Search Interface Research Articles

A Data-Driven Reference Standard for Adverse Drug Reaction (RS-ADR) Signal Assessment: Development and Validation.

BackgroundPharmacovigilance using real-world data (RWD), such as multicenter electronic health records (EHRs), yields massively parallel adverse drug reaction (ADR) signals. However, proper validation of computationally detected ADR signals is not possible due to the lack of a reference standard for positive and negative associations.ObjectiveThis study aimed to develop a reference standard for ADR (RS-ADR) to streamline the systematic detection, assessment, and understanding of almost all drug-ADR associations suggested by RWD analyses.MethodsWe integrated well-known reference sets for drug-ADR pairs, including Side Effect Resource, Observational Medical Outcomes Partnership, and EU-ADR. We created a pharmacovigilance dictionary using controlled vocabularies and systematically annotated EHR data. Drug-ADR associations computed from MetaLAB and MetaNurse analyses of multicenter EHRs and extracted from the Food and Drug Administration Adverse Event Reporting System were integrated as “empirically determined” positive and negative reference sets by means of cross-validation between institutions.ResultsThe RS-ADR consisted of 1344 drugs, 4485 ADRs, and 6,027,840 drug-ADR pairs with positive and negative consensus votes as pharmacovigilance reference sets. After the curation of the initial version of RS-ADR, novel ADR signals such as “famotidine–hepatic function abnormal” were detected and reasonably validated by RS-ADR. Although the validation of the entire reference standard is challenging, especially with this initial version, the reference standard will improve as more RWD participate in the consensus voting with advanced pharmacovigilance dictionaries and analytic algorithms. One can check if a drug-ADR pair has been reported by our web-based search interface for RS-ADRs.ConclusionsRS-ADRs enriched with the pharmacovigilance dictionary, ADR knowledge, and real-world evidence from EHRs may streamline the systematic detection, evaluation, and causality assessment of computationally detected ADR signals.

Archive Infrastructure and Spoken Language Corpora for Saami Languages in Finland

This study presents the results of an Aanaar Saami pilot project in the Saami Culture Archive, University of Oulu. The project has established a set of conventions to transcribe and annotate Aanaar Saami recordings in the archive’s collection and created a mechanism through which grammatically annotated but anonymous versions can be imported to the Korp search interface in the Language Bank of Finland. The practices include wide use of Saami language technology, the use of Finnish computational research infrastructure, and they can be extended later to other Saami languages in the archive.

Subjective variables in travel behavior models: a critical review and Standardized Transport Attitude Measurement Protocol (STAMP).

Understanding people’s travel behavior is necessary for achieving goals such as increased bicycling and walking, decreased traffic congestion, and adoption of clean-fuel vehicles. To understand underlying motivations, researchers increasingly are adding subjective variables to models of travel behavior. This article presents a systematic review of 158 such studies. Nearly every reviewed article finds subjective variables to be predictive of transport outcomes. However, the 158 reviewed studies include 2864 distinct subjective survey questions. This heterogeneity makes it difficult to reach definitive conclusions about which subjective variables are most important for which transport outcomes. In addition to heterogeneity, challenges of this literature also include an unclear direction of causality and tautological relationships between some subjective variables and behavior. Within the constraints imposed by these challenges, we attempt to evaluate the explanatory power of subjective variables, which subjective variables matter most for which transport choices, and whether the answers to these questions vary between continents. To reduce heterogeneity in future studies, we introduce the Standardized Transport Attitude Measurement Protocol, which identifies a curated set of subjective questions. We have also developed an open-access database of the reviewed studies, including all subjective survey questions and models, with an interactive, searchable interface.

IpaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues.

Functional interpretation of disease-associated non-coding variants remains a significant challenge in the post-GWAS era. Our recent study has identified 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) and connects APA events with QTLs as a major driver of human traits and diseases. Besides 3'UTR, APA events can also occur in intron regions, and increasing evidence has connected intronic polyadenylation with disease risk. However, systematic investigation of the roles of intronic polyadenylation in human diseases remained challenging due to the lack of a comprehensive database across a variety of human tissues. Here, we developed ipaQTL-atlas (http://bioinfo.szbl.ac.cn/ipaQTL) as the first comprehensive portal for intronic polyadenylation. The ipaQTL-atlas is based on the analysis of 15 170 RNA-seq data from 838 individuals across 49 Genotype-Tissue Expression (GTEx v8) tissues and contains ∼0.98 million SNPs associated with intronic APA events. It provides an interface for ipaQTLs search, genome browser, boxplots, and data download, as well as the visualization of GWAS and ipaQTL colocalization results. ipaQTL-atlas provides a one-stop portal to access intronic polyadenylation information and could significantly advance the discovery of APA-associated disease susceptibility genes.

Connecting IndExs Editors and exsiccata IDs with Wikidata for Disambiguation of People Names and Work in Botanical and Mycological Collections

Connecting IndExs Editors and exsiccata IDs with Wikidata for Disambiguation of People Names and Work in Botanical and Mycological Collections

Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements.

Protein phosphorylation plays a fundamental role in many cellular processes. Proteins are phosphorylated by kinases, which have been studied as drug targets for the treatment of various diseases, particularly cancer. Because kinases have multiple roles in interconnected molecular pathways, their specific regulation is required to enhance beneficial and reduce adversarial effects of drugs. Using our previously developed platform, we measured phosphorylation profiles of MCF7 and K562 cells treated with 94 clinical drugs. These phosphorylation profiles can provide insights into pathway activities and biological functions. Here, we introduce Phosprof, a novel database of drug response based on phosphorylation activity. Phosprof is able to present up- or downregulated phosphorylated signature proteins on pathway maps, significant pathways on the hierarchal tree in signal transduction and commonly perturbed pathways affected by the selected drugs. It also serves as a useful web interface for new or known drug profile search based on their molecular similarity with the 94 drugs. Phosprof can be helpful for further investigation of drug responses in terms of phosphorylation by utilizing the various approved drugs whose target phenotypes are known.Database URL https://phosprof.medals.jp/

Interactive visual facets to support fluid exploratory search

Exploratory search starts with ill-defined goals and involves browsing, learning, and formulating new targets for search. To fluidly support such dynamic search behaviours, we focus on devising interactive visual facets (IVF), visualising information facets to support user comprehension and control of the information space. We reviewed existing faceted search interfaces and derived two design requirements (DR) that have not been fully addressed to support fluid interactions in exploratory search. We then exemplified the requirements through devising an IVF tool, which coordinates a linear and a categorical facet representing the distribution and summarisation of items, respectively, and providing context for faceted exploration (DR1). To support rapid transitions between search criteria (DR2), the tool introduces a novel design concept of using facets to select items without filtering the item space. Particularly, we propose a filter-swipe technique that enables users to drag a categorical facet value sequentially over linear facet bars to view the items in the intersection of the two facets along with the categorical facet dynamically summarising the items in the intersection. Three applications with various datasets demonstrate how the features support information discovery with ease. A comparison with a baseline system provided evidence that the task performance of the IVF tool was comparable to the typical query search interface. Another study of 11 participants with realistic email search tasks shows that dynamic suggestions through the timeline navigation can help discover useful suggestions for search; the novel design concept was favoured over using facet values as filters. Based on these practices, we derive IVF design implications for fluid, exploratory searches.Graphical abstract

Keeping it under lock and keywords: exploring new ways to open up the web archives with notebooks

The UK Government Web Archive (UKGWA) has been archiving government websites since 1996 and now holds regular snapshots of over 5000 sites. Currently, this material can be accessed through browsing or a simple keyword search interface on their website and has also been catalogued in The National Archives’ online catalogue, Discovery. However, the scale of the UKGWA exposes the limits of the current search interface, and there is no facility to understand the archive in aggregate. This article seeks to go beyond the simple keyword search by exploring the data sources available, from APIs to web crawling, for computational analysis of the UKGWA. The article is accompanied by two Python Notebooks which present examples of analysis using each data source. Notebooks lower the technical barriers for the reader to explore and interpret the UKGWA as data, while surfacing the challenges around making web material computationally accessible.

Enhanced Electronic Grammars Online

Enhanced Electronic Grammars Online (EEG) is a full-text linguistics database available on the De Gruyter platform. EEG offers the ability to conduct searches across dozens of comprehensive grammars describing rare and endangered world languages. Intended for use by researchers into general linguistics and linguistic typology, EEG would also be a good resource for undergraduate teaching. The review notes some issues with the search interface and metadata.

Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer

Abstract Interpreting genomic variants in tumor samples presents a challenge in research and the clinical setting. A major barrier is that information about variants is fragmented across disparate databases, and aggregating information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one stop shop for variant annotation, equipped with a powerful API for bulk annotation of variants and a user friendly interface for cancer researchers. Genome Nexus is available at https://www.genomenexus.org. It a) aggregates variant information from a large number of sources that are relevant to cancer research and clinical applications; b) allows high-performance programmatic access to the aggregated data via a unified API; c) provides a search interface and a reference page for individual cancer variants; d) provides user-friendly tools for annotating variants in patients; e) is freely available under an open source license and can be installed in a private cloud or local environment. Genome Nexus contains annotations from more than a dozen resources, including those that provide variant effect information (VEP), protein sequence annotation (Uniprot, Pfam, dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, SIFT), population prevalence (gnomAD, dbSNP, ExAC), cancer population prevalence (Cancer Hotspots, SignalDB) and clinical actionability (OncoKB, CIViC, Clinvar). The annotations can be accessed through the website, the API, and a command line client. Genome Nexus is unique in providing a user friendly interface specific to cancer that allows high performance annotation of any variant. It is the main annotation service for the popular cancer genomics tool cBioPortal, which serves thousands of users daily. It is also offered as a standalone tool for annotation, allowing researchers and clinicians as well as genomic infrastructure developers to leverage it directly in their own workflows. For example, a local installation of Genome Nexus is used for annotating all variants in AACR Project GENIE. Citation Format: Ino de Bruijn, Xiang Li, Onur Sumer, Benjamin Gross, Robert Sheridan, Angelica Ochoa, Manda Wilson, Avery Wang, Hongxin Zhang, Aaron Lisman, Adam Abeshouse, Sander Rodenburg, Sjoerd van Hagen, Remond Fijneman, Gerrit Meijer, Nikolaus Schultz, Jianjiong Gao. Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1156.

Grateful Med: Direct access to MEDLINE for health professionals with personal computers.

Donald A.B. Lindberg M.D. arrived as Director, U.S. National Library of Medicine (NLM) in late 1984 with the intention of implementing a physician-friendly interface to MEDLINE, a prime example of his interest in making NLM information services more directly useful in medical care. By early 1986, NLM’s Grateful Med, an inexpensive PC search interface to MEDLINE useful for health professionals, had joined the group of end-user systems for searching MEDLINE that emerged in the 1980s. This chapter recounts Grateful Med’s rapid iterative development and the subsequent campaign to bring it to attention of health professionals. It emphasizes Lindberg’s role, the challenges faced by those introducing and using the interface in a pre-Internet world, and some longer-term effects of the effort to expand health professionals’ use of MEDLINE during the decade from 1986 to 1996.

Interactive Similarity-Based Search of Clinical Trials.

The rapid growth of clinical trials launched in recent years poses significant challenges for accurate and efficient trial search. Keyword-based clinical trial search engines require users to construct effective queries, which can be a difficult task given complex information needs. In this study, we present an interactive clinical trial search interface that retrieves trials similar to a target clinical trial. It enables user configuration of 13 clinical trial features and 4 metrics (Jaccard similarity, semantic-based similarity, temporal overlap and geographical distance) to measure pairwise trial similarities. Among 1,007 coronavirus disease 2019 (COVID-19) trials conducted in the United States, 91.9% were found to have similar trials with the similarity threshold being 0.85 and 43.8% were highly similar with the threshold 0.95. A simulation study using 3 groups of similar trials curated by COVID-19 clinical trial reviews demonstrates the precision and recall of the search interface.

Interactive Design of Personalized Website Search Interface Based on Visual Communication.

Aiming at the problems of low user satisfaction and long search time in the traditional interactive design method of the personalized website search interface, a personalized website search interface interactive design method based on visual communication is proposed. Under the analysis of personalized website users' search behavior, the interactive personalized website search interface is designed through a navigation module, search module, link module, interactive layout module, and visual rendering module; in the visual rendering module, the advanced texture mapping method is used to render the personalized website search interface; on the personalized website search interface, the disturbance function is imported along the normal vector, the simplified new normal vector is intelligently calculated through the concave convex texture mapping algorithm, the normal vector is solved to generate the intersection point of the high-precision interface, the illumination brightness value of each pixel of the interface is intelligently calculated, the visual communication rendering model is constructed, and the visual communication effect of the interface is improved. The simulation results show that the website interface search time of this method is within 4.9 s and the user satisfaction is up to 100%, indicating that the interaction effect of the personalized website search interface designed by this method is good.

HCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses.

In the twenty-first century, three new human coronaviruses have been identified with known zoonotic origins: severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, and Middle East respiratory syndrome coronavirus (MERS-CoV). SARS-CoV-2 was identified in November 2019 and is associated with an ongoing pandemic. Molecular surveillance and monitoring studies are essential for containing viral outbreaks, epidemics, and pandemics. In addition, the development and deployment of bioinformatics resources for highly pathogenic human coronaviruses are crucial for understanding the genetic and immunogenic landscape associated with these viruses. Here, we introduce an open-access, integrated resource for SARS-CoV, SARS-CoV-2, and MERS-CoV: the Human Coronaviruses Database and Analysis Resource (hCoronavirusesDB; http://hcoronaviruses.net/), which include nucleotide and protein sequence data obtained for these viruses. The database also offers a user-friendly search interface coupled with bioinformatics analytics and visualization tools. In addition, hCoronavirusesDB contains curated, experimentally validated B cell and T cell epitope data for these viruses. This resource can assist with the molecular surveillance necessary to trace virus circulation and contribute to microevolutionary studies. This application can also serve as a valuable resource for the development of rationally designed pan-coronavirus diagnostic tools, vaccines, and therapeutic agents.Database URL:http://hcoronaviruses.net/

"My words were completely gone." A qualitative study of the information seeking behaviour of people with aphasia

Introduction. Aphasia is an acquired language impairment, which affects the production and comprehension of speech, reading and writing. Aphasia is associated with great cognitive variation, but a common marker is impaired word retrieval. Searching for information requires several language related skills, such as naming, spelling and reading skills. Consequently, aphasia may have an impact on information seeking behaviour. Method. Seven participants with aphasia were interviewed about their information seeking. Analysis. The data were analysed and organized into categories, derived from themes in the interview guide and the dataset. Results. Information needs were typically solved by asking someone, or through word mobilising search strategies. The participants reported extensive searching for images and synonyms, with the overall purpose to identify adequate query terms. Browsing was preferred over direct searching. Furthermore, certain information needs did not result in any information seeking, because searching activities were considered too strenuous. Conclusions. The findings from this study suggest that an information architecture that facilitates browsing and image search can make Web content more accessible for people with aphasia. Moreover, there is a need for future research on search user interface design that better accommodate people with aphasia in general and impaired word retrieval skills in particular.

SCOPE and EaaSI: Software Emulation and the Future of Architectural History

SCOPE and EaaSI: Software Emulation and the Future of Architectural History

Designing Web-scale geographic search interface for libraries

PurposeThere are various online library databases available to access, but none of them include a geographic search option. The purpose of this study is to discover a suitable solution to solve this problem. To access information, it is critical to search using the geographic locations available in bibliographic databases. Geographic search functionality is available in Web-scale discovery system and services.Design/methodology/approachThe approach and methods for incorporating geographic search capabilities into VuFind open source discovery software for suitable and appropriate information resource discovery among users are straightforward. Library mash-up tools and techniques were integrated by using geographic locations into a Web-scale library discovery system.FindingsAs a result, bibliographic metadata descriptions help all library users to identify and access documents more quickly and easily. It can assist users and librarians in making better use of library resources by integrating various databases with VuFind and by providing them in a single window-based interface. This system has developed a standardised geographic search architecture, and it is entirely based on the Ubuntu operating system. Furthermore, the 034 MARC 21 tag will be adjusted using the latitude and longitude website.Originality/valueWeb-scale library services are provided by OCLC WorldCat Discovery Services, Summon Web-scale Discovery, EBSCO Discovery Services, Primo Central and others. This Web-scale discovery services platform relies heavily on geographic search interface functionalities.

An Exploratory Study on a Reinforcement Learning Prototype for Multimodal Image Retrieval Using a Conversational Search Interface

In the realm of information, conversational search is a relatively new trend. In this study, we have developed, implemented, and evaluated a multiview conversational image search system to investigate user search behaviour. We have also explored the potential for reinforcement learning to learn from user search behaviour and support the user in the complex information seeking process. A conversational image search system may mimic a natural language discussion with a user via text or speech, and then assist the user in locating the required picture via a dialogue-based search. We modified and improved a dual-view search interface that displays discussions on one side and photos on the other. Based on the states, incentives, and dialogues in the initial run, we developed a reinforcement learning model and a customized search algorithm in the back end that predicts which reply and images would be provided to the user among a restricted set of fixed responses. Usability of the system was validated using methodologies such as Chatbot Usability Questionnaire, System Usability Scale, and User Experience Questionnaire, and the values were tabulated. The result of this usability experiment proved that most of the users found the system to be very usable and helpful for their image search.

A study of visually linked keywords to support exploratory browsing in academic search

AbstractWhile the search interfaces used by common academic digital libraries provide easy access to a wealth of peer‐reviewed literature, their interfaces provide little support for exploratory browsing. When faced with a complex search task (such as one that requires knowledge discovery), exploratory browsing is an important first step in an exploratory search process. To more effectively support exploratory browsing, we have designed and implemented a novel academic digital library search interface (KLink Search) with two new features: visually linked keywords and an interactive workspace. To study the potential value of these features, we have conducted a controlled laboratory study with 32 participants, comparing KLink Search to a baseline digital library search interface modeled after that used by IEEE Xplore. Based on subjective opinions, objective performance, and behavioral data, we show the value of adding lightweight visual and interactive features to academic digital library search interfaces to support exploratory browsing.

Grateful Med: Direct Access to MEDLINE for Health Professionals with Personal Computers.

Donald A.B. Lindberg M.D. arrived as Director, U.S. National Library of Medicine (NLM) in late 1984 with the intention of implementing a physician-friendly interface to MEDLINE, a prime example of his interest in making NLM information services more directly useful in medical care. By early 1986, NLM's Grateful Med, an inexpensive PC search interface to MEDLINE useful for health professionals, had joined the group of end-user systems for searching MEDLINE that emerged in the 1980s. This chapter recounts Grateful Med's rapid iterative development and the subsequent campaign to bring it to attention of health professionals. It emphasizes Lindberg's role, the challenges faced by those introducing and using the interface in a pre-Internet world, and some longer-term effects of the effort to expand health professionals' use of MEDLINE during the decade from 1986 to 1996.