Saturday, April 25, 2015

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OATP primary

Open Access Policy [Draft] | Smith College Libraries

Posted: 25 Apr 2015 01:48 AM PDT

"The Faculty of Smith College is committed to disseminating the fruits of its research and scholarship as widely as possible. This Open Access Policy establishes the terms under which Faculty members permit distribution of their scholarly articles via open access channels. This policy relies on Creative Commons licenses, which are simple methods that permit an author to grant specific copyright permissions without transferring copyright ownership ..."

What are we going to call PLOS ONE-style peer-review? | Sauropod Vertebra Picture of the Week

Posted: 25 Apr 2015 01:45 AM PDT

"When a paper goes for peer-review at PLOS ONE, the reviewers are told not to make any judgement about how important or sexy or 'impacty' the paper is — to judge it only on methodical soundness. All papers that are judged sound are to be published without making guesses about which will and won't improve the journal's reputation through being influential down the line. (Such guesses are hopelessly inaccurate anyway.) When PLOS ONE was new, this approach drew scorn from established publishers, but now those publishers all have their own journals that use similar editorial criteria (Nature's Scientific Reports, AAAS's Science Advances, Elsevier's first attempt, Elsevier's second attempt, the Royal Society's Royal Society Open Science). Those editorial criteria have proved their worth. But what are we going to call this style of peer-review? It's not a new problem. I discussed it with with David Crotty three years ago without reaching any very satisfactory conclusion. But three years have not really helped us much as we try to agree on a term for this increasingly important and prevalent model. What are the options on the table? PLOS ONE-style peer-review. It's a cumbersome term, and it privileges PLOS ONE when that is now far from the only journal to use this approach to peer-review (and may not even have been first). Peer-review Lite. A snide term coined by people who wanted PLOS ONE to fail. It's not a good description, and it carries baggage. Scientific peer-review. This one came up in the discussion with David Crotty, but it's not really acceptable because it would leave us still needing a term for what the Open Library of Humanities does. Objective peer-review. This is the term that was used at the Royal Society meeting at the start of this week — the idea being that you review objectively for the quality of the research, but don't make a subjective judgement of its importance. Several people didn't like this on the grounds that even the 'objective' half is inevitably subjective. Any others that I missed? ..."

HowOpenIsIt? | PLOS

Posted: 25 Apr 2015 01:41 AM PDT

"The 'HowOpenIsIt?®' Open Access Spectrum (OAS) guide standardizes Open Access terminology in an easily understandable, comprehensive resource created by PLOS, the Scholarly Publishing and Academic Resources Coalition (SPARC) and the Open Access Scholarly Publishers Association (OASPA). The guide defines core components of Open Access derived from the articulation of basic tenets in the 2002 Budapest Open Access Initiative (BOAI) ..."

Why Mike is interested in Royal Society Open Science, and why Matt isn’t | Sauropod Vertebra Picture of the Week

Posted: 25 Apr 2015 01:36 AM PDT

Use the link to access the discussion thread.

First Paper with ‘Living Figure’ Published

Posted: 25 Apr 2015 01:32 AM PDT

"F1000Research, an open access scientific journal for life sciences, has debuted what it calls its first 'living article.'  Other scientists can contribute their own data to the published scientific paper, and the figure updates live online.   Authors of the first paper to have this option, Julien Colomb from Freie Universität and Björn Brembs from Universität Regensburg, two German behavioral neuroscientists, developed software in collaboration with F1000Research that allows figures in the paper to be auto-updated as new data in submitted by other scientists. Their paper finds that a commonly used strain of fruit flies sourced from different laboratories, which are meant to be nearly identical, actually show distinct differences in walking behaviors. One researcher, Gregg Roman from the University of Houston, Texas, has inserted his own data onto, Figure 4 of the paper – the so-called 'living figure'- and additional groups have agreed to add to it as well, the company said in a statement.  F1000Research launched in January 2013 and publishes scientific research immediately, and then invites peer review, avoiding the long delays associated with the traditional anonymous pre-publication peer-review process ..."

Successfully using research data management principles (I hope!) | Foster

Posted: 25 Apr 2015 01:28 AM PDT

"This presentation was delivered at 'Open research in Horizon 2020 - how to increase your chances of success' on Tuesday 14th April, 2015 in University College Cork , Ireland as part of a 2 day training event titled 'Open Access and Research Data Management: Horizon 2020 and Beyond' ..."

Varieties of Open Access | Leddy Library | University of Windsor

Posted: 25 Apr 2015 01:23 AM PDT

"There are a variety of ways in which authors can make their research available open access. As authors you are not simply restricted to trying to use a small set of journals that may not suit your research. This video discusses the variety of options for making research available OA. More more detail information please visit leddy.uwindsor.ca/open-access ..."

Why addressing brain health priorities requires open science (8-minute video) | SharpBrains

Posted: 25 Apr 2015 01:19 AM PDT

"Descrip­tion of talk (8 min­utes): Why open sci­ence? The rea­sons are many, but here are a few: our ser­vice mem­bers return­ing from 14 years of war, the rise in aware­ness of sports related brain injuries and new research that shows the inter­re­lat­ed­ness of neu­ro­log­i­cal ill­nesses. One Mind believes there are three key dri­vers to build­ing a strong foun­da­tion for brain dis­eases research – col­lab­o­ra­tion, big sci­ence, and data shar­ing focused on help­ing the patient, not the researcher. Gen­eral Peter Chiarelli, USA (Ret.) was appointed the Chief Exec­u­tive Offi­cer of ONE MIND in 2012. He is a retired Gen­eral with almost 40 years of experience."

The new science journalism and open science | R-bloggers

Posted: 25 Apr 2015 01:15 AM PDT

"The New York Times is quietly changing the practice of science journalism. The Tuesday April 21, 2015 article: Ebola Lying in Wait, reports on 'A growing body of scientific clues - some ambiguous, other substantive' that the Ebola virus may have lain dormant in West African rain forest for years before igniting last year's outbreak. In the 6th paragraph of the on-line edition mention is made of 'a detailed prediction of other likely Ebola dangers zones" made by a team of scientists. The words "detailed prediction' are innocuously provided with the hyper-link above. What I think is extraordinary is that this link points to the scientific paper: Mapping the zoonotic niche of Ebola virus disease in Africa by David M Piggot et al. published on the open science publishing platform eLife. This is the real science including the measured language of a scientific paper, the lengthly descriptions of the data sets, the innumerable references and even the reviewers comments and the authors' responses. I don't think that there is a better way to cultivate a scientific outlook than to make relevant, science open and accessible.  The following figure from the paper, illustrates one of the low level tools of open science: the digital object identifier (DOI). A DOI is a character string that uniquely identifies a document, or other digital object, that is meant to persist for the lifetime of the document.  The paper by Piggot et al. is replete with DOIs pointing to subsections of the document, figures and other documents.  The next step for data science along these lines is to use DOIs and other tools to make it easy to search eLife, Plos, Crossref, Entrez and other open science platforms. Towards this goal, the team at rOpenSci is well on their way. With limited resources, they have developed an impressive array of R packages for accessing public data as well as for searching the scientific literature. The code below shows some of my own early efforts to use rOpenSci functions to search the literature. rplos is a mature package available on CRAN. The fulltextpackage is under development. When finished, it will offer functions for working with multiple open science publishers. To go further have a look at the rOpenSci tutorials. However, interest in text mining aside, I think we should be grateful for the efforts of the PLOS, eLife and the other open science publishers, rOpenSci and the New York Times ..."

Is Figshare Open? "it is not just about open or closed, it is about control" | petermr's blog

Posted: 25 Apr 2015 01:09 AM PDT

"I have been meaning to write on this theme for some time, and more generally on the increasing influence of DigitalScience's growing influence in parts of the academic infrastructure. This post is sparked by a twitter exchange (follow backwards from https://twitter.com/petermurrayrust/status/591197043579813888 ) in the last few hours, which addresses the question of whether 'Figshare is Open'. This is not an easy question and I will try to be objective. First let me say - as I have said in public - that I have huge respect and admiration for how Mark Hahnel created Figshare while a PhD student. It's a great idea and I am delighted - in the abstract - that it gained some much traction so rapidly. Mark and I have discussed issues of Figshare on more than one occasion and he's done me the honour of creating a 'Peter Murray-Rust' slide (http://www.slideshare.net/repofringe/figshare-repository-fringe-2013 ) where he addresses some (but not all) of my concerns about Figshare after its 'acquisition' by Macmillan Digital Science (I use this term, although there are rumours of a demerger or merger). I use 'acquisition' because I have no knowledge of the formal position of Figshare as a legal entity (I assume it *is* one? Figshare FAQs ) and that's one of the questions to be addressed here ..."

Access to knowledge movement - Bee Hive

Posted: 25 Apr 2015 01:02 AM PDT

" ... The Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities from 2003 is a major declaration reflecting the goals of the movement in relation to academic publishing. In October 2004, the Geneva declaration on the future of the World Intellectual Property Organization emerged from a call from Brazil and Argentina for a development agenda for the World Intellectual Property Organization, and was supported by hundreds organizations. Supporters included the Free Software Foundation, with a statement Towards a 'World Intellectual Wealth Organisation': Supporting the Geneva Declaration. One of the proposals of the declaration was to a «call for a Treaty on Access to Knowledge and Technology. The Standing Committee on Patents and the Standing Committee on Copyright and Related Rights should solicit views from member countries and the public on elements of such a treaty». A shared discussion platform on A2K issues is the mailing list of that name, which was initiated around discussion of the Geneva declaration. A draft 'A2K treaty'  was later produced. The proposed treaty is intended to ease the transfer of knowledge to developing nations, and to secure the viability of open innovation systems all over the world ..."

Open Access Bills Stage A Return Engagement | Pasco Phronesis

Posted: 25 Apr 2015 12:58 AM PDT

"For the fifth consecutive Congress bills have been introduced to extend open access to government-funded research results.  In the last month three bills have been introduced, resembling bills introduced in previous years. For the 114th Congress there are House and Senate versions of the Fair Access to Science and Technology Research Act (FASTR).  Essentially the same bills were introduced in the 113th Congress with the same sponsors and the same terms.  Previous editions of these two bills were under a different name – the Federal Research Public Access Act.  The bills are assigned to the House Oversight and Government Reform Committee and the Senate Homeland Security and Government Affairs Committee, respectively.  The bills would require open access to federally funded research articles within six months of publication. Another open access bill in this Congress is the latest edition of the Public Access to Public Science Act.  It too was introduced in the previous Congress, and has the same sponsors this time around.  Compared to the FASTR bills, this act covers a smaller set of agencies (those under the jurisdiction of the House Science, Space and Technology Committee), and hews closer to the requirements of the February 2013 Policy Memo from the Office of Science and Technology on open access.  Like the FASTR bills, this legislation requires open access for covered articles within six months of publication. With nearly 10 years of legislative efforts to expand open access, I'm not optimistic that these bills will be much more successful than their predecessors.  A major difference in this Congress is that agency public access policies are in the process of final review and/or implementation.  (The difference in embargo periods between these bills and agency access policies is not likely a bill-killer, at least by itself.)  That might help get these bills out of committee, but I think it will take stronger effort by their legislative champions to get them to the President's desk. Then there's the matter of open access to research data, which is not covered by these bills.  Baby steps, I suppose."

Welcome to Unlocking Thesis Data | Unlocking Thesis Data

Posted: 25 Apr 2015 12:53 AM PDT

"Unlocking Thesis Data (UTD) is the short name for a project with a long title and a big ambition. 'Unlocking the UK's thesis data through persistent identifiers' will explore how the application of persistent identifiers, software and metadata enhancements, and guidance to institutions would kick-start a more widespread sharing of data generated in doctoral-level research in the UK. Here's our project summary: 'Unlocking Thesis Data (UTD) is a community-driven project to promote the use of persistent identifiers for theses, their underlying data and their authors. By their very nature, PhD theses break new ground and advance scholarly knowledge. Most make use of newly-created data but these data can be trapped in an appendix or DVD – either unavailable or not suited for reuse. UTD will make data more discoverable and citeable, thereby offering incentives to students to share their data in more appropriate formats, in the context of a sustainable national thesis framework. Funded by Jisc, UTD is led by the Universities of East London and Southampton and EThOS (the UK's national thesis service at the British Library). Phase one will explore current thesis practice through an online survey to EThOS member institutions, and individual case studies looking at the issues in more detail – including how institutions might apply DOI and ORCID identifiers. The survey and case study findings will be combined into a report with recommendations for further phases of the project. These are expected to enhance metadata and software for applying DOI and ORCID identifiers, to test them in live settings, and to offer comprehensive advice for institutions to adopt them. By summer 2016 we expect to have a sustainable infrastructure covering the whole UK, driving the wider availability of research data and introducing doctoral students to new norms of scholarly communication.'  The first phase of the project runs from late April to mid July 2015, and has three components ..."

Science Committee Gets In On Open Access Legislative Dance | Pasco Phronesis

Posted: 25 Apr 2015 12:49 AM PDT

"Last Thursday Representatives James Sensenbrenner (Wisconsin) and Eddie Berniece Johnson (Texas) introduced the Public Access to Public Science Act, H.R. 3157.  They are both members of the House Science, Space and Technology Committee and the bill was referred to that committee for review.  Like every other public access bill I've followed for the last several years, I expect to go nowhere. The bill is mostly an update of the legislation introduced earlier in the year in both the House and Senate.  But the major difference is that the bill attempts to put in place much of the guidance in the Policy Memo released by the Office of Science and Technology Policy (OSTP) in February.  Unlike the Policy Memo, but like the CHORUS plan advanced by scholarly publishers, H.R. 3157 focuses primarily on research publications.  While there are references to metadata and supplementary information, the bill reads to me as focused on research articles rather than research data. Another important distinction in this new bill is that it's narrower in scope compared to other legislation.  The standard has been to require public access policies from any agency with at least $100 million in annual research and development spending.  The new bill covers only the National Science Foundation, the National Institute of Science and Technology, the National Weather Service and NASA.  I suspect this is an effort to make sure that only the science committees in each house of Congress approve the bill prior to passage.  Given the track record of public access legislation and the current legislative calendar, it feels to me like an empty gesture ..."

Study of Open Access Publishing in Social Sciences and its Implications for Libraries | Rath | DESIDOC Journal of Library & Information Technology

Posted: 25 Apr 2015 12:46 AM PDT

Use the link to access the full text article.  "Abstract  ... The Open Access Movement (OAM), which started as a gradual realisation by authors mainly in biomedical sciences to make available results of public-funded research projects to the public without much barrier pertaining to cost, permission, copyright obligations, etc., gradually gained momentum across the world and India was no exception to it. Though the movement was confined mainly to science, technology and medical fields in India, since last few years, a number of open access repositories and open access journals in Social Science subjects have started appearing. The present study which is confined to the open access Social Science journals published from India as mentioned in the Directory of Open Access Journals, identified 60 open access Social Sciences journals in India. The study also analysed the journals on the basis of certain parameters as to trend of open access journals in Social Sciences, and was found that most of open access journals in Social Sciences appeared between 2009 and 2014 and about half of the journals charge authors for publishing their papers in the journals and only a few are published under Creative Commons Attribution. Lastly, the paper discusses about implications of open access publishing on Social Science research libraries made few suggestions towards encouraging open access publishing in Social Science subjects in India."

Bibliometrics: The Leiden Manifesto for research metrics : Nature News & Comment

Posted: 25 Apr 2015 12:41 AM PDT

" ... In 2005, Jorge Hirsch, a physicist at the University of California, San Diego, proposed the h-index, popularizing citation counting for individual researchers. Interest in the journal impact factor grew steadily after 1995 (see 'Impact-factor obsession'). Lately, metrics related to social usage and online comment have gained momentum — F1000Prime was established in 2002, Mendeley in 2008, and Altmetric.com (supported by Macmillan Science and Education, which owns Nature Publishing Group) in 2011. As scientometricians, social scientists and research administrators, we have watched with increasing alarm the pervasive misapplication of indicators to the evaluation of scientific performance. The following are just a few of numerous examples. Across the world, universities have become obsessed with their position in global rankings (such as the Shanghai Ranking and Times Higher Education's list), even when such lists are based on what are, in our view, inaccurate data and arbitrary indicators. Some recruiters request h-index values for candidates. Several universities base promotion decisions on threshold h-index values and on the number of articles in 'high-impact' journals. Researchers' CVs have become opportunities to boast about these scores, notably in biomedicine. Everywhere, supervisors ask PhD students to publish in high-impact journals and acquire external funding before they are ready. In Scandinavia and China, some universities allocate research funding or bonuses on the basis of a number: for example, by calculating individual impact scores to allocate 'performance resources' or by giving researchers a bonus for a publication in a journal with an impact factor higher than 15 (ref. 2). In many cases, researchers and evaluators still exert balanced judgement. Yet the abuse of research metrics has become too widespread to ignore. We therefore present the Leiden Manifesto, named after the conference at which it crystallized (see http://sti2014.cwts.nl). Its ten principles are not news to scientometricians, although none of us would be able to recite them in their entirety because codification has been lacking until now. Luminaries in the field, such as Eugene Garfield (founder of the ISI), are on record stating some of these principles3, 4. But they are not in the room when evaluators report back to university administrators who are not expert in the relevant methodology. Scientists searching for literature with which to contest an evaluation find the material scattered in what are, to them, obscure journals to which they lack access. We offer this distillation of best practice in metrics-based research assessment so that researchers can hold evaluators to account, and evaluators can hold their indicators to account ..."

Dataverse: an open source solution for data sharing | Savage Minds

Posted: 25 Apr 2015 12:36 AM PDT

"When you think of scholarship you might think first of publications, articles and books, but that is just the final product. Yes it is polished through countless hours of research, writing, and responding to reviewers, however all that work is built on an even more time consuming foundation of collecting raw materials. In cultural anthropology this includes field notes, journals, marked up literature, audio recordings, transcripts, and maybe photographs and video. I think I even have a few 3-D objects squirreled away in banker's boxes. Although we seldom refer to it as such all of this is 'data,' it is information awaiting interpretation. We take great pride in our finished products. Peer reviewed publications are still the coin of the realm. Our attitudes towards data in cultural anthropology are less clear. Are our data worth saving? What have you done with your data? How would you feel about sharing your data with others? ... In cultural anthropology, a discipline where so much of the self is invested and sacrificed in the work of collecting data I intuit that many of my colleagues would be very reluctant to share their raw materials. They are private for many reasons. Perhaps we see them as full of mistakes and prejudices. Perhaps they include confidential information. Perhaps they are embarrassing as that unfinished novel in your top desk drawer. We don't write fieldnotes for an audience! ... Dataverse is an open source, online repository for data. It's free to use and very user friendly, signing up is about as complicated as Gmail. Dataverse is for creators. It allows authors to control which data audiences are allowed to view, it preserves data files into the future, and generates citations for datasets. Dataverse is for readers too. It documents changes in data over time, allows audiences to check to see the data behind the claims, and allows an author to publicly distribute data without readers having to check for permission. Plus there's a nice GUI to simplify interaction with the digital archive. EXAMPLE 1: Using Dataverse at the end of a study ... EXAMPLE 2: Using Dataverse from the beginning of a study ..."

Over 300 Dissertations Available in IUScholarWorks | Indiana University Libraries

Posted: 25 Apr 2015 12:25 AM PDT

"Over 300 IUB graduate students have made their dissertations freely available in IUScholarWorks, IU's open access institutional repository. The dissertations collection is viewable online at http://go.iu.edu/wjU. Through recent collaborations with the University Graduate School, graduate students can now submit their dissertations to IUScholarWorks as a step in the ProQuest submission process. More information is available at https://scholarworks.iu.edu/dissertations.shtml. IUScholarWorks (http://scholarworks.iu.edu/dspace) is a digital repository that makes the work of IU scholars freely available, while insuring that these resources are preserved and organized for the future. Questions about this service should be directed to iusw@indiana.edu."
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