scholarly journals Mining Gene Ontology Data with AGENDA

2012 ◽  
Vol 6 ◽  
pp. BBI.S9101
Author(s):  
Guvanch Ovezmyradov ◽  
Qianhao Lu ◽  
Martin C. Göpfert
Keyword(s):  
Gene Ontology ◽  
Open Source ◽  
Genetic Information ◽  
Collaborative Effort ◽  
Controlled Vocabularies ◽  
Web Based ◽  
Commercial Use ◽  
Diverse Species ◽  
Go Terms ◽  
The Web

The Gene Ontology (GO) initiative is a collaborative effort that uses controlled vocabularies for annotating genetic information. We here present AGENDA (Application for mining Gene Ontology Data), a novel web-based tool for accessing the GO database. AGENDA allows the user to simultaneously retrieve and compare gene lists linked to different GO terms in diverse species using batch queries, facilitating comparative approaches to genetic information. The web-based application offers diverse search options and allows the user to bookmark, visualize, and download the results. AGENDA is an open source web-based application that is freely available for non-commercial use at the project homepage. URL: http://sourceforge.net/projects/bioagenda .

scholarly journals Using Open-Source Software for Sign Language Learning and Assessment

2019 ◽  
Vol 14 (19) ◽  
pp. 188
Author(s):  
Tobias Haug ◽  
Sarah Ebling
Keyword(s):  
Adult Learners ◽  
Language Learning ◽  
Open Source ◽  
Sign Language ◽  
Open Source Software ◽  
Self Assessment ◽  
Web Based ◽  
Swiss German ◽  
Feedback Questionnaire ◽  
The Web

This study reports on the use of an open-source software for sign language learning and (self-)assessment. A Yes/No vocabulary size test for Swiss German Sign Language (Deutschschweizerische Gebärdensprache, DSGS) was developed, targeting beginning adult learners. The Web-based test, which can be used for self-assessment or placement purposes, was administered to 20 DSGS adult learners of ages 24 to 55 (M = 39.3). The learners filled out a background questionnaire, took the Yes/No test tests, and filled out a feedback questionnaire. The comments provided by the learners about the suitability of the Web-based DSGS vocabulary self-assessment instrument provided concrete feedback towards improvement of the system.

scholarly journals The Scientific Comparison between Web-Based Site and Web-Builder (Open Source) Project: Functionalities, Usability, Design and Security

2018 ◽  
Vol 6 (06) ◽  
Author(s):  
Aso Mohammed Aladdin ◽  
Chnoor M. Rahman ◽  
Mzhda S. Abdulkarim
Keyword(s):  
Open Source ◽  
Programming Languages ◽  
Web Sites ◽  
Web Site ◽  
Business Organization ◽  
Web Based ◽  
Open Source Project ◽  
A Site ◽  
The Web

In developing web sites there are some rules that developers should depend on in order to create a site suitable to the users’ needs and also to make them as comfort as possible when they surf it. Before creating any website or operating any application, it is important for developers to address the functionality, design, usability and security of the work according to the demands.  Every developer has his/her own way to develop a website, some prefer to use website builders and while others prefer to what they have primarily formed in their mind What they have primarily formed in their mind preferred software and programming languages. Therefore, this paper will compare the web based sites and open source projects in terms of functionality, usability, design and security in order to help academic staffs or business organization for choosing the best way for developing an academic or e-commerce web site.  

Managing Operational Business Processes with Web-Based Information Technologies

2009 ◽  
pp. 217-225
Author(s):  
Ned Kock
Keyword(s):  
Information Technologies ◽  
Business Processes ◽  
The Internet ◽  
Team Coordination ◽  
Web Based ◽  
Commercial Use ◽  
Generic Framework ◽  
Starting Point ◽  
Use Of The Internet ◽  
The Web

Traditionally management schools of thought that emphasize certain types of work structures usually appear earlier than information technologies (IT) geared at supporting those work structures. This situation has undoubtedly changed recently, arguably around the mid-1990s, with the explosion in the commercial use of the Internet and particularly the Web. This calls for the development of a generic framework that ties together relevant management ideas that help organizations strategically and operationally align themselves with new Web-based IT. Our goal with this chapter is to provide some basic elements that can be used by managers and researchers as a starting point to develop this generic framework. As such, we focus on a particular set of activities associated with team coordination and communication in production and service delivery business processes through the Internet and the Web.

scholarly journals MonaGO: a novel Gene Ontology enrichment analysis visualisation system

2020 ◽  
Author(s):  
Ziyin Xin ◽  
Yujun Cai ◽  
Louis T. Dang ◽  
Hannah M.S. Burke ◽  
Jerico Revote ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Enrichment Analysis ◽  
Web Browser ◽  
Web Based ◽  
Single Output ◽  
Go Enrichment ◽  
Unbiased Manner ◽  
High Resolution Images ◽  
Interactive Visualisation ◽  
Go Terms

AbstractMonaGO is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing gene ontology (GO) enrichment analysis and visualising the results. MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is the only platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options. In summary, MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.

scholarly journals GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis

2009 ◽  
Vol 3 (1) ◽  
pp. 26-30 ◽  
Author(s):  
Mathur Sachin ◽  
Visvanathan Mahesh ◽  
Svojanovsky Stan ◽  
Yoo Byunggil ◽  
Srinivas Adagarla B. ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Protein Interactions ◽  
Microarray Data ◽  
Sources Of Information ◽  
Web Based ◽  
Gene Annotations ◽  
Functional Pathways ◽  
Microarray Datasets ◽  
User Friendly ◽  
The Web

We have developed the web based tool GOAPhAR (Gene Ontology, Annotations and Pathways for Array Research), that integrates information from disparate sources regarding gene annotations, protein annotations, identifiers associated with probe sets, functional pathways, protein interactions, Gene Ontology, publicly available microarray datasets and tools for statistically validating clusters in microarray data. Genes of interest can be input as Affymetrix probe identifiers, Genbank, or Unigene identifiers for human, mouse or rat genomes. Results are provided in a user friendly interface with hyperlinks to the sources of information. The tool is freely available at http://bioinformatics.kumc.edu/goaphar/.

Summary Visualisations of Gene Ontology Terms with GO-Figure!

2020 ◽  
Author(s):  
Maarten JMF Reijnders ◽  
Robert M Waterhouse
Keyword(s):  
Gene Ontology ◽  
Open Source ◽  
Large Scale ◽  
Semantic Space ◽  
Biological Data ◽  
Multiple Dataset ◽  
Term Enrichment ◽  
Genomics Research ◽  
Exploratory Data ◽  
Go Terms

AbstractThe Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large- scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualisations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualisation tools and resources there is a lack of standalone open-source software solutions that facilitate systematic comparisons of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together GO terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar GO terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualisations of lists of GO terms, designed to support exploratory data analyses and multiple dataset comparisons.

scholarly journals Mapping the Gene Ontology Into the Unified Medical Language System

2004 ◽  
Vol 5 (4) ◽  
pp. 354-361 ◽  
Author(s):  
Jane Lomax ◽  
Alexa T. McCray
Keyword(s):  
Gene Ontology ◽  
Clinical Medicine ◽  
Gene Products ◽  
National Library ◽  
Web Based ◽  
Language System ◽  
Unified Medical Language System ◽  
Medical Language ◽  
Large Numbers ◽  
Go Terms

We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics.

scholarly journals Feminist Science Interventions in Self-Tracking Technology

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Alessandra Mularoni
Keyword(s):  
Hormone Therapy ◽  
Open Source ◽  
Genetic Information ◽  
Feminist Art ◽  
Web Based ◽  
Feminist Science ◽  
Medical Products ◽  
Cell Track ◽  
Artistic Interventions ◽  
Tracking Technology

Contemporary self-tracking systems signal a new era of biological monitoring now entangled with the politics of ubiquitous computing. Is self-tracking technology, which is connected to major stakeholders in healthcare, essential for filling in gaps in care, or is it fueling an increasingly commercialized medical industry? This essay examines the complex biases embedded in self-tracking technologies and introduces three manifestations of feminist science that subvert the monetization of personal health information: feminist art collective subRosa, which investigates how personal genetic information is developed into marketable medical products in their web-based project, Cell Track: Mapping the Appropriation of Life Materials; media artist and biohacker Mary Maggic, who makes self-synthesized hormone therapy accessible with their Open Source Estrogen project; artist-researcher Heather Dewey-Hagborg, whose biohacking products provide a DIY science in a world marred by genetic policing. Against the lure of connectivity, feminist science looks to circumvention as a method for understanding and disrupting the gendered and raced politics embedded in self-tracking technology. Tracing alternative techno-politics in these three new media projects, this essay reveals the necessity for artistic interventions in the contemporary healthcare landscape. Feminist art collective subRosa investigates how personal genetic information is developed into marketable medical products in their web-based project, Cell Track: Mapping the Appropriation of Life Materials. Drawing attention to the corporate ownership of biology, Cell Track adds new meaning to the idea of tracking. Similarly emphasizing the potential in citizen science, media artist and biohacker Mary Maggic makes self-synthesized hormone therapy accessible with their Open-Source Estrogen project. Both subRosa and Maggic are interested in bypassing institutional gatekeepers, not unlike artist-researcher Heather Dewey-Hagborg whose biohacking products suggest a DIY science in a world marred by genetic policing. Feminist science aims to circumvent tracking and institutional biopower against targeted populations. Against the lure of connectivity, feminist science looks to circumvention as a method for understanding and disrupting the gendered and raced politics embedded in surveillance. Working through the three bioart projects above, this essay reveals the necessity for artistic interventions in the contemporary healthcare landscape. Where commercial self-tracking products shortchange consumers by requiring them to share their health data with third-party companies, a feminist science framework and practice critically examines – and in some cases offers a departure from – the neoliberal biotechnology and medical industries.

scholarly journals Summary Visualizations of Gene Ontology Terms With GO-Figure!

2021 ◽  
Vol 1 ◽  
Author(s):  
Maarten J. M. F. Reijnders ◽  
Robert M. Waterhouse
Keyword(s):  
Gene Ontology ◽  
Open Source ◽  
Large Scale ◽  
Semantic Space ◽  
Biological Data ◽  
Term Enrichment ◽  
Genomics Research ◽  
Exploratory Data ◽  
Data Summaries ◽  
Go Terms

The Gene Ontology (GO) is a cornerstone of functional genomics research that drives discoveries through knowledge-informed computational analysis of biological data from large-scale assays. Key to this success is how the GO can be used to support hypotheses or conclusions about the biology or evolution of a study system by identifying annotated functions that are overrepresented in subsets of genes of interest. Graphical visualizations of such GO term enrichment results are critical to aid interpretation and avoid biases by presenting researchers with intuitive visual data summaries. Amongst current visualization tools and resources there is a lack of standalone open-source software solutions that facilitate explorations of key features of multiple lists of GO terms. To address this we developed GO-Figure!, an open-source Python software for producing user-customisable semantic similarity scatterplots of redundancy-reduced GO term lists. The lists are simplified by grouping together terms with similar functions using their quantified information contents and semantic similarities, with user-control over grouping thresholds. Representatives are then selected for plotting in two-dimensional semantic space where similar terms are placed closer to each other on the scatterplot, with an array of user-customisable graphical attributes. GO-Figure! offers a simple solution for command-line plotting of informative summary visualizations of lists of GO terms, designed to support exploratory data analyses and dataset comparisons.

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