scholarly journals The Precision Medicine Knowledge Base: an online application for collaborative editing, maintenance and sharing of structured clinical-grade cancer mutations interpretations

2016 ◽  
Author(s):  
Linda Huang ◽  
Helen Fernandes ◽  
Hamid Zia ◽  
Peyman Tavassoli ◽  
Hanna Rennert ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Precision Medicine ◽  
Web Application ◽  
Cancer Genomics ◽  
Application Framework ◽  
Clinical Grade ◽  
Online Application ◽  
Collaborative Editing ◽  
Clinical Cancer ◽  
Cancer Mutations

ABSTRACTObjectiveThis 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 mutations interpretations.Materials and MethodsPMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as Human Genome Variation Society (HGVS) 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, detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically.ResultsAt 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. The PMKB’s interpretations have been used in over 1,500 AmpliSeq tests and 750 whole exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API.DiscussionAn 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.ConclusionThe PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitates 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 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 Genetic Gastric Cancer Susceptibility in the International Clinical Cancer Genomics Community Research Network

2017 ◽  
Vol 216-217 ◽  
pp. 111-119 ◽  
Author(s):  
Thomas Slavin ◽  
Susan L. Neuhausen ◽  
Christina Rybak ◽  
Ilana Solomon ◽  
Bita Nehoray ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Genomics ◽  
Cancer Susceptibility ◽  
Research Network ◽  
Community Research ◽  
Clinical Cancer

scholarly journals Use of Linked Data principles for semantic management of scanned documents

2016 ◽  
Vol 28 (2) ◽  
pp. 241-251 ◽  
Author(s):  
Luciane Lena Pessanha Monteiro ◽  
Mark Douglas de Azevedo Jacyntho
Keyword(s):  
Decision Making ◽  
Knowledge Base ◽  
Web Application ◽  
Linked Data ◽  
World Wide ◽  
Decision Making Process ◽  
Whole Process ◽  
The World ◽  
Scanned Documents ◽  
The Web

The study addresses the use of the Semantic Web and Linked Data principles proposed by the World Wide Web Consortium for the development of Web application for semantic management of scanned documents. The main goal is to record scanned documents describing them in a way the machine is able to understand and process them, filtering content and assisting us in searching for such documents when a decision-making process is in course. To this end, machine-understandable metadata, created through the use of reference Linked Data ontologies, are associated to documents, creating a knowledge base. To further enrich the process, (semi)automatic mashup of these metadata with data from the new Web of Linked Data is carried out, considerably increasing the scope of the knowledge base and enabling to extract new data related to the content of stored documents from the Web and combine them, without the user making any effort or perceiving the complexity of the whole process.

scholarly journals Prediction of Caption and Emoji of an Image using Deep Learning

2019 ◽  
Vol 8 (2S11) ◽  
pp. 3721-3724
Keyword(s):  
Deep Learning ◽  
Social Networking ◽  
Web Application ◽  
Automatic Generation ◽  
Application Framework ◽  
Challenging Problem ◽  
Artificial Intelligence Research ◽  
Learning Techniques ◽  
User Friendly ◽  
Visually Impaired Persons

With the invention of deep learning, there is a good progress in image classification. But automatic generation of captions for images is still a challenging problem and is in the initial stages of artificial intelligence research. Automatic description of images has applications in social networking and will be useful to visually impaired persons. This paper concentrates on designing a user-friendly web application framework which can predict the caption of an image using deep learning techniques. The verbs and objects present in the caption are used for forming the emoji and for predicting the major color of the image

scholarly journals Framework Design for Modular Web-based Application Using Model-CollectionService-Controller-Presenter (MCCP) Pattern

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Aryo Pinandito
Keyword(s):  
Information System ◽  
Web Application ◽  
Design Pattern ◽  
Data Exchange ◽  
Data Communication ◽  
Communication Process ◽  
Application Framework ◽  
Application Development ◽  
Web Based ◽  
Organization Model

Information system is one of the most important business supports in organizations. Web-based applications become an appropriate solution to overcome the dynamically changing environment among different units in an organization. Model-View-Controller (MVC) is a well-known design pattern in web-based application development due to the separation of an application into several parts, hence it is easy to reuse and maintain. However, such design pattern requires improvements since the information system handles business process choreography and integration between application. Therefore, modifying the interaction of object of class in a design pattern become a challenging problem. In this paper, an application framework based on Model-CollectionService-Controller-Presenter (MCCP) design pattern, which is a modification of an MVC, was proposed. The proposed framework allows multiple different applications to run and provides inter-application data exchange mechanisms to improve the data communication process between applications. Several performance comparisons with another popular web application framework are also presented.

scholarly journals Purwarupa Framework Aplikasi Desktop Menggunakan Teknologi Web

2015 ◽  
Vol 9 (1) ◽  
pp. 23
Author(s):  
Firmansyah Adiputra ◽  
Khabib Mustofa
Keyword(s):  
Web Application ◽  
Web Applications ◽  
Application Framework ◽  
Web Browser ◽  
Web Technologies ◽  
Desktop Application ◽  
New Type

AbstrakAplikasi desktop adalah aplikasi yang berjalan lokal dalam lingkungan desktop dan hanya dapat diakses oleh pengguna desktop. Ini berbeda dengan aplikasi web yang dapat diakses dari manapun melalui jaringan. Namun tidak seperti halnya aplikasi desktop, aplikasi web yang berjalan di atas web browser tidak dapat berintegrasi dengan aplikasi desktop yang berjalan pada sisi klien.Dalam penelitian ini dibangun purwarupa framework yang diberi nama HAF (Hybrid Application Framework). HAF digunakan untuk mengembangkan dan mengeksekusi jenis aplikasi desktop baru yang diberi nama HyApp (Hybrid Application). Melalui HAF, HyApp dibangun menggunakan teknologi web dan dapat diakses secara lokal maupun melalui jaringan. Saat diakses secara lokal, walaupun dikembangkan dengan teknologi web, HyApp dapat berkomunikasi dengan aplikasi desktop lainnya. Selain itu, melalui API yang disediakan oleh HAF, HyApp akan dapat menerapkan perilaku yang berbeda berdasarkan modus pengaksesan yang dilakukannya. Kata kunci—framework, aplikasi desktop, aplikasi web    AbstractDesktop application is an application that runs locally in a desktop environment and can be accessed only by desktop users. It differs from web application which can be accessed from anywhere through networks. But unlike desktop applications, web applications cannot integrate nicely with desktop applications from where it is accessed.This research developes a prototype of framework which is named HAF (Hybrid Application Framework). HAF is used for developing and executing a new type of desktop application, named HyApp (Hybrid Application). Through HAF, HyApp is built using web technologies and can be accessed either locally or from networks. When accessed locally, even though it is built using web technologies, it still can communicate with other desktop applications. Also by using APIs provided by HAF, HyApp is capable to behave differently based on whether it is accessed locally or remotely. Keywords—framework, desktop applications, web applications

The Johns Hopkins Molecular Tumor Board Precision Oncology elective for Medical Oncology fellows.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 11035-11035
Author(s):  
Kristen Marrone ◽  
Jessica Tao ◽  
Jenna VanLiere Canzoniero ◽  
Paola Ghanem ◽  
Emily Nizialek ◽  
...  
Keyword(s):  
Decision Making ◽  
Precision Medicine ◽  
Clinical Decision Making ◽  
Cancer Genomics ◽  
Medical Oncology ◽  
Clinical Decision ◽  
Tumor Board ◽  
Precision Oncology ◽  
Adaptive Expertise ◽  
Molecular Tumor Board

11035 Background: The accelerated impact of next generation sequencing (NGS) in clinical decision making requires the integration of cancer genomics and precision oncology focused training into medical oncology education. The Johns Hopkins Molecular Tumor Board (JH MTB) is a multi-disciplinary effort focused on integration of NGS findings with critical evidence interpretation to generate personalized recommendations tailored to the genetic footprint of individual patients. Methods: The JH MTB and the Medical Oncology Fellowship Program have developed a 3-month precision oncology elective for fellows in their research years. Commencing fall of 2020, the goals of this elective are to enhance the understanding of NGS platforms and findings, advance the interpretation and characterization of molecular assay outputs by use of mutation annotators and knowledgebases and ultimately master the art of matching NGS findings with available therapies. Fellow integration into the MTB focuses on mentored case-based learning in mutation characterization and ranking by levels of evidence for actionability, with culmination in form of verbal presentations and written summary reports of final MTB recommendations. A mixed methods questionnaire was administered to evaluate progress since elective initiation. Results: Three learners who have participated as of February 2021 were included. Of the two who had completed the MTB elective, each have presented at least 10 cases, with at least 1 scholarly publication planned. All indicated strong agreement that MTB elective had increased their comfort with interpreting clinical NGS reports as well as the use of knowledgebases and variant annotators. Exposure to experts in the field of molecular precision oncology, identification of resources necessary to interpret clinical NGS reports, development of ability to critically assess various NGS platforms, and gained familiarity with computational analyses relevant to clinical decision making were noted as strengths of the MTB elective. Areas of improvement included ongoing initiatives that involve streamlining variant annotation and transcription of information for written reports. Conclusions: A longitudinal elective in the JHU MTB has been found to be preliminarily effective in promoting knowledge mastery and creating academic opportunities related to the clinical application of precision medicine. Future directions will include leveraging of the MTB infrastructure for research projects, learner integration into computational laboratory meetings, and expansion of the MTB curriculum to include different levels of learners from multiple medical education programs. Continued elective participation will be key to understanding how best to facilitate adaptive expertise in assigning clinical relevance to genomic findings, ultimately improving precision medicine delivery in patient care and trial development.

Method Using Command Abstraction Library for Iterative Testing Security of Web Applications

2018 ◽  
pp. 192-215
Author(s):  
Seiji Munetoh ◽  
Nobukazu Yoshioka
Keyword(s):  
Web Application ◽  
Agile Development ◽  
Application Framework ◽  
Security Testing ◽  
Application Development ◽  
Security Assurance ◽  
Security Issues ◽  
Application Logic ◽  
Granularity Level ◽  
Scripting Language

A framework based on a scripting language is commonly used in Web application development, and high development efficiency is often achieved by applying several Agile development techniques. However, the adaptation of security assurance techniques to support Agile development is still underway, particularly from the developer's perspective. The authors have addressed this problem by developing an iterative security testing method that splits the security test target application into two parts on the basis of the code lifecycle, application logic (“active development code”) and framework (“used code”). For the former, detailed security testing is conducted using static analysis since it contains code that is changed during the iterative development process. For the latter, an abstraction library at the command granularity level is created and maintained. The library identifies the behavior of an application from the security assurance standpoint. This separation reduces the amount of code to be statically inspected and provides a mechanism for sharing security issues among application developers using the same Web application framework. Evaluation demonstrated that this method can detect various types of Web application vulnerabilities.

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