Open License Research Articles

MedTAG: a portable and customizable annotation tool for biomedical documents

BackgroundSemantic annotators and Natural Language Processing (NLP) methods for Named Entity Recognition and Linking (NER+L) require plenty of training and test data, especially in the biomedical domain. Despite the abundance of unstructured biomedical data, the lack of richly annotated biomedical datasets poses hindrances to the further development of NER+L algorithms for any effective secondary use. In addition, manual annotation of biomedical documents performed by physicians and experts is a costly and time-consuming task. To support, organize and speed up the annotation process, we introduce MedTAG, a collaborative biomedical annotation tool that is open-source, platform-independent, and free to use/distribute.ResultsWe present the main features of MedTAG and how it has been employed in the histopathology domain by physicians and experts to annotate more than seven thousand clinical reports manually. We compare MedTAG with a set of well-established biomedical annotation tools, including BioQRator, ezTag, MyMiner, and tagtog, comparing their pros and cons with those of MedTag. We highlight that MedTAG is one of the very few open-source tools provided with an open license and a straightforward installation procedure supporting cross-platform use.ConclusionsMedTAG has been designed according to five requirements (i.e. available, distributable, installable, workable and schematic) defined in a recent extensive review of manual annotation tools. Moreover, MedTAG satisfies 20 over 22 criteria specified in the same study.

Sonic Visualiser: Visualisation, Analysis, and Annotation of Music Audio Recordings

Sonic Visualiser: Visualisation, Analysis, and Annotation of Music Audio Recordings

Smartphone use among young drivers: Applying an extended Theory of Planned Behaviour to predict young drivers’ intention and engagement in concealed responding

Young drivers, aged 17–25 years, are more likely than other age groups to access social interactive technologies (e.g., Snapchat, Facebook) on their smartphones while driving. Many of these young drivers do so in a concealed manner, thereby diverting their eyes from the road for extended periods and increasing their crash risk. In accordance with previous research, an extended Theory of Planned Behaviour (TPB) was applied in this survey study to investigate psychosocial predictors of young drivers’ intention, and behaviour, of responding to social interactive technology on a smartphone in a concealed manner. Participants (N = 154) resided in Australia, were aged 17–25 years, owned a provisional or an open licence, and owned a smartphone. Participants completed two online surveys administered 1-week apart. The first survey measured intention and assessed the TPB standard constructs of attitude, subjective norm, and perceived behavioural control, as well as the additional constructs of anticipated action regret, anticipated inaction regret, and problematic mobile phone usage. The first survey also assessed whether there were any differences in the salient beliefs (elicited in a previous study) about smartphone use between high and low intenders to engage in this behaviour. The second survey measured engagement in the behaviour of responding in a concealed manner in the previous week. Hierarchical multiple regression analyses showed the standard TPB accounted for 69% of variance in intention, and a further 4% was accounted for by the extended constructs. In the final model, all variables, except anticipated inaction regret, were significant predictors of intention. Intention was the only significant predictor of behaviour. A series of MANOVAs found significant differences in the salient belief items between high and low intenders (e.g., high intenders were more likely to believe that friends/peers and other drivers would approve of them engaging in this behaviour). These key findings can be used as focal points for public education messages to persuade young drivers to reduce the frequency of their smartphone use, which is vital to improve road safety for all users.

Picking the crucial language technologies and how Wikipedia can help: the Welsh experience

When you're making plans to get people using your language as much and as often as possible, there's a list of things related to Wikipedia which can really help. I'll share our experience with the Welsh language.
 Supporting the Welsh-language Wikipedia community forms Work Package 15 of 27 in the Welsh Government's Welsh Language Technology Action Plan https://gov.wales/sites/default/files/publications/2018-12/welsh-language-technology-and-digital-media-action-plan.pdf. We like supporting Welsh language Wikipedia editing workshops, video workshops and other channels that encourage people to create and publish Welsh-language video, audio, graphic and text content because we're on a mission to try to help double daily use of Welsh by 2050.
 I'll share developments we're funding in speech, translation and conversational AI. The partners we're giving grants to publish what they develop under open licence. So we can share what we've funded with many companies. We think Microsoft might have used some to make their new synthetic voices in Welsh.
 We're excited by the potential Wikidata offers. We'll look at its potential in populating Welsh maps this year. We've already used Wikipedia search data as a way of prioritising the training of a Welsh virtual assistant.
 Welsh may not be spending as much as Icelandic and Estonian do on language technologies, but we'd like to share what we're learning as a smaller language about the important areas to focus on and how Wikipedia can help.

An analysis of open source software licensing questions in Stack Exchange sites

Free and open source software is widely used in the creation of software systems, whereas many organizations choose to provide their systems as open source. Open source software carries licenses that determine the conditions under which the original software can be used. Appropriate use of licenses requires relevant expertise by the practitioners, and has an important legal angle. Educators and employers need to ensure that developers have the necessary training to understand licensing risks and how they can be addressed. At the same time, it is important to understand which issues practitioners face when they are using a specific open source license, when they are developing new open source software products or when they are reusing open source software. In this work, we examine questions posed about open source software licensing using data from the following Stack Exchange sites: Stack Overflow, Software Engineering, Open Source and Law. We analyze the indication of specific licenses and topics in the questions, investigate the attention the posts receive and trends over time, whether appropriate answers are provided and which type of questions are asked. Our results indicate that practitioners need, among other, clarifications about licensing specific software when other licenses are used, and for understanding license content. The results of the study can be useful for educators and employers, organizations that are authoring open source software licenses and developers for understanding the issues faced when using licenses, whereas they are relevant to other software engineering research areas, such as software reusability.

PLoS Computational Biology Issue Image | Vol. 17(9) October 2021

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. DOI: pcbi.1009426 Image Credit: Priscila de CE1;ssia Souza AraFA;jo (co-author of the manuscript) photographed this bee visiting flowers of tomato plants grown at the experimental fields of the Federal University of ViE7;osa (Minas Gerais State, Brazil). We confirm that the image can publish under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). The authors own the copyright for the image and confirm that agree with open Access License of PLOS Computational Biology.

PLoS Computational Biology Issue Image | Vol. 1(9) October 2021.

The tomato flowers are characterized by possessing poricidal anthers, which restrict the exit of the pollen to a tiny opening on the apex of the anther. To extract pollen efficiently, some visiting bees grasp the anthers and quickly contracting their flight muscles, producing vibrations and an audible sound. The vibrations are transferred to the anthers, shaking and stimulating the pollen inside them to leave by the pores, a phenomenon known as floral sonication or buzz-pollination. DOI: pcbi.1009426 Image Credit: Priscila Souza AraFA;jo (co-author of the manuscript) photographed this bee visiting flowers of tomato plants grown at the experimental fields of the Federal University of ViE7;osa (Minas Gerais State, Brazil). We confirm that the image can publish under the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). The authors own the copyright for the image and confirm that agree with open Access License of PLOS Computational Biology.

Integration of solutions and services for multi-omics data analysis towards personalized medicine

Current advances in high-throughput and imaging technologies are paving the way next-generation healthcare, tailored to the clinical and molecular characteristics of each patient. The Big Data obtained from these technologies are of little value to society unless it can be analyzed, interpreted, and applied in a relatively customized and inexpensive way. We propose a flexible decision support system called IntelliOmics for multi-omics data analysis constituted with well-designed and maintained components with open license for both personal and commercial use. Our proposition aims to serve some insight how to build your own local end-to-end service towards personalized medicine: from raw data upload, intelligent integration and exploration to detailed analysis accompanying clinical medical reports.The high-throughput data is effectively collected and processed in a parallel and distributed manner using the Hadoop framework and user-defined scripts. Heterogeneous data transformation performed mainly on the Apache Hive is then integrated into a so called ‘knowledge base’. On its basis, manual analysis in the form of hierarchical rules can be performed as well as automatic data analysis with Apache Spark and machine learning library MLlib. Finally, diagnostic and prognostic tools, charts, tables, statistical tests and print-ready clinical reports for an individual or group of patients are provided. The experimental evaluation was performed as part of the clinical decision support for targeted therapy in non-small cell lung cancer. The system managed to successfully process over a hundred of multi-omic patient data and offers various functionalities for different types of users: researchers, bio-statisticians/bioinformaticians, clinicians and medical board.

Constructing Japanese MeSH term dictionaries related to the COVID-19 literature.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this research, it is necessary to promote sharing up-to-date knowledge from these papers. However, because most research papers are written in English, it is difficult for people who are not familiar with English medical terms to obtain knowledge from them. To facilitate sharing knowledge from COVID-19 papers written in English for Japanese speakers, we tried to construct a dictionary with an open license by assigning Japanese terms to MeSH unique identifiers (UIDs) annotated to words in the texts of COVID-19 papers. Using this dictionary, 98.99% of all occurrences of MeSH terms in COVID-19 papers were covered. We also created a curated version of the dictionary and uploaded it to PubDictionary for wider use in the PubAnnotation system.

Why are some Massive Open Online Courses more open than others?

This paper studies the determinants of the intellectual property license of the Massive Open Online Courses provided on a French platform. While they can opt for a traditional license, the majority of courses chooses among Creative Commons licenses. Considering the ordering in terms of degree of openness of the licenses, we study the course-, teacher- and institution-related factors driving the intellectual property decision of this pedagogical innovation. We observe that the field of study and the characteristics of the institution providing the course play a role. We explain these results by the heterogeneity in preferences and peer recognition with regard to open practices. We also find support for the idea that course providers willing to raise indirectly revenues by selling goods complementary to the MOOC (like a certificate of completion) are less likely to choose an open license.

BatRack: An open‐source multi‐sensor device for wildlife research

Abstract Bats represent a highly diverse group of mammals and are essential for ecosystem functioning. However, knowledge about their behaviour, ecology and conservation status is limited. Direct observation of marked individuals (commonly applied to birds) is not possible for bats due to their small size, rapid movement and nocturnal lifestyle, while neither popular observation methods such as camera traps nor conventional tracking technologies sufficiently capture the behaviour of individuals. The combination and networking of different sensors in a single system can overcome these limitations, but this potential has been explored only to a limited extent. We present BatRack, a multi‐sensor device that combines ultrasonic audio recordings, automatic radio telemetry and video camera recordings in a single modular unit. BatRack facilitates the individual or combined scheduling of sensors and includes a mutual triggering mode. It consists of off‐the‐shelf hardware and both its hardware blueprints and the required software have been published under an open license to allow scientists and practitioners to replicate the system. We tested the suitability of radio telemetry and audio sensors as camera triggers and evaluated the detection of individuals in video recordings compared to radio telemetry signals. Specifically, BatRack was used to monitor the individual swarming behaviour of six members of a maternity colony of Bechstein's bat. Preliminary anecdotal results indicate that swarming intensity is related to reproductive state and roost switching. BatRack allows researchers to recognize individual bats and monitor their behavioural patterns using an easily deployed and scalable system. BatRack is thus a promising approach to obtaining detailed insights into the behavioural ecology of bats.

SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology

Abstract Large‐scale digitization projects such as #ScanAllFishes and oVert are generating high‐resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them. Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research. We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python‐scriptable open‐source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open‐access 3D models or import users own 3D volumes, to annotate 3D curve and patch‐based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark‐driven and landmark‐free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology. Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.

Open Pedagogy: A Systematic Review of Empirical Findings

Open licensing used in open educational resources allows for teaching and learning practices that are not possible with traditional copyright. There is a growing body of empirical research on open pedagogy. However, definitions and instantiations of open pedagogy vary in the literature. The purpose of this review was to systematically search and synthesize empirical findings on open pedagogy. In this, the definitions of open pedagogy across empirical reports were examined. Generally, open pedagogy was defined in the context of open licensing affordances; however, there were exceptions particularly when examining faculty experiences with open pedagogy. Synthesized findings may be used by faculty to inform use of open pedagogy especially when considering issues with student confusion and changing power dynamics.

The Australian Acoustic Observatory

Abstract Fauna surveys are traditionally manual, and hence limited in scale, expensive and labour‐intensive. Low‐cost hardware and storage mean that acoustic recording now has the potential to efficiently build scale in terrestrial fauna surveys, both spatially and temporally. With this aim, we have constructed the Australian Acoustic Observatory. It provides a direct and permanent record of terrestrial soundscapes through continuous recording across Australian ecoregions, including those periodically subject to fire and flood, when manual surveys are dangerous or impossible. The observatory comprises 360 permanent listening stations deployed across Australia. Groups of four sensors are deployed at each of 90 sites, placed strategically across ecoregions, to provide representative datasets of soundscapes. Each station continuously records sound, resulting in year‐round data collection. All data are made freely available under an open access licence. The Australian Acoustic Observatory is the world's first terrestrial acoustic observatory of this size. It provides continental‐scale environmental monitoring of unparalleled spatial extent, temporal resolution and archival stability. It enables new approaches to understanding ecosystems, long‐term environmental change, data visualization and acoustic science that will only increase in scientific value over time, particularly as others replicate the design in other parts of the world.

Machine Learning Models Under the Copyright Microscope: Is EU Copyright Fit for Purpose?

Abstract This paper is based on a presentation given in December 2019 at the Lund’s University conference ‘Artificial Intelligence (AI), Data Protection and Intellectual Property in a European context’. The purpose of this article is to analyse the suitability of the copyright system over Machine Learning (ML) models, the so-called ‘core components’ of ML systems. Computer programs protection has always caused certain difficulties for intellectual property law. Internationally, agreement was reached in the 1970s to protect computer programs as literary works of copyright. ML models have been called ‘learning algorithms’, ‘AI computer programs’, and ‘software 2.0’. Yet there is no unanimity about what they are technically. This is relevant from a copyright perspective, because the regime of protection granted by copyright will be different depending on whether the ML model qualifies as a computer program, as a mathematical method, or as another type of work. Additionally, all proprietary and open source software licensing relies on copyright protection. In most open licenses, the license is not triggered if it is applied to something that is not protected by copyright (or related rights). Thus, it seems pertinent to question whether EU copyright law provides adequate protection for the core components of machine learning systems, the ML models.

Wikipedia for multilingual COVID-19 vaccine education at scale

We present the design of a project to develop Wikipedia content on general vaccine safety and the COVID-19 vaccines, specifically. This proposal describes what a team would need to distribute public health information in Wikipedia in multiple languages in response to a disaster or crisis, and to measure and report the communication impact of the same. Researchers at the School of Data Science at the University of Virginia made this proposal in response to a February 2021 call from a sponsor which was seeking to share public health information to respond globally to vaccine hesitancy related to the COVID-19 vaccines. This proposal was not selected for funding, and now the research team is sharing the proposal here with an open copyright license for anyone to reuse and remix. Most of the text here is from the original proposal, but there are modifications to remove the names of the funder, named partners, and for other details to make this text more reusable. The budget in this proposal has been converted from a dollar amount to equivalent descriptions in terms of labor hours, and the timeline was adapted from absolute to relative months.

Potret kepemilikan hak cipta dan penggunaan lisensi terbuka pada penerbitan ilmiah di Indonesia

Text-based content has become the type of content that is most accessed and disseminated by Internet users in Indonesia, including scientific article content. The method of how scientific copyrights are organized and content distributed has become a key factor in the development of scientific journal. This situation is supported by the presence of Creative Commons with its CC open licensing concept. By extracting data from the Directory of Open Access Journal (DOAJ) on 13 February 2020, this article presents the distribution of the use of copyright and licenses in journals in Indonesia. The 1578 journals observed show that copyright ownership in scientific articles in Indonesia tends to be held by publishers, while forty percent of journals apply CC BY open licenses in their management. The phenomenon of the emergence of openness amidst the possible illiteracy of journal managers about the licenses types, which become blessing in disguise, is explained as the contribution of Indonesian culture as part of Eastern society that contributes to the preference of applying copyright and open licenses in Indonesian scientific journals.

Advancing open access in the Netherlands after 2020: from quantity to quality

The purpose of this article is to explore options to further open access in the Netherlands from 2021. Its premise is that there is a need to look at the qualitative aspects of open access, alongside quantitative ones. The article first takes stock of progress that has been made. Next, we suggest broadening the agenda by involving more types of actors and other scholarly formats (like books, chapters, proceedings, preprints and textbooks). At the same time we suggest deepening the open access agenda by including several open access dimensions: immediacy, diamond open access, open metadata, open peer review and open licences. To facilitate discussion, a framework is proposed that allows specifying these actions by the a) aspects of open access they address (what is made open access, how, when and where it is made open access, and copyright and rights retention), b) the actors that play a role (government, research institutions, funders) and c) the various levels at which these actions can be taken: state as goal, set as policy, legalize and promote, recognize and reward, finance, support with infrastructure. A template is provided to ease the use of the framework.

Open government data licensing in the Gulf Cooperation Council

The Cooperation Council of the Arab States of the Gulf (‘GCC’) is a political and economic bloc made up of Bahrain, Kuwait, Oman, Qatar, Saudi Arabia (‘Saudi’) and the United Arab Emirates (UAE). As these countries start publishing more of their government-produced copyright works through open data portals, it has become important to analyse the legal terms under which these works are licensed and the extent to which members of the public are allowed to use and utilize them. This article examines the different open licensing approaches of open government data in Bahrain, Kuwait, Oman, Qatar, Saudi Arabia and the UAE by analysing each of their licensing provisions and identifying the key differences between them. Open government data are a trending topic among the GCC Member States with Saudi issuing a brand new open data policy in September 2020,1 Oman issuing a revised open data policy in June 2020,2 and the UAE issuing a Smart Data Framework in February 2019 that included open data licensing provisions.3 This section provides an introduction to open government data, an overview of copyright restrictions on government works within the GCC, and an outline of the different approaches to licensing that are available to overcome these restrictions.

Role of 3D Printing and Modeling to Aid in Neuroradiology Education for Medical Trainees.

Applications of 3-dimensional (3D) printing in medical imaging and health care are expanding. Currently, primary uses involve presurgical planning and patient and medical trainee education. Neuroradiology is a complex subdiscipline of radiology that requires further training beyond radiology residency. This review seeks to explore the clinical value of 3D printing and modeling specifically in enhancing neuroradiology education for radiology physician residents and medical trainees. A brief review summarizing the key steps from radiologic image to 3D printed model is provided, including storage of computed tomography and magnetic resonance imaging data as digital imaging and communications in medicine files; conversion to standard tessellation language (STL) format; manipulation of STL files in interactive medical image control system software (Materialise) to create 3D models; and 3D printing using various resins via a Formlabs 2 printer. For the purposes of demonstration and proof of concept, neuroanatomy models deemed crucial in early radiology education were created via open-source hardware designs under free or open licenses. 3D-printed objects included a sphenoid bone, cerebellum, skull base, middle ear labyrinth and ossicles, mandible, circle of Willis, carotid aneurysm, and lumbar spine using a combination of clear, white, and elastic resins. Based on this single-institution experience, 3D-printed complex neuroanatomical structures seem feasible and may enhance resident education and patient safety. These same steps and principles may be applied to other subspecialties of radiology. Artificial intelligence also has the potential to advance the 3D process.