In this work we present Publication Access Through Tiered Interaction & Exploration (PATTIE) -an information foraging, sense-making, and exploratory spatial-semantic information retrieval (IR) system (http://pattie.unc.edu/plos). Non-spatial, spatial IR systems, and some recent studies focused on their principal functions are discussed and compared. To interactively work through a use-case from the biomedical domain, instructions are provided for readers to conduct exploratory searches directly on the PLOS archive based on the software embedded in the online version of this paper (http://vzlib.unc.edu/software/). To carefully evaluate some of the critical parameters of the PATTIE algorithm, and the core functions of the implemented system, a set of experiments were conducted. Along with details on the experimental methods and their rationale, key findings from the experiments are analyzed and presented. Finally, with an eye toward the future of software-embedded scientific papers, their potential benefits for supporting direct engagement with scientific content, replication, and validation are discussed.Information retrieval (IR) systems are essential tools for finding relevant documents.2 Current IR systems dominantly adopt the ranking-based retrieval model, which returns 3 a list of documents ranked in descending order of predicted relevance for a user query 4 (i.e., search keywords). Such an architecture and information access point rely on the 5 user having and understanding on how and what to search for. The evidence base 6 suggests that this is often an incorrect assumption to make [1, 2]. Despite a user 7 overcoming these assumptions by searching appropriately, a Search Engine Result Page 8 (SERP) can retrieve an extraordinarily large set of documents which makes it difficult 9 to locate and comprehend all the relevant information. This is especially true for the 10 biomedical domain given the ever-growing body of the literature; a position that IR 11 researchers have been discussing for decades now.
12For instance, consider a scenario where a researcher unfamiliar with the PLOS 13 digital archive is curious to understand the topical structure. Without issuing a query, a 14 October 14, 2019 2/22 dynamic spatial-semantic table-of-contents can be generated as shown in Fig 1. The 15 PATTIE Map presents the most recently published topical content within the PLOS 16 digital archive. We will demonstrate the access point, mechanism of navigation, and 17 information acquisition in the System design and implementation details and Discussion 18 sections. 19 Fig 1. A screenshot of PLOS digital archive PATTIE Map, no query issued.Alternative modes of access or metaphors for representing and presenting 20 information spaces in IR that incorporate spatial-semantic context may prove beneficial, 21and have been discussed with works on exploratory search, sense-making, information 22 foraging [3-9], and visualization of concept spaces [10]. Moreover, when we consider 23 individual differences in verbal and spatial reasonin...
