The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

<p>Abstract</p> <p>Background</p> <p>Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data.</p> <p>Results</p> <p>The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks.</p> <p>Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents.</p> <p>We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe <it>Halobacterium salinarum NRC-1 </it>in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved.</p> <p>Conclusion</p> <p>The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.</p

Abmash: Mashing Up Legacy Web Applications by Automated Imitation of Human Actions

Many business web-based applications do not offer applications programming interfaces (APIs) to enable other applications to access their data and functions in a programmatic manner. This makes their composition difficult (for instance to synchronize data between two applications). To address this challenge, this paper presents Abmash, an approach to facilitate the integration of such legacy web applications by automatically imitating human interactions with them. By automatically interacting with the graphical user interface (GUI) of web applications, the system supports all forms of integrations including bi-directional interactions and is able to interact with AJAX-based applications. Furthermore, the integration programs are easy to write since they deal with end-user, visual user-interface elements. The integration code is simple enough to be called a "mashup".Comment: Software: Practice and Experience (2013)

Virtual Notes:Annotations on the WWW for Learning Environments

This paper describes Virtual Notes, small yellow stickers which can be freely placed on instrumented HTML-pages using standard Internet technology. In a teaching and research environment they provide a user- friendly and flexible way of improving collaboration by annotations, feedback, post-its and blackboards

Extending the 5S Framework of Digital Libraries to support Complex Objects, Superimposed Information, and Content-Based Image Retrieval Services

Advanced services in digital libraries (DLs) have been developed and widely used to address the required capabilities of an assortment of systems as DLs expand into diverse application domains. These systems may require support for images (e.g., Content-Based Image Retrieval), Complex (information) Objects, and use of content at fine grain (e.g., Superimposed Information). Due to the lack of consensus on precise theoretical definitions for those services, implementation efforts often involve ad hoc development, leading to duplication and interoperability problems. This article presents a methodology to address those problems by extending a precisely specified minimal digital library (in the 5S framework) with formal definitions of aforementioned services. The theoretical extensions of digital library functionality presented here are reinforced with practical case studies as well as scenarios for the individual and integrative use of services to balance theory and practice. This methodology has implications that other advanced services can be continuously integrated into our current extended framework whenever they are identified. The theoretical definitions and case study we present may impact future development efforts and a wide range of digital library researchers, designers, and developers

The Semantic Shadow : Combining User Interaction with Context Information for Semantic Web-Site Annotation

This thesis develops the concept of the Semantic Shadow (SemS), a model for managing contentual and structural annotations on web page elements and their values. The model supports a contextual weighting of the annotated information, allowing to specify the annotation values in relation to the evaluation context. A procedure is presented, which allows to manage and process this context-dependent meta information on web page elements using a dedicated programming interface. Two distinct implementations for the model have been developed: One based on Java objects, the other using the Resource Description Framework (RDF) as modeling backend. This RDF-based storage allows to integrate the annotations of the Semantic Shadow with other information of the Semantic Web. To demonstrate the application of the Semantic Shadow concept, a procedure to optimize web based user interfaces based on the structural semantics has been developed: Assuming a mobile client, a requested web page is dynamically adapted by a proxy prototype, where the context-awareness of the adaptation can be directly modeled alongside with the structural annotations. To overcome the drawback of missing annotations for existing web pages, this thesis introduces a concept to derive context-dependent meta-information on the web pages from their usage: From the observation of the users' interaction with a web page, certain context-dependent structural information about the concerned web page elements can be derived and stored in the annotation model of the Semantic Shadow concept.In dieser Arbeit wird das Konzept des Semantic Shadow (dt. Semantischer Schatten) entwickelt, ein Programmier-Modell um Webseiten-Elemente mit inhaltsbezogenen und strukturellen Anmerkungen zu versehen. Das Modell unterstützt dabei eine kontextabhängige Gewichtung der Anmerkungen, so dass eine Anmerkung in Bezug zum Auswertungs-Kontext gesetzt werden kann. Zur Verwaltung und Verarbeitung dieser kontextbezogenen Meta-Informationen für Webseiten-Elemente wurde im Rahmen der Arbeit eine Programmierschnittstelle definiert. Dazu wurden zwei Implementierungen der Schnittstelle entwickelt: Eine basiert ausschließlich auf Java-Objekten, die andere baut auf einem RDF-Modell auf. Die RDF-basierte Persistierung erlaubt eine Integration der Semantic-Shadow-Anmerkungen mit anderen Anwendungen des Semantic Webs. Um die Anwendungsmöglichkeiten des Semantic-Shadow-Konzepts darzustellen, wurde eine Vorgehensweise zur Optimierung von webbasierten Benutzerschnittstellen auf Grundlage von semantischen Strukturinformationen entwickelt: Wenn ein mobiler Benutzer eine Webseite anfordert, wird diese dynamisch durch einen Proxy angepasst. Die Kontextabhängigkeit dieser Anpassung wird dabei bereits direkt mit den Struktur-Anmerkungen modelliert. Für bestehende Webseiten liegen zumeist keine Annotationen vor. Daher wird in dieser Arbeit ein Konzept vorgestellt, kontextabhängige Meta-Informationen aus der Benutzung der Webseiten zu bestimmen: Durch Beobachtung der Benutzer-Interaktionen mit den Webseiten-Elementen ist es möglich bestimmte kontextabhängige Strukturinformationen abzuleiten und als Anmerkungen im Modell des Semantic-Shadow-Konzepts zu persistieren

From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results

Beyond the Feed and Board: Holistic Principles for Expressive Web Curation

We develop holistic principles for expressive web curation through the iterative design and study of a new medium and system, IdeaMâché. Web curation is the process of gathering and assembling content into online exhibits. The linear organization of the feed - e.g., Facebook and Twitter - and board - e.g., Pinterest - constrains authors in expressing themselves. We conducted a field study of IdeaMâché with 472 undergraduate student users. Quantitative, qualitative, and visual data show how students expressed themselves and developed ideas. Interaction logs show how students utilized expressive operations. We analyze students' creative works with ideation metrics of curation. Interviews expose users' underlying motivations and experiences. Visual data is compelling. While iteratively designing IdeaMâché features in conjunction with the mixed methods data, we derive holistic design principles for media and systems supporting expressive web curation: direct clipping with context, diverse and heterogeneous media, freeform non-linear medium of assemblage, multi-scale organization, sketching as annotation, and novice-friendly direct manipulation command selection and parameter adjustment