ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available softw

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation

FINDbase: a worldwide database for genetic variation allele frequencies updated

Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding

Mining Domain-Specific Design Patterns: A Case Study †

Domain-specific design patterns provide developers with proven solutions to common design problems that arise, particularly in a target application domain, facilitating them to produce quality designs in the domain contexts. However, research in this area is not mature and there are no techniques to support their detection. Towards this end, we propose a methodology which, when applied on a collection of websites in a specific domain, facilitates the automated identification of domain-specific design patterns. The methodology automatically extracts the conceptual models of the websites, which are subsequently analyzed in terms of all of the reusable design fragments used in them for supporting common domain functionalities. At the conceptual level, we consider these fragments as recurrent patterns consisting of a configuration of front-end interface components that interrelate each other and interact with end-users to support certain functionality. By performing a pattern-based analysis of the models, we locate the occurrences of all the recurrent patterns in the various website designs which are then evaluated towards their consistent use. The detected patterns can be used as building blocks in future designs, assisting developers to produce consistent and quality designs in the target domain. To support our case, we present a case study for the educational domain

Mining Domain-Specific Design Patterns: A Case Study †

Domain-specific design patterns provide developers with proven solutions to common design problems that arise, particularly in a target application domain, facilitating them to produce quality designs in the domain contexts. However, research in this area is not mature and there are no techniques to support their detection. Towards this end, we propose a methodology which, when applied on a collection of websites in a specific domain, facilitates the automated identification of domain-specific design patterns. The methodology automatically extracts the conceptual models of the websites, which are subsequently analyzed in terms of all of the reusable design fragments used in them for supporting common domain functionalities. At the conceptual level, we consider these fragments as recurrent patterns consisting of a configuration of front-end interface components that interrelate each other and interact with end-users to support certain functionality. By performing a pattern-based analysis of the models, we locate the occurrences of all the recurrent patterns in the various website designs which are then evaluated towards their consistent use. The detected patterns can be used as building blocks in future designs, assisting developers to produce consistent and quality designs in the target domain. To support our case, we present a case study for the educational domain

Mining Domain-Specific Design Patterns

Part 10: Mining Humanistic Data Workshop (MHDW)International audienceMost catalogues of web design patterns contain patterns of general purpose, making it difficult for developers to properly apply them. This has led to the advent of domain-specific design patterns, encapsulating design experience which is in alignment with the natural constraints of a particular domain. Towards this end, we have developed a methodology which when applied on a collection of websites in a particular domain, leads to the automated identification of domain-specific design patterns. At the level of a single website, the methodology analyzes its conceptual model in terms of the incorporated recurrent patterns and evaluates their consistent use. The identified design patterns are stored in a central repository. By applying the methodology on a set of websites of the same application domain, we can populate a repository containing all the design patterns identified within the various websites designs, categorized towards various aspects such as the domain functionalities they perform. In this work, we focus on the domain of educational websites and present our preliminary results

An Approach for Domain-Specific Design Pattern Identification Based on Domain Ontology

Part 2: 8th Mining Humanistic Data WorkshopInternational audienceIn this work, we present an approach for supporting the identification of domain-specific design patterns based on domain’s ontology, since the latter encapsulates the knowledge about the problem domain. More specifically, the proposed approach automatically analyzes the designs of a collection of domain-specific websites in terms of all the recurrent patterns occurring among them, both in the organization of their content and the front-end interface of their pages, resulting in a set of reusable design solutions which are commonly used in them by designers as building blocks for addressing typical domain problems. Then, evaluation is performed according to a number of inspection steps. At a first level, the recurrent patterns occurring at content organization, i.e., the common configurations of domain concepts occurring among website pages are evaluated by matching them against the domain’s ontology and selecting the ones which are in alignment with the domain’s context. At a second level, the recurrent patterns occurring at front-end organization (i.e., the common configurations of front-end design elements) are evaluated towards their consistent and effective use in designs of the collected websites. Finally, the approach categorizes the various reusable design solutions and recommends the ones with the best evaluation results as candidate domain-specific design patterns

Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies

FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft’s PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase