Tag Archives: citations

There’s a database for everything, even uber-operons

I was playing around with Google Scholar’s new citation feature that allowed me to collect my papers in one place easily (worked pretty well, btw, save a few glitches, see below) when I noticed it missed a paper of mine from 2000: “Gene context conservation of a higher order than operons.” The abstract:

Operons, co-transcribed and co-regulated contiguous sets of genes, are poorly conserved over short periods of evolutionary time. The gene order, gene content and regulatory mechanisms of operons can be very different, even in closely related species. Here, we present several lines of evidence which suggest that, although an operon and its individual genes and regulatory structures are rearranged when comparing the genomes of different species, this rearrangement is a conservative process. Genomic rearrangements invariably maintain individual genes in very specific functional and regulatory contexts. We call this conserved context an uber-operon.

The uber-operon. It was my PI’s suggested term. Living and working in Germany at the time, I thought it was kind of funny. Anyway, I never really expanded more than another paper or so on that research and kind of lost track whether that paper resulted in much. I typed in ‘uber-operon’ in google today and found that it’s been cited a few times (88) and, I found this interesting: there have been a few databases built of “uber-operons.”

A Chinese research group created the Uber-Operon Database. The paper looks interesting, but unfortunately the server is down (whether this is temporary or permanent, I do not know), the ODB (Operon Database) uses uber-operons (which they call reference operons) to predict operons in the database , Nebulon is another, HUGO is another. Read the chapter on computational methods for predicting uber-operons :)

Just goes to show you, there’s a database for everything.

Oh, and back to Google Scholar citation. It did find nearly every paper I’ve published, though it missed two (including the one above) and had two false positives. Additionally, many citations are missing (like the 88 for this paper, and many others from other papers). That’s not to say it’s not useful, I find it a nice tool but it’s not perfect. You can find out more about google scholar citation here, and about Microsoft’s similar feature here.

Oh, and does this post put me in the HumbleBrag Hall of Fame? If that’s reserved for twitter, than maybe I should twitter this so I can get there :). (though I’m not sure pointing out relatively small databases based a relatively minor paper constitutes bragging, humbly or not LOL).

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.”

PubMed citation sensor

citation sensorPubMed has added a few features to it’s search capabilities including a new Automatic Term Mapping and Citation Sensor, both help make the search a bit more powerful and simple.

I’m liking the citation sensor. If you enter a last name and year, the search will sense that it is a citation and give you the citations that match. So, if you search “lathe 2001” you’ll find 8 citations by someone with the last name of Lathe in the year 2001, 3 of them mine ;). These are listed with a yellow backround at the top of the search results. Of course you could just also type in “lathe[Author] AND 2001[Publication Date]” and get the same 8 citations, but why type in the added 27 characters when you could just type 9. Makes searching a bit nicer.

Research Blogging and CrossRef

At the Science Blogging Conference we were introduced to researchblogging.org. I made mention of this earlier and have we have been using it since. It’s a great service and I’ve been reading many of the blog posts. One of the other things they announced at that same session (and in a previous newsletter) was a WordPress plugin from CrossRef. This would allow you to look up (by title, author) a reference and get the DOI citation to put into your blog post. It was supposed to come out that week, but I hadn’t seen it (and asked, they said “soon”). Well, I found it today ;) (update at end)

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