Weird Specific Requirement from Journal

[physci]

One of the manuscripts that was submitted to a journal got a response specifically requiring me to:

1. Add Pubmed citation numbers (PMID) and DOI to the reference list. You will find PMID in http://www.ncbi.nlm.nih.gov/sites/entrez; and you will find DOI in http://www.crossref.org/SimpleTextQuery/
Please provide the web address of references which do not have PMID or DOI.

2. References must be exactly formatted as in the example shown below:
Tian D, Araki H, Stahl E, Bergelson J, Kreitman M. Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci U S A 2006;22: 2909-2918 [PMID: 161182455] doi:29.1304/ps.41951.09.1125

Questions:
a) How do I add PMID and DOI to bibliography list?
b) How do I format references with the first author in bold?

Thanks.

[Jon]

a) How do I add PMID and DOI to bibliography list?
b) How do I format references with the first author in bold?

Hi,

PMID is designated by u17, doi by u18.

In the format for journal articles, you'd add this at the end (after the page range, or p-)

...[$PMID: $u18] $doi:$u17

You can't tell Bookends to output just one author's name in bold. You'd have to modify the actual reference (put the author's name in bold).

Jon
Sonny Software

[physci]

...[$PMID: $u18] $doi:$u17
You can't tell Bookends to output just one author's name in bold. You'd have to modify the actual reference (put the author's name in bold).
Jon
Sonny Software

Thanks, Jon.

It's awesome that I can add PMID and doi.

Re: author's name, it's a bummer that I have to go into each reference to change it. I'd rather not change it in the database though, since I can use them for other journals.. Since this is a journal specific requirement, I'm going to change it in my final outputted list. Grr.. 200 references to change..

Thanks again.

[Jon]

I agree, changing in the db is a pain, and I don't recommend it (FWIW, changing back is easy -- Global Change -> Restore Default Font and Style).

BTW, unless this submission is going directly to publication, you might just submit it properly formatted and not worry about the bold face, leaving that up to the publisher. Just a thought.

Jon
Sonny Software

[physci]

BTW, unless this submission is going directly to publication, you might just submit it properly formatted and not worry about the bold face, leaving that up to the publisher. Just a thought.
Jon
Sonny Software

Thanks, Jon. It is going directly to publication. I'll give it a shot.

[Eingang]

I have a sort of related question... Related in that it involves DOIs! I'd prefer to include a DOI in my references *IF* I have a DOI. If I don't have a DOI but I have a URL then I'd like to use that. Is there any way to construct a biblio format that can automatically do that, a kind of "conditional" punctuation? Or...?

Thanks,

[Jon]

Hi,

Perhaps, depending on just what you want. Here's an example of Author (Date) DOI/URL (z = url, u17 = doi):

a (d) u17z.

Note that if you have both, both will be output, which may defeat the purpose of this. In that case, you can create a Type to assign to such references, and define the Type in the format so that the DOI is used.

Jon
Sonny Software

[Eingang]

The latter's what I suspected, Jon. It's not useful to have the DOI and a separate URL, I wouldn't think.
Hmmm... I'll have to think about what I want to do.

Thanks for the response.

[Jon]

I've been thinking of other solutions I could implement, too. Maybe in the release after this weeks'...

Jon
Sonny Software

[Jon]

Hi,

You'll be able to include conditional commands in the next Bookends update (if field x exists use it, if not then use field y).

Jon
Sonny Software

[ozean]

Wow, this sounds like a really useful addition – looking forward to the next release! (This is not to say that the 10.4 release isn’t wonderful too, of course )

Somewhat off-topic: Maybe it would then also be possible to add some conditionally linked element logic to the Formats Manager too? (I still miss the ability to link the (non)appearance of an element to the (non)existence of an entity that is _not_ adjacent.)

[Jon]

Hi ozean,

The new feature is in the formats definition process (which is what I think you mean by the Formats Manager). If you give me a concrete example of what you'd like to achieve, I can tell you if it will be possible.

Jon
Sonny Software

[ozean]

Well, I think I thought that something like this would be neat several times when I was designing / overhauling formats. Currently, however, I can only think of one example:

I want to give both the original publishing date of a book and the publishing date of the editing that I cite from:
Marx (1867/1968) Das Kapital

the simplest code here would be (u11 is original publishing date)

Code: Select all

a (u11/d) t

however, most of my books have only the publishing date d, thus I have to put ´ around the opening parenthesis ( to keep it appearing in any case

Code: Select all

a ´(´u11/d) t

the problem appears if I them stumble upon a book which doesn’t have any kind of date at all. Then the output would look like this
anonymous ( My Diary

of course, I can define a new type for these kinds of documents, but it would be more elegant if this wouldn’t be necessary. Therefore, it would be great if the appearance of the ( could be tied to the existence of element d.

Another way to solve this problem (and others that are similar) is to allow bracketing. ` is the bracketing character here:

Code: Select all

a (`u11/d`) t

in this example, as soon as there is any content inside the bracket ``, the adjacent elements/characters will be displayed.

[Jon]

Yes, you should be able to do that in 10.4.1. You can contact me off-forum if you like and I'll show you how this will work (I don't want to post in the forum because things may change before release).

Jon
Sonny Software