Cohen-Boulakia, Sarah
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Publication Selecting Biological Data Sources and Tools with XPR, a Path Language for RDF(2006-01-01) Cohen-Boulakia, Sarah; Froidevaux, Christine; Pietriga, EmmanuelAs the number, richness and diversity of biological sources grow, scientists are increasingly confronted with the problem of selecting appropriate sources and tools. To address this problem, we have designed BioGuide, a user-centric framework that helps scientists choose sources and tools according to their preferences and strategy, by specifying queries through a user-friendly visual interface. In this paper, we provide a complete RDF representation of BioGuide and introduce XPR (eXtensible Path language for RDF), an extension of FSL that is expressive enough to model all BioGuide queries. BioGuide queries modeled as XPR expressions can then be saved, compared, evaluated and exchanged through the Web between users and applications.Publication Selecting biomedical data sources according to user preferences(2005-07-01) Cohen-Boulakia, Sarah; Lair, Severine; Stransky, Nicolas; Graziani, Stephane; Radvanyi, Francois; Barillot, Emmanuel; Froidevaux, ChristineMotivation: Biologists are now faced with the problem of integrating information from multiple heterogeneous public sources with their own experimental data contained in individual sources. The selection of the sources to be considered is thus critically important. Results: Our aim is to support biologists by developing a module based on an algorithm that presents a selection of sources relevant to their query and matched to their own preferences. We approached this task by investigating the characteristics of biomedical data and introducing several preference criteria useful for bioinformaticians. This work was carried out in the framework of a project which aims to develop an integrative platform for the multiple parametric analysis of cancer. We illustrate our study through an elementary biomedical query occurring in a CGH analysis scenario.Publication Addressing the Provenance Challenge using ZOOM(2007-05-01) Cohen-Boulakia, Sarah; Biton, Olivier; Cohen, Shirley; Davidson, Susan BZOOM*UserViews presents a model of provenance for scientific workflows that is simple, generic, and yet sufficiently expressive to answer questions of data and step provenance that have been encountered in a large variety of scientific case studies. In addition, ZOOM builds on the concept of composite step-classes – or sub-workflows – which is present in many scientific workflow systems to develop a notion of user views. This paper discusses the design and implementation of ZOOM in the context of the queries posed by the provenance challenge, and shows how user views affect the level of granularity at which provenance information can be seen and reasoned about.Publication Path-based systems to guide scientists in the maze of biological data sources(2006-08-24) Cohen-Boulakia, Sarah; Davidson, Susan B.; Froidevaux, Christine; Lacroix, Zoe; Vidal, Maria-EstherFueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer. Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data. In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.Publication BioGuideSRS: Querying Multiple Sources with a user-centric perspective(2007-01-01) Cohen-Boulakia, Sarah; Biton, Olivier; Davidson, Susan B; Froidevaux, ChristineSummary: Biologists are frequently faced with the problem of integrating information from multiple heterogeneous sources with their own experimental data. Given the large number of public sources, it is difficult to choose which sources to integrate without assistance. When doing this manually, biologists differ in their preferences concerning the sources to be queried as well as the strategies, i.e. the querying process they follow for navigating through the sources. In response to these findings, we have developed BioGuide to assist scientists search for relevant data within external sources while taking their preferences and strategies into account. In this paper, we present BioGuideSRS, a user-friendly system which automatically retrieves instances of data by using BioGuide on top of the SRS system. BioGuideSRS is an Applet that can be run from its web page on any system with Java 5.0. Availability: http://www.bioguide-project.net