scholarly journals DGIdb 3.0: a redesign and expansion of the drug-gene interaction database

2017 ◽  
Author(s):  
Kelsy C. Cotto ◽  
Alex H. Wagner ◽  
Yang-Yang Feng ◽  
Susanna Kiwala ◽  
Adam C. Coffman ◽  
...  
Keyword(s):  
User Interface ◽  
Web Application ◽  
Response Times ◽  
Gene Interaction ◽  
Application Programming Interface ◽  
Gene Interactions ◽  
Application Framework ◽  
Interaction Database ◽  
Search Filters ◽  
Ease Of Access

ABSTRACTThe Drug-Gene Interaction Database (DGIdb, www.dgidb.org) consolidates, organizes, and presents drug-gene interactions and gene druggability information from papers, databases, and web resources. DGIdb normalizes content from more than thirty disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API), and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included twenty-eight sources were updated. Six new resources were added, bringing the total number of sources to thirty-three. These updates and additions of sources have cumulatively resulted in 56,309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and antineoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times, and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes, and drug-gene interactions, including listings of PubMed IDs (PMIDs), interaction type, and other interaction metadata.

scholarly journals Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

2020 ◽  
Vol 49 (D1) ◽  
pp. D1144-D1151
Author(s):  
Sharon L Freshour ◽  
Susanna Kiwala ◽  
Kelsy C Cotto ◽  
Adam C Coffman ◽  
Joshua F McMichael ◽  
...  
Keyword(s):  
Interaction Network ◽  
Gene Interaction ◽  
Application Programming Interface ◽  
Application Framework ◽  
Interaction Data ◽  
Gene Interaction Network ◽  
Web Based ◽  
Web Resource ◽  
Interaction Database ◽  
Primary Focus

Abstract The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major version release of this database. A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations. Seven new sources have been added since the last major version release, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include the introduction of a more sophisticated Query Score for interaction search results, an updated Interaction Score, the inclusion of interaction directionality, and several additional improvements to search features, data releases, licensing documentation and the application framework.

scholarly journals Serverless Computing: An Investigation of Deployment Environments for Web APIs

Computers ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 50
Author(s):  
Ivan ◽  
Vasile ◽  
Dadarlat
Keyword(s):  
Web Application ◽  
Web Applications ◽  
Virtual Machines ◽  
Response Times ◽  
Application Programming Interface ◽  
Resource Provisioning ◽  
Dynamic Scaling ◽  
Application Programming ◽  
Test Scenarios ◽  
Additional Labor

Cloud vendors offer a variety of serverless technologies promising high availability and dynamic scaling while reducing operational and maintenance costs. One such technology, serverless computing, or function-as-a-service (FaaS), is advertised as a good candidate for web applications, data-processing, or backend services, where you only pay for usage. Unlike virtual machines (VMs), they come with automatic resource provisioning and allocation, providing elastic and automatic scaling. We present the results from our investigation of a specific serverless candidate, Web Application Programming Interface or Web API, deployed on virtual machines and as function(s)-as-a-service. We contrast these deployments by varying the number of concurrent users for measuring response times and costs. We found no significant response time differences between deployments when VMs are configured for the expected load, and test scenarios are within the FaaS hardware limitations. Higher numbers of concurrent users or unexpected user growths are effortlessly handled by FaaS, whereas additional labor must be invested in VMs for equivalent results. We identified that despite the advantages serverless computing brings, there is no clear choice between serverless or virtual machines for a Web API application because one needs to carefully measure costs and factor-in all components that are included with FaaS.

WED 224 Building causality networks for inherited neuropathies

2018 ◽  
Vol 89 (10) ◽  
pp. A32.4-A33 ◽  
Author(s):  
Tiet May Yung ◽  
Barnes Michael R
Keyword(s):  
Gene Interaction ◽  
Drug Binding ◽  
Sensory Nerves ◽  
Functional Enrichment ◽  
Gene Interactions ◽  
Human Phenotype ◽  
Interaction Database ◽  
Large Gene ◽  
Inherited Neuropathy ◽  
Inherited Neuropathies

BackgroundInherited neuropathies are genetic conditions affecting the peripheral motor and sensory nerves. The number of causative genes are continuing to expand. As more genes are being discovered, more phenotypes are attributed. Despite our rapidly growing knowledge, inherited neuropathies remain incurable diseases.With the wealth of information now available, bioinformatic platforms are available to visualise functional enrichment of genes and gene-phenotype annotations to enhance our understanding of the mechanism of disease and support hypothesis-driven research.MethodsThe interactors of inherited neuropathy genes were explored using the Search Tool for Recurring Incidences of Neighbouring Genes (STRING) database. Drug-phenotype interactions were assessed using PhenogramViz, human phenotype ontology terms (HPO). We used the Drug Gene Interaction Database (DGIdb) to find drug-gene interactions then used DoGSiteScorer to view potential drug binding pockets.ResultsInherited neuropathy genes were associated with gene ontology terms related to axonal transport. A total of 380 HPO terms were annotated to the genes which shared a phenotypic spectrum with neurodegenerative disorders. We identified 221 drug-gene interactions.ConclusionBioinformatic platforms are available to rapidly visualise and explore large gene-sets. Platforms to annotate drug-gene interactions need to be developed to assist drug discovery and identify potential agents that can be repurposed.

scholarly journals Multiplatform Application Technology – Based Heutagogy on Learning Batik: A Curriculum Development Framework

2020 ◽  
Vol 5 (1) ◽  
pp. 45-61 ◽  
Author(s):  
Isma Widiaty ◽  
Lala Septem Riza ◽  
Ade Gafar Abdullah ◽  
Sugeng Rifqi Mubaroq
Keyword(s):  
High School Students ◽  
Web Application ◽  
Application Programming Interface ◽  
Application Framework ◽  
Vocational High School ◽  
School Students ◽  
Web Based ◽  
Development Framework ◽  
Application Programming ◽  
Main Components

This  study  aimed  to  design  a  batik  learning  medium  for vocational high school students in based on multiplatform. The application  made was expected  to support heutagogy approach – based learning and to deal with the development of  science  and  technology  integrated  in  the  curriculum  of vocational high schools. The application developed, namely e-botik,  was  an  integration  of  several  previously-designed applications using Code ignitor (CI) framework. The database used was My-SQL. It is commonly known that Code igniter is an open source web application framework utilized to create dynamic PHP applications. In this study, e-botik consisted of three main  components  including interface, database,  and application  programming  interface  (API).  Some  of  the applications combined were ARtikon_joyful (Android-based), Video Kasumedangan Batik (movie player), Nalungtik  Batik (desktop-based),  Digi_Learnik  (web-based),  Batik  UPI (manual),  Batik  Cireundeu  (manual),  and  Lembar  Balik (manual). The combination proceeded web-based so that it was  compatible  with  various  operating  systems.  The application (e-botik) was designed and then tested. The test was  performed  through  whitebox  testing  and  blackbox testing. The results of the test showed that it ran well and was able to be used a batik learning media. It is expected that students  can  utilize  e-botik  in  selecting  topics  of  learning batik in accordance with their competences and needs. This condition enables e-botik to support learning batik through heutagogical approach. In addition, the application was also validated in terms of both system and usage aspects. 

scholarly journals Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

2020 ◽  
Author(s):  
Sharon Freshour ◽  
Susanna Kiwala ◽  
Kelsy C. Cotto ◽  
Adam C. Coffman ◽  
Joshua F. McMichael ◽  
...  
Keyword(s):  
Routine Data ◽  
Gene Interaction ◽  
Application Programming Interface ◽  
Web Based ◽  
Web Resource ◽  
Interaction Database ◽  
Manual Curation ◽  
Application Programming ◽  
Further Development ◽  
Programming Interface

ABSTRACTThe Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from various sources including publications, databases, and other web-based sources in one resource. These drug, gene, and interaction claims are normalized and grouped to identify aliases, merge concepts, and reduce redundancy. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major update of this database. Seven new sources have been added, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include further development of automatic jobs for routine data updates, more sophisticated query scores for interaction search results, extensive manual curation of interaction source link outs, and the inclusion of interaction directionality. A major focus of this update was integration with crowd-sourced efforts, including leveraging the curation activities of Drug Target Commons, using Wikidata to facilitate term normalization, and integrating into NDEx for producing network representations.

scholarly journals The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

2016 ◽  
Vol 24 (3) ◽  
pp. 513-519 ◽  
Author(s):  
Linda Huang ◽  
Helen Fernandes ◽  
Hamid Zia ◽  
Peyman Tavassoli ◽  
Hanna Rennert ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Precision Medicine ◽  
Web Application ◽  
Cancer Genomics ◽  
Application Programming Interface ◽  
Application Framework ◽  
Clinical Grade ◽  
Online Application ◽  
Collaborative Editing ◽  
Clinical Cancer

Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.

scholarly journals Analysis of the Optimal Application of Blockchain-Based Smart Lockers in the Logistics Industry Based on FFD-SAGA and Grey Decision-Making

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 329
Author(s):  
Shen-Tsu Wang ◽  
Meng-Hua Li ◽  
Chun-Chi Lien
Keyword(s):  
Web Application ◽  
Success Factors ◽  
Service Providers ◽  
Cost Effective ◽  
Application Programming Interface ◽  
Fractional Factorial ◽  
Office Workers ◽  
Logistics Industry ◽  
Blockchain Technology ◽  
Multiple Attribute

Blockchain technology has been applied to logistics tracking, but it is not cost-effective. The development of smart lockers has solved the problem of repeated distribution to improve logistics efficiency, thereby becoming a solution with convenience and privacy compared to the in-store purchase and pickup alternative. This study prioritized the key factors of smart lockers using a simulated annealing–genetic algorithm by fractional factorial design (FFD-SAGA) and grey relational analysis, and investigated the main users of smart lockers by grey multiple attribute decision analysis. The results show that the Web application programming interface (API) concatenation and money flow provider are the key success factors of smart lockers, and office workers are the main users of the lockers. Hence, how to better meet the needs of office workers will be an issue of concern for service providers.

The Design of Embedded Systems GUI Message Based on Mobile and Intelligent Materials

2012 ◽  
Vol 460 ◽  
pp. 210-213
Author(s):  
Shu Zhou
Keyword(s):  
Information Technology ◽  
User Interface ◽  
Embedded Systems ◽  
Graphical User Interface ◽  
Application Framework ◽  
The Novel ◽  
Interaction Interface ◽  
Novel Method ◽  
Personal Assistant ◽  
Embedded Gui

Research and development of embedded systems is the hot information technology and the graphical user interface (GUI) is the most important part of human-computer interaction interface. These embedded GUI system has been widely used because of its strong and powerful functionality. But many times , it is necessary to sacrifice performance for its versatility. In this paper, the embedded GUI systems based on the message mechanism is study considering the short of current embedded GUI systems. The novel method of a message-driven application framework is suggested to solve the problem of the current message mechanisms for the implementation. Meanwhile, a circular queue algorithm is given in order to achieve messaging unit. Then, the message has been classified considering of efficiency. In the end, the design example of personal assistant is given.

scholarly journals Safety Measures and Auto Detection against SQL Injection Attacks

2019 ◽  
Vol 8 (4) ◽  
pp. 2827-2833
Keyword(s):  
Web Application ◽  
Application Programming Interface ◽  
Database Management System ◽  
Transport Layer ◽  
Prototype System ◽  
Large Network ◽  
Security Measures ◽  
Sql Injection ◽  
Sql Injection Attack ◽  
The Web

The SQL injection attack (SQLIA) occurred when the attacker integrating a code of a malicious SQL query into a valid query statement via a non-valid input. As a result the relational database management system will trigger these malicious query that cause to SQL injection attack. After successful execution, it may interrupts the CIA (confidentiality, integrity and availability) of web API. The vulnerability of Web Application Programming Interface (API) is the prior concern for any programming. The Web API is mainly based of Simple Object Access Protocol (SOAP) protocol which provide its own security and Representational State Transfer (REST) is provide the architectural style to security measures form transport layer. Most of the time developers or newly programmers does not follow the standards of safe programming and forget to validate their input fields in the form. This vulnerability in the web API opens the door for the threats and it’s become a cake walk for the attacker to exploit the database associated with the web API. The objective of paper is to automate the detection of SQL injection attack and secure the poorly coded web API access through large network traffic. The Snort and Moloch approaches are used to develop the hybrid model for auto detection as well as analyze the SQL injection attack for the prototype system

scholarly journals AUTOMATED INFORMA¬TION SYSTEM FOR GPS MONITORING DATA PROCESSING

2021 ◽  
Vol 2 (37) ◽  
pp. 88-92
Author(s):  
K. Yalova ◽  
K. Yashyna ◽  
O. Tarasiyk
Keyword(s):  
User Interface ◽  
Data Processing ◽  
System Architecture ◽  
Web Application ◽  
Gps Tracking ◽  
System Software ◽  
Web Interfaces ◽  
Application Service ◽  
Functional Features ◽  
Tion System

Using of automated information systems in the field of geolocation data processing increases the control and management efficiency of freight and passenger traffic. The article presents the results of design and software implementation of the automated information system that allows monitoring of GPS tracking data in real time, build routes and set control points for it, generate system messages about the status of vehicles on the route and generate reporting information on the base of user requests. The design of the system architecture and interface was carried out on the basis of developed object and functional data domain models, which take into account its structural and functional features. The microservice approach principles were applied during the developing of the system architecture. The system software is a set of independent services that work in their own process, implement a certain business logic algorithm and communicate with other services through the HTTP protocol. The set of the system software services consists of: a service for working with GPS data, a service for implementing geolocation data processing functions, and a web application service. The main algorithms of the developed system services and their functional features are described in the work. Article’s figures graphically describe developed system site map and system typical Web forms. This data displays the composition of web pages, paths between them and shows the user interface. The design of the user interface was carried out taking into account quality requirements of user graphical web interfaces.

Sign in / Sign up

Export Citation Format

Share Document