EN

Data publication with the structural biology data grid supports live analysis

Posted on by Hans Dillaerts

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications.

Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures.

SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

URL : Data publication with the structural biology data grid supports live analysis

DOI : 10.1038/ncomms10882

EN

Open Access, Open Science, Open Society

Posted on by Hans Dillaerts

Open Access’ main goal is not the subversion of publishers’ role as driving actors in an oligopolistic market characterised by reduced competition and higher prices. OA’s main function is to be found somewhere else, namely in the ability to subvert the power to control science’s governance and its future directions (Open Science), a power that is more often found within the academic institutions rather than outside.

By decentralising and opening-up not just the way in which scholarship is published but also the way in which it is assessed, OA removes the barriers that helped turn science into an intellectual oligopoly even before an economic one. The goal of this paper is to demonstrate that Open Access is a key enabler of Open Science, which in turn will lead to a more Open Society.

Furthermore, the paper argues that while legislative interventions play an important role in the top-down regulation of Open Access, legislators currently lack an informed and systematic vision on the role of Open Access in science and society. In this historical phase, other complementary forms of intervention (bottom-up) appear much more “informed” and effective.

This paper, which intends to set the stage for future research, identifies a few pieces of the puzzle: the relationship between formal and informal norms in the field of Open Science and how these impact on intellectual property rights, the protection of personal data, the assessment of science and the technology employed for the communication of science.

URL : http://ssrn.com/abstract=2751741

EN

Scientific Production on Open Access: A Worldwide Bibliometric Analysis in the Academic and Scientific Context

Posted on by Hans Dillaerts

This research aims to diachronically analyze the worldwide scientific production on open access, in the academic and scientific context, in order to contribute to knowledge and visualization of its main actors.

As a method, bibliographical, descriptive and analytical research was used, with the contribution of bibliometric studies, especially the production indicators, scientific collaboration and indicators of thematic co-occurrence.

The Scopus database was used as a source to retrieve the articles on the subject, with a resulting corpus of 1179 articles. Using Bibexcel software, frequency tables were constructed for the variables, and Pajek software was used to visualize the collaboration network and VoSViewer for the construction of the keywords’ network.

As for the results, the most productive researchers come from countries such as the United States, Canada, France and Spain. Journals with higher impact in the academic community have disseminated the new constructed knowledge. A collaborative network with a few subnets where co-authors are from different countries has been observed.

As conclusions, this study allows identifying the themes of debates that mark the development of open access at the international level, and it is possible to state that open access is one of the new emerging and frontier fields of library and information science.

URL : Scientific Production on Open Access: A Worldwide Bibliometric Analysis in the Academic and Scientific Context

DOI : http://www.mdpi.com/2304-6775/4/1/1

FR

De l’usage des revues juridiques dématérialisées : A propos des interactions entre TIC et recherche juridique

Posted on by Hans Dillaerts

Si la réussite d’une revue juridique se traduit tant par la diversité des thématiques abordées et de ses auteurs que par l’actualité des propos, force est de reconnaître que sa longévité est un critère tout aussi pertinent. Une existence qui doit essentiellement sa pérennité à l’investissement originel de ses créateurs et continu de ses contributeurs.

Il faut avouer que le support dématérialisé évince toute contrainte financière substantielle pour une revue et que l’accès libre aux articles (le fameux open-access) facilite grandement la diffusion des travaux de recherche. La revue Neptunus du Centre de Droit Maritime et Océanique de l’Université de Nantes a ainsi été précurseur dans la diffusion des idées sans contrainte matérielle ou financière.

D’ailleurs, quelques années après sa création en 1994, des prises de position et des appels en ce sens, hors de nos frontières nationales, initient une réflexion, désormais ancrée dans toutes les politiques d’innovation et de recherche…

URL : https://hal.archives-ouvertes.fr/halshs-01288752

EN

Wikidata as a semantic framework for the Gene Wiki initiative

Posted on by Hans Dillaerts

Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia.

In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata.

In total, 59 721 human genes and 73 355 mouse genes have been imported from NCBI and 27 306 human proteins and 16 728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike.

The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified.

Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias.

Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists.

In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.

URL : Wikidata as a semantic framework for the Gene Wiki initiative

DOI : 10.1093/database/baw015

EN

Current state of open access to journal publications from the University of Zagreb School of Medicine

Posted on by Hans Dillaerts

AIMS

To identify the share of open access (OA) papers in the total number of journal publications authored by the members of the University of Zagreb School of Medicine (UZSM) in 2014.

METHODS

Bibliographic data on 543 UZSM papers published in 2014 were collected using PubMed advanced search strategies and manual data collection methods. The items that had « free full text » icons were considered as gold OA papers.

Their OA availability was checked using the provided link to full-text. The rest of the UZSM papers were analyzed for potential green OA through self-archiving in institutional repository. Papers published by Croatian journals were particularly analyzed.

RESULTS

Full texts of approximately 65% of all UZSM papers were freely available. Most of them were published in gold OA journals (55% of all UZSM papers or 85% of all UZSM OA papers). In the UZSM repository, there were additional 52 freely available authors’ manuscripts from subscription-based journals (10% of all UZSM papers or 15% of all UZSM OA papers).

CONCLUSION

The overall proportion of OA in our study is higher than in similar studies, but only half of gold OA papers are accessible via PubMed directly. The results of our study indicate that increased quality of metadata and linking of the bibliographic records to full texts could assure better visibility. Moreover, only a quarter of papers from subscription-based journals that allow self-archiving are deposited in the UZSM repository.

We believe that UZSM should consider mandating all faculty members to deposit their publications in UZSM OA repository to increase visibility and improve access to its scientific output.

URL : http://www.ncbi.nlm.nih.gov/pubmed/26935617

EN

Open Access Publishing in Higher Education: Charting the Challenging Course to Academic and Financial Sustainability

Posted on by Hans Dillaerts

The benefits, pitfalls, and sustainability of open access publishing are hotly debated. Commercial publishers dominate the marketplace and oppose alternative publishing models that threaten their bottom line. Scholars’ use of open access remains relatively limited due to awareness and perceived benefits to their professional goals.

Readership of open access publications is generally strong, but some people disagree that more readers leads to increased citations and research impact. Libraries have grown their influence by supporting and promoting open access, but these efforts come with significant financial costs.

Today, open access has flourished most significantly as a philosophy: the belief that the world’s scholarship should be freely available to readers and that publicly funded research, in particular, should be accessible to the taxpayers who paid for it.

Transforming a moral good into a sustainable publishing model rests with lawmakers, scholars, and institutions of higher education. Without laws designed to ensure participation by authors and publishers, Green Open Access cannot effectively replace journal subscriptions.

Scholars need to call upon each other to archive their work, utilize open access repository web sites to find quality content, and embrace Gold Open Access journals as a professionally beneficial publishing venue.

Institutions must allocate additional internal resources to spur more and better institutional and disciplinary archives, new Gold Open Access journals, and myriad other professional, technical, and financial services necessary to promote open access as a fiscally and academically sustainable publishing solution.

URL : http://cedar.wwu.edu/jec/vol10/iss1/5/