tag:blogger.com,1999:blog-3467242881996852098.post1020638249215586219..comments2024-01-08T08:39:39.026-08:00Comments on The Open Source Paleontologist: Citation Format WarsAndyhttp://www.blogger.com/profile/16171447306687358664noreply@blogger.comBlogger19125tag:blogger.com,1999:blog-3467242881996852098.post-374143059827519212012-01-06T04:14:05.361-08:002012-01-06T04:14:05.361-08:00I personally like the footnote variant with supers...I personally like the footnote variant with superscript numbers. The full reference is put on the bottom of the same page.<br /><br />It does not clutter the text.<br />The reader does not have to flip back and forth.<br />It is easy to add small comments to the citation such as "cp".<br />The bibliography at the end is sorted alphabetically.<br /><br />It was once quite common in Europe. Now most Universities prefer numbered endnotes. Anyone knows why it came out of fashion?Arminhttps://www.blogger.com/profile/04981136965070438208noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-48423937267953482092011-02-07T19:11:42.915-08:002011-02-07T19:11:42.915-08:00As Mike T. Keesey said, no problem for digital med...As Mike T. Keesey said, no problem for digital media, but for printed media, is there any real obstacles to reaching a creative, compromise solution?<br /><br />How about restructuring the page layout so that it allows the use of numbered in-line citations AND the number-referenced corresponding author-year citation on the margin, in close proximity, or in a special box or something?<br />Best of both worlds?Paleontology Studentnoreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-37467828491183436942011-01-13T08:00:58.195-08:002011-01-13T08:00:58.195-08:00Most color-blind individuals have a red-green defi...Most color-blind individuals have a red-green deficit, so this can (usually) be overcome by careful choice of color schemes (having a color-blind prof in grad school made me much more aware of this fact!). And, there are some types of graphics - for instance, photographs of anatomical dissections or outcrops - that really benefit from color but cannot be adjusted by a simple change in fill. However, in an age where many people still print out their stuff in grayscale (or journals only allow this), it's critical to make sure that the figures are at least passable in both formats.Andyhttps://www.blogger.com/profile/16171447306687358664noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-70669298902685465062011-01-12T13:00:07.223-08:002011-01-12T13:00:07.223-08:00@ Mike: I'll take you up on that one ;)
@ And...@ Mike: I'll take you up on that one ;)<br /><br />@ Andy: and I'll add a gripe with that mark-up stuff right here and now (wikipedia solved this better, albeit only slightly): you click the link, it takes you to the ref, you're happy. Now you click------ uhm, what DO I click to go back????<br /><br />on wiki, you can hover the mouse over the link and see which instance of this particular ref you're on (i.e., is it being used the first, second, fivehundredth time), click it and be taken to the ref list, then click the corresponding number to be taken back. OK, you must remember to check before you click, otherwise you're lost, but at least you CAN. In PDFs and on web pages it is not that easy. You may be able to use the back button, but sometimes that is not possible, it takes you back the correct page but not the correct paragraph.Heinrich Mallisonhttps://www.blogger.com/profile/14195098490352297671noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-15509717853923713552011-01-12T10:53:14.058-08:002011-01-12T10:53:14.058-08:00"The (current) lack of color can be a hindran..."The (current) lack of color can be a hindrance for some papers"<br /><br />It shouldn't be. Papers should not rely on being in color, for the simple reason that some people are colorblind.<br /><br />"So, geeks: shut up or money up!"<br /><br />Looks like a decent project when I have some spare time. Would make a good JavaScript library....Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-52624291669099152722011-01-12T10:26:36.516-08:002011-01-12T10:26:36.516-08:00@Randy - I completely agree with all of your point...@Randy - I completely agree with all of your points about PDFs on the Kindle. The (current) lack of color can be a hindrance for some papers (yes, I know that the iPad has color, but its screen is not nearly as comfortable to read from for long periods; and, I don't own a pair of hipster glasses).<br /><br />On a related note, someone at another forum pointed out that Nature has already implemented hover-over citations. Their appearance is a little clunky (it would be great to have a hanging indent, and full journal titles), but it's a great start. Science has a similar feature, and similarly clunky (and occasionally buggy, when I tried it; sometimes the reference didn't pop up).Andyhttps://www.blogger.com/profile/16171447306687358664noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-70873120965346849982011-01-12T10:13:05.501-08:002011-01-12T10:13:05.501-08:00@Andy: One of my colleagues recently showed me PDF...@Andy: One of my colleagues recently showed me PDFs of paleo papers she had uploaded on the Kindle. I was quite impressed with the readability and image quality. The only drawback was that the zoom feature seemed a bit clunky. Otherwise ereaders/iPads may be the wave of the future!<br /><br />@Heinrich: I completely agree!220myahttps://www.blogger.com/profile/06403919493457640549noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-75172893652049031482011-01-12T06:20:19.884-08:002011-01-12T06:20:19.884-08:00@Heinrich - it would be completely awesome if jour...@Heinrich - it would be completely awesome if journal websites instituted customizable presentations of their papers. Most major journals these days (including PE, I see!) are already marking up their published manuscripts appropriately, so it <i>should</i> be rather trivial (on some levels). At the same time, though, it would probably require a rewrite of the web publishing software that won't happen for awhile.<br /><br />I got an eReader (Kindle) for Christmas, and have been reading quite a bit of both scientific and non-scientific work on there. It's making me realize that academic publishing has a long, long way to go in order to catch up to the evolving reading technologies.Andyhttps://www.blogger.com/profile/16171447306687358664noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-70454534148072377842011-01-12T04:27:05.913-08:002011-01-12T04:27:05.913-08:00I must say I strongly dislike numbered citations f...I must say I strongly dislike numbered citations for the simple reason of having to flip to the refs again and again and again each time the <b>same</b> paper crops up again, within the same article. Or do you learn the numbers by heart afresh for each paper you read?<br /><br />DOH!<br /><br />however, slowly entering the shiny digital future, I know a wonderful way of combining the advantages of both methods, and avoiding the disadvantages:<br /><br />I have seen journals that use numbers in their text, and online have a side bar giving the full citation in the same line. Others use pop-ups: hover the mouse over the number and you get the full citation.<br /><br />So far, so good, but what do we do about print-outs and PDFs?<br />Well, the way I hear computers people talk it should be a piece of cake for them to program websites and databases to give me all options: <br />1) author-year, reflist alphabetically sorted at the end<br />2) author-year, refs of each page as footnote<br />3) author-year, refs on margin<br />4) numbers, refs on margin<br />5) numbers, refs number-sorted at end<br />6) numbers, refs as footnote<br />7) any combination of the above.<br /><br />So, geeks: shut up or money up!Heinrich Mallisonhttps://www.blogger.com/profile/14195098490352297671noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-89346849895417622002011-01-11T07:09:09.113-08:002011-01-11T07:09:09.113-08:00Excellent discussion here, and many of you bring u...Excellent discussion here, and many of you bring up some issues I hadn't thought of. Jeff, you're absolutely right that an alphabetized bibliography is essential for usability (no matter what one's level of familiarity with the topic). One alternative, I suppose, would be to combine alphabetized and numbered. The minor problem with this (I'm thinking out loud here) is that when folks cite a series of 4 papers in an intro, you get [3,12,19,43], rather than [1-4].<br /><br />Mike brings up an interesting point about the advancing wave of digital formatting, but I think one way or another we're still going to be tied to a paper-influenced format for a long time. Of course, it's so easy to switch citation formats (particularly if documents are marked-up properly) that it will probably be a non-issue. I love the image of roll-over citations, and think the effective implementation of this is essential for scholarly publishing in a digital format.<br /><br />@Randy, I mainly mentioned my spouse as a counter-example to Mike's claim that All Science used author-year. You're completely right that this format is common in biosciences. . .so maybe it's more of an issue for PLoS ONE than we thought? I guess to some extent the journal is "hampered" by a presumed common publishing platform and format between all of the PLoS-labeled journals (although again the argument would be why we can't have author-year for all of them, and just be done with it - maybe it does come down to GlamourMag syndrome?).<br /><br />As a follow-up to Randy's comment on citation management, sharing documents between authors without such software is a major headache.<br /><br />Anonymous's comment on numbered citations for grants is pure gold.<br /><br />Anyhow, good stuff all around. There was also <a href="http://svpow.wordpress.com/2011/01/07/an-open-letter-to-plos-one-a-pox-on-your-numbered-references/#comment-9462" rel="nofollow">some interesting discussion</a> at SV-POW! about how to reference a specific "page number" in digital documents (esp. when quoting text or referring to a particular section). Definitely worth checking out.Andyhttps://www.blogger.com/profile/16171447306687358664noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-88843781078240693462011-01-10T17:38:01.822-08:002011-01-10T17:38:01.822-08:00Andrea--Zotero is probably the easiest open source...Andrea--Zotero is probably the easiest open source ref manager (and it has been featured here before). BibTEX is also great, if you're a LaTeX user.<br /><br />I think I agree with the previous sentiments that it simply isn't that large of a deal. If you read digitally, it will probably soon turn into hyperlinks. If you read a print out, just keep the references unstapled. It only matters if you are looking at the print journal, and that makes it inapplicable to PLoS.Jonhttps://www.blogger.com/profile/13728872012920505418noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-51894531080350688432011-01-09T19:25:15.145-08:002011-01-09T19:25:15.145-08:00How about a compromise? First time a reference is...How about a compromise? First time a reference is cited in a paper it needs to be done in full text with the year and following this in brackets the citation number. Then for the rest of the paper only the citation number can be used to say space and clutter. <br /><br />This is analogous in some ways to the oldtime usage of "ibid" or the full write out in the first usage of all author names instead of "et al" in citations with three authors, which is used by some journals.Bill Parkerhttps://www.blogger.com/profile/05941940882532354219noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-81341900000764898592011-01-09T18:12:02.802-08:002011-01-09T18:12:02.802-08:00On Andrea's point, most word processing softwa...On Andrea's point, most word processing software automates numbered references. Since this is an open-source-themed blog, I'll mention <a href="http://openoffice.org/" rel="nofollow">OpenOffice</a>'s Write, wherein adding a numbered reference is as simple as <b>Insert > Footnote</b>.<br /><br />There is absolutely no reason these days for anyone to put themselves through the hell of manually creating numbered references.<br /><br />(I do use Harvard-style on my blog, where there is no automated footnote system.)Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-32142618666408607792011-01-09T15:50:46.880-08:002011-01-09T15:50:46.880-08:00I still prefer to have a hard-copy of a paper in h...I still prefer to have a hard-copy of a paper in hand to read or edit more than reading off a screen, but that is an issue of page cost at my end, not the jounral's. This is probably going to continue to be the case for years to come, until things like iPads and Nooks get sophiticated enough that I can carry around a single clipboard sized (and weight) screen which can hold my entire library and has a stylus that I can scribble notes with. Still, I'm willing to lose a few more cents printing out 13% more pages for the reading convenience.<br /><br />The point about numbered citations in grant-writing is an excellent point though. I wish I had thought of that a few months ago...Jeffrey W. Martz, PhDhttps://www.blogger.com/profile/08923720923588241488noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-3379496388486320222011-01-09T13:53:45.334-08:002011-01-09T13:53:45.334-08:00While the space saving argument doesn't hold m...While the space saving argument doesn't hold much weight with largely electronic media, numbered citations do significantly cut down on length. I prefer to use the author, year style while writing but found on a recent grant proposal that by switching to a numbered format I bought myself a whole extra page to write about the project. Using the author, year style approximately 13% of the text would have been in-text citations. <br /><br />For those who lament the demise of print media the cost savings associated with printing should be considered. That would also translate into thinner volumes saving space on library and office shelves. I'd love it if I could free-up 13% of my bookshelves and filing cabinets. That might help me get away from the "stratigraphic filing system" that seems to have taken over any horizontal surface in my office.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-16045262794414847752011-01-09T13:08:43.140-08:002011-01-09T13:08:43.140-08:00Regarding the pros/cons of point #1, I completely ...Regarding the pros/cons of point #1, I completely agree with Jeff. If I'm not familiar with a particular citation (e.g., Doofus, 2011), I'll surely flip to the back to see what it is the first time. However, after I've learned what reference "Doofus, 2011" is, its alot easier to remember when the author/year are cited, then when its just a number. Its very easy to forget whether "Doofus, 2011" was ref. 1 or ref. 3 in the numerical citation style.<br /><br />I think your physicist wife example is a bit of a red herring. Yes - as paleontologists we are conditioned by the literature we read. However, <i>PLoS One</i> is largely a biosciences journal (and I would consider paleo to be part of the biosciences). Beyond <i>Nature</i>, <i>Science</i>, and a few other journals (where there are good space saving reasons for numerical citations), the vast majority of biosciences journals use author/year citations, including <i>Cell</i>. Shouldn't <i>PLoS One</i> cater to their major audience (i.e., bioscientists)?<br /><br />I agree with Mike Keesey's comments that new technology should make this argument obsolete in the near future. However, I don't think hyperlinks do the job, because they still navigate you away from the text that you were reading. Only mouse-over pop-ups will solve the problem, because you can stay where you were reading.<br /><br />Finally, in terms of the practical aspects of writing a manuscript, citation management software (e.g., EndNote) does not fully solve the problem. If one uses this software to manage in-text citations, it can be a real problem if any of your collaborators has this same software installed. If they try to change an in-text citation, it causes huge issues in screwing up the order and content of the citations. Therefore, although I use EndNote to format my references, I do not use it to manage any in-text citations.220myahttps://www.blogger.com/profile/06403919493457640549noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-4456314802386423722011-01-09T12:54:36.529-08:002011-01-09T12:54:36.529-08:00From a reader's point of view, I see no big di...From a reader's point of view, I see no big differences among them. <br />At the same time, I could be also a potential writer, so, when writing a papers, I prefer the most functional and faster way to edit the ms. Re-ordering the citations every time a change in the text occurs (before and after the review) is an absurd loss of time (and energy).<br />Since this is the blog... are there OPEN SOURCE citation managers online? <br />If the answer is "yes", both methods are almost equivalent.<br />If "no", I think I would prefer the Author-Year one.Andrea Cauhttps://www.blogger.com/profile/10855060597677361866noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-44226391129736065062011-01-09T11:06:15.995-08:002011-01-09T11:06:15.995-08:00I think this is going to become a non-issue within...I think this is going to become a non-issue within our lifetimes. As digital media become more frequently used, we'll have a more elegant system than either of these. Probably the best system would be hyperlinked text with rollover popups listing the cited sources. That would be even less obtrusive than numbered references and much more informative than Harvard-style.<br /><br />Of course, printed media are not going to vanish (nor should they), so this issue will still be relevant there. But people are probably going to increasingly favor digital media. (I, for one, can't even remember the last time I read an article from a scientific journal in print--probably a couple of years ago.)Mike Keeseyhttps://www.blogger.com/profile/00147156174467903264noreply@blogger.comtag:blogger.com,1999:blog-3467242881996852098.post-14948759211590496592011-01-09T10:10:52.589-08:002011-01-09T10:10:52.589-08:00glI'd like to point out an additional advantag...glI'd like to point out an additional advantage of the author-year citation: Its a lot easier to find a particular reference that you are looking for if they are alphabetized, rather than trying to remember the number. Just to give one example where this is useful, I will sometimes be trying to remember the full citation for a particular article, and pick up a paper where I am pretty sure it was cited to get it. If the refs are alphabetized, I can go straight to it instead of having to scan the pages for it.<br /><br />"The author-year format is helpful only if you are already familiar with the relevant literature. Otherwise, you're still in the game of flipping back and forth to the reference section."<br /><br />Only the first time, though. Once you do the first flip and see the full citation, you will recognize it when you see it subsequently in the text. At least for me it's pretty common to find a useful new reference by seeing it cited once, and then encountering other information attributed to it later in the text. I'm more likely to recognize the citation from previous times I saw it if it is given by name, rather than number, which I am less likely to remember.<br /><br />"The author-year format clutters the text."<br /><br />I've personally never had any particular problem with this. Once you've been reading it a while, your eyes learn to skip over the citations if you don't happen to be interested.<br /><br />I don't think the issue is whether or not numbered citations are a "great evil". The issue is simply whether or not they offer more or fewer advantages than the author-date. The only real advantage of numbered citations you gave was not "cluttering the text"; the first three disadvantages that you list for author-year really boil down to the same thing.Jeffrey W. Martz, PhDhttps://www.blogger.com/profile/08923720923588241488noreply@blogger.com