Internet based molecular collaborative and publishing tools

The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web. The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing. The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks

Electronic information sharing in local government authorities: Factors influencing the decision-making process

This is the post-print version of the final paper published in International Journal of Information Management. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2013 Elsevier B.V.Local Government Authorities (LGAs) are mainly characterised as information-intensive organisations. To satisfy their information requirements, effective information sharing within and among LGAs is necessary. Nevertheless, the dilemma of Inter-Organisational Information Sharing (IOIS) has been regarded as an inevitable issue for the public sector. Despite a decade of active research and practice, the field lacks a comprehensive framework to examine the factors influencing Electronic Information Sharing (EIS) among LGAs. The research presented in this paper contributes towards resolving this problem by developing a conceptual framework of factors influencing EIS in Government-to-Government (G2G) collaboration. By presenting this model, we attempt to clarify that EIS in LGAs is affected by a combination of environmental, organisational, business process, and technological factors and that it should not be scrutinised merely from a technical perspective. To validate the conceptual rationale, multiple case study based research strategy was selected. From an analysis of the empirical data from two case organisations, this paper exemplifies the importance (i.e. prioritisation) of these factors in influencing EIS by utilising the Analytical Hierarchy Process (AHP) technique. The intent herein is to offer LGA decision-makers with a systematic decision-making process in realising the importance (i.e. from most important to least important) of EIS influential factors. This systematic process will also assist LGA decision-makers in better interpreting EIS and its underlying problems. The research reported herein should be of interest to both academics and practitioners who are involved in IOIS, in general, and collaborative e-Government, in particular

Process evaluation of complex interventions tested in randomised controlled trials in musculoskeletal disorders: A systematic review protocol

Introduction The effectiveness of complex interventions for the management of musculoskeletal disorders has been estimated in many randomised clinical trials (RCTs). These trials inform which interventions are the most effective, however they do not always inform how an intervention achieved its clinical outcomes, nor how and what elements of an intervention were delivered to patients. Such information is useful for translating findings into clinical practice. A few process evaluation studies have been conducted alongside RCTs and a variety of methods have been used. To gain a better understanding of current practices of process evaluation in RCTs in musculoskeletal disorders, this systematic review is designed to answer the following research question: How are process evaluation of complex interventions tested in RCTs in musculoskeletal disorders being conducted? Methods and analysis We will systematically search seven electronic databases (MEDLINE, SCOPUS, CINAHL, PsycINFO, EMBASE, Web of Science and Cochrane database) from the date of inception to August 2018 for studies on process evaluation of RCTs on non-surgical and non-pharmacological management of musculoskeletal disorders. We will include qualitative and quantitative studies conducted alongside RCTs, reported with the RCTs or separate studies that assessed interventions for musculoskeletal disorders. Two reviewers will screen abstracts and apply prespecified inclusion criteria to identify relevant studies, extract the data and assess the risk of bias within included studies. We will follow recommendations from the Cochrane Qualitative and Implementation Methods Group Guidance Series' when assessing methodological strengths and limitations of included studies. We will use a narrative synthesis to describe findings. Ethics and dissemination Ethical approval is not required as this review will not collect original data. Findings from this systematic review will be presented at a scientific conference and published in a peer reviewed journal. PROSPERO registration number CRD4201810960

So You Want to Be a Publisher: Planning and Publishing the Journal of eScience Librarianship

Objective: To describe the planning process and activities of the University of Massachusetts Medical School\u27s Lamar Soutter Library around the publication of the new Journal of eScience Librarianship (JESLIB). Methods: The University of Massachusetts Medical School’s Lamar Soutter Library through funding from the National Network of Libraries of Medicine has been a leader in educating librarians about eScience and its impact on librarianship. In spring 2011 the Library began to explore the idea of publishing a peer-reviewed, open access electronic journal about eScience and data management for librarians. Planning and implementation considerations included: choosing a unique and appropriate name; infrastructure and hosting options; organizational and governance structure; roles and responsibilities; journal structure and content; aims and scope; editorial, peer review and other policies and procedures; and dissemination. Results: The inaugural issue of the Journal of eScience Librarianship (http://escholarship.umassmed.edu/jeslib/) was published on February 15, 2012 via the journal management platform of the Library\u27s institutional repository, eScholarship@UMMS. JESLIB has been assigned ISSN 2161-3974. The medical school joined CrossRef so that article metadata could be deposited into their system and each article assigned a DOI (Digital Object Identifier). Conclusion: Libraries can successfully publish as well as host online journals. Helpful planning guides and other resources are available to assist libraries and academic groups in publishing open access peer-reviewed journals. Lessons learned include: consider professional copy editing services to assist the Editorial Board; Editorial Team roles and responsibilities should be clearly defined but allow room for flexibility; and have a clear marketing communication and promotion strategy

Engaging Novice Scholars with the Lure of Publication: Embedding Research, Writing and Analytical Skills into the Curriculum through an Electronic-Journal Project

This presentation showcases an electronic-journal project that embeds information literacy, analytical thinking, and writing into the first year nanoscience curriculum. The speaker will showcase a suite of pedagogical tools that provides first year, first semester students with a true-to-life experience of writing for publication. The central component of this project is da Vinci’s Notebook, an electronic, open-access, writing-in-the sciences journal developed at the University of Guelph that offers full journal functionality (e.g. document management, version control; double blind peer review). Custom-designed learning activities, assessment rubrics, and just-in-time skill development tutorials provide intentional support for student learning and the development of academic literacies such as information literacy, academic writing, and analytical thinking.Learning outcomes. At the end of this session participants will:1) recognize the potential of “Open Journal Systems (OJS)” as a pedagogical tool for improving scientific writing;2) be able to describe an approach to embedding information literacy, analytical thinking and writing into the curriculum that parallels the scholarly communication process;3) understand how to develop resources that will scaffold student learning and academic literacies development

Complying with the NIH Public Access Policy - Copyright Considerations and Options

On January 11, 2008, the National Institutes of Health ('NIH') adopted a revised Public Access Policy for peer-reviewed journal articles reporting research supported in whole or in part by NIH funds. Under the revised policy, the grantee shall ensure that a copy of the author's final manuscript, including any revisions made during the peer review process, be electronically submitted to the National Library of Medicine's PubMed Central ('PMC') archive and that the person submitting the manuscript will designate a time not later than 12 months after publication at which NIH may make the full text of the manuscript publicly accessible in PMC. NIH adopted this policy to implement a new statutory requirement under which: The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law. This White Paper is written primarily for policymaking staff in universities and other institutional recipients of NIH support responsible for ensuring compliance with the Public Access Policy. The January 11, 2008, Public Access Policy imposes two new compliance mandates. First, the grantee must ensure proper manuscript submission. The version of the article to be submitted is the final version over which the author has control, which must include all revisions made after peer review. The statutory command directs that the manuscript be submitted to PMC 'upon acceptance for publication.' That is, the author's final manuscript should be submitted to PMC at the same time that it is sent to the publisher for final formatting and copy editing. Proper submission is a two-stage process. The electronic manuscript must first be submitted through a process that requires input of additional information concerning the article, the author(s), and the nature of NIH support for the research reported. NIH then formats the manuscript into a uniform, XML-based format used for PMC versions of articles. In the second stage of the submission process, NIH sends a notice to the Principal Investigator requesting that the PMC-formatted version be reviewed and approved. Only after such approval has grantee's manuscript submission obligation been satisfied. Second, the grantee also has a distinct obligation to grant NIH copyright permission to make the manuscript publicly accessible through PMC not later than 12 months after the date of publication. This obligation is connected to manuscript submission because the author, or the person submitting the manuscript on the author's behalf, must have the necessary rights under copyright at the time of submission to give NIH the copyright permission it requires. This White Paper explains and analyzes only the scope of the grantee's copyright-related obligations under the revised Public Access Policy and suggests six options for compliance with that aspect of the grantee's obligation. Time is of the essence for NIH grantees. As a practical matter, the grantee should have a compliance process in place no later than April 7, 2008. More specifically, the new Public Access Policy applies to any article accepted for publication on or after April 7, 2008 if the article arose under (1) an NIH Grant or Cooperative Agreement active in Fiscal Year 2008, (2) direct funding from an NIH Contract signed after April 7, 2008, (3) direct funding from the NIH Intramural Program, or (4) from an NIH employee. In addition, effective May 25, 2008, anyone submitting an application, proposal or progress report to the NIH must include the PMC reference number when citing articles arising from their NIH funded research. (This includes applications submitted to the NIH for the May 25, 2008 and subsequent due dates.) Conceptually, the compliance challenge that the Public Access Policy poses for grantees is easily described. The grantee must depend to some extent upon the author(s) to take the necessary actions to ensure that the grantee is in compliance with the Public Access Policy because the electronic manuscripts and the copyrights in those manuscripts are initially under the control of the author(s). As a result, any compliance option will require an explicit understanding between the author(s) and the grantee about how the manuscript and the copyright in the manuscript are managed. It is useful to conceptually keep separate the grantee's manuscript submission obligation from its copyright permission obligation because the compliance personnel concerned with manuscript management may differ from those responsible for overseeing the author's copyright management. With respect to copyright management, the grantee has the following six options: (1) rely on authors to manage copyright but also to request or to require that these authors take responsibility for amending publication agreements that call for transfer of too many rights to enable the author to grant NIH permission to make the manuscript publicly accessible ('the Public Access License'); (2) take a more active role in assisting authors in negotiating the scope of any copyright transfer to a publisher by (a) providing advice to authors concerning their negotiations or (b) by acting as the author's agent in such negotiations; (3) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License; (4) enter into a side agreement with NIH-funded authors that grants a non-exclusive copyright license to the grantee sufficient to grant NIH the Public Access License and also grants a license to the grantee to make certain uses of the article, including posting a copy in the grantee's publicly accessible digital archive or repository and authorizing the article to be used in connection with teaching by university faculty; (5) negotiate a more systematic and comprehensive agreement with the biomedical publishers to ensure either that the publisher has a binding obligation to submit the manuscript and to grant NIH permission to make the manuscript publicly accessible or that the author retains sufficient rights to do so; or (6) instruct NIH-funded authors to submit manuscripts only to journals with binding deposit agreements with NIH or to journals whose copyright agreements permit authors to retain sufficient rights to authorize NIH to make manuscripts publicly accessible

Editorial

It is tradition that the Electronic Journal of Information Systems Evaluation (EJISE) publish a special issue containing the full versions of the best papers that were presented in a preliminary version during the 8th European Conference on Information Management and Evaluation (ECIME 2014). The faculty of Economics and Business Administration of the Ghent University was host for this successful conference on 11-12th of September 2014. ECIME 2014 received a submission of 86 abstracts and after the double-blind peer review process, thirty one academic research papers, nine PhD research papers, one master research paper and four work-in-progress papers were accepted and selected for presentation. ECIME 2014 hosted academics from twenty-two nationalities, amongst them: Australia, Belgium, Bosnia and Herzegovina, Brazil, Finland, France, Greece, Ireland, Lebanon, Lithuania, Macedonia (FYROM), Norway, Portugal, Romania, Russia, South Africa, South Korea, Spain, Sweden, The Netherlands, Turkey and the UK. From the thirty-one academic papers presented during the conference nine papers were selected for inclusion in this special issue of EJISE. The selected papers represent empirical work as well as theoretical research on the broad topic of management and evaluation of information systems. The papers show a wide variety of perspectives to deal with the problem

Repository Interface for Overlaid Journal Archives: costs estimates and sustainability issues

The RIOJA project (http://www.ucl.ac.uk/ls/rioja) investigated the feasibility of an overlay journal model in collaboration with the arXiv and in the scientific domain of astrophysics and cosmology. Scientists in this community are active users of e-prints repositories such as the arXiv. Furthermore, they have the support of Professional Associations and Learned Societies that have been pioneers in adapting to new publishing models and in particular electronic journals. Long term access to information as well as maintaining provision to sustainable systems/services is important to various parties in the scholarly communication system: the creators of information, developers and managers of services, libraries, publishers, funders and also users. Although scientific journals have been in existence since the 18th century (Lawal, 2001), factors such as increased journal subscription prices in the last decades and the emergence of new technologies have triggered discussions on the potential of new business models for publishing research. Furthermore, the advent of the open access movement also contributed to exploration of the issues around free access to information and provision of sustainable services. Exploring aspects of sustainability is something that should be seen over a period of time and whether launching, converting or simply maintaining a new or existing system/service the needs of the community it serves should be taken into account. Scientific journal publishing is a complex process. Besides disseminating scientific knowledge, registration of a claim for new discovery and a quality “stamp” it also facilitates social factors. Besides making research findings available and contributing to the advancement of knowledge, publishing is also a means for measuring quality of the work of scientists, allocating funding, and acknowledging contributions to knowledge. In this report, we will try to provide an overview of a new publishing model, that of the overlay journal. We will discuss the use of the arXiv by scientists in astrophysics and cosmology as well as the role of professional associations and learned societies in the publishing process for this community. We will briefly explain the methods employed to compile this report. We will also briefly present the RIOJA toolkit before we try and identify costs in the publishing process associated with the functions of registration, certification, and awareness and archiving. This report does not aim to provide a comprehensive report of actual journal publishing costings. Despite the fact that there are studies in existence that tried to document costs associated with journal publishing, the information presented there rarely corresponds to the actual costs of individual journal functions. In addition, the interviews with publishers and editors did not reveal any substantial information about costings that have not already been reported in the literature or are available on some publishers' websites. Where appropriate, this report aims to acknowledge studies conducted previously as pointers to further reading and, where applicable, to compare reported findings to observations made during the development and implementation of the RIOJA toolkit (described below). We will conclude this report with some of the issues reported in the literature around sustainability of services and some brief suggestions for further work