Digital Repository of the Southern Federal University in the Scientific and Educational Space of the University

The article reveals the experience of creating a Digital Repository by the Zonal Scientific Library of the Southern Federal University. It is organized and technically supported as the central repository of the SFedU intellectual property objects. Having studied the experience of other universities, it was decided to develop its own software platform built in Python. As a result, a high level of service was provided for the use of the repository not only by librarians and users, but also by other structural divisions of the university. The repository contains the intellectual products of the university, provides access to the results of scientific research of the university, has the ability to exchange metadata through the API interface, has a customized search interface, ensures the safety of content, and minimizes the labor costs of users and service personnel.

Automatically Producing Semantically Tagged Bilingual Terminologies

Even though many NLP resources and tools claim to be domain independent, their application to specific tasks is restricted to some specific domain, otherwise their performance degrade notably. As the accuracy of NLP resources drops heavily when applied in environments different from which they were built a tuning to the new environment is needed. This paper proposes a method for automatically compile terminologies from potentially any domain. The proposed method takes as reference the set of domains defined by Magnini, the Multilingual Central Repository (a resource based on WordNet 3.0) together with DBpedia, an open knowledge source that had proven to be reliable for restricted domains. Using the method described in this article, we have produced a big set of reliable terminologies for 164 domains and 2 languages totalling 635,527 terms. The proposed method has been applied to English and Spanish languages but it is potentially applicable to any language that has its own a DBpedia evolved enough. The obtained results have been intensively evaluated in several ways.

Zebrafish Information Network, the knowledgebase for Danio rerio research

The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for zebrafish genetic and genomic data. ZFIN expertly curates, integrates, and displays zebrafish data including genes, alleles, human disease models, gene expression, phenotype, gene function, orthology, morpholino, CRISPR, TALEN, and antibodies. ZFIN makes zebrafish research data Findable, Accessible, Interoperable, and Reusable (FAIR) through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. ZFIN is a founding member of the Alliance of Genome Resources, providing zebrafish data for integration into the cross species platform as well as contributing to model organism data harmonization efforts.

Integrative annotation of genomic features reveal functional elements and epigenetic landscapes in the developing zebrafish

Despite being a popular model for embryonic development and diseases, zebrafish have lacked systematic functional annotation programmes seen in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1802 sets of unpublished and reanalysed published genomics data, with which we improve existing annotations and show its usefulness in experimental design. We define over 140,000 cis-regulatory elements and decribe novel classes with distinct features depending on time and space of activity. We delineate the difference between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of their relatedness. Finally, we match regulatory elements between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals.

Employability: Smart learning in extracurricular activities for developing college graduates' competencies

Nowadays, employers expect college graduates (or simply “graduates”) to be for ready in taking up challenges when they enter into their careers. Most competencies that employers are looking for cannot be learned but can be developed by participating in extracurricular activities. However, planning on participation in extracurricular activities is difficult, given the lack of measurement standards together with their unstructured and non-systematic nature. To provide a smarter way for activity organisers, advisers and students to plan for extracurricular activities, our university has launched the central repository on student development activities system and codified the information about participation in extracurricular activities in a quantified and systematic way. This paper has collected data from three consecutive years from the system, the employers' feedback data and the academic performance data of placement students in the Department of Computer Science. Participation level, with logarithm transformation, had a positive and significant relationship with academic performance. Moreover, the competency developed by most students had a positive relationship with job performance in the placement year of 2019/2020. In this article, we discuss contributions, limitations and future directions.

Advancing Ocean Science Through Open Science and Software on the Cloud

This Ocean-Shot will seek to advance community awareness and practice around open science, based on the activities and outcomes generated by a growing cadre of U.S.-based and international developers working with open software libraries and in cloud computing environments. This practice will require additional software and tooling and required a shift in thinking toward a philosophy of trust and transparency. Key to this endeavor will be to take advantage of innovative development tools and practices that will better enable science by decreasing barriers to collaborations, reproducibility, and interdisciplinary research.For data, this will mark a shift from a central repository model to central service model, enabling data-proximate computing. Most commonly today, data are downloaded from central locations for analysis on local environments. We hope to advance data-proximate computing that facilitates the accessing of data in central locations and running analysis there. This will mark a move from current reliance on locally deployed packages and servers to making products and services readily available on the cloud. The project will contribute to a step change of how datasets are accessed and used across the community. Throughout the decade it will build on the training and capacity development currently supported by NASA, and upon the professional development activities of other stakeholders.

Pertinent Knowledge Storage Processes for Central Repository Design in Domain of Interlocking Institutional Worlds

Designing a Central Repository (CR) for supporting the domain of Interlocking Institutional Worlds (IWs) requires a theory or model from Knowledge Storage Process (KSP) literature to govern the stakeholders' participation in the CR platform. However, current KSP theories or models have limited capabilities, so there are clear gaps in the context of designing a CR for the domain of IWs. Therefore, this paper suggests processes which include Identification, Standard, Service, and Maintain (ISSM) as a new KSP model to fill these gaps. To understand the stakeholders' participation, the authors use the case study of Flood Management (FM) to make sense of the proposed ISSM model. This gives us better understanding towards CR design using the KSP model.

IMI—Bigpicture: A Central Repository for Digital Pathology

To address the challenges posed by large-scale development, validation, and adoption of artificial intelligence (AI) in pathology, we have constituted a consortium of academics, small enterprises, and pharmaceutical companies and proposed the BIGPICTURE project to the Innovative Medicines Initiative. Our vision is to become the catalyst in the digital transformation of pathology by creating the first European, ethically compliant, and quality-controlled whole slide imaging platform, in which both large-scale data and AI algorithms will exist. Our mission is to develop this platform in a sustainable and inclusive way, by connecting the community of pathologists, researchers, AI developers, patients, and industry parties based on creating value and reciprocity in use based on a community model as the mechanism for ensuring sustainability of the platform.

BioCommons: a robust java library for RNA structural bioinformatics

Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.