scholarly journals Linking PubDictionaries with UniBioDicts to support Community Curation

2020 ◽  
Author(s):  
John Zobolas ◽  
Jin-Dong Kim ◽  
Martin Kuiper ◽  
Steven Vercruysse
Keyword(s):  
Data Exchange ◽  
Ad Hoc ◽  
General Purpose ◽  
Controlled Vocabularies ◽  
New Information ◽  
Community Curation ◽  
Biological Concepts ◽  
Rest Api ◽  
Easy Integration ◽  
The Many

One of the many challenges that biocurators face, is the continuous evolution of ontologies and controlled vocabularies and their lack of coverage of biological concepts. To help biocurators annotate new information that cannot yet be covered with terms from authoritative resources, we produced an update of PubDictionaries: a resource of publicly editable, simple-structured dictionaries, accessible through a dedicated REST API. PubDictionaries was equipped with both an enhanced API and a new software client that connects it to the Unified Biological Dictionaries (UBDs) uniform data exchange format. This client enables efficient search and retrieval of ad hoc created terms, and easy integration with tools that further support the curator’s specific annotation tasks. A demo that combines the Visual Syntax Method (VSM) interface for general-purpose knowledge formalization, with this new PubDictionaries-powered UBD client, shows it is now easy to incorporate the user-created PubDictionaries terminologies into biocuration tools.

Computing Cores for Existential Rules with the Standard Chase and ASP

2020 ◽  
Author(s):  
Markus Krötzsch
Keyword(s):  
Large Class ◽  
Data Exchange ◽  
Answer Set Programming ◽  
Query Answering ◽  
Universal Model ◽  
The Core ◽  
Universal Models ◽  
General Terms ◽  
Special Cases ◽  
The Many

To reason with existential rules (a.k.a. tuple-generating dependencies), one often computes universal models. Among the many such models of different structure and cardinality, the core is arguably the “best”. Especially for finitely satisfiable theories, where the core is the unique smallest universal model, it has advantages in query answering, non-monotonic reasoning, and data exchange. Unfortunately, computing cores is difficult and not supported by most reasoners. We therefore propose ways of computing cores using practically implemented methods from rule reasoning and answer set programming. Our focus is on cases where the standard chase algorithm produces a core. We characterise this desirable situation in general terms that apply to a large class of cores, derive concrete approaches for decidable special cases, and generalise these approaches to non-monotonic extensions of existential rules.

scholarly journals Where the Sidewalk Ends: Automobility and Shame in Tbilisi, Georgia

2018 ◽  
Vol 33 (3) ◽  
pp. 444-472 ◽  
Author(s):  
Perry Maxfield Waldman Sherouse
Keyword(s):  
Social Media ◽  
Public Space ◽  
Ad Hoc ◽  
Private Company ◽  
Urban Public Space ◽  
Social Actors ◽  
The Public ◽  
Physical Barriers ◽  
The Many ◽  
The City

In recent years, cars have steadily colonized the sidewalks in downtown Tbilisi. By driving and parking on sidewalks, vehicles have reshaped public space and placed pedestrian life at risk. A variety of social actors coordinate sidewalk affairs in the city, including the local government, a private company called CT Park, and a fleet of self-appointed st’aianshik’ebi (parking attendants) who direct drivers into parking spots for spare change. Pedestrian activists have challenged the automotive conquest of footpaths in innovative ways, including art installations, social media protests, and the fashioning of ad hoc physical barriers. By safeguarding sidewalks against cars, activists assert ideals for public space that are predicated on sharp boundaries between sidewalk and street, pedestrian and machine, citizen and commodity. Politicians and activists alike connect the sharpness of such boundaries to an imagined Europe. Georgia’s parking culture thus reflects not only local configurations of power among the many interests clamoring for the space of the sidewalk, but also global hierarchies of value that form meaningful distinctions and aspirational horizons in debates over urban public space. Against the dismal frictions of an expanding car system, social actors mobilize the idioms of freedom and shame to reinterpret and repartition the public/private distinction.

Equity and Sustainability in the Old Growth Forests of the Central Highlands of Victoria

1997 ◽  
Author(s):  
A. Dragun
Keyword(s):  
Forest Management ◽  
Ad Hoc ◽  
Well Being ◽  
Economic Power ◽  
General Issue ◽  
The Face ◽  
Human Effort ◽  
Forest Use ◽  
The Many ◽  
Variable Efficiency

The general issue of forest use has been highly contentious in Victoria and considerable human effort has been exerted to establish the “best” use of forests. This economic, bureaucratic and political contemplation has yielded a multitude of different policy prescriptions with quite variable efficiency and equity outcomes. However, a feature of the analysis is that nowhere-on the grounds of efficiency or equity-is forestry logging the clearly desired outcome. Yet in the face of insurmountable evidence against logging, governments in Victoria prevaricate over making a formal decision not to log the forests-in fact the ad hoc approach to forest management favours the established forest interests. Clearly the narrow economic power and interests of a few logging companies are sufficient to counterbalance the much greater-but diffuse-well being of the many citizens in the state.

Information Sharing in VANETs

2010 ◽  
pp. 75-96
Author(s):  
Marco Fiore ◽  
Claudio Casetti ◽  
Carla-Fabiana Chiasserini
Keyword(s):  
Information Sharing ◽  
Data Exchange ◽  
Ad Hoc ◽  
Network Simulator ◽  
Content Sharing ◽  
Content Caching ◽  
Peer Network ◽  
Future Challenges ◽  
Technical Issues ◽  
Peer To Peer Network

This chapter looks at a vehicular ad hoc network (VANET) as a peer-to-peer network, where mobile users may request information contents as well as provide them to other nodes, and it addresses the major technical issues that emerge when dealing with information sharing in VANETs. After briefly reviewing some proposals appeared in the literature on application and network protocols for data exchange in VANETs, the chapter focuses on a possible application for data sharing between vehicular users, which exploits the pull-based approach. It then highlights the main challenges in such a scenario and introduces some mechanisms that can be applied to solve two major issues in content sharing: content query propagation and content caching. A comparison among the schemes presented for query propagation, as well as between the mechanisms introduced for data caching, is shown through simulation results derived using the network simulator ns2. Finally, future challenges and emerging research topics for content sharing and dissemination in VANETs are outlined.

Document SQL (DSQL)

2011 ◽  
pp. 316-344
Author(s):  
Arijit Sengupta ◽  
V. Ramesh
Keyword(s):  
Query Optimization ◽  
Ad Hoc ◽  
Query Language ◽  
Optimization Techniques ◽  
Order Logic ◽  
First Order Logic ◽  
Tree Structures ◽  
Easy Integration ◽  
Query Semantics ◽  
Theoretical Foundations

This chapter presents DSQL, a conservative extension of SQL, as an ad-hoc query language for XML. The development of DSQL follows the theoretical foundations of first order logic, and uses common query semantics already accepted for SQL. DSQL represents a core subset of XQuery that lends well to query optimization techniques; while at the same time allows easy integration into current databases and applications that use SQL. The intent of DSQL is not to replace XQuery, the current W3C recommended XML query language, but to serve as an ad-hoc querying frontend to XQuery. Further, the authors present proofs for important query language properties such as complexity and closure. An empirical study comparing DSQL and XQuery for the purpose of ad-hoc querying demonstrates that users perform better with DSQL for both flat and tree structures, in terms of both accuracy and efficiency.

Sensed Data Sharing in Cloud Federation for Advances in Health Information Exchange

2013 ◽  
Vol 3 (4) ◽  
pp. 36-50
Author(s):  
Antonio Celesti ◽  
Maria Fazio ◽  
Antonio Puliafito ◽  
Massimo Villari
Keyword(s):  
Data Model ◽  
Information Exchange ◽  
Data Exchange ◽  
Health Information Exchange ◽  
Distributed Approach ◽  
Efficient Management ◽  
Sensing Systems ◽  
New Information ◽  
Open Source Framework ◽  
Administrative Domains

In this paper the authors focus on sensing systems supporting data exchange among several healthcare administrative domains. The challenge in this area is twofold: efficient management of a huge amount of data produced by medical devices, bio-sensors and information systems, sharing sensed data for scientific and clinical purposes. The authors present a new information system that exploits Cloud computing capabilities to overcome such issues, also guaranteeing patients' privacy. Their proposal integrates different healthcare institutions into a federated environment, thus establishing a trust context among the institutions themselves. The storage service is designed according to a fully distributed approach and it is based on the wide-used Open Source framework Hadoop, which is enriched to establish a compelling federated system. They adopt the XRI technology to formalize an XML-based data model which allows to simplify the classification, searching and retrieval of medical data.

Designing Document SQL (DSQL)

2009 ◽  
Vol 20 (4) ◽  
pp. 26-53 ◽  
Author(s):  
Arijit Sengupta ◽  
V. Ramesh
Keyword(s):  
Ad Hoc ◽  
Query Language ◽  
Optimization Techniques ◽  
Order Logic ◽  
Conservative Extension ◽  
Tree Structures ◽  
First Order ◽  
Easy Integration ◽  
Query Semantics ◽  
Theoretical Foundations

This article presents DSQL, a conservative extension of SQL, as an ad-hoc query language for XML. The development of DSQL follows the theoretical foundations of first order logic, and uses common query semantics already accepted for SQL. DSQL represents a core subset of XQuery that lends well to optimization techniques, while at the same time allows easy integration into current databases and applications that useSQL. The intent of DSQL is not to replace XQuery, the current W3C recommended XML query language, but to serve as an ad-hoc querying frontend to XQuery. Further, the authors present proofs for important query language properties such as complexity and closure. An empirical study comparing DSQL and XQuery for the purpose of ad-hoc querying demonstrates that users perform better with DSQL for both flat and tree structures, in terms of both accuracy and efficiency.

scholarly journals Benchmarking a Many-Core Neuromorphic Platform With an MPI-Based DNA Sequence Matching Algorithm

Electronics ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1342
Author(s):  
Gianvito Urgese ◽  
Francesco Barchi ◽  
Emanuele Parisi ◽  
Evelina Forno ◽  
Andrea Acquaviva ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Parallel Architecture ◽  
General Purpose ◽  
Sequence Matching ◽  
Matching Algorithm ◽  
Computing Platform ◽  
Globally Asynchronous Locally Synchronous ◽  
Efficient Communication ◽  
The Many ◽  
Many Core

SpiNNaker is a neuromorphic globally asynchronous locally synchronous (GALS) multi-core architecture designed for simulating a spiking neural network (SNN) in real-time. Several studies have shown that neuromorphic platforms allow flexible and efficient simulations of SNN by exploiting the efficient communication infrastructure optimised for transmitting small packets across the many cores of the platform. However, the effectiveness of neuromorphic platforms in executing massively parallel general-purpose algorithms, while promising, is still to be explored. In this paper, we present an implementation of a parallel DNA sequence matching algorithm implemented by using the MPI programming paradigm ported to the SpiNNaker platform. In our implementation, all cores available in the board are configured for executing in parallel an optimised version of the Boyer-Moore (BM) algorithm. Exploiting this application, we benchmarked the SpiNNaker platform in terms of scalability and synchronisation latency. Experimental results indicate that the SpiNNaker parallel architecture allows a linear performance increase with the number of used cores and shows better scalability compared to a general-purpose multi-core computing platform.

scholarly journals Partial Compilation of ASP Programs

2019 ◽  
Vol 19 (5-6) ◽  
pp. 857-873 ◽  
Author(s):  
BERNARDO CUTERI ◽  
CARMINE DODARO ◽  
FRANCESCO RICCA ◽  
PETER SCHÜLLER
Keyword(s):  
Experimental Analysis ◽  
Ad Hoc ◽  
Blow Up ◽  
State Of The Art ◽  
Answer Set Programming ◽  
General Purpose ◽  
Combinatorial Problems ◽  
New Approach ◽  
Input Program ◽  
Evaluation Algorithm

AbstractAnswer Set Programming (ASP) is a well-known declarative formalism in logic programming. Efficient implementations made it possible to apply ASP in many scenarios, ranging from deductive databases applications to the solution of hard combinatorial problems. State-of-the-art ASP systems are based on the traditional ground&solve approach and are general-purpose implementations, i.e., they are essentially built once for any kind of input program. In this paper, we propose an extended architecture for ASP systems, in which parts of the input program are compiled into an ad-hoc evaluation algorithm (i.e., we obtain a specific binary for a given program), and might not be subject to the grounding step. To this end, we identify a condition that allows the compilation of a sub-program, and present the related partial compilation technique. Importantly, we have implemented the new approach on top of a well-known ASP solver and conducted an experimental analysis on publicly-available benchmarks. Results show that our compilation-based approach improves on the state of the art in various scenarios, including cases in which the input program is stratified or the grounding blow-up makes the evaluation unpractical with traditional ASP systems.

De-biasing role induced bias using Bayesian networks

2019 ◽  
Author(s):  
Mark Schweizer
Keyword(s):  
Probability Theory ◽  
Bayesian Networks ◽  
Subjective Probability ◽  
Ad Hoc ◽  
Decision Aids ◽  
Decision Makers ◽  
Normative Standard ◽  
The Many ◽  
Legal Fact ◽  
Assessment Of Evidence

Abstract The merits of using subjective probability theory as a normative standard for evidence evaluation by legal fact-finders have been hotly debated for decades. Critics argue that formal mathematical models only lead to an apparent precision that obfuscates the ad-hoc nature of the many assumptions that underlie the model. Proponents of using subjective probability theory as normative standard for legal decision makers, specifically proponents of using Bayesian networks as decision aids in complex evaluations of evidence, must show that formal models have tangible benefits over the more natural, holistic assessment of evidence by explanatory coherence. This article demonstrates that the assessment of evidence using a Bayesian network parametrized with values obtained from the decision makers reduces role-induced bias, a bias that has been largely resistant to de-biasing attempts so far.

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