Bibliographies for the 21st century, why Zotero rules!

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

via PLoS Computational Biology: Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

zoteroInteresting look at how to manage scientific information. I use zotero these days. Zotero is a firefox addon that works within the browser, hence is platform independent. It is incredibly powerful, automatically imports meta data from a lot of journal sites, links to microsoft word and openoffice for “cite as you write” and bibliographic generation behaviour, stores pdfs, word docs, excel files, etc as attachments to your citations so if you have a little calculation routine you got from a paper, you can put that in an excel spreadsheet and always have it linked to the paper.

You can synchronize the database to the cloud. And, if you have access to a server with webdav, you can synchronize your attachments as well (i have not tried this yet).

Best of all, it is free and open source.

Anyway, the days of ridiculously expensive and arcane tools like endnote are over.

Similar Posts

  • Harvard votes on Open Access

    Faculty members are scheduled to vote on a measure that would permit Harvard to distribute their scholarship online, instead of signing exclusive agreements with scholarly journals that often have tiny readerships and high subscription costs.Although the outcome of Tuesday’s vote would apply only to Harvard’s arts and sciences faculty, the impact, given the university’s prestige, could be significant for the open-access movement, which seeks to make scientific and scholarly research available to as many people as possible at no cost.

    Harvard Proposal to Publish Scholarly Research Free on the Internet – New York Times

    This could be huge. Of course, expect ACS, Elsevier and others to complain, but their lobbyists can’t touch Harvard, with its giant endowment.

    Blogged with Flock

    Tags:

  • | |

    The LA Times and the American Chemistry Council

    Giving the American Chemistry Council a forum to sing paeans to its chemical du jour is kinda like giving Donald Trump an Op-Ed column on the harmlessness of gambling. The ACC is a trade association that gets all its funding from the chemical industry and is the reliable source on producing just about enough fudge to create “reasonable doubt” about chemicals. The ACC is notorious for its various astroturf websites including the Phthalate information center, the Plastic Resource, dioxin facts (seeing a pattern here?), and many other websites that propagate biased industry funded research, outright misinformation, and unrestrained cheerleading. They also spend vast amounts of money lobbying congress. Bora, and other Open Access advocates, note the similarities in the arguments used in the above websites to some recent attacks on Open Access, the imprint of Nicholas-Dezenhall is all over the ACC’s strategies!

  • One Strike for Open Access Journals

    Now, if only the US government, which funds the bulk of all research in this country, insists on open access for all research it funds! A man can dream!

    Chemical & Engineering News: Latest News – HHMI Will Require Free Access To Journal Articles

    Howard Hughes Medical Institute has announced a new policy regarding articles authored by biomedical researchers supported by the prestigious philanthropic organization. Beginning in January 2008, HHMI investigators will be required to publish only in those journals that make articles freely accessible in a public repository within six months of publication.

    HHMI supports more than 300 investigators, some of whom publish in American Chemical Society journals. Investigators who publish in an ACS journal can satisfy HHMI’s requirement by utilizing the society’s AuthorChoice option. For a $1,000—$3,000 fee, ACS provides free reader access to an article via the ACS website immediately upon online publication and deposits a copy of the article in the National Institutes of Health’s free PubMed Central repository.

    HHMI may be the first U.S. funding institution to impose a mandatory public-access policy on its investigators. In the U.K., the Wellcome Trust, which funds biomedical research, already has a mandatory public-access policy.

    Technorati Tags:

  • Harvard Open Access Update

    Yes they can, and they did! Harvard votes for Open Access!

    Harvard University’s arts and sciences faculty approved a plan on Tuesday that will post finished academic papers online free, unless scholars specifically decide to opt out of the open-access program. While other institutions have similar repositories for their faculty’s work, Harvard’s is unique for making online publication the default option.

    Harvard Opts In to ‘Opt Out’ Plan :: Inside Higher Ed :: Jobs, News and Views for All of Higher Education

    Blogged with Flock

    Tags:

  • | |

    Organic agriculture can feed the world

    That’s the conclusion reached by the authors of this study based on 293 examples in the developing and developed world.The authors also conclude that yields in the developing world are higher for organic agriculture than for conventional agriculture. Why? Well, since the paper is not open access, I can’t read it, or critique it, I’ll have to wait to get to the library before I can download it. But, maybe it’s because organic agriculture tends to be more labor intensive than conventional agriculture as practised by the developed world, and in the developing world, labor is cheap!

    Anyway, this is a good news study and should be examined a little more thoroughly.

    CJO – Abstract – Organic agriculture and the global food supply

    The principal objections to the proposition that organic agriculture can contribute significantly to the global food supply are low yields and insufficient quantities of organically acceptable fertilizers. We evaluated the universality of both claims. For the first claim, we compared yields of organic versus conventional or low-intensive food production for a global dataset of 293 examples and estimated the average yield ratio (organic:non-organic) of different food categories for the developed and the developing world. For most food categories, the average yield ratio was slightly 1.0 for studies in the developing world. With the average yield ratios, we modeled the global food supply that could be grown organically on the current agricultural land base. Model estimates indicate that organic methods could produce enough food on a global per capita basis to sustain the current human population, and potentially an even larger population, without increasing the agricultural land base. We also evaluated the amount of nitrogen potentially available from fixation by leguminous cover crops used as fertilizer. Data from temperate and tropical agroecosystems suggest that leguminous cover crops could fix enough nitrogen to replace the amount of synthetic fertilizer currently in use. These results indicate that organic agriculture has the potential to contribute quite substantially to the global food supply, while reducing the detrimental environmental impacts of conventional agriculture. Evaluation and review of this paper have raised important issues about crop rotations under organic versus conventional agriculture and the reliability of grey-literature sources. An ongoing dialogue on these subjects can be found in the Forum editorial of this issue.

  • |

    India's Environmental Portal

    Home | India Environment Portal

    This is a very useful undertaking by the Centre for Science and Environment (CSE) to gather up a lot of technical information about India’s environmental research and activism.

    They have a small multimedia section as well and I found this movie, appropriately titled Faecal Attraction to be an informative watch…

    [youtube=’http://in.youtube.com/watch?v=bUlkOLLa31s’]