Tag Archives: literature

Open Access Publishing… funding it

Five universities, Harvard, Cornell, Dartmouth, UC Berkeley and MIT, have compacted to support open-access publishing by funding publishing fees. Many open access journals, because the do not charge readers, use the model of charging for publication. This could be a barrier to publishing in an OA journal, so the compact:

…supports equity of the business models by committing each university to the timely establishment of durable mechanisms for underwriting reasonable publication fees for open-access journal articles written by its faculty for which other institutions would not be expected to provide funds.

Open access isn’t free, someone has to pay for it.. the provider, the user or some other model. I, personally, like the idea behind open access publishing of research. I believe it can be one model, among several, to make access to research free and available to help advance further research. Two years ago, the Consolidated Appropriations Act made it a requirement that NIH-funded research be published in such a manner that it was open after a certain period of time, a boon to open access publishing. Publishers of all stripes are attempting to develop ways to make research available to researchers, and pay for it.

I look forward to seeing how these universities underwrite those fees and which other universities join the compact.

Tip of the Week: PLAN2L for Arabidopsis literature

plan2L_jingFor this tip of the week we look at a text-mining tool for the Arabidopsis literature, Plan2L, or PLant ANnotation to Literature.  It has a very straightforward interface that permits searching of the paper space, and you can do that with a variety of focal points: the bibliome as a whole, or with emphasis on interactions, regulation, cell cycle, and more.  The results offer links to the PubMed abstracts, and tabular results of the statistics of the term occurance in that area of focus.  Green results indicate positive scores and likely relevance, red are likely to be non-relevant, a graphical guide to quickly finding the data of interest. Links to other resources including the BioCreative server, WikiGenes, iHOP and TAIR are provided as well.

The current emphasis for this resource is Arabidopsis, but it would be quite useful for other species too.  If you are interested in text mining Arabidopisis I would also encourage you to compare the results with the Textpresso installation at TAIR to see what you discover in a different text miner interface as well.

Plan2L site: http://zope.bioinfo.cnio.es/plan2l/plan2l.html

For their recent paper on Plan2L see: http://www.ncbi.nlm.nih.gov/pubmed/19520768 or the full article freely available in PubMedCentral:  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=19520768

iPhone and research

Ok, so I just got my new iPhone 3Gs. I couldn’t resist. Anyway, my contract on my first generation iPhone was up. So, it was time to reconfigure and explore the huge number of apps out there for the iPhone.

I use the iPhone for a lot of things, directions, finding out what stores are in the area, keeping my grocery list, listening to music, watching shows, browsing the web, keeping my calendar and contacts and a bunch more. Oh, and to make and receive phone calls :).

I’ve read past posts on other blogs about scientific apps for the iphone, I decided it was time to check out what apps there are now.

I’ve found a few I like, some that might work (I do computational genomics now, so I haven’t tried the ones for the bench), and one that has nothing to do with biology (directly anyway), but I am in love with. Follow me below the fold.

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Tip of the Week: It's a duplicate

dejavu_thumbThere are a lot of research papers out there, more than ever. Along with the good news (increasing knowledge), comes some bad news: increasing duplication and plagiarism, more often than not going undetected. The developers of eTBLAST, which is a great tool we’ve had a tip on before, have created another tool using an eTBLAST search of Medline and other databases to find highly similar citations: Deja Vu.

These similar citations could be legitimate; a review of a previous article, an author using similar wording of an abstract from a previous paper for new research (the eTBLAST search can only search titles and abstracts), sanctioned duplications, etc, etc. as the author of the post “Deja Boo” points out. There are some real instances of duplications (authors attempting to pad their CVs) and plagiarism (stealing words and research). An earlier example (before Deja Vu) found at Panda’s Thumb is of a creationist attempting to pad a CV and look more legitimate. Errami and Gardner (two of the developers of the tool) published a paper in Nature earlier this year with many such instances of (and another in Science, reported on here with some interesting discussion) duplication and plagiarism.

Still, the database needs to be viewed with caution. Of the 74,792 ‘highly similar and duplicate citations’ found, 92% have not be verified. Of the 8% left that have been verified (this has to be done by manual curation), 65% have been found to be probably legitimate (as stated above) and 35% to be duplicates. But even the duplicates aren’t necessarily nefarious. Since full texts are not available, it is often the case that the duplication might be perfectly understandable (reusing an abstract with some minor changes for new research, etc). Still, it is a tool that, with some work, can help tremendously in that search for true duplicates and plagiarism, and perhaps even just the threat of it might lower the instances?  :D

So, with that in mind, this week’s tip of the week is a quick view of “Deja Vu.”

Adventures in publishing

A new open access journal, Ideas in Ecology and Evolution, has, well, opened. It’s published at Queen’s College in Canada.

“So?” you ask, “there are lots of journals up starting all the time”.

This one is different. It’s experimenting with a lot of things (ok, so there seem to be a lot of journals experimenting with the model lately). The subject matter is not research per se, but ideas. Having been to my share of ecology and evolution conferences and discussion, I can see this journal has opened itself up to some quite lovely discussions.

As explained by Bob O’hara, there are some interesting review process experiments going on here too. Authors pay to get their ideas published, reviewers are paid, reviewers are not anonymous and they get to publish their views of the article as a companion piece. Bob discusses the issues we’ve all heard about the pros of anonymity (and they are valid ones), but this might work in this case. I also agree with Bob on one point, this structure (reviewers publishing their views) will indeed increase discussion, but I’d too like to see some mechanism for a broader discussion. As it is designed now, it will be like watching TV pundits arguing the finer points of health policy, which I guess is informative, but I’d like to see some mechanism that allows a broader discussion of the article. Something like PLoS has, which I think would actually work better in a journal of ideas like this.

Well, we’ll see. Right now there is nothing there but the editorial. I’ll be watching though.

hat tip: Coturnix

Tip of the Week: Subscribing to journal updates with NCBI

NCBI RSSTwo weeks ago, I showed you how to use HubMed, an alternative search interface to PubMed, to subscribe to a feed for a specific journal, allowing you to stay up-to-date on new articles and issues of that journal. As mentioned earlier, many journals have feeds to their updates, but using PubMed and HubMed are good alternatives if you can not find a feed, want to customize it a bit or just like a single place to go to for all your feeds. This week, I’m going to show you how to do the same thing, subscribe to a feed for a specific journal, using NCBI as suggested by a commenter in the Tip of the Week a couple weeks ago.

Tip of the Week: Subscribing to journal updates with HubMed

hubmed subscriptionsAs one of the tools (along with Connotea, Faculty1000, MyNCBI, HubMed, etc) to keep abreast of the fire hose of literature that is published, I also use RSS feeds to keep up-to-date on the latest publications from journals of interest. There are a lot of journals out there that publish a lot of data interesting to me, but subscribing to them all IRL of course is cost prohibitive (and environmentally unfriendly). Many will send updates by email of new issues, but the last thing I need is another email in my inbox screaming for my attention. Getting an RSS feed from a journal is a good way to keep up-to-date on new issues (if you haven’t used RSS feeds, read up on them here, find a reader here). Many journals include RSS feeds to new content, others don’t. Another way to get RSS feeds to a specific journal is to use HubMed in a nice feature that allows you to get an RSS news feed for a ‘search.’ I’ll show you how to do that here.

Defrosting the Digital Library

Defrosting the Digital LibraryThat’s the title of a recent paper in PLoS Computational Biology paper I read. This paper is a good read on two levels. It discusses the problems and difficulties (and solutions) with the rising number of digital libraries, published papers and research. Difficulties like identity (identifying papers in a persistent and standard way) and metadata (being able to pull out publication data from a paper in a standard and simple manner, if at all) and solutions like simple and persistent  URIs,  exposing metadata and identifying people and publications.

It was also a good read on another level, here, now and me. The authors discuss several digital libraries and their scope (the graphic here is a representation of some and their overlap) and tools to ‘defrost’ these libraries at a personal level. Many of these tools I use or know about (MyNCBI, CiteULike, Connotea and HubMed) and some I’m not particularly familar with (Zotero, Mendeley and Mekentosj Papers-Mac only! :), but the paper did give me a pretty decent understanding on some better ways for me to start to get a handle on the growing body of literature.

Now I should go do two things… reorganize and reinvigorate my references (back to Connotea! and try out Papers!) and to add the DOI link from CrossRef to this post, you know to standardize!

Tip of the Week: eTBlast

etBlasteTBlast is a great tool for searching the literature, not only PubMed, but also CRISP (a database of federally funded biomedical research). Unlike PubMed or CRISP, you don’t use a few well chosen (hopefully) keywords, you can just paste in an entire paragraph or abstract and eTBlast will search and find papers similar to the entire paragraph. It saves you the time and effort of trying to narrow your search down. Just wrote that amazing research up and need to find citations for it? or granting agencies, experts in the field or the best journal to submit it to? eTBlast can help you with that. Want to do some boning up on a new field? eTBlast can help you create that reading list. This 5 minute tip shows you quickly how to use eTBlast and obtain some relevant results.

The eTBlast server site at Virginia Tech also hosts the handy ARGH search tool, allowing searches for acronyms used in biomedical contexts.

Don't blink, PubMed adds a feature

It’s not ground breaking and you probably hadn’t noticed it yet, but it looks like something that could add some more, possibly useful, info to your PubMed searches. Last week, Pubmed announced on their technical bulletin that they’ve added a column to the right of the PubMed search summary which will contain results from other resources based on your search. Think of it as kind of an Amazon’s “you might also like” feature.

You might be forgiven for missing it because unless you are searching for one of the 200 drugs they’ve added this feature for (or read their technical bulletin), like “lovastatin,” you won’t see the column and links to the other resource. This other resource is the “Clinical Q&A” for the first implementation of this feature. It will be interesting to see how that develops and grows over time.