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Les revues de sciences humaines et sociales en France: libre accès et audience

Posted on by Hans Dillaerts

« La Commission européenne a émis le 17 juillet 2012 une recommandation en faveur du libre accès aux résultats de la recherche financée sur fonds publics.

La question posée aux politiques publiques est celle de la durée pendant laquelle l’accès peut être payant avant le passage à la gratuité de l’article. Il s’agit donc de prendre la mesure des gains et des coûts d’une telle politique de libre accès pour déterminer quel serait le délai optimal d’embargo. »

URL : http://www.ipp.eu/wp-content/uploads/2015/07/revues-shs-rapport-IPP-juillet2015.pdf

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Accelerating Scientific Publication in Biology

Posted on by Hans Dillaerts

« Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. Considerably more experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training.

Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for the life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and scientific community. »

URL : http://biorxiv.org/content/early/2015/07/11/022368

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Mining and Analyzing the Future Works in Scientific Articles

Posted on by Hans Dillaerts

« Future works in scientific articles are valuable for researchers and they can guide researchers to new research directions or ideas. In this paper, we mine the future works in scientific articles in order to 1) provide an insight for future work analysis and 2) facilitate researchers to search and browse future works in a research area.

First, we study the problem of future work extraction and propose a regular expression based method to address the problem. Second, we define four different categories for the future works by observing the data and investigate the multi-class future work classification problem. Third, we apply the extraction method and the classification model to a paper dataset in the computer science field and conduct a further analysis of the future works.

Finally, we design a prototype system to search and demonstrate the future works mined from the scientific papers. Our evaluation results show that our extraction method can get high precision and recall values and our classification model can also get good results and it outperforms several baseline models. Further analysis of the future work sentences also indicates interesting results. »

URL : http://arxiv.org/abs/1507.02140

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Wikidata through the Eyes of DBpedia

Posted on by Hans Dillaerts

« DBpedia is one of the first and most prominent nodes of the Linked Open Data cloud. It provides structured data for more than 100 Wikipedia language editions as well as Wikimedia Commons, has a mature ontology and a stable and thorough Linked Data publishing lifecycle. Wikidata, on the other hand, has recently emerged as a user curated source for structured information which is included in Wikipedia.

In this paper, we present how Wikidata is incorporated in the DBpedia ecosystem. Enriching DBpedia with structured information from Wikidata provides added value for a number of usage scenarios. We outline those scenarios and describe the structure and conversion process of the DBpediaWikidata dataset. »

URL : Wikidata through the Eyes of DBpedia

Related URL : http://arxiv.org/abs/1507.04180

 

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Barriers to Initiation of Open Source Software Projects in Libraries

Posted on by Hans Dillaerts

« Libraries share a number of core values with the Open Source Software (OSS) movement, suggesting there should be a natural tendency toward library participation in OSS projects. However Dale Askey’s 2008 Code4Lib column entitled “We Love Open Source Software. No, You Can’t Have Our Code,” claims that while libraries are strong proponents of OSS, they are unlikely to actually contribute to OSS projects. He identifies, but does not empirically substantiate, six barriers that he believes contribute to this apparent inconsistency.

In this study we empirically investigate not only Askey’s central claim but also the six barriers he proposes. In contrast to Askey’s assertion, we find that initiation of and contribution to OSS projects are, in fact, common practices in libraries. However, we also find that these practices are far from ubiquitous; as Askey suggests, many libraries do have opportunities to initiate OSS projects, but choose not to do so. Further, we find support for only four of Askey’s six OSS barriers. Thus, our results confirm many, but not all, of Askey’s assertions. »

URL : http://journal.code4lib.org/articles/10665

EN

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Posted on by Hans Dillaerts

Motivation

Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed.

The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.

Results

Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings.

The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. »

URL : From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

DOI : 10.1371/journal.pone.0127612

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Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

Posted on by Hans Dillaerts

« Context

Biobanks are important resources which enable large-scale genomic research with human samples and data, raising significant ethical concerns about how participants’ information is managed and shared. Three previous studies of the Canadian public’s opinion about these topics have been conducted. Building on those results, an online survey representing the first study of public perceptions about biobanking spanning all Canadian provinces was conducted. Specifically, this study examined qualitative views about biobank objectives, governance structure, control and ownership of samples and data, benefit sharing, consent practices and data sharing norms, as well as additional questions and ethical concerns expressed by the public.

Results

Over half the respondents preferred to give a one-time general consent for the future sharing of their samples among researchers. Most expressed willingness for their data to be shared with the international scientific community rather than used by one or more Canadian institutions. Whereas more respondents indicated a preference for one-time general consent than any other model of consent, they constituted less than half of the total responses, revealing a lack of consensus among survey respondents regarding this question. Respondents identified biobank objectives, governance structure and accountability as the most important information to provide participants.

Respondents’ concerns about biobanking generally centred around the control and ownership of biological samples and data, especially with respect to potential misuse by insurers, the government and other third parties. Although almost half the respondents suggested that these should be managed by the researchers’ institutions, results indicate that the public is interested in being well-informed about these projects and suggest the importance of increased involvement from participants. In conclusion, the study discusses the viability of several proposed models for informed consent, including e-governance, independent trustees and the use of exclusion clauses, in the context of these new findings about the views of the Canadian public. »

URL : Fair Shares and Sharing Fairly: A Survey of Public Views on Open Science, Informed Consent and Participatory Research in Biobanking

DOI : 10.1371/journal.pone.0129893