Discovery Interface Research Articles

Non-isothermal stability by linear heating: a fast method for preformulation stability screening of drugs at the discovery and development interface

The non-isothermal method for prediction of chemical stability of pharmaceuticals has been discussed in the literature for almost half a century but it has not yet been systematically evaluated. The purpose of this study was to carry out a comprehensive experimental evaluation of the non-isothermal method against the conventional isothermal method for a fast preformulation stability screening. The chemical stabilities of 20 pharmaceutical compounds in aqueous based solution were investigated. Degradation rate constants (k), activation energies (Ea), t90% and t98% (times for 10 and 2% loss of potency, respectively) were determined by applying the Arrhenius equation to stability data generated by both non-isothermal and isothermal methods. A comparison of the results indicated that the ‘1 week’ non-isothermal experiment is as accurate as the ‘8 weeks’ isothermal experiment for placing compounds (15 out of 16 cases) into the same binning categories based on t90% and t98% values. The absolute values of k, t90% and t98% at 25 °C determined by the non-isothermal method for compounds with first order (or pseudo-first order) degradation kinetics were within a factor of two compared to those determined by the isothermal method. The non-isothermal method proved to be not applicable for accurate prediction of the shelf-lives of pharmaceuticals, however, when used to bin discovery compounds based on likely issues related to chemical instability, the non-isothermal method can be carefully implemented as a cost effective, fast, and relatively ‘high-throughput’ method to support drug stability screening at the discovery and development interface.

When ERM Met Alma: The Intricacies of Content Management in a Shared Consortia Landscape

ABSTRACTIn 2013, after nearly two decades of operating in a distributed legacy Integrated Library System (ILS) environment on local servers, the Orbis Cascade Alliance, a consortium of public and private academic libraries in Washington, Oregon, and Idaho, began a two-year-long process to migrate its 37 members to a shared implementation of Ex Libris's cloud-based Alma library management system (LMS) and Primo discovery interface. Although much has been written on electronic resource management (ERM) functionality at an institution level, little has been written on serials and ERM functionality and workflows within a shared consortial environment. This article discusses the challenges and opportunities of implementing a consortial-based LMS, with particular emphasis on serials and ERM functionality. Key migration issues related to serials control, acquisitions, licensing, administration, cataloging, statistics, and interoperability are examined at the institutional and large-scale networked levels. Benefits and limitations of using a shared consortial cloud-based LMS are explored, and the overall capabilities of the Alma LMS for electronic resource management are reviewed.

Using Primo for undergraduate research: a usability study

Purpose The purpose of this paper is to observe how undergraduate students approach open-ended searching for a research assignment, specifically as it affected their use of the discovery interface Primo. Design/methodology/approach In total, 30 undergraduate students were provided with a sample research assignment and instructed to find resources for it using web tools of their choice, followed by the Primo discovery tool. Students were observed for 30 minutes. A survey was provided at the end to solicit additional feedback. Sources students found were evaluated for relevance and utility. Findings Students expressed a high level of satisfaction with Primo despite some difficulty navigating through more complicated tasks. Despite their interest in the tool and previous exposure to it, it was usually not the first discovery tool students used when given the research assignment. Students approached the open-ended search environment much like they would with a commercial search engine. Originality/value This paper focused on an open-ended search environment as opposed to a known-item scenario in order to assess students’ preferences for web search tools and how a library discovery layer such as Primo was a part of that situation. Evaluation of the resources students found relevant were also analyzed to determine to what degree the students understood the level of quality they exhibited and from which tool they were obtained.

Evolution of thesauri and the history of knowledge organization

Thesauri are considered as an optimum between maximum ontological modelling (best knowledge mapping) and minimal alphabetic ordering (less expensive access). From this point of view a swift history of its evolution is provided. The recent evolutions in Internet searching are also analysed from this perspective. In this context, there is an immediate role for thesauri to ensure interoperability and feed up the new Internet semantic engines; and in the long term as a simple semantic user interface for resource discovery and navigation, which ensures proper transparency and control by the user who wants to take the effort to supervise and analyse its search processes. It is proposed that better devices for ensuring semantic sorting are provided when necessary, and that a distributed hub for thesauri interconnection is provided, perhaps using the existent big open Internet semantic facilities, as Wikipedia

The evolution of thesauri and the history of knowledge organization: between the sword of mapping knowledge and the wall of keeping it simple

Thesauri are considered as an optimum between maximum ontological modelling (best knowledge mapping) and minimal alphabetic ordering (less expensive access). From this point of view a swift history of its evolution is provided. The recent evolutions in Internet searching are also analysed from this perspective. In this context, there is an immediate role for thesauri to ensure interoperability and feed up the new Internet semantic engines; and in the long term as a simple semantic user interface for resource discovery and navigation, which ensures proper transparency and control by the user who wants to take the effort to supervise and analyse its search processes. It is proposed that better devices for ensuring semantic sorting are provided when necessary, and that a distributed hub for thesauri interconnection is provided, perhaps using the existent big open Internet semantic facilities, as Wikipedia

Visualization: A Mind–Machine Interface for Discovery

Computation is critical for enabling us to process data volumes and model data complexities that are unthinkable by manual means. However, we are far from automating the sense-making process. Human knowledge and reasoning are critical for discovery. Visualization offers a powerful interface between mind and machine that should be further exploited in future genome analysis tools.

Library Users Attempt to Access a Wide Range of Information Beyond Books and Articles through a Single Search Box

A Review of:
 Lown, C., Sierra, T., & Boyer, J. (2013). How users search the library from a single search box. College & Research Libraries, 74(3), 227-241. Retrieved from http://dx.doi.org/10.5860/crl-321
 
 Abstract
 
 Objective – To identify how users use a single search box.
 
 Design – Transaction log analysis.
 
 Setting – A large research university in North Carolina, United States of America.
 
 Subjects – Search results from a customized single search box on the library’s home page, consisting of 739,180 searches and 655,388 hyperlink selections.
 
 Methods – The authors used custom logging software to generate transaction logs of all searches that took place over two semesters (August to December 2010 and January to May 2011) in QuickSearch, a custom-made, combined search application. The study tracked search queries and hyperlink selections, noting which modules in the discovery interface (articles, catalogue, databases, and others) were selected and, from these modules, which hyperlinks were clicked. 
 
 Main Results – Transaction log analysis was conducted on over 739,000 searches during the two semesters and over 655,000 hyperlink selections from the results interface. The 20 most frequent queries made in QuickSearch were primarily for specific resources (database titles or journal titles), administrative information, and library services. The 153 most popular searches made up 10% of all searches. Hyperlinks to full-text articles (41.5%) and the catalogue (35.2%) accounted for about 76% of the links selected. About 23% of links selected were for other modules (e.g., FAQs, “best bets,” and journal titles). Hyperlinks that led directly to specific items were selected more frequently than hyperlinks to a full list of results.
 
 Conclusion – Analysis of user transaction logs suggests that users do not understand what is being searched in a combined search box and that search applications need to direct users more effectively to resources beyond the catalogue and article databases. Users attempt to access a wide range of information from a single search box, and the most commonly used modules in QuickSearch do not serve many of the most frequent queries. Many of the most common queries can be defined and addressed with a predefined list of results, improving the quality of results and the search experience for users. Ongoing evaluation and analysis of the search interface and subsequent optimization for the most frequent queries can improve user experience.

A Hybrid Approach to Discovery Services

Over the last few years, changing user expectations and new technologies have led libraries to rethink their approach to helping users more easily discover the breadth of print and electronic resources offered by the library As a central component of this rethinking, many libraries have chosen to subscribe to one of the new web-scale discovery services provided by various library vendors. These services are designed to search quickly and seamlessly across a vast range of local and remote preharvested and indexed content, providing relevancy-ranked results. (1) Princeton University Library (PUL) has also chosen to go this route but with a twist: we have adopted a hybrid combination of Ex Libris's Primo and ProQuest's Summon services. As a member of PUL's Discovery Implementation Group (LDIG) and Website Steering Group, I have been involved with this effort for more than three years. I believe our experience can prove helpful to other libraries implementing a discovery service. BACKGROUND In February 2010, PUL convened a Library Discovery Assessment Group to assess the landscape of these new discovery systems and recommend whether the library should adopt one. Ultimately, the group recommended adopting Primo, primarily because it felt that Primo offered the best option for updating our aging catalog interface. Since PUL uses Ex Libris's Voyager ILS, Primo held out the promise of a smoother transition and better integration of circulation functions and other features. However, there was some hesitation. Primo Central had only just been launched in beta testing in January 2010, and there were no live installations that the group could examine. (2) Also, there were concerns about the amount of content in Primo's unified index, especially compared to Summon, which at the time had broader article coverage and boasted a significant body of news content. In the end, PUL opted for a hybrid approach: using Primo (without its centralized index) as the new discovery interface to Princeton's local content--cataloging data and other repositories, like senior theses and finding aids--while also subscribing to Summon to leverage its unified index of article and news content. In fall 2010, PUL created the LDIG to implement this hybrid solution. Over the past three years, LDIG's work has gone through three main phases. PHASE 1: CONFIGURING AND PREPARING TO LAUNCH The first phase of implementation involved becoming familiar with and configuring the new discovery systems. This primarily meant Primo, as there were numerous configuration choices necessary to prepare and normalize the Library's local data for ingestion. PUL contracted with Ex Libris to integrate the Summon content into the Primo interface via Summon's API, so Summon required little set up beyond turning on our full text packages in the ProQuest knowledgebase. (3) The new system was hosted by Ex Libris on a custom domain, and the Library branded this new system SearchIt@PUL. LDIG initially planned for a public beta launch in early 2011, but that timetable proved too ambitious. LDIG introduced the new system to staff in April 2011, while the public beta launch was pushed back to the beginning of the fall 2011 semester. Various issues contributed to the delay. For one, it took time to learn how PUL's MARC records mapped to Primo's new PNX records, and figuring out which fields were being displayed and indexed for search often required investigation and experimentation. We also ran into significant challenges trying to tailor algorithms for search, deduplication of records, and FRBRization in Primo to work well with our large and diverse collections. For example, there were numerous issues related to the indexing and retrieval of records in foreign characters, especially Chinese, Japanese, and Korean, which was of particular concern because PUL has a highly regarded East Asian library. Working through these and other issues was time-intensive for LDIG members. …

Discovering Music: Small-Scale, Web-Scale, Facets, and Beyond

In this presentation, two music librarians addressed the issues related to the discovery of library music resources. Rebecca Belford talked about the Music Library Association’s “Music Discovery Requirements” (MLA MDR) document, and how it applies to some contexts. Tracey Snyder then described the incorporation of MLA MDR into the development of a specific discovery interface. The presenters identified some of the challenges characteristic of music resources and ways in which those challenges may be met, reasoning that a tool capable of handling music will be capable of handling most things in a general collection.

Geo-Enrichment and Semantic Enhancement of Metadata Sets to Augment Discovery in Geoportals

Geoportals are established to function as main gateways to find, evaluate, and start “using” geographic information. Still, current geoportal implementations face problems in optimizing the discovery process due to semantic heterogeneity issues, which leads to low recall and low precision in performing text-based searches. Therefore, we propose an enhanced semantic discovery approach that supports multilingualism and information domain context. Thus, we present workflow that enriches existing structured metadata with synonyms, toponyms, and translated terms derived from user-defined keywords based on multilingual thesauri and ontologies. To make the results easier and understandable, we also provide automated translation capabilities for the resource metadata to support the user in conceiving the thematic content of the descriptive metadata, even if it has been documented using a language the user is not familiar with. In addition, to text-enable spatial filtering capabilities, we add additional location name keywords to metadata sets. These are based on the existing bounding box and shall tweak discovery scores when performing single text line queries. In order to improve the user’s search experience, we tailor faceted search strategies presenting an enhanced query interface for geo-metadata discovery that are transparently leveraging the underlying thesauri and ontologies.

Site based data curation: Developing a data portal for geobiologists at yellowstone national park

The Site-Based Data Curation (SBDC) project at the University of Illinois at Urbana-Champaign has developed a framework of policies and processes for the curation of research data generated at scientifically significant sites. In this poster, we report on the implementation of packaging methods for submission of geobiology data to repositories, templates for organizing data for better management, aggregation, and discovery, and the implementation of a prototype repository interface. The poster will be paired with a demonstration of the discovery interface for the repository.

Next-Gen Library Catalogs

This work was published in cooperation with the Library Information and Technology Association, a division of the American Library Association. Marshall Breeding is a well-known author in library automation. He is the director for innovative technologies and research at the Jean and Alexander Heard Library at Vanderbilt University. He publishes the Library Technology Guides website , the “Systems Librarian” column in Computers in Libraries, and the “Annual Automation Marketplace” series in Library Journal, among many other articles, book chapters, and books. With his background, Breeding writes with authority on the transformation of the traditional online catalog into a discovery interface. The chapters are logically organized to lead the reader through the process of selecting and implementing a discovery interface, as evidenced by the chapter titles: “Introduction: Next-Gen Library Catalog Basics,” “Planning,” “Implementation, “Marketing,” “Best Practices,” and “Measures of Success.” At 125 pages, the book provides a very useful guide and project outline of discovery interfaces for systems and technology librarians. Library administrators and staff who need an overview on the next generation library catalog will also benefit from Breeding's clear descriptions of this complex subject. The information in this book is applicable to any type of library, whether it is a public, academic, or special library. The crux of the book is its chapters on planning and implementation. When planning, Breeding reminds readers that the discovery interface is a visual tool to guide library users to the information they need. As such, discovery interfaces combine disparate collections into a searchable front end that displays results according to relevancy. He is careful to point out that discovery tools are not aimed at library staff but are used to break down the barriers that users encounter as they try to navigate a library's various resources and website. Chapter highlights include the features of a discovery interface, a review of the major discovery products, change management for staff and library users, and the selection process. The implementation chapter covers such topics as the integration of discovery and the integrated library system (ILS), the importance of accurate metadata, and data transfer between the ILS and discovery. Breeding also discusses trends and ways to keep current with the changing technology in discovery interfaces. Once the discovery tool is implemented, the chapters on marketing the new interface, best practices, and impact measurement naturally conclude the entire process. Web 2.0 tools such as a wiki, Facebook page, and Twitter are used to update the book's content in this quickly changing environment.

From the Editor: From Discovery to Delivery

Our library implemented a web-scale discovery interface at the beginning of the fall semester. One major reason given by many libraries opting for these tools is that they increase the library's re...

Taking Discovery Systems for a Test Drive

Researchers at American University investigated user preferences for discovery layer features, interface design, and content. They tested local implementations of WorldCat Local and Aquabrowser by conducting a group test with eighteen students and individual tests with ten students. Students searched a given question and a topic of their choosing and talked about their experiences. The group usability session yielded preliminary findings and informed the individual tests. Using the constant comparative method, the researchers coded qualitative data collected during the individual tests and grouped participant preferences into three primary categories: functionality, interface display, and content. Findings revealed that underclassmen tended to prefer WorldCat Local, while upperclassmen and graduates tended to prefer Aquabrowser. Participants most preferred the following features: links to full-text articles using a link resolver, results incorporating both articles and books, and facets like date, format, and subject. They viewed word clouds, the ability to search libraries beyond the local library or consortium, and user-generated reviews as optional rather than required features. While one system did not emerge as the preferred system, understanding their preferences informed the decision to implement Summon as the permanent discovery layer for the Library and determined configuration options for the new system. Other libraries may benefit from the coding system developed during the study and the methodology for testing potential systems with users.

DRUG DISCOVERY INTERFACE: Functional Group Dependence of Solute Partitioning to Various Locations within a DOPC Bilayer: A Comparison of Molecular Dynamics Simulations with Experiment

Atomic-level molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers containing small, amphiphilic, drug-like molecules were carried out to examine the influence of polar functionality on membrane partitioning and transport. Three related molecules (tyramine, phenethylamine, and 4-ethylphenol) were chosen to allow a detailed study of the isolated effects of the amine and hydroxyl functionalities on the preferred solute location, free energies of transfer, and the effect of combining both functional groups in a same molecule. Transfer free energy profiles (from water) generated from molecular dynamics (MD) simulations as a function of bilayer depth compared favorably to comparable experimental results. The simulations allowed the determination of the location of the barrier domain for permeability where the transfer free energy is highest and the preferred binding region at which the free energy is a minimum for each of the three solutes. Comparisons of the free energy profiles reveal that the hydrocarbon chain interior is the region most selective to chemical structure of different solutes because the free energies of transfer in that region vary to a significantly greater extent than in other regions of the bilayer. The contributions of the hydroxyl and amino groups to the free energies of solute transfer from water to the interfacial region were close to zero in both the MD simulations and experimental measurements. This suggests that the free energy decrease observed for solute transfer into the head group region occurs with minimal loss in solvation by hydrogen bonding to polar functional groups on the solute and is largely driven by hydrophobicity. Overall, the joint experimental and simulation studies suggest that the assumption of additivity of free energy contributions from multiple polar functional groups on the same molecule may hold for predictions of passive bilayer permeability coefficients providing that the groups are well isolated. However, this assumption does not hold for predictions of relative liposome-binding affinities.

Usability of the VuFind Next-Generation Online Catalog

The VuFind open–source, next-generation catalog system was implemented by the Consortium of Academic and Research Libraries in Illinois as an alternative to the WebVoyage OPAC system. The University of Illinois at Urbana-Champaign began offering VuFind alongside WebVoyage in 2009 as an experiment in next generation catalogs. Using a faceted search discovery interface, it offered numerous improvements to the UIUC catalog and focused on limiting results after searching rather than limiting searches up front. Library users have praised VuFind for its Web 2.0 feel and features. However, there are issues, particularly with catalog data.

Meet the Guest Editor

Larry C. Wienkers is currently the Executive Director for the Department of Pharmacokinetics and Drug Metabolism at Amgen in Seattle, WA. Larrys areas of scientific interest include: understanding of the mechanisms of cytochrome P450 oxidation reactions; the application of novel in vitro metabolism techniques to understand the enzymatic basis for biotransformation of potential therapeutic agents at the drug discovery interface; and the prospective application of in vitro metabolism data to predict clinically relevant pharmacokinetically based drug-drug interactions. Larry holds a BSc. and MS. in Chemistry from Western Washington University (1986 & 1988) and Ph.D. in Medicinal Chemistry from the University of Washington (1993). Larry worked as a Postdoctoral Fellow, in the Department of Drug Metabolism at the Upjohn Company (1993-1995) and he joined Pharmacia and Upjohn as a Research Scientist (1995). Larry became Director of Drug Metabolism Enabling Technologies and Scientific Fellow at Pharmacia, Kalamazoo MI (1998). In 2003, Larry became Executive Director in the Department of Pharmacokinetics, Dynamics and Metabolism at Pfizer St Louis, MO. Larry has co-authored more than 50 peer reviewed manuscripts, 4 book chapters and currently holds 1 patent. He is co-Editor of the Handbook of Drug Metabolism, and is a member of the Editorial Board for the journals: Drug Metabolism and Disposition, Open Medicinal Chemistry Letters, and Current Drug Metabolism.

Service-oriented Access to Next Generation Networks—from Service Creation to Execution

Existing telecommunication networks and classical roles of operators are subject to fundamental change. Many network operators are currently seeking for new sources to generate revenue by exposing network capabilities to 3rd party service providers. At the same time we can observe that services on the World Wide Web (WWW) are becoming mature in terms of the definition of APIs that are offered towards other services. The combinations of those services are commonly referred to as Web 2.0 mash-ups. Rapid service design and creation becomes therefore important to meet the requirements in a changing technology and competitive market environment. This report describes our approach to include Next Generation Networks (NGN)-based telecommunications application enabler into complex services by defining a service broker that mediates between 3rd party applications and NGN service enablers. It provides policy-driven orchestration mechanisms for service enablers, a service authorization functionality, and a service discovery interface for Service Creation Environments. The work has been implemented as part of the Open SOA Telco Playground testbed at Fraunhofer FOKUS.

Towards a Unifying View of QoS-Enhanced Web Service Description and Discovery Approaches

The number of web services increased vastly in the last years. Various providers offer web services with the same functionality, so for web service consumers it is getting more complicated to select the web service, which best fits their requirements. That is why a lot of the research efforts point to discover semantic means for describing web services taking into account not only functional characteristics of services, but also the quality of service (QoS) properties such as availability, reliability, response time, trust, etc. This motivated us to research current approaches presenting complete solutions for QoS enabled web service description, publication and discovery. In this paper we present comparative analysis of these approaches according to their common principals. Based on such analysis we extract the essential aspects from them and propose a pattern for the development of QoS-aware service-oriented architectures. The number of web services increased vastly in the last years. Various providers offer web services with the same functionality, so for web service consumers it is getting more complicated to select the web service, which best fits their requirements. That is why many research efforts point to discovering semantic approaches for describing web services including both functional and non-functional properties. This will give consumers the opportunity to find web services according to their QoS requirements such as availability, reliability, response time, trust, etc. Most of the current solutions are based on Web Service Definition Language (WSDL) and Universal Description and Discovery Interface (UDDI) registry. WSDL documents provide functional description of web services without semantic specifications concerning QoS. UDDI registry provides catalog-based searching without control over the quality of registered services. UDDI APIs allow publishing and discovering data for a particular service, but do not provide an opportunity for a quality-based retrieval. The problem becomes more complicated when the discovery process returns several web services with the same functionality. Such mentioned disadvantages motivated us to research principal current approaches for QoS-aware web service description and discovery in order to find better solutions giving more accurate and productive service retrieval. These approaches have common principals that can be summarized as follows:

Towards a Repository-enabled Scholar's Workbench

Between April 2005 and March 2009, the e-Services Integration Group at the University of Hull undertook two Joint Information Systems Committee (JISC)-funded projects, RepoMMan and REMAP. The RepoMMan tool developed a browser-based interface through which a user could interact with a private digital repository space to support the development of their works-in-progress. It went on to look at the processes involved in publishing such works to a public-facing repository and to investigate the possibility of generating metadata for the published object automatically. The follow-on REMAP Project implemented the publishing process and also investigated how triggers might be embedded in the objects that were created that would help with management and possible preservation of the object over time. The work of RepoMMan and REMAP has now been taken up in an international collaboration, the Hydra Project, which seeks to develop a repository-enabled Scholars' Workbench. This will be a highly flexible system that will provide a search and discovery interface for a Fedora repository and that can be configured to provide interactive workflows around it for pre-publication development of materials and their post-publication management. © 2009 Richard Green and Chris Awre.