Existing Web Resources Research Articles

Pesti-DGI-Net: A multi-modal deep learning architecture based on dual interpretability for pesticide-likeness prediction

“Pesticide-likeness” represents an extension of the pharmaceutical concept of “drug-likeness” to the field of pesticides. The development of algorithmic tools for predicting pesticide-likeness holds great significance for the rational design of pesticide molecules. Among various computational approaches, artificial intelligence techniques, especially deep learning, stand out due to their distinctive advantages. However, the application of deep learning models in the field of pesticide-likeness remains relatively limited. To address this gap, we proposed a multi-modal deep learning architecture, termed Pesti-DGI-Net, which took the standard Simplified Molecular Input Line Entry System (SMILES) of compounds as input and combined molecular representations across multiple dimensions. Through this fusion, Pesti-DGI-Net made accurate predictions of the pesticide-likeness for candidate compounds, as substantiated by extensive evaluations on internal test sets and an external independent test set. Additionally, Pesti-DGI-Net provided two interpretable methods to elucidate the relationship between chemical structure and pesticide-likeness. Comparison with domain experts showed that Pesti-DGI-Net enabled researchers to better understand the prediction results. Finally, we integrated Pesti-DGI-Net with existing web resources to comprehensively assess the potential of compounds as pesticide-like molecules. Our cloud platform is freely available at http://chemyang.ccnu.edu.cn/ccb/server/CoPLE/.

GlyComb: A novel glycoconjugate data repository that bridges glycomics and proteomics

The glycosylation of proteins and lipids is known to be closely related to the mechanisms of various diseases such as influenza, cancer, and muscular dystrophy. Therefore, it has become clear that the analysis of post-translational modifications of proteins, including glycosylation, is important to accurately understand the functions of each protein molecule and the interactions among them. In order to conduct large-scale analyses more efficiently, it is essential to promote the accumulation, sharing, and reuse of experimental and analytical data in accordance with the FAIR (Findability, Accessibility, Interoperability, and Re-usability) data principles. However, a FAIR data repository for storing and sharing glycoconjugate information, including glycopeptides and glycoproteins, in a standardized format did not exist. Therefore, we have developed GlyComb (https://glycomb.glycosmos.org) as a new standardized data repository for glycoconjugate data. Currently, GlyComb can assign a unique identifier to a set of glycosylation information associated with a specific peptide sequence or UniProt ID. By standardizing glycoconjugate data via GlyComb identifiers and coordinating with existing web resources such as GlyTouCan and GlycoPOST, a comprehensive system for data submission and data sharing among researchers can be established. Here we introduce how GlyComb is able to integrate the variety of glycoconjugate data already registered in existing data repositories to obtain a better understanding of the available glycopeptides and glycoproteins, and their glycosylation patterns. We also explain how this system can serve as a foundation for a better understanding of glycan function.

Location-Aware Resource Discovery and QoR-Driven Resource Selection for Hybrid Web Environments.

In the Web of Things (WoT) context, an increasing number of stationary and mobile objects provide functions as RESTful services, also called resources, that can be combined with other existing Web resources, to create value-added processes. However, nowadays resource discovery and selection are challenging, due to (1) the growing number of resources providing similar functions, making Quality of Resource (QoR) essential to select appropriate resources, (2) the transient nature of resource availability due to sporadic connectivity, and (3) the location changes of mobile objects in time. In this paper, we first present a location-aware resource discovery that relies on a 3-dimensional indexing schema, which considers object location for resource identification. Then, we present a QoR-driven resource selection approach that uses a Selection Strategy Adaptor (SSA) to form i-compositions (with i ) offering different implementation alternatives. The defined SSA allows forming resource compositions while considering QoR constraints and Inputs/Outputs matching of related resources, as well as resource availability and users different needs (e.g., optimal and optimistic compositions obtained using a scoring system). Analyses are made to evaluate our service quality model against existing ones, and experiments are conducted in different environments setups to study the performance of our solution.

University of Portsmouth library subject pages: a flexible in-house system for guidance and resource discovery

Guiding students to library resources, and supporting users in their discovery and use, is a key role of academic librarians. Subject pages are a traditional way of asynchronously managing some of the complexity that exists, with off-the-shelf software packages often a solution.The University of Portsmouth Library (https://library.port.ac.uk/) decided to provide this support through an addition to our existing in-house content management system (CMS). This would be flexible and powerful in allowing freedom of design for Faculty Librarians within a shell that provided some similarity – and thus familiarity – between subject areas. It would also be easy to maintain technically. The Library's Web Developer, in consultation with the six Faculty Librarians and the Enquiry team lead, has built a PHP/MySQL based application which is tightly integrated to our existing web resources providing enhanced delivery mechanisms allowing for open ended content development while retaining support for legacy web pages.This allows new pages to be quickly and easily added to the system in real time, existing pages to be either edited alone, ‘linked to’ or copied and modified. Resource lists can be simply constructed which rely on Library metadata rather than copies of data which need updating; support material can be added whether video, slides or images; guidance can be included to help students navigate their information literacy journey.Despite a pressured summer period of lockdown and working from home due to Covid-19, the rollout of the system has been successful from the point of view of the faculty librarian construction and development, as well as in usage by our enquiries team supporting students requiring help. Student feedback has been positive.

Web repositories of natural agents promote pests and pathogenic microbes management.

The grand challenge to meet the increasing demands for food by a rapidly growing global population requires protecting crops from pests. Natural active substances play a significant role in the sustainable pests and pathogenic microbes management. In recent years, natural products- (NPs), antimicrobial peptides- (AMPs), medicinal plant- and plant essential oils (EOs)-related online resources have greatly facilitated the development of pests and pathogenic microbes control agents in an efficient and economical manner. However, a comprehensive comparison, analysis and summary of these existing web resources are still lacking. Here, we surveyed these databases of NPs, AMPs, medicinal plants and plant EOs with insecticidal, antibacterial, antiviral and antifungal activity, and we compared their functionality, data volume, data sources and applicability. We comprehensively discussed the limitation of these web resources. This study provides a toolbox for bench scientists working in the pesticide, botany, biomedical and pharmaceutical engineering fields. The aim of the review is to hope that these web resources will facilitate the discovery and development of potential active ingredients of pests and pathogenic microbes control agents.

Mapping the Knowledge of Dante Commentaries in the Digital Context: A Web Ontology Approach

AbstractWith digital repositories and databases available since the 1990s, Dante scholarship has always been at the forefront of the digital humanities and the digitization of medieval texts and manuscripts. However, the amount of information available about such aspects is imposing, and its location subject to the extreme dispersion of traditional scholarly publications: commentaries first but also academic journals, miscellanies, and so forth. Rather than being based on traditional word searches, a true advancement of knowledge needs to overcome the rigidity of text-based queries (and in-line markup embedded in text). Such paramount evolution is now made possible by the Semantic Web, an extension of the current web by description standards that help machines to understand and connect the information already available on the web. To achieve this, the latter is mapped using formal description and classification patterns, called ontologies. Ontologies are a key factor in managing meaningful search/data extraction, publishing relevant results on the web, search existing web resources, and offering answers to more sophisticated queries. Due to its vastness and complexity, Dante scholarship has calls for an ontology-based mapping, and specific tools have been designed to express the most difficult and articulate aspects of Dante’s literary production, such as its use of biblical, classical, and medieval sources. This paper aims to introduce the aims and scope of a new digital library of Dante commentaries, built according to the aforementioned standards and aiming to refine and extend the ontologies developed for Dante’s minor works to the more complex world of the Commedia.

Information resources for communication of priests with parishioners

The article considers the problem of using modern means of communication in the field of religion. This topic has become extremely relevant today, given the unfavorable situation due to the establishment of quarantine restrictions that directly affect the communication process between priests and parishioners.The main information resources for providing religious communications in the modern world are analyzed in the work, their main advantages and disadvantages are highlighted. Particular attention is paid to comprehensive religious web resources. All web resources are divided into 6 categories: Christian sites, religious portals, sites of individual religious institutions, societies, YouTube channels, sites of electronic Christian libraries and electronic databases. It was found that the main disadvantage of most of the analyzed resources is the poor design and disorder of information. Based on the analysis of religious web resources, it is proposed to develop a website for the Parish. Such a site has a complex structure in the form of the main and additional menus, which, in turn, are structured by sections, and sections - by subsections. Thanks to the sections of the main menu, users will be able to see when, where, at what time an event will take place. Using the additional menu "Communication", the user will be able to anonymously send questions to the priest using the service "Ask a priest" and receive a response to the specified e-mail address. Equally important is the section "Library", which contains religious publications, and which are structured in alphabetical order and by category. The conclusion of the article presents the prospects of development of religious information resources on the basis of their comprehensive and complex analysis. Recommendations for improving religious communication web resources are offered. In particular, it is recommended to conduct constant monitoring in the world of Internet technologies, to research the preferences of users, and on this basis, to make changes to existing web resources in the field of religion.

Evaluation of Neuroanatomy Web Resources for Undergraduate Education: Educators' and Students' Perspectives.

Despite the development of novel teaching strategies and the abundance of adjunct teaching web resources, students and early career physicians have continuously reported difficulties in learning and clinically applying neuroanatomy. Differences in instructional design of these resources, the lack of assessment of their capacity to meet intended educational goals, and a poor understanding of the user's perspective may have hindered their success in increasing understanding and retention of neuroanatomical knowledge. To decipher the limitations of existing web resources, an online search for neuroanatomy web resources was performed and distilled through a strict filtration rubric. A selection of resources were analyzed by a panel of educators and rated using Likert scales, focusing on the identification of features influencing their usefulness in learning the anatomy of the spinal pathways. The top three ranked web resources were subsequently evaluated by a panel of medical and neuroscience students to assess how specific features aided in their learning of the subject. This detailed analysis has identified features of neuroanatomy web resources that are valued by both educators and users with regard to instructional design. One resource was rated highest by end users and educators on a series of Likert scale questions in terms of clarity of explanation, step-wise teaching design, summarization of information, control of instructional-pace, integration with neurophysiology, neuroradiology and clinical correlates, deployment of a wide array of pedagogical tools, and factors for visualizing neuroanatomical inter-relationships. These results have provided a novel user perspective on the influence of specific elements of neuroanatomy web resources to improve instructional design and enhance learner performance.

Abstract 5280: A web-based platform for exploring ‘omics and clinical data from healthy breast tissues

Abstract Integrating ‘omics, epidemiology and clinical data from healthy patients and their biologic samples is important for identifying the determinants of early carcinogenesis. In a cross-sectional study of 249 women with no history of cancer and who underwent reduction mammoplasty, whole transcriptome (i.e., gene expression) and epigenome (i.e., methylation and microRNA) data were collected from dissected breast tissues. An extensive epidemiologic questionnaire ascertained data on breast cancer risk factors. Subjects with benign lesions considered at risk for future cancer were excluded. In order to manage, analyze, and share these data efficiently, we organized the data into a relational database to support a series of web-based tools for analyzing and visualizing the multidimensional data in an intuitive graphical user interface (GUI). The current platform improves upon existing web resources that integrate ‘omics and clinical data by including novel features that allow for greater flexibility of bioinformatics analyses. It also focuses on the ‘omics as an outcome, rather, e.g., what epidemiology risk factor or particular gene is associated with downstream effects across the ‘omics. Such features include: 1) a plot function that can visualize up to 4 dimension data chosen by a user from the 3 types of genetic profiles and more than 100 clinical and biomedical variables; 2) a differentiation visualization tool based on the ‘omics data of 2 groups of samples; and 3) miRNA target gene network generated by the correlations between gene expression and miRNA expression of our patient samples and validated miRNA target gene database. The GUI facilitates the discovery of research scientists by reducing complex biological and clinical data into easily understandable views. Even without the expertise of computational biology, researchers can integrate and analyze the high dimensional data that they are interested conveniently on our user-friendly designed platform. Citation Format: Xingyan Kuang, Catalin Marian, Cenny Taslim, Min-Ae Song, Daniel Weng, Jo L. Freudenheim, Theodore Brasky, Kun Huang, Kevin Coombes, Peter G. Shields. A web-based platform for exploring ‘omics and clinical data from healthy breast tissues. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5280.

Domain Adaptation for Ontology Localization

Ontology localization is the task of adapting an ontology to a different cultural context, and has been identified as an important task in the context of the Multilingual Semantic Web vision. The key task in ontology localization is translating the lexical layer of an ontology, i.e., its labels, into some foreign language. For this task, we hypothesise that the translation quality can be improved by adapting a machine translation system to the domain of the ontology. To this end, we build on the success of existing statistical machine translation (SMT) approaches, and investigate the impact of different domain adaptation techniques on the task. In particular, we investigate three techniques: i) enriching a phrase table by domain-specific translation candidates acquired from existing Web resources, ii) relying on Explicit Semantic Analysis as an additional technique for scoring a certain translation of a given source phrase, as well as iii) adaptation of the language model by means of weighting n-grams with scores obtained from topic modelling. We present in detail the impact of each of these three techniques on the task of translating ontology labels. We show that these techniques have a generally positive effect on the quality of translation of the ontology and that, in combination, they provide a significant improvement in quality.

Domain adaptation for ontology localization

Ontology localization is the task of adapting an ontology to a different cultural context, and has been identified as an important task in the context of the Multilingual Semantic Web vision. The key task in ontology localization is translating the lexical layer of an ontology, i.e., its labels, into some foreign language. For this task, we hypothesize that the translation quality can be improved by adapting a machine translation system to the domain of the ontology. To this end, we build on the success of existing statistical machine translation (SMT) approaches, and investigate the impact of different domain adaptation techniques on the task. In particular, we investigate three techniques: (i) enriching a phrase table by domain-specific translation candidates acquired from existing Web resources, (ii) relying on Explicit Semantic Analysis as an additional technique for scoring a certain translation of a given source phrase, as well as (iii) adaptation of the language model by means of weighting n-grams with scores obtained from topic modelling. We present in detail the impact of each of these three techniques on the task of translating ontology labels. We show that these techniques have a generally positive effect on the quality of translation of the ontology and that, in combination, they provide a significant improvement in quality.

Increasing the quality, comparability and accessibility of phytoplankton species composition time-series data

Phytoplankton diversity and its variation over an extended time scale can provide answers to a wide range of questions relevant to societal needs. These include human health, the safe and sustained use of marine resources and the ecological status of the marine environment, including long-term changes under the impact of multiple stressors. The analysis of phytoplankton data collected at the same place over time, as well as the comparison among different sampling sites, provide key information for assessing environmental change, and evaluating new actions that must be made to reduce human induced pressures on the environment. To achieve these aims, phytoplankton data may be used several decades later by users that have not participated in their production, including automatic data retrieval and analysis. The methods used in phytoplankton species analysis vary widely among research and monitoring groups, while quality control procedures have not been implemented in most cases. Here we highlight some of the main differences in the sampling and analytical procedures applied to phytoplankton analysis and identify critical steps that are required to improve the quality and inter-comparability of data obtained at different sites and/or times. Harmonization of methods may not be a realistic goal, considering the wide range of purposes of phytoplankton time-series data collection. However, we propose that more consistent and detailed metadata and complementary information be recorded and made available along with phytoplankton time-series datasets, including description of the procedures and elements allowing for a quality control of the data. To keep up with the progress in taxonomic research, there is a need for continued training of taxonomists, and for supporting and complementing existing web resources, in order to allow a constant upgrade of knowledge in phytoplankton classification and identification. Efforts towards the improvement of metadata recording, data annotation and quality control procedures will ensure the internal consistency of phytoplankton time series and facilitate their comparability and accessibility, thus strongly increasing the value of the precious information they provide. Ultimately, the sharing of quality controlled data will allow one to recoup the high cost of obtaining the data through the multiple use of the time-series data in various projects over many decades.

Research of Adaptive Transformation Method Based on Webpage Semantic Features for Small-Screen Terminals

Small-screen mobile terminals have difficulty accessing existing Web resources designed for large-screen devices. This paper presents an adaptive transformation method based on webpage semantic features to solve this problem. According to the text density and link density features of the webpages, the webpages are divided into two types: index and content. Our method uses an index-based webpage transformation algorithm and a content-based webpage transformation algorithm. Experiment results demonstrate that our adaptive transformation method is not dependent on specific software and webpage templates, and it is capable of enhancing Web content adaptation on small-screen terminals. Keywords: Webpage transformation, mobile terminals, semantic features, text density, link density.

Techniques for Building a Read/Write/Execute-Able Web

In recent years, the usage pattern of the Web has been undergoing dramatic changes. The traditional definition of the Web, “a system of interlinked hyper-text documents”, can no longer describe the situation accurately today. Instead, users want to interact with Web resources and even want to create their own Web resources that can interact with others. This is what we call “Web 2.0”, a new Web that is both read-able and write-able. However, considering Web-based services around us: the calendar services, the traveling services, and the messaging services, etc., one can draw a conclusion that what Web users nowadays expect from the Web are not only contents and interactions but also services. To meet this expectation, a read/write/execute-able Web is demanded. In this paper, new technologies for building such a Web are proposed. A virtual browsing environment is employed to transform existing Web resources into executable services. Furthermore, an HTML-to-XML annotation/transformation technology is integrated into the virtual browsing environment to form the data model part. With these technologies, the Web will be transformed into “a system of interlinked services.”

Web-based Architecture for Mobile Learning

The availability of multimedia web resources and the development of mobile phones are two major factors that have opened the way towards the development of M-learning systems. These systems are designed for nomadic learners; they are designed to deliver learning material that adapts to the learner context. In this research we developed a mobile learning system that exploits existing web resources to generate learning material which fits the actual needs of the learner. The system constructs a personalized learning web for a mobile user who needs to learn about a specific topic. The system manages the gathering, authoring, packaging and delivery of learning material. The architecture of the implemented system uses a set of web services to retrieve information and learning resources from the web. These learning resources are packaged into lightweight learning objects designed according to preset layouts. Besides, the system constructs an ontology-like hierarchical content structure to organize learning objects into a learning web allowing the learner to navigate freely according to his/her needs and constraints. The paper presents the design, implementation and an evaluation of the system.

"An AJAX-based Graphical Cooperative Ontology Editor" by Rajinder Singh, with Jessica Rubart as Coordinator

The Semantic Web is best described as an evolving extension of the current World Wide Web (WWW), where not only humans but machines are able to interpret Web content. To enable these machines to interpret the meaning of Web content, this meaning must be described in a machine processable form. Several standards have been proposed to facilitate in adding meaning to existing Web resources. One such standard that has gained a significant amount of interest is the Web Ontology Language (OWL), which enables knowledge to be represented through well-defined constructs.

MetaTIGER: a metabolic evolution resource

Metabolic networks are a subject that has received much attention, but existing web resources do not include extensive phylogenetic information. Phylogenomic approaches (phylogenetics on a genomic scale) have been shown to be effective in the study of evolution and processes like horizontal gene transfer (HGT). To address the lack of phylogenomic information relating to eukaryotic metabolism, metaTIGER (www.bioinformatics.leeds.ac.uk/metatiger) has been created, using genomic information from 121 eukaryotes and 404 prokaryotes and sensitive sequence search techniques to predict the presence of metabolic enzymes. These enzyme sequences were used to create a comprehensive database of 2257 maximum-likelihood phylogenetic trees, some containing over 500 organisms. The trees can be viewed using iTOL, an advanced interactive tree viewer, enabling straightforward interpretation of large trees. Complex high-throughput tree analysis is also available through user-defined queries, allowing the rapid identification of trees of interest, e.g. containing putative HGT events. metaTIGER also provides novel and easy-to-use facilities for viewing and comparing the metabolic networks in different organisms via highlighted pathway images and tables. metaTIGER is demonstrated through evolutionary analysis of Plasmodium, including identification of genes horizontally transferred from chlamydia.

Services Mashups: The New Generation of Web Applications

Web services are becoming a major technology for deploying automated interactions between distributed and heterogeneous applications, and for connecting business processes. Service mashups indicate a way to create new Web applications by combining existing Web resources utilizing data and Web APIs. They facilitate the design and development of novel and modern Web applications based on easy-to-accomplish end-user service compositions.

An interactive Web-based teaching tool for simplified 3D analysis of solar rhythms

This case study presents the World Wide Web as an appropriate medium for architectural teaching. The prototypical tool VRSolar uses simple programming and existing Web resources to help in the teaching of topics related to the movement of the sun and its effects on the built environment. Using JavaScript, this tool is capable of generating real time Web content in html and VRML based on user input. Accessible on the Web from within a standard Web browser, this tool calculates the solar positions of any location on earth and indicates the solar access to a given site in the form of a three-dimensional Web page, which the user can view, navigate through, and animate.