Publications scientifiques

Recueil d'informations sur les publications scientifiques en libre accès ou sous licence libre : journaux, réflexions, débats...

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Préambule

Afin de ne pas alourdir cette page, les publications n'entrant pas dans le cadre des revues scientifiques mais plus de l'information et de la vulgarisation se trouve sur cette page. Ici nous gardons les éléments permettant la réflexion des licences associées aux productions alors que l'autre page renvoie d'avantage à la diffusion de l'information.

Libre accès

Sur la thématique du libre accès

• Le long chemin du Libre Accès au Savoir à l'Université (Framablog)

• Open-Access Science: A Necessity for Global Public Health

Josefina Coloma, Eva Harris

PLoS Pathog 1(2): e21. doi:10.1371/journal.ppat.0010021 (texte complet)

• Usages des ressources en libre accès dans les bibliothèques universitaires et services communs de documentation. Le cas de Revues.org

Résumé :

Comment les ressources en libre accès sont-elles traitées par les bibliothèques universitaires et services communs de documentations ? Entre les deux voies " or " et " verte " du libre accès, les bibliothèques se sont logiquement investies davantage dans le mouvement des archives ouvertes plutôt que dans le développement de revues électroniques en libre accès. La question qui se pose est celle de la prise en compte de ces dernières par les bibliothèques. Une enquête effectuée en 2009 tente d'y répondre en évaluant la visibilité des revues en libre accès diffusées par le portail Revues.org dans une vingtaine d'établissements de la région parisienne. A partir de résultats contrastés, il est possible d'analyser les points de blocage et les leviers qui permettraient d'améliorer la prise en compte de ce type de ressources par les bibliothèques.

Lien : [1]

Sur la thématique des licences libres

• Pour libérer les sciences, par Christophe Masutti

Dépôt en libre accès et autres infos

• Arxiv
• HAL : archives ouvertes
• CEL : cours en ligne
• TEL : thèse en ligne
• Medihal : image en ligne Il est possible de déposer ses images sous licence creative commons.
• Mars 2011 : l'UPMC ouvre HAL-UPMC
• Compte-rendu de la réunion sur la publication en libre accès Bethesda Statement on Open Access Publishing, 11 avril 2003
• Sherpa - Romeo : sur la possibilité de publier sous pré ou post-print selon les journaux, donc de libérer l'accès
• http://openaccess.inist.fr/

Listes de journaux en libre accès

• DOAJ : Directory of Open Access journals : Moteur de recherche et liste des journaux en open access.

Journaux

Journaux sous licence "libre"

Physical Review

Publications scientifiques : Physical Review permet l’usage de creative commons paternité (Licence CC BY 3.0) Coût : 1700 et 2700$ pour Physical Review et Physical Review Letters resp.

EPJ : European physical journal

EPJ Selon leur document, les droits d'exploitation commerciale sont données à l'éditeur et l'article est sous CC BY NC 2.5. Coût : 1000€.

Informatique : lmcs

Revue en informatique théorique sous licence CC BY-ND 2.0 Coût : gratuit (?)

PLOS

PLoS Public Library of Science. Licence CC BY : "All material published by the Public Library of Science, whether submitted to or created by PLoS, is published under an open access license that allows unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."

PLoS est un journal scientifique couvrant plusieurs disciplines (biologie, physique,...). Les publications ne se font qu'en ligne : il n'y a pas de version papier. Les articles publiés dans PLoS sont indexés dans les bases publiques PubMed Central, Scopus, CrossRef, ainsi que par Google Scholar.

La philosophie de PLoS est différente de celle des journaux scientifiques classiques tels que Nature, Science,... qui traduisent l'obsession universitaire générale de l'impact factor (réf) du journal. En effet, l'idée est qu'une publication en ligne implique de publier plus rapidement les résultats de sa recherche et de laisser l'évaluation du travail scientifique à une discussion ouverte entre pairs. De plus, le journal ne se limite pas à un domaine scientifique restreint, mais souhaite favoriser et rendre possible la publication d'articles interdisciplinaires.

Coût : http://www.plos.org/publish/pricing-policy/publication-fees/

Semantics and Pragmatics

Semantics and Pragmatics : journal à accès ouvert en linguistique (philosophie, psychologie, informatique) sous licence licence CC BY-NC 3.0 et possibilité de publier sous licence CC BY-NC-ND

BioMed Central

BioMed Central (BMC) ainsi que Chemistry Central et PhysMath Central sont depuis 2008 propriété de Springer Science ; les articles ne sont publiés qu'en ligne. Leur philosophie est semblable à celle de PLoS :

All original research articles published by BioMed Central are made freely and permanently
accessible online immediately upon publication. BioMed Central views open access to research
as essential in order to ensure the rapid and efficient communication of research findings.

Les publications sont indexées dans les bases publiques PubMed Central, Scopus, CrossRef, ainsi que par Google Scholar.

BMC publie 204 journaux dont les articles sont sous Creative Commons Attribution Licence (CCAL) et couvrant une large palette de domaines scientifiques et médicaux. L'accès à certaines revues est ouvert seulement aux universitaires (par exemple, Genome Research).

European Journal of Taxonomy

cf News_education_juillet_2011#Appel_.C3.A0_manuscrits_-_revue_European_Journal_of_Taxonomy

Conférences, débats...

• Conférence internationale sur l’édition scientifique en libre accès a eu lieu à Prague - août 2010

Articles sur le sujet pour alimenter la réflexion

En vrac...

Pour l'instant, juste les titres et les résumés (abstracts) sont donnés. La plupart des articles étant en accès payant, les pdf ne sont pas publiés...

• When speed truly matters, openness is the answer.

Marturano A.

Sacred Heart Catholic University of Rome and LUISS University of Rome, Italy. marturanoa A luiss DOT it Bioethics. 2009 Sep;23(7):385-93. Epub 2009 Apr 21.

In this paper I analyse the ethical implications of the two main competing methodologies in genomic research. I do not aim to provide another contribution from the mainstream legal and public policy perspective; rather I offer a novel approach in which I analyse and describe the patent-and-publish regime (the proprietary regime) led by biologist J. Craig Venter and the 'open-source' methodologies led by biotechnology Nobel laureate John Sulston. The 'open-source methodologies' arose in biotechnology as an alternative to the patent-and-publish regime in the wake of the explosion in computer technology. Indeed, the tremendous increase in computer technology has generated a corresponding increase in the pace of genomics research. I conclude this paper by arguing that while the patent-and-publish method is a transactional method based on the exchange of extrinsic goods (patents in exchange for research funds), the free and open-source methodology (FLOSS) is a transformational method based on a visionary ideal of science, which leads to prioritizing intrinsic goods in scientific research over extrinsic goods.

• Open source and healthcare in Europe - time to put leading edge ideas into practice.

Murray PJ, Wright G, Karopka T, Betts H, Orel A.

CHIRAD - Centre for Health Informatics Research and Development, Lincolnshire, UK. peterjmurray A gmail DOT com Stud Health Technol Inform. 2009;150:963-7.

Free/Libre and Open Source Software (FLOSS) is a process of software development, a method of licensing and a philosophy. Although FLOSS plays a significant role in several market areas, the impact in the health care arena is still limited. FLOSS is promoted as one of the most effective means for overcoming fragmentation in the health care sector and providing a basis for more efficient, timely and cost effective health care provision. The 2008 European Federation for Medical Informatics (EFMI) Special Topic Conference (STC) explored a range of current and future issues related to FLOSS in healthcare (FLOSS-HC). In particular, there was a focus on health records, ubiquitous computing, knowledge sharing, and current and future applications. Discussions resulted in a list of main barriers and challenges for use of FLOSS-HC. Based on the outputs of this event, the 2004 Open Steps events and subsequent workshops at OSEHC2009 and Med-e-Tel 2009, a four-step strategy has been proposed for FLOSS-HC: 1) a FLOSS-HC inventory; 2) a FLOSS-HC collaboration platform, use case database and knowledge base; 3) a worldwide FLOSS-HC network; and 4) FLOSS-HC dissemination activities. The workshop will further refine this strategy and elaborate avenues for FLOSS-HC from scientific, business and end-user perspectives. To gain acceptance by different stakeholders in the health care industry, different activities have to be conducted in collaboration. The workshop will focus on the scientific challenges in developing methodologies and criteria to support FLOSS-HC in becoming a viable alternative to commercial and proprietary software development and deployment.

• osni.info-Using free/libre/open source software to build a virtual international community for open source nursing informatics.

Oyri K, Murray PJ.

The Interventional Centre, Rikshospitalet University Hospital, 0027 Oslo, Norway. karl.oyri A klinmed DOT uio DOT no Int J Med Inform. 2005 Dec;74(11-12):937-45. Epub 2005 Aug 19.

Many health informatics organizations seem to be slow to take up the advantages of dynamic, web-based technologies for providing services to, and interaction with, their members; these are often the very technologies they promote for use within healthcare environments. This paper aims to introduce some of the many free/libre/open source (FLOSS) applications that are now available to develop interactive websites and dynamic online communities as part of the structure of health informatics organizations, and to show how the Open Source Nursing Informatics Working Group (OSNI) of the special interest group in nursing informatics of the International Medical Informatics Association (IMIA-NI) is using some of these tools to develop an online community of nurse informaticians through their website, at . Some background introduction to FLOSS applications is used for the benefit of those less familiar with such tools, and examples of some of the FLOSS content management systems (CMS) being used by OSNI are described. The experiences of the OSNI will facilitate a knowledgeable nursing contribution to the wider discussions on the applications of FLOSS within health and healthcare, and provides a model that many other groups could adopt.

• Open Source software in medical informatics--why, how and what.

McDonald CJ, Schadow G, Barnes M, Dexter P, Overhage JM, Mamlin B, McCoy JM.

Department of Medicine, Indiana University School of Medicine, 1001 W. 10th St., RG5th Floor, Indianapolis, IN 46202, USA. cmcdonald A regenstrief DOT org. Int J Med Inform. 2003 Mar;69(2-3):175-84. Comment in: Int J Med Inform. 2003 Sep;71(2-3):165.

'Open Source' is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General's COSTAR and the Veterans Administration's VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.

• How the role of computing is driving new genetics' public policy.

Marturano A, Chadwick R.

Centre for Leadership Studies, School of Business and Economics, University of Exeter, Streatham Court, Reenes Drive, Exeter EX 4 4PU, UK. antonio.marturano A ex DOT ac DOT uk. Ethics Inf Technol. 2004;6(1):43-53.

In this paper we will examine some ethical aspects of the role that computers and computing increasingly play in new genetics. Our claim is that there is no new genetics without computer science. Computer science is important for the new genetics on two levels: (1) from a theoretical perspective, and (2) from the point of view of geneticists practice. With respect to (1), the new genetics is fully impregnate with concepts that are basic for computer science. Regarding (2), recent developments in the Human Genome Project (HGP) have shown that computers shape the practices of molecular genetics; an important example is the Shotgun Method's contribution to accelerating the mapping of the human genome. A new challenge to the HGP is provided by the Open Source Philosophy (I computer science), which is another way computer technologies now influence the shaping of public policy debates involving genomics.

• The case for open-source software in drug discovery.

DeLano WL.

DeLano Scientific LLC, 400 Oyster Point Blvd., Suite 213, San Francisco, CA 94080, USA. Drug Discov Today. 2005 Feb 1;10(3):213-7.

Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consu

Autres liens

• SciELO : Scientific Electronic Library Online, publication électronique coopérative orientée pour les pays en voie de développement. Voir aussi cet article sur le site de l'UNESCO.
• BOAI Budapest open access initiative