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WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects. [ABSTRACT FROM AUTHOR]

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans , Drosophila , zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML). [ABSTRACT FROM AUTHOR]

PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community. [ABSTRACT FROM AUTHOR]

Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein–protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community. [ABSTRACT FROM AUTHOR]

Background: With the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing. Methods: In this study, we have developed "Consensus Cancer Core" (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis. Results: The knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial. Conclusions: The novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org, and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets. [ABSTRACT FROM AUTHOR]

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO--a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations--evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)--mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project. [ABSTRACT FROM AUTHOR]

As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community. [ABSTRACT FROM AUTHOR]

Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface. KRiShI collects and integrates widely scattered and unstructured information from various scientific literatures, stores it under a single window, and makes it available to the community in a user-friendly manner. From basic information, best management practices, host resistance, differentially expressed genes, proteins, metabolites, resistance genes, pathways, and OMICS scale experiments, KRiShI presents these in the form of easy and comprehensive tables, diagrams, and pictures. The "Search" tab allows users to verify if their input rice gene id(s) are Rhizoctonia solani (R. solani) responsive and/or resistant. KRiShI will serve as a valuable resource for easy and quick access to data and information related to rice SB disease for both the researchers and the farmers. To encourage community curation a submission facility is made available. KRiShI can be found at http://www.tezu.ernet.in/krishi. [ABSTRACT FROM AUTHOR]

Library knowledgebases (kbs) have improved generation by generation, product by product over the last three or four decades. Functionality, completeness, integration with other library systems, and the standardization of useful data elements have all increased particularly via the Knowledgebases and Related Tools (KBART) Recommended Practice (RP), KBART Automation RP, and the upcoming NISO recommendation for package identifiers. However, several more fields and limiters would greatly enhance kbs for staff users. These include additional date fields, indicators for consortia- or region-specific packages, curator/responsible party, and more. [ABSTRACT FROM AUTHOR]

• We describe a repository of FDA-approved protein- or peptide-based drugs. • We discuss the various routes used to administer therapeutic proteins. • The manually curated THPdb2 database contains comprehensive information describing 894 unique therapeutic proteins and peptides. • User-friendly search and similarity search tools are integrated into the database. During the past 20 years, there has been a significant increase in the number of protein-based drugs approved by the US Food and Drug Administration (FDA). This paper presents THPdb2, an updated version of the THPdb database, which holds information about all types of protein-based drugs, including peptides, antibodies, and biosimilar proteins. THPdb2 contains a total of 6,385 entries, providing comprehensive information about 894 FDA-approved therapeutic proteins, including 354 monoclonal antibodies and 85 peptides or polypeptides. Each entry includes the name of therapeutic molecule, the amino acid sequence, physical and chemical properties, and route of drug administration. The therapeutic molecules that are included in the database target a wide range of biological molecules, such as receptors, factors, and proteins, and have been approved for the treatment of various diseases, including cancers, infectious diseases, and immune disorders. [ABSTRACT FROM AUTHOR]

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein--protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides. [ABSTRACT FROM AUTHOR]

The Zebrafish Information Network (zfin.org) is the central repository for Danio rerio genetic and genomic data. The Zebrafish Information Network has served the zebrafish research community since 1994, expertly curating, integrating, and displaying zebrafish data. Key data types available at the Zebrafish Information Network include, but are not limited to, genes, alleles, human disease models, gene expression, phenotype, and gene function. The Zebrafish Information Network makes zebrafish research data Findable, Accessible, Interoperable, and Reusable through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. Recently, the Zebrafish Information Network and 6 other model organism knowledgebases have collaborated to form the Alliance of Genome Resources, aiming to develop sustainable genome information resources that enable the use of model organisms to understand the genetic and genomic basis of human biology and disease. Here, we provide an overview of the data available at the Zebrafish Information Network including recent updates to the gene page to provide access to single-cell RNA sequencing data, links to Alliance web pages, ribbon diagrams to summarize the biological systems and Gene Ontology terms that have annotations, and data integration with the Alliance of Genome Resources. [ABSTRACT FROM AUTHOR]

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease. [ABSTRACT FROM AUTHOR]

Objective: Overconsumption of processed foods has led to an increase in chronic diet-related diseases such obesity and type 2 diabetes. Although diets high in fresh fruits and vegetables are linked with healthier outcomes, the specific mechanisms for these relationships are poorly understood. Experiments examining plant phytochemical production and breeding programs, or separately on the health effects of nutritional supplements have yielded results that are sparse, siloed, and difficult to integrate between the domains of human health and agriculture. To connect plant products to health outcomes through their molecular mechanism an integrated computational resource is necessary. Results: We created the Aliment to Bodily Condition Knowledgebase (ABCkb) to connect plants to human health by creating a stepwise path from plant → plant product → human gene → pathways → indication. ABCkb integrates 11 curated sources as well as relationships mined from Medline abstracts by loading into a graph database which is deployed via a Docker container. This new resource, provided in a queryable container with a user-friendly interface connects plant products with human health outcomes for generating nutritive hypotheses. All scripts used are available on github (https://github.com/atrautm1/ABCkb) along with basic directions for building the knowledgebase and a browsable interface is available (https://abckb.charlotte.edu). [ABSTRACT FROM AUTHOR]

Background: Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Query Language) databases are popular in the biomedical domain, NoSQL database technologies have been used as a more relationship-based, flexible and scalable method of data integration. Results: We have created a graph database integrating data from multiple sources. In addition to using a graph-based query language (Cypher) for data retrieval, we have developed a web-based dashboard that allows users to easily browse and plot data without the need to learn Cypher. We have also implemented a visual graph query interface for users to browse graph data. Finally, we have built a prototype to allow the user to query the graph database in natural language. Conclusion: We have demonstrated the feasibility and flexibility of using a graph database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to discover novel relationships among heterogeneous biological data and metadata. [ABSTRACT FROM AUTHOR]

This article describes the unique database of zooplankton collected by the large Juday net in 1984-2013 in the Chukchi, Bering, Okhotsk, Japan seas and the North Pacific Ocean: the sources and extent of the information contained therein, its benefits and drawbacks, the first operating experience and prospects. The information in this database has already been used to quantify the inventory of marine biological resources and appraise the waters of the North Pacific. In particular, in 2016, five tabular reference books were created and printed containing the species composition, occurrence and abundance of zooplankton in the surveyed area. The data is aggregated by species, developmental stages, size fractions, regions, vertical layers of water, light and dark time of day, four seasons of the year and perennial periods. This information has recently been verified, corrected, translated into English and from text to digital format to increase its availability to the scientific community worldwide (Volvenko, 2021 https://doi.org/10.5281/zenodo.4448646). The substantial volume and high quality of the collated data, along with the information presented in reference books and previously published data on macrofauna and the nutrition of common fish and squid, will enable the next important steps to be taken to understand the Far Eastern seas and the Pacific – one of the most productive and economically important regions of the world ocean. The scope of application of this data is fundamental to the management of marine resources, aquaculture development, nature conservation, and assessment of the damage of various anthropogenic factors on nature. [ABSTRACT FROM AUTHOR]

Background: Precision oncology pharmacotherapy relies on precise patient-specific alterations that impact drug responses. Due to rapid advances in clinical tumor sequencing, an urgent need exists for a clinical support tool that automatically interprets sequencing results based on a structured knowledge base of alteration events associated with clinical implications.Results: Here, we introduced the Oncology Pharmacotherapy Decision Support System (OncoPDSS), a web server that systematically annotates the effects of alterations on drug responses. The platform integrates actionable evidence from several well-known resources, distills drug indications from anti-cancer drug labels, and extracts cancer clinical trial data from the ClinicalTrials.gov database. A therapy-centric classification strategy was used to identify potentially effective and non-effective pharmacotherapies from user-uploaded alterations of multi-omics based on integrative evidence. For each potentially effective therapy, clinical trials with faculty information were listed to help patients and their health care providers find the most suitable one.Conclusions: OncoPDSS can serve as both an integrative knowledge base on cancer precision medicine, as well as a clinical decision support system for cancer researchers and clinical oncologists. It receives multi-omics alterations as input and interprets them into pharmacotherapy-centered information, thus helping clinicians to make clinical pharmacotherapy decisions. The OncoPDSS web server is freely accessible at https://oncopdss.capitalbiobigdata.com . [ABSTRACT FROM AUTHOR]

Modified residues present in proteins are the result of post‐translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non‐redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/. [ABSTRACT FROM AUTHOR]

In order to build upon the research of Brett, the author categorized over three hundred e-resources troubleshooting tickets at The University of Alabama Libraries into a coding scheme originally created by Goldfinger and Hemhauser with the goal of cross-comparing the results with that of two other research libraries. The results of the analysis shed light upon the most commonly reported types of problems among the three institutions, and patterns emerged that could be indicative of industry-wide concerns. The author also developed a more specific, local classification schema in order to identify areas in which local solutions could be implemented to improve user experience. [ABSTRACT FROM AUTHOR]

Opinion mining tools enable users to efficiently process a large number of online reviews in order to determine the underlying opinions. This paper presents a Hybrid Semantic Knowledgebase-Machine Learning approach for mining opinions at the domain feature level and classifying the overall opinion on a multi-point scale. The proposed approach benefits from the advantages of deploying a novel Semantic Knowledgebase approach to analyse a collection of reviews at the domain feature level and produce a set of structured information that associates the expressed opinions with specific domain features. The information in the knowledgebase is further supplemented with domain-relevant facts sourced from public Semantic datasets, and the enriched semantically-tagged information is then used to infer valuable semantic information about the domain as well as the expressed opinions on the domain features by summarising the overall opinions about the domain across multiple reviews, and by averaging the overall opinions about other cinematic features. The retrieved semantic information represents a valuable resource for modelling a machine learning classifier to predict the numerical rating of each review. Experimental evaluation revealed that the proposed Hybrid Semantic Knowledgebase-Machine Learning approach improved the precision and recall of the extracted domain features, and hence proved suitable for producing an enriched dataset of semantic features that resulted in higher classification accuracy. [ABSTRACT FROM AUTHOR]

To abstract missing interests of microblog users, this paper proposed an data mining approach based on posting mes- sage analysis. Using the phrase-LDA and the user interest knowledge base constructed automatically, it could extract high-quality candidate interest phrases from posting messages and implement the interest classification. The experimental results on SMP CUP 2016 dataset show that the phrase-LDA can achieve better results than traditional topic model on perplexity and phrase quality. The accuracy rate and the recall rate of user interest mining can reach 78% and 82% at best respectively. [ABSTRACT FROM AUTHOR]

Understanding a tumor's detailed molecular profile has become increasingly necessary to deliver the standard of care for patients with advanced cancer. Innovations in both tumor genomic sequencing technology and the development of drugs that target molecular alterations have fueled recent gains in genome-driven oncology care. 'Basket studies,' or histology-agnostic clinical trials in genomically selected patients, represent one important research tool to continue making progress in this field. We review key aspects of genome-driven oncology care, including the purpose and utility of basket studies, biostatistical considerations in trial design, genomic knowledgebase development, and patient matching and enrollment models, which are critical for translating our genomic knowledge into clinically meaningful outcomes. [ABSTRACT FROM AUTHOR]

Accurate holdings information for electronic serials is essential to librarians and users. Collection management staff spent copious amounts of time creating and updating links and public notes in electronic serials bibliographic records. This effort not only duplicated the work of our e-resource access and management software, but the updated information also quickly became outdated and inaccurate. This article describes our project to replace platform-specific Uniform Resource Locators (URLs) with an International Standard Serial Number–specific, static URL that points to the e-resource access and management software resource page and details the. process, from generating the URL and batch-editing machine-readable cataloging records, to garnering support from stakeholders and teaching users to navigate new steps. [ABSTRACT FROM PUBLISHER]

Ontario Council of University Libraries (OCUL) is a consortium of Ontario’s twenty-one university libraries. Scholars Portal E-journals (SP E-Journals) is an OCUL-sponsored digital repository containing over 45 million full text scholarly articles drawn from 19,000 journals covering every academic discipline. SP E-Journals exports its holdings to various knowledge bases including SFX. Scholars Portal (SP), OCUL’s shared technology infrastructure provider, maintains a central SFX instance for member libraries’ content subscribed via OCUL. The University of Windsor’s library is an OCUL member library that, until recently, used SFX as its Open Uniform Resource Locator link resolver for OCUL and local subscription content. This study will examine the work flow and problems encountered in maintaining central and local SFX instances, as well as discuss the advantages and challenges of providing and maintaining access to electronic serials at the consortium and member library levels. [ABSTRACT FROM PUBLISHER]

In 2015, Radford University’s McConnell Library migrated to OCLC Online Computer Library Center, Inc. (OCLC)’s WorldShare Management Services, relinquishing three legacy systems in the process. As a result, many of the Collection and Technical Services Department’s workflows changed considerably beginning months before the contract was signed. An extensive temporary departmental focus on data clean-up and training was required while maintaining core duties. New opportunities for collaboration and communication emerged. In light of developing new workflows, NASIG Core Competencies for Electronic Resources Librarians and NASIG Core Competencies for Print Serials Management were consulted in revising positions. What follows is the process, management, communication, and outcomes involved in migrating to a new next-generation library management system. [ABSTRACT FROM PUBLISHER]

Antimicrobial resistance (AMR), a top threat to global health, challenges preventive and treatment strategies of infections. AMR strains of microbial pathogens arise through multiple mechanisms. The underlying "antibiotic resistance genes" (ARGs) spread through various species by lateral gene transfer thereby causing global dissemination. Human methods also augment this process through inappropriate use, non-compliance to treatment schedule, and environmental waste. Worldwide significant efforts are being invested to discover novel therapeutic solutions for tackling resistant pathogens. Diverse therapeutic strategies have evolved over recent years. In this work we have developed a comprehensive knowledgebase by collecting alternative antimicrobial therapeutic strategies from literature data. Therapeutic strategies against bacteria, virus, fungus and parasites were extracted from PubMed literature using text mining. We have used a subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities and subsequently add objective data like entity name (including IUPAC), potency, and safety information. The extracted data was organized in a freely accessible web platform, KOMBAT. The KOMBAT comprises 1104 Chemical compounds, 220 of newly identified antimicrobial peptides, 42 bacteriophages, 242 phytochemicals, 106 nanocomposites, and 94 novel entities for phototherapy. Entities tested and evaluated on AMR pathogens are included. We envision that this database will be useful for developing future therapeutics against AMR pathogens. The database can be accessed through http://kombat.igib.res.in/. [Display omitted] • Therapeutic strategies against bacteria, virus, fungus and parasites, extracted from PubMed literature. • Subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities. • Objective approach for extraction of specific data like entity name (including IUPAC), potency, and safety information. • Coverage of multifaceted antimicrobial therapeutics. [ABSTRACT FROM AUTHOR]

The Global Open Knowledgebase Project (GOKb) is providing an open, community-based solution to resource metadata curation. The project's success pivots between data accumulation and enhancement, quality control, open data, and community involvement. In the following, participants in the project respond to questions about where GOKb is today, its usefulness in current workflows, and GOKb's future. [ABSTRACT FROM AUTHOR]

University of North Carolina at Greensboro (UNCG), like many libraries, recently migrated to a new knowledgebase and integrated library system (ILS) and found they had to clean up a great deal of messy serial title list data. In their search for solutions, they discovered the free, open source tool OpenRefine, a software program specifically designed for data normalization, transformation, and cleaning. This article describes the steps that UNCG used to take a publisher's title list file and transform it into a file format usable by their ILS. In doing so, this article will discuss major types of functionality in OpenRefine: downloading the software, importing data correctly, using the interface, transforming data on a column and cell level, exploring and normalizing data, and exporting files out of OpenRefine. At the end of this article, the readers should understand how to use OpenRefine on a basic level and be able to begin to use it on their own data. [ABSTRACT FROM PUBLISHER]

There is a growing trend toward a consolidation of services for electronic resources management, A–Z journal listings, full text link resolving, and discovery services under a single service provider. In many cases, the adoption of a discovery service from a provider that is not the same as the libraries’ existing link resolver service means managing multiple knowledgebases. In this session, three librarians gave an overview of their experiences and strategies for maintaining separate link resolving and discovery services in lieu of adopting a full suite of services from a single service provider. Each speaker presented a case study on the advantages and challenges of managing their chosen discovery service: EBSCO Discovery Service, Ex Libris’ Primo and ProQuest’s Summon, in conjunction with the CUFTS/GODOT open source knowledgebase and link resolver service. [ABSTRACT FROM PUBLISHER]

Troubleshooting electronic resource linking issues can seem to be an insurmountable task—so many resources, so little time. Using interlibrary loan (ILL) data on requests for materials available online, the electronic resources staff at the Samford University Library detected problems with the implementation of their new link resolver. This data also provided a window into some systemic issues within the metadata of certain sources and the link resolver knowledgebase. In addition to helping us improve linking for our users, the establishment of a workflow for communicating cancelled ILL transaction data on an ongoing basis has also improved the communication between electronic resources staff and the ILL department regarding the overall linking process. [ABSTRACT FROM PUBLISHER]

Since product regulations contain important rules or codes that manufacturers must follow, automatic verification of product design with the regulations related to a product is necessary. For this, this study presents a new method for the verification of product design using regulation knowledgebase and Web services. Regulation knowledgebase consisting of product ontology and rules was built with a hybrid technique combining ontology and programming languages. Web service for design verification was developed ensuring the flexible extension of knowledgebase. By virtue of two technical features, design verification is served to various products while the change of system architecture is minimized. [ABSTRACT FROM AUTHOR]

This article details Idaho State University (ISU) Library’s experience implementing and using an SFX service package in the mode that Ex Libris defines as the total care level of customer support. Although we entered into the SFX package subscription with high expectations due to the ISU Library’s earlier positive experience with another Ex Libris product, our experience using the SFX package on a day-to-day basis was consistently unsatisfactory. After objective evaluation and extensive documentation of lapses in Ex Libris personnel responsiveness to the Library’s concerns as well as lapses in basic functionality, we felt compelled to forego renewing with Ex Libris at the end of the three-year subscription period. The decision not to renew was also influenced in part by conflicts between a third party content provider and Ex Libris. [ABSTRACT FROM PUBLISHER]

The Global Open Knowledgebase (GOKb) is a project to develop and maintain a freely available repository of metadata that describes electronic journals and books using a community-managed approach. In preparation for GOKb's public preview at the end of 2014, the North Carolina State University (NCSU) Libraries launched a pilot to create a partnership model for participating libraries. Based on a presentation at the 2015 North Carolina Serials Conference, Eric Hanson, Xiaoyan Song, and Kristen Wilson from NCSU Libraries share their experiences partnering with GOKb, including the workflows and tools that NCSU has established for contributing to GOKb, opportunities for library and vendor partners, and GOKb's linked data service. [ABSTRACT FROM PUBLISHER]

An adverse outcome pathway (AOP) is a conceptual framework that organizes existing knowledge concerning biologically plausible, and empirically supported, links between molecular-level perturbation of a biological system and an adverse outcome at a level of biological organization of regulatory relevance. Systematic organization of information into AOP frameworks has potential to improve regulatory decision-making through greater integration and more meaningful use of mechanistic data. However, for the scientific community to collectively develop a useful AOP knowledgebase that encompasses toxicological contexts of concern to human health and ecological risk assessment, it is critical that AOPs be developed in accordance with a consistent set of core principles. Based on the experiences and scientific discourse among a group of AOP practitioners, we propose a set of five fundamental principles that guide AOP development: (1) AOPs are not chemical specific; (2) AOPs are modular and composed of reusable components—notably key events (KEs) and key event relationships (KERs); (3) an individual AOP, composed of a single sequence of KEs and KERs, is a pragmatic unit of AOP development and evaluation; (4) networks composed of multiple AOPs that share common KEs and KERs are likely to be the functional unit of prediction for most real-world scenarios; and (5) AOPs are living documents that will evolve over time as new knowledge is generated. The goal of the present article was to introduce some strategies for AOP development and detail the rationale behind these 5 key principles. Consideration of these principles addresses many of the current uncertainties regarding the AOP framework and its application and is intended to foster greater consistency in AOP development. [ABSTRACT FROM AUTHOR]

Organization of existing and emerging toxicological knowledge into adverse outcome pathway (AOP) descriptions can facilitate greater application of mechanistic data, including those derived through high-throughput in vitro, high content omics and imaging, and biomarker approaches, in risk-based decision making. The previously ad hoc process of AOP development is being formalized through development of internationally harmonized guidance and principles. The goal of this article was to outline the information content desired for formal AOP description and some rules of thumb and best practices intended to facilitate reuse and connectivity of elements of an AOP description in a knowledgebase and network context. For example, key events (KEs) are measurements of change in biological state that are indicative of progression of a perturbation toward a specified adverse outcome. Best practices for KE description suggest that each KE should be defined as an independent measurement made at a particular level of biological organization. The concept of “functional equivalence” can help guide both decisions about how many KEs to include in an AOP and the specificity with which they are defined. Likewise, in describing both KEs and evidence that supports a causal linkage or statistical association between them (ie, a key event relationship; KER), best practice is to build from and contribute to existing KE or KER descriptions in the AOP knowledgebase rather than creating redundant descriptions. The best practices proposed address many of the challenges and uncertainties related to AOP development and help promote a consistent and reliable, yet flexible approach. [ABSTRACT FROM AUTHOR]

Increasing efforts are being dedicated towards improving cancer care via personalized medicine. These efforts depend to a large degree on the availability of a knowledge foundation. Unfortunately, existing knowledge linking cancer drugs and potential efficacy biomarkers is in its infancy; and where links are known, they are frequently unstructured and poorly documented. We have developed a new open-access knowledgebase for precision cancer medicine (the PCM Wiki and Knowledgebase). This knowledgebase was constructed using an innovative, two-pronged approach involving a structured knowledgebase at the back-end, and an intuitive knowledge-sharing interface and user-friendly query engine in front. The knowledgebase was seeded with several patient case reports and information was mined via text-mining and literature review by human curators. Using our novel Wiki-based platform to present and share knowledge stored in the PCM knowledgebase, users are able to suggest corrections, propose additions or point to errors in the knowledgebase. The result is a community-driven evolving knowledgebase holding integrated and consolidated knowledge of markers and indications for personalized cancer medicine. We suggest that the PCM Knowledgebase and Wiki could serve as an important tool for the advancement of clinical trials and care in the field of precision cancer medicine. [ABSTRACT FROM AUTHOR]

Background Neurodegenerative diseases (NDs) are characterized by the progressive loss of neurons in the human brain. Although the majority of NDs are sporadic, evidence is accumulating that they have a strong genetic component. Therefore, significant efforts have been made in recent years to not only identify disease-causing genes but also genes that modify the severity of NDs, so-called genetic modifiers. To date there exists no compendium that lists and crosslinks genetic modifiers of different NDs. Description In order to address this need, we present NeuroGeM, the first comprehensive knowledgebase providing integrated information on genetic modifiers of nine different NDs in the model organisms D. melanogaster, C. elegans, and S. cerevisiae. NeuroGeM cross-links curated genetic modifier information from the different NDs and provides details on experimental conditions used for modifier identification, functional annotations, links to homologous proteins and color-coded protein-protein interaction networks to visualize modifier interactions. We demonstrate how this database can be used to generate new understanding through meta-analysis. For instance, we reveal that the Drosophila genes DnaJ-1, thread, Atx2, and mub are generic modifiers that affect multiple if not all NDs. Conclusion As the first compendium of genetic modifiers, NeuroGeM will assist experimental and computational scientists in their search for the pathophysiological mechanisms underlying NDs. http://chibi.ubc.ca/neurogem. [ABSTRACT FROM AUTHOR]

Background: Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools. Description: Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 7,000 genes to 2,000 different phenotypes. Conclusions: Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development. [ABSTRACT FROM AUTHOR]

In modern control systems, identification is an integral part of adaptive control where process models are adjusted using real-time operation data and control actions optimal with respect to some performance criterion are developed. A variety of identification methods based on mathematical statistics techniques have been developed. Algorithms optimal for certain classes of objects and external disturbances were categorized dependent on the available a priori information about the control object. The limits of approximating models development and application were outlined. Against this background, the paper presents novel associative search techniques enabling the development of a new dynamic object's model on each time step rather than plant approximation pertaining to time. The model is build using the data samples from process history (associations) developed at the learning phase. The new techniques employs the models of human individual's (process operator's, stock analyst's or trader's) behavior based on professional knowledge formalization. Application examples from oil refining and chemical industries, power engineering, and banking are adduced. [ABSTRACT FROM AUTHOR]

With the dramatic increase in the volume of experimental results in every domain of life sciences, assembling pertinent data and combining information from different fields has become a challenge. Information is dispersed over numerous specialized databases and is presented in many different formats. Rapid access to experiment-based information about well-characterized proteins helps predict the function of uncharacterized proteins identified by large-scale sequencing. In this context, universal knowledgebases play essential roles in providing access to data from complementary types of experiments and serving as hubs with cross-references to many specialized databases. This review outlines how the value of experimental data is optimized by combining high-quality protein sequences with complementary experimental results, including information derived from protein 3D-structures, using as an example the UniProt knowledgebase (UniProtKB) and the tools and links provided on its website (). It also evokes precautions that are necessary for successful predictions and extrapolations. [ABSTRACT FROM AUTHOR]

Knowledge Bases and Related Tools (KBART) is a joint project between the National Information Standards Organization (NISO) and the UK Serials Group (UKSG) that is now underway with a focus on improving the functioning of OpenURL by providing standards for the quality and timeliness of data provided by publishers to knowledgebases. In this presentation Peter McCracken, Co-founder of Serials Solutions, provided an overview of KBART and discussed the future plans of this new initiative. A major goal of KBART is to develop a best practices guide that can be used by content providers as they focus on quality control as it relates to the data they provide to the knowledgebase. By bringing together librarians, publishers, aggregators, and e-resource and access management services (ERAMS) vendors the hope is that the real beneficiaries will be library patrons. Several problems that impact the ability of users to get to full-text content include OpenURL data errors and syntax errors. Peter provided an overview of the problems facing library patrons, the various factors that can lead to errors in the knowledgebase and what the KBART project may be able to do to contribute to better data for everyone. The various groups are meeting monthly and presentations are planned at several national-level conferences. KBART will be successful if it results in better data for everyone including those who provide it, those who process it, those who present it, and those who use it. [ABSTRACT FROM AUTHOR]

The stability of bilinear systems is investigated using spectral techniques such as selective modal analysis. Predictive models of bilinear systems based on inductive knowledge extracted by big data mining techniques are applied with associative search of statistical patterns. A method and an algorithm for the elementwise solution of the generalized matrix Lyapunov equation are developed for discrete bilinear systems. The method is based on calculating the sequence of values of a fixed element of the solution matrix, which depends on the product of the eigenvalues of the dynamics matrix of the linear part and the elements of the nonlinearity matrixes. A sufficient condition for the convergence of all sequences is obtained, which is also a BIBO (bounded input bounded output) systems stability condition for the bilinear system. [ABSTRACT FROM AUTHOR]

The innate immune system is fundamental to the recognition of pathogens, triggering of immune-inflammatory response and host defense. Recent advance in this area has resulted in enormous amount of data, which are stored across different databases. Integrating relevant information from these different data sources is difficult because of their heterogeneous nature and dispersed physical location. We present here a single portal system, Cell Interaction Knowledgebase, with focus on the innate immunity. In particular, the knowledgebase houses comprehensive information on innate immune cells and cytokines/chemokines which are the principal mediators of communication among the immune cells. Currently the knowledgebase consists of extensive information on 2 major innate immune cell types (Macrophages and Dendritic cells) and 7 6 cytokines/chemokines for both human and mouse. In addition, intra-cellular molecular interactions and inter-cellular interactions involved in the innate immunity are curated and presented in an interactive and dynamic manner by animated pathways and query-driven cell-interaction map respectively. This is one of the first databases that houses extensive phenotypic, signaling, genomic, proteomic and knockout data on both the innate immune cells and their attendant cytokines/chemokines, and is aimed to evolve as a one-stop-shop for immunologists. The first version of database is available at http://cell-interaction.bii.a-star.edu.sg/. [ABSTRACT FROM AUTHOR]

The major bottlenecks in expert system development lie within the processes of eliciting and representing knowledge. Knowledge representation schemes combine data structures, and interpretative procedures that enable the extraction of the knowledge embedded in the data structures. A broad spectrum of knowledge types need to be represented, but available representation techniques are not optimum systems since they vary in level of expressiveness and power. Knowledge demands more than the conventional representation structures used for databases and information. This is because information is derived from processing, refining and analysing raw data. The extra refinement, analysis and addition of heuristics to information converts it to knowledge. This paper discusses the major issues in the quest for an efficient knowledge representation technique and assesses the performance and level of usefulness of some of the most successful approaches in knowledge representation. [ABSTRACT FROM AUTHOR]

Although environmental management projects typically must collect large quantities of data and information from a variety of related fields, these data and information often are not used effectively. In this study, an experimental version of a knowledge management system (Learning Acceleration and Knowledge Enhancement System) was developed to solve problems related to the acquisition and accumulation of large quantities of information being applied to an international project on lake management. Two functions were incorporated in the system, including (i) a function for previewing retrieved documents so that the information obtained using a specific search word could be easily accessed; and (ii) a thesaurus function to facilitate the sourcing and understanding by decision-makers and other stakeholders of information in unfamiliar, but related, fields of study. As these functions enable users to search for data and information in fields that might be unfamiliar to them, the application of knowledge management to projects involving environmental issues can be a valuable tool for such projects in the future. [ABSTRACT FROM AUTHOR]

The World-Wide Web provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies have become apparent, one of which is the inability to programmatically identify locally named objects that may be widely distributed over the network. This shortcoming limits our ability to integrate multiple knowledgebases, each of which gives partial information of a shared domain, as is commonly seen in bioinformatics. The Life Science Identifier (LSID) and LSID Resolution System (LSRS) provide simple and elegant solutions to this problem, based on the extension of existing internet technologies. LSID and LSRS are consistent with next-generation semantic web and semantic grid approaches. This article describes the syntax, operations, infrastructure compatibility considerations, use cases and potential future applications of LSID and LSRS. We see the adoption of these methods as important steps toward simpler, more elegant and more reliable integration of the world's biological knowledgebases, and as facilitating stronger global collaboration in biology. [ABSTRACT FROM AUTHOR]

This work is an attempt to lay foundations for a theory of interactive computation and bring logic and theory of computing closer together. It semantically introduces a logic of computability and sets a program for studying various aspects of that logic. The intuitive notion of (interactive) computational problems is formalized as a certain new, procedural-rule-free sort of games (called static games) between the machine and the environment, and computability is understood as existence of an interactive Turing machine that wins the game against any possible environment. The formalism used as a specification language for computational problems, called the universal language, is a non-disjoint union of the formalisms of classical, intuitionistic and linear logics, with logical operators interpreted as certain—most basic and natural—operations on problems. Validity of a formula is understood as being “always computable”, and the set of all valid formulas is called the universal logic. The name “universal” is related to the potential of this logic to integrate, on the basis of one semantics, classical, intuitionistic and linear logics, with their seemingly unrelated or even antagonistic philosophies. In particular, the classical notion of truth turns out to be nothing but computability restricted to the formulas of the classical fragment of the universal language, which makes classical logic a natural syntactic fragment of the universal logic. The same appears to be the case for intuitionistic and linear logics (understood in a broad sense and not necessarily identified with the particular known axiomatic systems). Unlike classical logic, these two do not have a good concept of truth, and the notion of computability restricted to the corresponding two fragments of the universal language, based on the intuitions that it formalizes, can well qualify as “intuitionistic truth” and “linear-logic truth”. The paper also provides illustrations of potential applications of the universal logic in knowledgebase, resourcebase and planning systems, as well as constructive applied theories. The author has tried to make this article easy to read. It is fully self-contained and can be understood without any specialized knowledge of any particular subfield of logic or computer science. [Copyright &y& Elsevier]

The paper offers an approach to the investigation of the dynamics of nonlinear non-stationary processes with the focus on the risk of dynamic system stability loss. The risk is assessed on the basis of the accumulated knowledge about power supply system operation. New methods for power supply modes analysis are developed and applied as follows: linear discrete point knowledge-based models are developed for nonlinear non-stationary objects; wavelet analysis is used for non-stationary processes; stability loss risks are analyzed through the investigation of spectral decompositions of Gramians of these linear predictive models. Case studies are included. [ABSTRACT FROM AUTHOR]