Open Access Knowledge Research Articles

InteractOA: Showcasing the representation of knowledge from scientific literature in Wikidata

Knowledge generated during the scientific process is still mostly stored in the form of scholarly articles. This lack of machine-readability hampers efforts to find, query, and reuse such findings efficiently and contributes to today’s information overload. While attempts have been made to semantify journal articles, widespread adoption of such approaches is still a long way off. One way to demonstrate the usefulness of such approaches to the scientific community is by showcasing the use of freely available, open-access knowledge graphs such as Wikidata as sustainable storage and representation solutions. Here we present an example from the life sciences in which knowledge items from scholarly literature are represented in Wikidata, linked to their exact position in open-access articles. In this way, they become part of a rich knowledge graph while maintaining clear ties to their origins. As example entities, we chose small regulatory RNAs (sRNAs) that play an important role in bacterial and archaeal gene regulation. These post-transcriptional regulators can influence the activities of multiple genes in various manners, forming complex interaction networks. We stored the information on sRNA molecule interaction taken from open-access articles in Wikidata and built an intuitive web interface called InteractOA, which makes it easy to visualize, edit, and query information. The tool also links information on small RNAs to their reference articles from PubMed Central on the statement level. InteractOA encourages researchers to contribute, save, and curate their own similar findings. InteractOA is hosted at https://interactoa.zbmed.de and its code is available under a permissive open source licence. In principle, the approach presented here can be applied to any other field of research.

TracerDB: a crowdsourced fluorescent tracer database for target engagement analysis

Investigating ligand-protein complexes is essential in the areas of chemical biology and drug discovery. However, detailed information on key reagents such as fluorescent tracers and associated data for the development of widely used bioluminescence resonance energy transfer (BRET) assays including NanoBRET, time-resolved Förster resonance energy transfer (TR-FRET) and fluorescence polarization (FP) assays are not easily accessible to the research community. We created tracerDB, a curated database of validated tracers. This resource provides an open access knowledge base and a unified system for tracer and assay validation. The database is freely available at https://www.tracerdb.org/.

Training in open access for doctoral students: results of a survey of current and recent students and supervisors

Introduction. This study aimed to understand the extent to which doctoral students receive training relating to open access publishing, and the form of that training. Method. An international online survey of 1,569 current and recent doctoral students and supervisors was undertaken. Questions covered the extent and nature of training in open access offered to doctoral students, sources of respondents’ open access knowledge, and their perspectives on open access. Analysis. Descriptive statistical analysis was conducted with some non-parametric tests. Free-text data were thematically analysed. Results. The large majority of current and recent doctoral students and supervisors indicated there was no mandatory open access training at their institutions. More than half of respondents thought they had good or excellent understanding of open access, with those who had completed training more likely to highly rate their understanding. Only 27% of respondents felt the level of training offered was sufficient. Respondents suggested that institutions could take further action to support understanding of open access. Conclusion. There is a need for institutions to develop further training in open access. Researchers who undertake training in report a better level of understanding of open access and place more importance on it as a factor in selecting a journal.

Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits.

Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.

Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits

Hippocampome.org is a mature open-access knowledge base of the rodent hippocampal formation focusing on neuron types and their properties. Previously, Hippocampome.org v1.0 established a foundational classification system identifying 122 hippocampal neuron types based on their axonal and dendritic morphologies, main neurotransmitter, membrane biophysics, and molecular expression (Wheeler et al., 2015). Releases v1.1 through v1.12 furthered the aggregation of literature-mined data, including among others neuron counts, spiking patterns, synaptic physiology, in vivo firing phases, and connection probabilities. Those additional properties increased the online information content of this public resource over 100-fold, enabling numerous independent discoveries by the scientific community. Hippocampome.org v2.0, introduced here, besides incorporating over 50 new neuron types, now recenters its focus on extending the functionality to build real-scale, biologically detailed, data-driven computational simulations. In all cases, the freely downloadable model parameters are directly linked to the specific peer-reviewed empirical evidence from which they were derived. Possible research applications include quantitative, multiscale analyses of circuit connectivity and spiking neural network simulations of activity dynamics. These advances can help generate precise, experimentally testable hypotheses and shed light on the neural mechanisms underlying associative memory and spatial navigation.

Going Open Access: The Attitudes and Actions of Scientific Journal Editors in China

This study aims to investigate the attitudes and actions of scientific journal editors in China towards open access. Semi-structured interviews were conducted with 17 Chinese editors from various scientific journals during September and October of 2022. The results indicate that the editors generally possess knowledge of open access and have implemented an appropriate open access model for their respective journals. However, the Chinese-language journal editors expressed a lack of motivation to adopt open access, unless there is a reform in the mechanism of academic publishing or a policy is imposed. On the other hand, the English-language journal editors acknowledged that they have no other choice but to adopt open access. This study helps us learn about Chinese editors’ understanding and attitudes towards open access, the current status of open access in China’s scientific journals, and the mechanisms of academic publishing in China.

EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances

The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field each year, the absence of dedicated open-access databases for endophytic microorganism natural products research is evident. To address the increasing demand for mining and sharing of data resources related to endophytic microorganism natural products, this study introduces EMNPD, a comprehensive endophytic microorganism natural products database comprising manually curated data. Currently, EMNPD offers 6632 natural products from 1017 endophytic microorganisms, targeting 1286 entities (including 94 proteins, 282 cell lines, and 910 species) with 91 diverse bioactivities. It encompasses the physico-chemical properties of natural products, ADMET information, quantitative activity data with their potency, natural products contents with diverse fermentation conditions, systematic taxonomy, and links to various well-established databases. EMNPD aims to function as an open-access knowledge repository for the study of endophytic microorganisms and their natural products, thereby facilitating drug discovery research and exploration of bioactive substances. The database can be accessed at http://emnpd.idrblab.cn/ without the need for registration, enabling researchers to freely download the data. EMNPD is expected to become a valuable resource in the field of endophytic microorganism natural products and contribute to future drug development endeavors.

Framework for a living systematic review and meta-analysis for the surgical treatment of bladder cancer: introducing EVIglance to urology.

Knowledge of current and ongoing studies is critical for identifying research gaps and enabling evidence-based decisions for individualized treatment. However, the increasing number of scientific publications poses challenges for healthcare providers and patients in all medical fields to stay updated with the latest evidence. To overcome these barriers, we aim to develop a living systematic review and open-access online evidence map of surgical therapy for bladder cancer (BC), including meta-analyses. Following the guidelines provided in the Cochrane Handbook for Systematic Reviews of Interventions and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement, a systematic literature search on uro-oncological therapy in BC will be performed across various literature databases. Within the scope of a meta-analysis and living systematic review, relevant randomized controlled trials will be identified. Data extraction and quantitative analysis will be conducted, along with a critical appraisal of the quality and risk of bias of each study. The available research evidence will be entered into an open-access framework (www.evidencemap.surgery) and will also be accessible via the EVIglance app. Regular semi-automatic updates will enable the implementation of a real-living review concept and facilitate resource-efficient screening. A regularly updated evidence map provides professionals and patients with an open-access knowledge base on the current state of research, allowing for decision-making based on recent evidence. It will help identify an oversupply of evidence, thus avoiding redundant work. Furthermore, by identifying research gaps, new hypotheses can be formulated more precisely, enabling planning, determination of sample size, and definition of endpoints for future trials.

Narrative review on open access institutional repositories and knowledge sharing in South Africa

AbstractThis brief communication conveys a critical assessment of the benefits, challenges, and potential of Open Access Institutional Repositories (OAIRs) for knowledge sharing in South Africa. The review identifies best practices and recommendations to promote and improve their usage. Researchers need training and support to understand guidelines and best practices for depositing their work. Limited funding for OAIRs can be addressed by government funding or exploring alternative models. Legal and policy frameworks must support OAIRs and ensure they comply with international standards. Proper management and indexing policies enhance institutional visibility and information retrieval. OAIRs promote collaboration and cooperation among researchers and provide a platform for knowledge sharing and feedback. Standardized platforms and frameworks ensure digital outputs are accessible and usable for the academic community. Sharing knowledge on self‐archiving encourages researchers to deposit their works. Formal reviews must focus on metadata and ensure that articles are from DHET‐accredited journals and that theses and dissertations meet institutional requirements. These efforts promote open access and preserve scholarly works for future generations.

Science and policy lessons learned from a decade of adaptation to the emergent risk of sargassum proliferation across the tropical Atlantic

Climatic and anthropogenic changes appear to be driving the emergence of new ecosystem and human health risks. As new risks emerge, and the severity or frequency of known risks change, we ask: what evidence is there of past adaptations to emergent risks? What scientific and policy processes lead to adaptive solutions that minimise the impacts of these events, and draw out opportunities? We identify science and policy lessons learned from coping with, and responding to, the sudden arrival of brown macroalgae (pelagic sargassum) that has proliferated across the tropical Atlantic since 2011. Drawing on an evidence base developed from a systematic search of literature relating to sargassum seaweed, and using event timelines and word clouds, we provide an analysis of lessons learned from a case study of adaptive responses across three continents to an emergent risk over the course of a decade. We reflect on successes and failures as well as opportunities taken in building adaptive capacity to address the risk in four key domains: policy, knowledge and evidence, monitoring and early warning, and technology and valorisation. Failures include: lack of environmental risk registries; missed opportunities to share monitoring data; and lack of a shared approach to manage the risk. Successes include: development of national management strategies; open-access knowledge hubs, networks and webinars sharing information and best practice; semi-operational early advisory systems using open access remote sensing data; numerous innovations customising clean-up and harvesting equipment, and research and development of new uses and value-added products.

P05 Developing an open-access knowledge exchange platform for breast surgeons

Abstract Introduction Compiling information for best practice and exams is time-consuming. Furthermore, having this on-demand is not always feasible. A group of breast surgery trainees sought to develop a resource that could easily be accessed from a computer or mobile device, and that consolidated all relevant literature. The aim of this survey was to assess the needs for such a resource and inform its design. Methods An online survey was sent to current breast trainees and consultants working in the North East, Northwest and Yorkshire. Oncology trainees in the Northeast were also canvassed. Questions included demographics;, stage of training and qualifications;, online resources used;, potential gains and needs from a resource and preferred learning methods (visual, auditory, kinesthetic, note-making). Results A total of 33 participants completed the survey:24 breast surgeons and 9 oncologists. 60% of the respondents were in higher training (ST5-ST7). The most commonly used resources by breast trainees were ABS (87.5%), NICE guidance (75%) and iBreastbook (45.8%)., Oncology trainees commonly reported using NICE guidance (77.8%), ESMO (77.8%) and NCCN (55.6%). The majority of the respondents identified as visual learners (N=20, 60.6%). 93.9% of respondents would like to have access to recent papers on the online resource, 90% would like access to consolidated guidance. Conclusion Based on the pilot survey results, we have developed an online learning resource (Best of Breast Resource) that addresses these needs. This has been released and is being collaboratively iterated with participants with the aim to release it more widely in the breast community.

Developing an open-access knowledge exchange platform for breast surgeons

Developing an open-access knowledge exchange platform for breast surgeons

The Main Directions of the Russian Federation State Policy in the Field of Intellectual Property

Introduction . The growth of social engagement in innovation activity reflects the global trend for developing cooperation in the field of commercialisation of the Intellectual Activity Results (hereinafter — IAR) and their throughout dissemination. The balanced regulation of the intellectual products protection and dissemination implies the interference from behalf of the state, including establishment of the system of governing bodies managing the national innovation- driven economy. The purpose of this study is to identify the main directions of the state policy ensuring the Russian economy competitiveness and growth of the gross domestic product, national security, technological sovereignty in the areas important for the state and society. Materials and Methods . The object of the study is the Russian Federation state policy in the field of intellectual property. In the research the methods of sociological case-study, analysis, synthesis and modeling, as well as statistical, system- structural, logical, historical methods have been used. Results . The author highlights and characterises five main directions of the Russian Federation state policy in the field of intellectual property. In the article the conclusions are made about the mission of the state to stimulate social engagement by removing the excessive legislative barriers and simplifying the administrative procedures for IAR registration and licensing, by opening access to the intellectual products that are not in commercial demand or do not have a copyright holder, by creating the national information and communication platform of digital content. Only the state, being the main source of law in the 21st century, can provide the balanced approach to the harmonious coexistence and interaction of the material and digital economic environment. Discussion and Conclusions . Any disbalance in favour of either public interest in open access knowledge and information or prioritised protection of the creative subjects aggravates the conflict of interests, creates the condition of the legislative system uncertainty and obstructs the formation of beneficial conditions for reproduction of culture and technological progress. At the same time, the creative subjects are defined as subjects creating the new knowledge and technologies that represent the public interest to the intellectual property turnover as the most commercially valuable information. As follows from the above, the principle of reasonable balance between the legitimate interests and fair use of IAR by copyright holders, users and consumers, expressed in the adequate legal form, should be recognised as the fundamental principle of the state policy in the field of intellectual property.

Narrative Review on Open Access Institutional Repositories and Knowledge Sharing in South Africa

Narrative Review on Open Access Institutional Repositories and Knowledge Sharing in South Africa

Open Science Practices in Communication Sciences and Disorders: A Survey.

Open science is a collection of practices that seek to improve the accessibility, transparency, and replicability of science. Although these practices have garnered interest in related fields, it remains unclear whether open science practices have been adopted in the field of communication sciences and disorders (CSD). This study aimed to survey the knowledge, implementation, and perceived benefits and barriers of open science practices in CSD. An online survey was disseminated to researchers in the United States actively engaged in CSD research. Four-core open science practices were examined: preregistration, self-archiving, gold open access, and open data. Data were analyzed using descriptive statistics and regression models. Two hundred twenty-two participants met the inclusion criteria. Most participants were doctoral students (38%) or assistant professors (24%) at R1 institutions (58%). Participants reported low knowledge of preregistration and gold open access. There was, however, a high level of desire to learn more for all practices. Implementation of open science practices was also low, most notably for preregistration, gold open access, and open data (< 25%). Predictors of knowledge and participation, as well as perceived barriers to implementation, are discussed. Although participation in open science appears low in the field of CSD, participants expressed a strong desire to learn more in order to engage in these practices in the future. Supplemental Material and Open Science Form: https://doi.org/10.23641/asha.21569040.

KBANZSL

KBANZSL, the Knowledge Bank of Australia and New Zealand School Libraries, is an open access knowledge bank collating key documents, collections and other resources for and about Australian and New Zealand school libraries and teacher librarianship. The resource was created in response to recommendations from the Australian Parliament over a decade ago but still highly relevant in today’s educational climate. KBANZSL holds strong potential in supporting advocacy, professional development, and research for school libraries and teacher librarianship in the Oceania region and beyond. This paper shares ways KBANZSL can be used for research and advocacy projects.

84. Benefits of integrating an open-source knowledgebase in a precision oncology workflow

Next-generation sequencing is revolutionizing precision oncology, but vast amounts of sequence data must be processed and mined to reveal clinically relevant alterations that can inform patient care. The Personalized OncoGenomics (POG) program at BC Cancer utilizes whole genome and transcriptome analysis, providing a comprehensive view of advanced cancer patient tumours. This analysis relies on curated clinical knowledgebases linking cancer variants and their clinical relevance, but the breadth and utility of these can be limited by proprietary access or limited coverage. CIViC (Clinical Interpretation of Variants in Cancer) is an open-access, crowd-sourced knowledgebase of clinically relevant cancer variants that aims to address these limitations, and is one of several sources used for variant interpretation in POG. Based on a retrospective cohort of POG cases, we evaluated the knowledgebase coverage of genes and variants involved in treatment recommendations from the molecular tumour board (MTB). In a preliminary analysis, we found more than 95% of patients had an alteration considered clinically actionable by the MTB, demonstrating the benefit of combined genome and transcriptome analysis. We found that knowledge from CIViC represented nearly 50% of therapeutic evidence reported at the MTB, emphasizing the role of open-access knowledge in precision oncology. Additionally, by prospectively examining the levels and sources of evidence in patient reports, we identified areas where additional knowledgebase curation would most impact alignment with clinical utility, highlighting genome signatures as a critical area for future curation efforts. We also considered the impact of quality of evidence on MTB recommendations and patient treatments.

FDup: a framework for general-purpose and efficient entity deduplication of record collections.

Deduplication is a technique aiming at identifying and resolving duplicate metadata records in a collection. This article describes FDup (Flat Collections Deduper), a general-purpose software framework supporting a complete deduplication workflow to manage big data record collections: metadata record data model definition, identification of candidate duplicates, identification of duplicates. FDup brings two main innovations: first, it delivers a full deduplication framework in a single easy-to-use software package based on Apache Spark Hadoop framework, where developers can customize the optimal and parallel workflow steps of blocking, sliding windows, and similarity matching function via an intuitive configuration file; second, it introduces a novel approach to improve performance, beyond the known techniques of “blocking” and “sliding window”, by introducing a smart similarity matching function T-match. T-match is engineered as a decision tree that drives the comparisons of the fields of two records as branches of predicates and allows for successful or unsuccessful early-exit strategies. The efficacy of the approach is proved by experiments performed over big data collections of metadata records in the OpenAIRE Research Graph, a known open access knowledge base in Scholarly communication.

Bioactive Natural Products Identification Using Automation of Molecular Networking Software.

Secondary metabolites from natural sources are promising starting points for discovering and developing drug prototypes and new drugs, as many current treatments for numerous diseases are directly or indirectly related to such compounds. Recent advances in bioinformatics tools and molecular networking methods have made it possible to identify novel bioactive compounds. In this study, a workflow combining network-based methods for identifying bioactive compounds found in natural products was streamlined by innovating an automated bioinformatics software. The workflow relies on Global Natural Product Social Molecular Networking (GNPS), a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data. By combining computational tools including MZmine2, GNPS, and Cytoscape, the integrated dashboard quickly creates bioactive molecular networks with minimal user intervention and reduces the processing time of the original workflow by over 80%. This newly automated workflow quickens the process of discovering bioactive compounds from natural products. This study uses extracts from Psidium guajava leaves to demonstrate the application of our automated software.

COVID-19 GPH: tracking the contribution of genomics and precision health to the COVID-19 pandemic response

The scientific response to the COVID-19 pandemic has produced an abundance of publications, including peer-reviewed articles and preprints, across a wide array of disciplines, from microbiology to medicine and social sciences. Genomics and precision health (GPH) technologies have had a particularly prominent role in medical and public health investigations and response; however, these domains are not simply defined and it is difficult to search for relevant information using traditional strategies. To quantify and track the ongoing contributions of GPH to the COVID-19 response, the Office of Genomics and Precision Public Health at the Centers for Disease Control and Prevention created the COVID-19 Genomics and Precision Health database (COVID-19 GPH), an open access knowledge management system and publications database that is continuously updated through machine learning and manual curation. As of February 11, 2022, COVID-GPH contained 31,597 articles, mostly on pathogen and human genomics (72%). The database also includes articles describing applications of machine learning and artificial intelligence to the investigation and control of COVID-19 (28%). COVID-GPH represents about 10% (22983/221241) of the literature on COVID-19 on PubMed. This unique knowledge management database makes it easier to explore, describe, and track how the pandemic response is accelerating the applications of genomics and precision health technologies. COVID-19 GPH can be freely accessed via https://phgkb.cdc.gov/PHGKB/coVInfoStartPage.action.