tool (TASMAN) has been developed to ease the build up and maintenance of TAP_SCHEMA-ta including also ObsCore maintenance capability. Future work will be devoted at widening the range of VO protocols covered by the set of available modules, improve the configuration management and develop specific purpose modules common to all the service components.Comment: SPIE Astronomical Telescopes + Instrumentation 2018, Software and Cyberinfrastructure for Astronomy V, pre-publishing draft proceeding (reduced abstract

Learner-centred Accessibility for Interoperable Web-based Educational Systems

This paper describes the need for an information model and specifications that support a new strategy for delivering accessible computer-based resources to learners based on their specific needs and preferences in the circumstances in which they are operating. The strategy augments the universal accessibility of resources model to enable systems to focus on individual learners and their particular accessibility needs and preferences. A set of specifications known as the AccessForAll specifications is proposed

Metadata and ontologies for organizing students’ memories and learning: standards and convergence models for context awareness

Este artículo trata de las ontologías que sirven para la comprensión en contexto y la Gestión de la Información Personal (PIM)y su aplicabilidad al proyecto Memex Metadata(M2). M2 es un proyecto de investigación de la Universidad de Carolina del Norte en Chapel Hill para mejorar la memoria digital de los alumnos utilizando tablet PC, la tecnología SenseCam de Microsoft y otras tecnologías móviles(p.ej. un dispositivo de GPS) para capturar el contexto del aprendizaje. Este artículo presenta el proyecto M2, dicute el concepto de los portafolios digitales en las actuales tendencias educativas, relacionándolos con las tecnologías emergentes, revisa las ontologías relevantes y su relación con el proyecto CAF (Context Awareness Framework), y concluye identificando las líneas de investigación futuras.This paper focuses on ontologies supporting context awareness and Personal Information Management (PIM) and their applicability in Memex Metadata (M2) project. M2 is a research project of the University of North Carolina at Chapel Hill to improve student digital memories using the tablet PC, Microsoft’s SenseCam technology, and other mobile technologies (e.g., a GPS device) to capture context. The M2 project offers new opportunities studying students’ learning with digital technologies. This paper introduces the M2 project; discusses E-portfolios and current educational trends related to pervasive computing; reviews relevant ontologies and their relationship to the projects’ CAF (context awareness framework), and concludes by identifying future research directions

Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie