Web Services Tools Research Articles

Multi-scale window transformer for cervical cytopathology image recognition

Cervical cancer is a major global health issue, particularly in developing countries where access to healthcare is limited. Early detection of pre-cancerous lesions is crucial for successful treatment and reducing mortality rates. However, traditional screening and diagnostic processes require cytopathology doctors to manually interpret a huge number of cells, which is time-consuming, costly, and prone to human experiences. In this paper, we propose a Multi-scale Window Transformer (MWT) for cervical cytopathology image recognition. We design multi-scale window multi-head self-attention (MW-MSA) to simultaneously integrate cell features of different scales. Small window self-attention is used to extract local cell detail features, and large window self-attention aims to integrate features from smaller-scale window attention to achieve window-to-window information interaction. Our design enables long-range feature integration but avoids whole image self-attention (SA) in ViT or twice local window SA in Swin Transformer. We find convolutional feed-forward networks (CFFN) are more efficient than original MLP-based FFN for representing cytopathology images. Our overall model adopts a pyramid architecture. We establish two multi-center cervical cell classification datasets of two-category 192,123 images and four-category 174,138 images. Extensive experiments demonstrate that our MWT outperforms state-of-the-art general classification networks and specialized classifiers for cytopathology images in the internal and external test sets. The results on large-scale datasets prove the effectiveness and generalization of our proposed model. Our work provides a reliable cytopathology image recognition method and helps establish computer-aided screening for cervical cancer. Our code is available at https://github.com/nmyz669/MWT, and our web service tool can be accessed at https://huggingface.co/spaces/nmyz/MWTdemo.

A Survey on the Media Information Flow to Contribute Bulgaria’s Destination Image and Perception

Travel and tourism business has proved to be powerful accelerator and contributor to the global economy. As a flexible and highly adaptive to many disruptive events industry, it has been handling crises of various nature, origin and background. The current publication is focused on the role the media information flow exerts on to the image and perception of destination Bulgaria. The survey aims to perform a quality analysis of the news published and announced by leading media broadcasts and to evaluate their influence when making a decision to undertake travel. The study period is limited to the 2023 summer season. For the purposes of the survey, Web service tool for semantic analysis is implemented. In the course of the research, it is revealed that negative news related to tourism prevails and this could have a negative impact on the destination.

Interactive Dynamic Presentation (IDP) and Semantic Faceted Search and Browsing (SFB) of the Wittgenstein Nachlass

Abstract In 2000 the Wittgenstein Archives at the University of Bergen (WAB) published the CD-ROM edition of Wittgenstein’s Nachlass: The Bergen Electronic Edition (BEE). Moreover, since then WAB has worked towards complementing the static CD-ROM edition with an interactive web platform that additionally allows more user-specific and more user-tailored utilizations of WAB’s Nachlass resources. The paper describes two specific web service tools of this platform: Interactive Dynamic Presentation (IDP) of the Wittgenstein Nachlass and Semantic Faceted Search and Browsing (SFB) of Wittgenstein domain metadata. The paper argues that it is only when these two tools are fully implemented and functional that WAB can adequately serve the scholarly needs of the Wittgenstein Nachlass user community. The paper discusses some selected features and functionalities of the two tools in detail. An earlier version of this paper was published as „Complementing Static Scholarly Editions with Dynamic Research Platforms: Interactive Dynamic Presentation (IDP) and Semantic Faceted Search and Browsing (SFB) for the Wittgenstein Nachlass“ in Selected Papers from the CLARIN Annual Conference 2020, ed. by C. Navarretta & M. Eskevich (Utrecht: CLARIN ERIC). In writing this paper I have benefitted from comments by K. De Smedt, N. Gangopadhyay, Ø. Gjesdal, J. Hendrickson, C. Huitfeldt, H. Al Ruweh, the Clarin 2020 conference reviewers and editors as well as Jasmin Trächtler.

S-ProvFlow. Storing and Exploring Lineage Data as a Service

Abstract We present a set of configurable Web service and interactive tools, s-ProvFlow, for managing and exploiting records tracking data lineage during workflow runs. It facilitates detailed analysis of single executions. It helps users manage complex tasks by exposing the relationships between data, people, equipment and workflow runs intended to combine productively. Its logical model extends the PROV standard to precisely record parallel data-streaming applications. Its metadata handling encourages users to capture the application context by specifying how application attributes, often using standard vocabularies, should be added. These metadata records immediately help productivity as the interactive tools support their use in selection and bulk operations. Users rapidly appreciate the power of the encoded semantics as they reap the benefits. This improves the quality of provenance for users and management. Which in turn facilitates analysis of collections of runs, enabling users to manage results and validate procedures. It fosters reuse of data and methods and facilitates diagnostic investigations and optimisations. We present S-ProvFlow's use by scientists, research engineers and managers as part of the DARE hyper-platform as they create, validate and use their data-driven scientific workflows.

A Dynamic Nomogram to Predict the Risk of Stroke in Emergency Department Patients With Acute Dizziness.

ObjectiveTo develop a risk prediction tool for acute ischemic stroke (AIS) for patients presenting to the emergency department (ED) with acute dizziness/vertigo or imbalance.MethodA prospective, multicenter cohort study was designed, and adult patients presenting with dizziness/vertigo or imbalance within 14 days were consecutively enrolled from the EDs of 4 tertiary hospitals between August 10, 2020, and June 10, 2021. Stroke was diagnosed by CT or MRI performed within 14 days of symptom onset. Participants were followed-up for 30 days. The least absolute shrinkage and selection operator (LASSO) logistic regression analysis was conducted to extract predictive factors that best identified patients at high risk of stroke to establish a prediction model. Model discrimination and calibration were assessed and its prediction performance was compared with the age, blood pressure, clinical features, duration, and diabetes (ABCD2) score, nystagmus scheme, and finger to nose test.ResultsIn this study, 790 out of 2,360 patients were enrolled {median age, 60.0 years [interquartile range (IQR), 51–68 years]; 354 (44.8%) men}, with complete follow-up data available. AIS was identified in 80 patients. An online web service tool (https://neuroby.shinyapps.io/dynnomapp/) was developed for stroke risk prediction, including the variables of sex, trigger, isolated symptom, nausea, history of brief dizziness, high blood pressure, finger to nose test, and tandem gait test. The model exhibited excellent discrimination with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.889 (95% CI: 0.855–0.923), compared with the ABCD2 score, nystagmus scheme, and finger to nose test [0.712 (95% CI, 0.652–0.771), 0.602 (95% CI, 0.556–0.648), and 61.7 (95% CI, 0.568–0.666) respectively].ConclusionOur new prediction model exhibited good performance and could be useful for stroke identification in patients presenting with dizziness, vertigo, or imbalance. Further externally validation study is needed to increase the strength of our findings.

Converting Biomedical Text Annotated Resources into FAIR Research Objects with an Open Science Platform

Today, there are excellent resources for the semantic annotation of biomedical text. These resources span from ontologies, tools for NLP, annotators, and web services. Most of these are available either in the form of open source components (i.e., MetaMap) or as web services that offer free access (i.e., Whatizit). In order to use these resources in automatic text annotation pipelines, researchers face significant technical challenges. For open-source tools, the challenges include the setting up of the computational environment, the resolution of dependencies, as well as the compilation and installation of the software. For web services, the challenge is implementing clients to undertake communication with the respective web APIs. Even resources that are available as Docker containers (i.e., NCBO annotator) require significant technical skills for installation and setup. This work deals with the task of creating ready-to-install and run Research Objects (ROs) for a large collection of components in biomedical text analysis. These components include (a) tools such as cTAKES, NOBLE Coder, MetaMap, NCBO annotator, BeCAS, and Neji; (b) ontologies from BioPortal, NCBI BioSystems, and Open Biomedical Ontologies; and (c) text corpora such as BC4GO, Mantra Gold Standard Corpus, and the COVID-19 Open Research Dataset. We make these resources available in OpenBio.eu, an open-science RO repository and workflow management system. All ROs can be searched, shared, edited, downloaded, commented on, and rated. We also demonstrate how one can easily connect these ROs to form a large variety of text annotation pipelines.

ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures

Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. The new web service features an integrated and customizable protein viewer with an option to analyze and view more than one structure at once. This feature facilitates side-by-side comparisons of pores in different conformations of the same protein or of identified pores before and after opening gates within the same protein. ProPores2 is freely and publicly available at https://service.bioinformatik.uni-saarland.de/propores.

Exploring Teacher Perceptions of Using E-portfolios in Public Schools in the United Arab Emirates

This study explores e-portfolio practices among K-12 teachers and investigates their perceptions, attitudes and skills towards the potentials of e-portfolios to enhance the required 21st century competencies. Both qualitative and quantitative methods were used to investigate teachers’ perceptions of the use of e-portfolios in both public and private sectors in the seven Emirates of the UAE. In addition, 10 school leaders were interviewed to explore how willing and able they were in supporting a hypothetical change in the practice of documentation by using e-portfolios. A survey was conducted with over 400 teachers responding to 54 questions via an online questionnaire supported by the Survey Monkey web service tool. Data analysis results revealed that a substantial proportion of participants felt positively towards the possibility of using e-portfolios. However, the survey also revealed that the majority of teachers in the field need to acquire knowledge, associated skills, and competencies, through professional developmental training programs to cultivate and improve reflective, selective, organizational, constructive feedback skills, along with familiarity and proficiency in using online collaborative and professional networking tools. The study concludes with implications for policy-makers and stakeholders to consider before introducing requirements and regulations on e-portfolios.

Cano-wgMLST_BacCompare: A Bacterial Genome Analysis Platform for Epidemiological Investigation and Comparative Genomic Analysis.

With the decreasing cost of next-generation sequencing, whole-genome sequence-based bacterial genome comparisons are expected to become a mainstream process in the public health domain. Extended multilocus sequence typing (MLST) methods are becoming increasingly popular for use in comparing bacterial genetic relatedness in epidemiological investigations. Several extended MLST schemes based on biological signatures have been reported. Among them, whole-genome MLST (wgMLST) has gradually become one of the most widely used approaches for bacterial strain typing. In addition to using bacterial typing, many researchers aim to identify differences in the genes of compared strains. Because these differences might provide insights into critical bacterial functions, such as virulence and pathogenicity, researchers usually study these genes that differ between strains. Hence, we designed a web service tool based on wgMLST-constructed tree topology coupled with the feature selection method to create the “canonical wgMLST (cano-wgMLST) tree.” The genes that differ between strains are shown at each split of the tree, thereby directly providing information for performing a comparative genomic analysis for each strain pair. We demonstrated that this web service tool could be operated efficiently on two datasets consisting of 22 Campylobacter jejuni isolates and 59 S. Heidelberg isolates, respectively. We imposed this tool on a designated web server, cano-wgMLST_BacCompare, to enable users to create a wgMLST tree and canonical wgMLST tree automatically from their uploaded bacterial genomes for not only epidemiological investigation but also comparative genomic analysis. Additionally, detailed information on how to use this service is provided. The cano-wgMLST_BacCompare is available at http://baccompare.imst.nsysu.edu.tw.

An integrated approach towards service composition life cycle: A transportation process case study

Abstract In Web Service research, providing methods and tools to cater for automatic composition of services on the Web is still the object of ongoing research activity. Despite the proposed approaches, this issue remains open. Our current contribution deals with this topic and presents a Dynamic Web Service Composition Framework (DWSC). The DWSC behavior is based mainly on two components: service dynamic designer (WSDD) and service selection based on popularity (WSSP) to propose a composite service. The DWSC architecture, designed to automatically compose services based on popularity, has the advantage of proposing a list of suggested web services according the user request from a service repository and presenting a dynamic orchestration based on the selected web services. Further, we present a practical case study according the transportation process on supply chain, examples and experimental results that demonstrate the feasibility and effectiveness of our work.

PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence.

We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the −35 and −10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the −35 and −10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the −10 and −35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts −10 and −35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.

FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation

AbsatractAlong with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/. This new web-based annotator will shed light on field studies involving organisms without a reference genome.

PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing.

With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon’s study used for discerning among epidemiologically related and non-related isolates.

Automating bibliometric analyses using Taverna scientific workflows: A tutorial on integrating Web Services

Quantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad analyses and statistics. The Europe PubMed Central (PMC) and its Web Services is one of these resources, providing a rich platform to retrieve information and metadata on scientific publications. However, a complete bibliometric analysis that involves gathering information and deriving statistics on an author, topic, or country is laborious when consuming Web Services on the command-line or using low level automation. In contrast, scientific workflow managers can integrate different types of software tools to automate multi-step processes. The Taverna workflow engine is a popular open-source scientific workflow manager, giving easy access to availableWeb Services. In this tutorial, we demonstrate how to design scientific workflows for bibliometric analyses in Taverna by integrating Europe PubMed Central Web Services and statistical analysis tools. To our knowledge, this is also the first time scientific workflow managers have been used to perform bibliometric analyses using these Web Services.

Designing vulnerability testing tools for web services: approach, components, and tools

This paper proposes a generic approach for designing vulnerability testing tools for web services, which includes the definition of the testing procedure and the tool components. Based on the proposed approach, we present the design of three innovative testing tools that implement three complementary techniques (improved penetration testing, attack signatures and interface monitoring, and runtime anomaly detection) for detecting injection vulnerabilities, thus offering an extensive support for different scenarios. A case study has been designed to demonstrate the tools for the particular case of SQL Injection vulnerabilities. The experimental evaluation demonstrates that the tools can effectively be used in different scenarios and that they outperform well-known commercial tools by achieving higher detection coverage and lower false-positive rates.

Elucidation of an Array of Nitrate Transporter Paralogs in Arabidopsis Thaliana Genome

Plants derive gene paralogs after both small-scale duplication (SSD) and whole genome duplication (WGD). Plants are known to retain duplicated genes and enhance their gene repertoire which intensively contributes to the evolution of their genomes. The general view is that such paralogs are both selected and preserved in evolution because they express variable levels of proteins in different temporal and spatial patterns. In Arabidopsis thaliana, paralogs involved in signalling and transcriptional regulation are very often retained after gene and genome duplication events. We analysed duplication events of a primitive nitrate transporter gene NTR across the genome of Arabidopsis thaliana. Majority of the paralogs have acquired the function of both high, low and also dual affinity nitrate transporters, some being regulated by nitrate levels themselves and involved in a variety of plant functions such as embryonic development, repression of lateral root initiation, stomatal opening, xylem and phloem transport and wound response etc. For the present analysis, 19 nitrate transporter protein sequences were retrieved from TAIR database and analysed by a web service tool PINDA as well as manually which gave analogous results. Several transporters were found to be acting as paralogs as close sequence homology was observed amongst them. The results point towards the idea that sub functionalization of nitrate transporter proteins in higher plants happened as a result of a series of gene duplication events.

A Practical Approach Towards Automatic Testing of Web Services Interoperability

Web Services are a technology designed to support the invocation of remote elements by client applications, with the goal of providing interoperable application-to-application interaction while assuring vendor and platform independence. In business-critical environments, the occurrence of interoperability issues can have disastrous consequences, including direct financial costs, reputation, and client fidelity losses. Despite this, experience shows that services interoperability is still quite difficult to achieve. The goal of this paper is to propose a practical testing process to understand the real level of interoperability provided by web services platforms. An extensible tool, that implements the proposed approach, has been used to run a large campaign during which we have tested the interoperability of a large number of web services, comprising both home-implemented and publicly available services, deployed on top of several web service platforms and against 11 client-side web service platforms. Numerous issues have been disclosed, showing the effectiveness of the proposed approach and the importance of having an automatic tool for testing web services for interoperability.

Assessing and Comparing Vulnerability Detection Tools for Web Services: Benchmarking Approach and Examples

Selecting a vulnerability detection tool is a key problem that is frequently faced by developers of security-critical web services. Research and practice shows that state-of-the-art tools present low effectiveness both in terms of vulnerability coverage and false positive rates. The main problem is that such tools are typically limited in the detection approaches implemented, and are designed for being applied in very concrete scenarios. Thus, using the wrong tool may lead to the deployment of services with undetected vulnerabilities. This paper proposes a benchmarking approach to assess and compare the effectiveness of vulnerability detection tools in web services environments. This approach was used to define two concrete benchmarks for SQL Injection vulnerability detection tools. The first is based on a predefined set of web services, and the second allows the benchmark user to specify the workload that best portrays the specific characteristics of his environment. The two benchmarks are used to assess and compare several widely used tools, including four penetration testers, three static code analyzers, and one anomaly detector. Results show that the benchmarks accurately portray the effectiveness of vulnerability detection tools (in a relative manner) and suggest that the proposed benchmarking approach can be applied in the field.

Identification of temozolomide resistance factors in glioblastoma via integrative miRNA/mRNA regulatory network analysis.

Drug resistance is a major issue in the treatment of glioblastoma. Almost all glioblastomas are intrinsically resistant to chemotherapeutic temozolomide (TMZ) or develop resistance during treatment. The interaction networks of microRNAs (miRNAs) and mRNAs likely regulate most biological processes and can be employed to better understand complex processes including drug resistance in cancer. In this study, we examined if integrative miRNA/mRNA network analysis using the web-service tool mirConnX could be used to identify drug resistance factors in glioblastoma. We used TMZ-resistant glioblastoma cells and their integrated miRNA/mRNA networks to identify TMZ-sensitizing factors. TMZ resistance was previously induced in glioblastoma cell lines U87, Hs683, and LNZ308. miRNA/mRNA expression profiling of these cells and integration of the profiles using mirConnX resulted in the identification of plant homeodomain (PHD)-like finger 6 (PHF6) as a potential TMZ-sensitizing factor in resistant glioblastoma cells. Analysis of PHF6 expression showed significant upregulation in glioblastoma as compared to normal tissue. Interference with PHF6 expression in three TMZ-resistant subclones significantly enhanced TMZ-induced cell kill in two of these cell lines. Altogether, these results demonstrate that mirConnX is a feasible and useful tool to investigate miRNA/mRNA interactions in TMZ-resistant cells and has potential to identify drug resistance factors in glioblastoma.

Analysis Tool Web Services from the EMBL-EBI

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.