Research RESOURCES INFORMATION Research Articles

ScPerturb: harmonized single-cell perturbation data.

Analysis across a growing number of single-cell perturbation datasets is hampered by poor data interoperability. To facilitate development and benchmarking of computational methods, we collect a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We apply uniform quality control pipelines and harmonize feature annotations. The resulting information resource, scPerturb, enables development and testing of computational methods, and facilitates comparison and integration across datasets. We describe energy statistics (E-statistics) for quantification of perturbation effects and significance testing, and demonstrate E-distance as a general distance measure between sets of single-cell expression profiles. We illustrate the application of E-statistics for quantifying similarity and efficacy of perturbations. The perturbation-response datasets and E-statistics computation software are publicly available at scperturb.org. This work provides an information resource for researchers working with single-cell perturbation data and recommendations for experimental design, including optimal cell counts and read depth.

Research Knowledge Management using Mobile Technologies: Challenges and Solutions at the National Museum of Kenya

Knowledge is widely acknowledged as a pivotal asset, and various perspectives underscore the significance of effectively marshaling, deploying, and sharing knowledge within an organization for achieving organizational success. The National Museum of Kenya (NMK) was established with the primary goal of enriching knowledge and facilitating sustainable utilization of research information resources by stakeholders. However, the increasing diversification of knowledge sources has rendered content creation and knowledge management processes complex and laborious. Consequently, this complexity has resulted in inefficiencies throughout the knowledge management process, leading to inadequacies and disorganization. Despite the adoption of knowledge management systems, the integration of mobile phone technology in research activities at the museum has been neglected. This study aimed to scrutinize knowledge management practices at the NMK through the use of mobile apps, examine the associated challenges, and propose viable solutions. The study’s objectives were to investigate the challenges faced by researchers in generating knowledge and recommend feasible mobile technological solutions to address these challenges. The study was guided by the Knowledge Management Process Model, and employed a qualitative case study approach. The target population comprised researchers, knowledge managers, and ICT staff at the museum. Since this study was purely qualitative, data collection was achieved through interviews, and analyzed using narrative methods. The findings indicated that the NMK has implemented web-based systems supporting knowledge management activities. However, mobile phone technology has not been incorporated into any aspect of the museum’s knowledge management support tools. The study highlighted challenges such as; delayed data acquisition, misplacement of specimens, time consuming processes, data inaccuracies, and inefficiencies in knowledge management processes. Further, it was established that relying solely on web-based systems limits the flexibility of researchers in adapting to dynamic field conditions. Thus, this study recommends integrating mobile technologies into the knowledge management process at the National Museum of Kenya as a solution to the highlighted challenges. Mobile apps, known for their effectiveness and reliability, particularly in remote areas, offer a practical solution. This integration empowers researchers with more accessible and versatile tools, fostering improved content creation and knowledge management while ensuring inclusivity and efficiency, even in resource-constrained environments.

Attainment of sustainable food security in Nigeria: the role of libraries

PurposeThe quest for sustainable food security (SFS) is fundamental to United Nations Sustainable Development Goals. In furtherance of their pivotal role in providing the required information resources in support of education and research, libraries are expected to assist the economy in ensuring SFS. The purpose of this study is to investigate how libraries provide information to support research in agriculture towards the attainment of SFS in Nigeria.Design/methodology/approachDescriptive research design was used for the study. Interview and questionnaire were used as the instruments of data collection.FindingsThis study found that the extent of use of library information resources for SFS in Nigeria is high. Libraries, though facing some challenges, contribute significantly to the attainment of food security in Nigeria. It was recommended that libraries should intensify efforts to embark on media literacy programmes and provide information resources for research on agriculture and food production with a view to actualising food security goals specified in Sustainable Development Goals. Libraries should be well-funded to acquire the relevant information resources to aid research into food security and end hunger and poverty across the world.Practical implicationsThis study suggests having better sponsored libraries that can perform as required in advancing agricultural information needs.Originality/valueThis study is a creative attempt to know how libraries can contribute to SFS through the provision of information to farmers and lecturers in agriculture.

Accessibility, Awareness and Use of Egranary Digital Library Technology in Academic Library by Lecturers of Umaru Musa Yar’adua University Katsina, Nigeria

The study investigated on the Accessibility, Awareness and Use of EGranary Library System by Academic Staff of Umaru Musa Yar’adua University. A null hypothesis was formed to investigate the influence of eGranary on enhanced access and usage of information resources by academic staff. The study used a quantitative research paradigm and a survey as the research method. Through the usage of the eGranary digital library system, a questionnaire was employed as the primary instrument for data collection on accessibility and utilization of information resources. The study used a population of 506 academic employees and a sample size of 150 academic staff, with a response rate of 95.0 % for data analysis. The study's data was broken down into percentage and frequency tables. According to the findings of the study, demographic characteristics (gender, age, education, and professional rank) had no significant impact on access to and use of information resources at the surveyed university. The study advised that the surveyed university to invest more in ICT facilities in order to improve academic staff's access to and use of eGranary and information resources for research.

СПРОЩЕНА СИСТЕМА ОПОДАТКУВАННЯ: СУЧАСНИЙ СТАН, ПЕРЕВАГИ, НЕДОЛІКИ ТА ПЕРСПЕКТИВИ

UDC 336.2; JEL Classification: H 30Purpose. Investigation of the peculiarities of the enterprise different taxation systems functioning. Formation of actions algorithm for enterprise when choosing an effective taxation system in accordance with the main activity aspects. Methodology of research. Analysis and synthesis methods, logical analysis method were used during the study. Research information resources were electronic information resources and periodical material. Results. Today there is a rather exhaustive list of applying conditions of different taxation systems according to the peculiarities of a enterprise functioning. However, the choice a general or simplified tax system has certain advantages, disadvantages, and consequences. The main advantages of the general system of taxation: taxation solely the financial result of the enterprise; reduced tax rate at dividend payment; no need for quarterly income control; lack of restrictions for expansion of activities; no restrictions on the number of employees; no restrictions at the choice of activity kind. The benefits of applying a simplified tax system are a significant reduction in the tax list; significant simplification of accounting and reporting; the right not to use RST; the right to choose whether or not to pay VAT; payment of the fixed tax in the first and second group, regardless of the actual level of profitability and income, if the activity is highly profitable. Therefore, at choice of taxation system, the business owner should analyze the type of activity, the need to use barter operations, netting, the need to use hired labor, seasonal fluctuations in the income volume, the level of enterprise profitability, should formulate a tax burden forecast for each taxation system. Originality. The list of disadvantages and advantages of different systems of enterprise taxation is determined. The algorithm of the enterprise actions at the choice of the optimum tax system is formed. Practical value. The findings will be able to use by researchers, business owners, and executives at selection of an effective tax system.

With open science gaining traction, do we need an Australasia PubMed Central (PMC)? A qualitative investigation.

Open biomedical repositories, such as PubMed Central (PMC), are a means to make research discoverable and permanently accessible. Assessing the potential interest of key stakeholders in an Australasia PubMed Central was the objective of this research. The investigation is novel, assisting in the development of open science infrastructure through its systematic analysis of the potential interest in, and viability of a biomedical repository for managing openly accessible research outputs for the Australasia region. The research adopted a qualitative approach based on semi-structured interviews and a focus group. Forty-four stakeholders located throughout Australia and New Zealand participated in the research. Participants expanded upon their experience of PubMed, MEDLINE, PMC and their use of information resources for research and clinical practice. The Evidence Based Healthcare (EBHC) pyramid was the theoretical model adopted to explain open biomedical repository processes. A strengths, weaknesses, opportunities and threats (SWOT) analysis identified support for exploring membership of an international PMC system, in particular Europe PMC. Lessons learnt from PMC US, Europe PMC and PMC Canada (collectively known as PubMed Central International) informed the investigation. A major strength identified was that PubMed Central International has been able to achieve high levels of compliance way beyond that of most institutional repositories. A great threat faced is overcoming the difficulties of working together with other major world bodies and financially sustaining an Australasia PMC. Improving Australasian biomedical knowledge management processes may be possible from adopting a PMC for retrieving and transferring research, linked to the data underlying the research. This in turn could help put regional research under a brighter spotlight, potentially leading to improvements in research quality. There is an opportunity for a potential Australasia PMC to harvest biomedical research from the National Library of Australia’s aggregator database, Trove and work closely with Europe PMC to avoid duplication of effort. Overall, establishment of an Australasia permanent biomedical digital open repository is perceived as important, with significant potential flow-on benefits to healthcare, industry and society.

Personalised anonymity for microdata release

Individual privacy protection in the released data sets has become an important issue in recent years. The release of microdata provides a significant information resource for researchers, whereas the release of person-specific data poses a threat to individual privacy. Unfortunately, microdata could be linked with publicly available information to exactly re-identify individuals’ identities. In order to relieve privacy concerns, data has to be protected with a privacy protection mechanism before its disclosure. The k-anonymity model is an important method in privacy protection to reduce the risk of re-identification in microdata release. This model necessitates the indistinguishably of each tuple from at least k − 1 other tuples in the released data. While k-anonymity preserves the truthfulness of the released data, the privacy level of anonymisation is same for each individual. However, different individuals have different privacy needs in the real world. Thereby, personalisation plays an important role in supporting the notion of individual privacy protection. This study proposes a personalised anonymity model that provides distinct privacy levels for each individual by offering them to control their anonymity on the released data. To satisfy the personal anonymity requirements with low information loss, the authors introduce a clustering based algorithm.

Attractiveness of Intangible Cultural Heritage of Ukraine: Tourism Discussion

The article deals with the scientific exploration of the detection in tourist attraction of elements in the intangible cultural heritage (hereinafter – ICH), which are included in the National List of Ukraine. It has been indicated that the tourism discourse of disclosing of the attractiveness essence/attractiveness of the elements in the NKS is aimed at the use of a wide range in research information resources. It is noted that in the conditions of globalization there is a mutually beneficial influence of NSC on the sustainable tourism development, and vice versa. A special mission has been carried out in the process of such interaction by the state, which ensures the processes of state regulation of the relevant spheres. The support analysis for the development in the element of the NSC at the community level and the ability to provide protection measures with the relevant legal documents has been carried out. Among practical events, master classes, festivals, contests, excursions, thematic meetings, competitions, art awards, etc. are singled out.

Biocuration: Distilling data into knowledge

Data, including information generated from them by processing and analysis, are an asset with measurable value. The assets that biological research funding produces are the data generated, the information derived from these data, and, ultimately, the discoveries and knowledge these lead to. From the time when Henry Oldenburg published the first scientific journal in 1665 (Proceedings of the Royal Society) to the founding of the United States National Library of Medicine in 1879 to the present, there has been a sustained drive to improve how researchers can record and discover what is known. Researchers’ experimental work builds upon years and (collectively) billions of dollars’ worth of earlier work. Today, researchers are generating data at ever-faster rates because of advances in instrumentation and technology, coupled with decreases in production costs. Unfortunately, the ability of researchers to manage and disseminate their results has not kept pace, so their work cannot achieve its maximal impact. Strides have recently been made, but more awareness is needed of the essential role that biological data resources, including biocuration, play in maintaining and linking this ever-growing flood of data and information. The aim of this paper is to describe the nature of data as an asset, the role biocurators play in increasing its value, and consistent, practical means to measure effectiveness that can guide planning and justify costs in biological research information resources’ development and management.

Faculty Still Rely on Library Resources and Services for their Research

A Review of: 
 Borrego, Á., & Anglada, L. (2016). Faculty information behaviour in the electronic environment: Attitudes towards searching, publishing and libraries. New Library World, 117(3/4): 173-185. doi:10.1108/NLW-11-2015-0089
 
 Objective – To determine faculty’s information behaviour and their perception of academic libraries in the current transition between print and electronic scholarly communication.
 
 Design – Online survey.
 
 Setting – A consortium of 12 large universities in Spain.
 
 Subjects – More than 17,380 faculty members.
 
 Methods – The researchers used a questionnaire based on a subset of the questionnaire used for the Ithaka S+R Faculty Survey, with 20 closed and 2 open-ended questions. The survey was implemented via Google Forms and sent through mailing lists. The number of recipients was not known, but university statistics for 11 of the 12 universities list 17,380 faculty (statistics were not available for one university, located in a different administrative area). The questions aimed to identify the types of documents used by scholars for teaching and research, the search tools used, the strategies used to keep up-to-date in their disciplines, preferences for print or electronic books, the sources used to access documents, their preferred channels to disseminate their own research, and their views regarding library services.
 
 Main Results – The response rate was 12.7%. Based on the results, scholarly journals were the most used information resource for research across all academic disciplines, with 94% of respondents rating them as important. For teaching, faculty preferred to use textbooks for undergraduates, and journal articles for Master’s students. To search the literature, faculty chose bibliographic databases and Internet search engines over the library catalog and physical collections, although the catalog was the first choice for known-item searches. Respondents favored print to read entire books or chapters but preferred the electronic format for skimming. Of the respondents, 78% rated the library as an important channel to access resources, while 61% also considered free online materials important. If the material was not available at their library, 71% frequently chose to search for a free online version and 42% used the inter-library loan service. For their own research, faculty have published in scholarly journals more often than other channels and have selected the journal based on its impact factor (77.5% ranked it as important) and on its area of coverage (73.4%). When asked to rank library services, faculty placed paying for resources highest, with 86.2% identifying it as important. Next were facilitating teaching and helping students develop information literacy skills. Finally, a majority of faculty considered themselves highly dependent on the library.
 
 Conclusion – Journal articles are the most widely used information resource for research and teaching purposes, regardless of discipline. This includes arts and humanities, which are known for heavy monograph usage. Articles are also scholars’ preferred channel for publishing. With regards to books, faculty have mixed feelings about print and electronic formats. Spanish faculty display information behaviours similar to their British and American counterparts, as documented in the Ithaka S+R 2012 surveys. Blogs and social networks are not widely used in spite of growing attention to such channels for research output and altmetrics. Open access is also relatively unimportant for faculty when they choose where to publish. A majority of respondents still consider library services as important, for collections as well as teaching and learning support, which may present opportunities for librarians.

Faculty Research and Publication Practices

Understanding faculty work practices can translate into improved library services. This study documents how education and behavioral science faculty locate, retrieve, and use information resources for research and writing and how they publish and store their research materials. The authors interviewed twelve professors using a structured interview instrument and analyzed the data. Findings cover the role of library services in scholarly research processes, as well as the use of software and technologies and the challenges faculty face.

Accessibility and Utilization of Electronic Information Resources for Research by Academic Staff at Selected Nigerian Universities Between 2005 and 2012

This paper explored the extent of the accessibility and utilization of electronic resources by academic staff at two Nigerian universities: the University of Calabar and the University of Ibadan. A quantitative research method was adopted in the study and a questionnaire was used as the instrument for data collection. The study population comprised 2035 academic staff at the surveyed universities, and a sample size of 586 academics was used in the study. A total of 324 completed copies of the questionnaires were retrieved and used for data analysis representing a response rate of 55.3%. The findings of the study revealed a poor electronic information environment at the surveyed universities. There was no significant influence of demographic variables (discipline, gender, age, education and professional rank) on the accessibility and utilization of electronic resources among respondents in the survey. The paper concluded that an increase in investment in ICT facilities by university management will lead to improvement in electronic information environment at the surveyed universities and recommended that, Nigerian universities should considerably increase their investments in ICT infrastructural facilities to be in line with the emerging digital trend at universities around the world.

リサーチ・アドミニストレーターと図書館の研究情報資源

リサーチ・アドミニストレーターと図書館の研究情報資源

ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins

ProGlycProt (http://www.proglycprot.org/) is an open access, manually curated, comprehensive repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). To facilitate maximum information at one point, the database is arranged under two sections: (i) ProCGP—the main data section consisting of 95 entries with experimentally characterized glycosites and (ii) ProUGP—a supplementary data section containing 245 entries with experimentally identified glycosylation but uncharacterized glycosites. Every entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information. Interestingly, ProGlycProt contains as many as 174 entries for which information is unavailable or the characterized glycosites are unannotated in Swiss-Prot release 2011_07. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology.

The use and sharing of information from Wikipedia by high‐tech professionals for work purposes

PurposeThe aim of this paper is to focus on discovering whether high‐tech professionals as a user community search for information from Wikipedia to fulfill their job duties and, if they do, how they share information with co‐workers and clients.Design/methodology/approachAn online questionnaire was used, administered by a commercial provider. The questionnaire consisted of 15 Likert‐scaled questions to assess participants' agreement with each question along with an optional open‐ended explanation. A total of 68 participants successfully answered the questionnaire. Participants' Likert rating scores were analyzed by two‐way ANOVA, one‐way ANOVA and correlational analyses using SPSS.FindingsThe analyses examined relationships among participants' characteristics, their use of information resources for research and teaching, information‐sharing behaviors, and use/non‐use of Wikipedia. Findings indicated that the participants treated Wikipedia as a ready reference for general information. Their concern is that Wikipedia only has a limited number of entries available at this point. They suggested that Wikipedia needed to improve the contribution and editorial process and to make it more rigorous.Originality/valuePersonal information infrastructure affects how the high‐tech professionals surveyed use‐and‐share information from Wikipedia for work. In the current situation, the participants consider Wikipedia to be a developing information resource and show less interest in contributing to it. The project is an exploratory study and more considerations are needed for this research area.

Dynamic exploration and editing of KEGG pathway diagrams

The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database is a very valuable information resource for researchers in the fields of life sciences. It contains metabolic and regulatory processes in the form of wiring diagrams, which can be used for browsing and information retrieval as well as a base for modeling and simulation. Thus it helps in understanding biological processes and higher-order functions of biological systems. Currently the KEGG website uses semi-static visualizations for the presentation and navigation of its pathway information. While this visualization style offers a good pathway presentation and navigation, it does not provide some of the possibilities related to dynamic visualizations, most importantly, the creation and visualization of user-specific pathways. This paper presents methods for the dynamic visualization, interactive navigation and editing of KEGG pathway diagrams. These diagrams, given as KEGG Markup Language (KGML) files, can be visually explored using novel approaches combining semi-static and dynamic visualization, but also edited or even newly created and then exported into KGML files. KGML-ED, a program implementing the presented methods, is available free of charge to the scientific community at http://kgml-ed.ipk-gatersleben.de.

메타데이터 기반의 연구성과정보 검색시스템의 개념적 설계

It has lately been recognized that the sharing and exchanging of the research results information is the critical factor to improve the research productivity. So many institutions are planning or developing the information systems which provide the research information services for researcher. But it has very difficulty in integrating the research resources information due to the dispersion and heterogeneity in data sources, and semantic and structural difference in describing data. We propose the semantic web based methodology and conceptual framework for raising the interoperability of metadata about research results information, which will support the integration of the distributed research data for information services in the end. We first introduce the ontology which is developed based on Standard Metadata of Research Results Information published by STISC. Then to show the applicability in real-world environment, we express the metadata of research information in RDF/RDFS according to ontology. Finally we proposed the conceptual architecture of research information service system which shows the main components, the functional requirements, and the principal and design direction at implementing the system.

How digital libraries can support e‐learning

PurposeDigital libraries have the potential to offer unprecedented resources for supporting e‐learning. This paper addresses and discusses such aspects as what is meant by “e‐learning”, and how can it be supported by the library environment, the functionality of the digital library; and how e‐learning resources are included and organized in the digital library.Design/methodology/approachThe paper explores the advantages of digital libraries for e‐learning and the types of learning that can be supported by digital libraries.FindingsThere is undoubtedly a keenness to use online information resources for research and teaching, but this seems to be matched by a lack of awareness of how best to integrate these resources into the e‐learning environment.Originality/valueThe paper provides a useful insight into the role and influence of digital libraries and online resources on e‐learning.

How can university and national libraries achieve deeper collaboration?

Governments are placing great store in "the knowledge economy" as a key engine for economic and social development in a post-manufacturing world. One result is an acceptance for much increased expenditure on research and advanced teaching and there is much debate, at least in the UK, about how these matters should be organised. Since much of the research (excluding defence) and virtually all the graduate teaching will be undertaken in the universities it follows that one key question in the UK is just what proportion and number of the 100 UK universities should be truly "research-intensive"? The trend, although it can be exaggerated, is towards greater concentration and last year I estimated (Follett, 2002) that the faculty in about 12 of the universities will spend on average 50% of their working year on research and graduate teaching, and 50% on undergraduate teaching. In another 30 universities faculty will spend about 25% of their annual working year on research and 75% on undergraduate teaching. In the remaining 60 universities the time available for research will be much smaller. A second key question relates to the "research infrastructure" needed to support the researchers. It is my contention that access to world-class "research information resources" - at a reasonable cost - is a pre-requisite for any nation's research base. In parallel, of course, the actual means of providing those "research information resources" is changing rapidly and the existing provision through "local" research libraries in individual universities or research institutes, often set alongside other services from the "national" library, is under both financial and technological strain: · Electronic provision of delivering research information "direct to the desk-top" has inverted the means of delivery. This has been developed most strongly in the natural sciences but is likely to develop in all areas of research. · The generation of primary research data on a huge scale - from telescopes, particle physics machines and genomics - is leading to electronic grids and the associated metadata being established so as to process and deliver this material direct to the researcher. Similar opportunities exist for using these technologies in the humanities and the social sciences. · Overall growth in the volume of the world's research continues unabated and is likely to do so for the foreseeable future. · Costs of purchasing research information outstrip inflation (even at constant volume), partly because a true market does not exist.

A Prototype of PubMed Central Japan

“PubMed Central (PMC) is the U.S. National Library of Medicine’s digital archive of life sciences journal literature. Access to PMC is free and unrestricted.” [3]. It covers 78 journals and also 57 journals of BioMed Central [1]. It provides not only bibliographic information and abstracts but also full texts including figures and tables. Thus PMC is a rich and valuable information resource for research and development in biology and medicine.