Thursday, 27 August 2009

Using the correct tool for the job

I mentioned a long time back about receiving an e-mail from someone in another country with a question about the use of the program Perple_X. My initial reply to him turned out to be helpful enough that I’ve received the occasional follow up question from him, and a few months back he wrote to me with a request for me to check over the Perple_X results he’d obtained for his samples, and asked if I would be interested in being a co-author on the paper he was preparing. At the time my reply was a brief “Not now, sorry”, as I was in “frantic” mode trying to finish up my thesis before getting on an airplane, but I did add “check back when I’ve arrived in Europe, if you want”. He did, and we’ve been working on the document off and on since. After seeing the first draft I asked him if he’d done the references by hand, or if he was using a program to do them automatically. I strongly suspected I knew the answer to this question based upon the condition of that portion of the text (it can be difficult to keep references in a consistent style when adding them by hand, over the course of preparing a document). His reply confirmed my suspicions, and he asked me if I’d be kind enough to send him the copy of the program I use (EndNote). When I explained that the zip file on my computer for that program is 59,780 KB he agreed that he didn’t really want an attachment of that size (it is a pity that it is so large—my Uni library in Tassie provided the program free to all students, and so it would have felt reasonable to share it, were the folder not an unreasonably sized for mailing).

Instead I took over the sorting of the references. Step one was easy—I opened his list of references, opened up some of the on-line library databases I use, and went into assembly-line mode:

Copy the name of the first author.

Paste into database (in the field “first author”)

Change range of dates in the database search page to match that in the citation.

Hit “search”.

Select the correct result and hit “download to EndNote”.

Repeat with next reference.

Often this resulted in a single (correct) citation being suggested, but sometimes the author’s name was too common and even for a single year there were many (sometimes more than 100) choices. In that case I would glance at the paper title, choose a key word (like “melt” or “granulite”) and “search within results”. This usually got me the article in question. More rarely the reference was for a section within a book or conference proceedings and didn’t show up in one of the major databases. In that case I’d switch to GeoRef (which isn’t as nicely set up for downloading results, but has a much better geology database available) and do a bit of fiddling to get the results (once found) into EndNote. Only once or twice did I need to actually type in the data from his list into EndNote. I did, however, occasionally need to edit the data I downloaded. Sometimes accent marks or mathematical symbols don’t translate correctly, but it is easy to copy-paste the correct version into EndNote when that happens (so long as you remember to check to see if it needed).

Once I’d completed step one I then went through the document and replaced his in-line citations with EndNote field codes. This is a delightfully easy task which involves searching for the next left-hand closed parentheses in the document, if it was a citation (as opposed to some other reason to have parentheses) clicking upon the matching entry for that author(s)/date in EndNote, then pushing a single button to insert the citation within the text (and automatically adding the full reference details to the new reference list at the end of the document, if it had not yet been cited). This process revealed a number of places where he’d added a citation, but the reference wasn’t listed in his first draft list of references. I highlighted these in the document, and made a list of each occurrence for him as I went. In the time it took me to finished that process and send it back to him with a request for the list of missing references he’d completed the edits I’d suggested for the first draft and sent the document back to me.

In the time it took me to read the paper over and do a fresh round of edits he sent me a list of the “new” references, so I added them into EndNote using the same routine as before, and once again when through the document converted the previously highlighted document citations to field codes, in the process finding another handful of citations that he’d missed. Because I was curious I then compared the number of references I’ve entered into EndNote with the number that are now listed at the bottom of the document as actually cited, and, sure enough, there are more on the list than are cited in the text. This is another reason I strongly prefer to use a program for this. If a citation gets deleted from the text, it is also automatically deleted from the list. I pointed out the discrepancy to him, and suggested that he look to see which ones they are and if he wants to cite them somewhere after all. (This is not a decision I can make, while I’m useful for editing for grammar and looking at the Perple_X results he’s presented to see if he is describing them correctly, I haven’t worked with this rock type hitherto, and have not read the papers we are citing, so wouldn’t have a clue if the ones which are now “extra” should be cited or not.)

I’ve just sent that list back to him, and now he’s got a choice. I fly off to a conference tomorrow, and will have limited (if any) internet access till I return in two weeks. He can either add these last few references by hand (I gave him two copies of the document, one with the field codes intact, and one with all of the EndNote field codes converted to plain text—the latter is the one he’d have to change if he wants to do it by hand) or wait till I once again have the time (and internet access) to complete the task myself. Given the delay in the project that happened between him asking if I’d like to be on board and my being free to participate, it won’t surprise me if he chooses to do it by hand. But, if he does, I will probably still add those references to the EndNote file I created for this paper. You never know when I might need to read one of these papers, and if I do I won’t have to re-do the data entry.

(A bonus amusing side-note: I mentioned the other day that there were 10 people who will be attending next week’s conference whose papers I’ve consulted whilst doing my own research. Yesterday I received an e-mail from one of the conference coordinators letting me know of a minor change to the field trip plans, and was delighted to realize that I now recognize his name as well—his was the one most frequently cited in this paper for which I’ve just revised the reference list.)

1 comment:

sbioggio said...

Hi, scholar,

Try using Refruns to find missing citations.

You paste your file online ( and get back a list of misses.

I use it for copy editing.