OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database

BACKGROUND: The dysfunction of OPA1, a dynamin GTPase involved in mitochondrial fusion, is responsible for a large spectrum of neurological disorders, each of which includes optic neuropathy. The database dedicated to OPA1 ( https://www.lovd.nl/OPA1 ), created in 2005, has now evolved towards a centralized and more reliable database using the Global Variome shared Leiden Open-source Variation Database (LOVD) installation. RESULTS: The updated OPA1 database, which registers all the patients from our center as well as those reported in the literature, now covers a total of 831 patients: 697 with isolated dominant optic atrophy (DOA), 47 with DOA "plus", and 83 with asymptomatic or unclassified DOA. It comprises 516 unique OPA1 variants, of which more than 80% (414) are considered pathogenic. Full clinical data for 118 patients are documented using the Human Phenotype Ontology, a standard vocabulary for referencing phenotypic abnormalities. Contributors may now make online submissions of phenotypes related to OPA1 mutations, giving clinical and molecular descriptions together with detailed ophthalmological and neurological data, according to an international thesaurus. CONCLUSIONS: The evolution of the OPA1 database towards the LOVD, using unified nomenclature, should ensure its interoperability with other databases and prove useful for molecular diagnoses based on gene-panel sequencing, large-scale mutation statistics, and genotype-phenotype correlations

Using DBpedia as a knowledge source for culture-related user modelling questionnaires

In the culture domain, questionnaires are often used to obtain profiles of users for adaptation. Creating questionnaires requires subject matter experts and diverse content, and often does not scale to a variety of cultures and situations. This paper presents a novel approach that is inspired by crowdwisdom and takes advantage of freely available structured linked data. It presents a mechanism for extracting culturally-related facts from DBpedia, utilised as a knowledge source in an interactive user modelling system. A user study, which examines the system usability and the accuracy of the resulting user model, demonstrates the potential of using DBpedia for generating culture-related user modelling questionnaires and points at issues for further investigation

ACO2 clinicobiological dataset with extensive phenotype ontology annotation

Pathogenic variants of the aconitase 2 gene (ACO2) are responsible for a broad clinical spectrum involving optic nerve degeneration, ranging from isolated optic neuropathy with recessive or dominant inheritance, to complex neurodegenerative syndromes with recessive transmission. We created the first public locus-specific database (LSDB) dedicated to ACO2 within the "Global Variome shared LOVD" using exclusively the Human Phenotype Ontology (HPO), a standard vocabulary for describing phenotypic abnormalities. All the variants and clinical cases listed in the literature were incorporated into the database, from which we produced a dataset. We followed a rational and comprehensive approach based on the HPO thesaurus, demonstrating that ACO2 patients should not be classified separately between isolated and syndromic cases. Our data highlight that certain syndromic patients do not have optic neuropathy and provide support for the classification of the recurrent pathogenic variants c.220C>G and c.336C>G as likely pathogenic. Overall, our data records demonstrate that the clinical spectrum of ACO2 should be considered as a continuum of symptoms and refines the classification of some common variants.Molecular Technology and Informatics for Personalised Medicine and Healt

Contextual Metadata in Digital Aggregations: Application of Collection-Level Subject Metadata and Its Role in User Interactions and Information Retrieval

Article discussing a study of contextual metadata in digital aggregations. Results of this study prove importance of provision of collection-level metadata in general and subject metadata in particular to enhance user experiences and information retrieval in digital libraries

Open Government Data Driven Co-creation: Moving Towards Citizen-Government Collaboration

Part 2: Open Data, Linked Data, and Semantic WebInternational audienceIt is believed that co-creation may lead to public service quality improvements, the provision and creation of new and innovative services, and bring public service providers closer to their service users. There has been an increased interest and focus on how new technological innovations are enabling and facilitating co-creation; one such digital innovation is open government data (OGD). This paper examines a relatively new concept, that of co-created OGD-driven public services and aims to understand how the availability and exploitation of OGD to co-create new public services allows service users to become collaborators rather than customers of public service providers. An exploratory case study is conducted on a pilot project within Estonia where a new public service has been co-created through the exploitation of OGD. The initial results show that in order for an OGD-driven public service to be effectively co-created, a new understanding of the role of stakeholders is needed