Closed cparnot closed 12 years ago
rmzelle
commented
12 years ago There are two styles with apostrophes in the file name, which isn't allowed:
http://www.zotero.org/styles/bmc-women%27s-health http://www.zotero.org/styles/alzheimer%27s-research-and-therapy
cparnot
commented
12 years ago Thanks! The script was updated accordingly (see above), and the styles committed again: https://github.com/citation-style-language/styles/commit/676b029106f53129ed166d5cb31f82aa51faff23
rmzelle
commented
12 years ago Two more things:
adam3smith
commented
12 years ago Just looking at the code w/o regard for accuracy: neither is fantastic, but BMC Bioinformatics is cleaner code. (It'd be better still if it used more groups and fewer affixes.)
rmzelle
commented
12 years ago Oh, and @cparnot, you deserve a box of cookies!
adam3smith
commented
12 years ago yes, this is awesome.
cparnot
commented
12 years ago this is just a matter of preference, but I'd prefer to see an independent journal named "BioMed Central" (now all journals point to "BMC Bioinformatics"
Yes, was thinking about that. I will do that move.
the only thing my quality control scripts picked up was that we now have one duplicate, genome-biology.csl, which exists as both a dependent and independent style. I don't know which style, bmc-bioinformatics.csl or the independent genome-biology.csl, is the better one of the two.
I also picked it up as I updated the styles in Paper itself. For now, I've kept the original style, and will use the bmc-bioinformatics for the BioMed Central style, based on @adam3smith's comments.
Oh, and @cparnot, you deserve a box of cookies!
Ah, nice. I'll talk about it to my kids, they'll bake some for my coffee :-)
cparnot
commented
12 years ago I switched to a generic 'BioMed Central' style as the parent for all BMC styles: https://github.com/citation-style-language/styles/commit/56d62a62380ae12b28bc3f9bf1a0990aab642d01
Only styles still independent are "Genome Biology" and "BMC Bioinformatics", the latter because it's still being linked from all the BMC journal websites. We will need to coordinate with BMC so they change the links on their websites.
For this, I updated the template and reran the script:
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0">
<!-- This style was generated automatically from a script created by Charles Parnot. This was done based on the assumption that all BMC journals follow the same reference style. In general, this style should not be modified and made independent: any adjustment would likely have be made to the parent style instead, "biomed-central". See also: https://github.com/citation-style-language/styles/issues/190 -->
<info>
<title>#TITLE#</title>
<id>http://www.zotero.org/styles/#IDENTIFIER#</id>
<link href="http://www.zotero.org/styles/biomed-central" rel="independent-parent"/>
<link href="#URL#/authors/instructions" rel="documentation"/>
<category citation-format="numeric"/>
<category field="biology"/>
<category field="medicine"/>
<issn>#ISSN#</issn>
<updated>2012-06-29T12:00:00+00:00</updated>
<rights>This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/</rights>
</info>
</style>
emaxwell
commented
12 years ago I believe I found a minor error in the .csl file.
Per BioMed Central: "Citations in the reference list should contain all named authors up to the first 10, followed by et al."
This is not correct in the .csl file. Line 70 should be changed to:
cparnot
commented
12 years ago @maxwell Could you let me know in which document you found the info? I am looking in that page: http://www.biomedcentral.com/bmcbioinformatics/authors/instructions/researcharticle#formatting-references, and it says here "Citations in the reference list should include all named authors, up to the first 30 before adding 'et al.'."
In any case, we need to correct this!
rmzelle
commented
12 years ago Googling that sentence gives http://www.biomedcentral.com/authors/instprepdoc , which details instructions specific to journal supplements.
rmzelle
commented
12 years ago Also, to conform to those supplement requirements, you'd need <bibliography et-al-min="11" et-al-use-first="10">.
cparnot
commented
12 years ago rmzelle
commented
12 years ago Uhm, @cparnot, I think we might just need a separate style for BMC journal supplements. E.g. http://genomebiology.com/authors/instructions/research#formatting-references also mentions: "Citations in the reference list should include all named authors, up to the first 30 before adding 'et al.'."
emaxwell
commented
12 years ago I was looking at the BioMed Central instructions here, in the "References" section: http://www.biomedcentral.com/authors/instprepdoc
emaxwell
commented
12 years ago Actually, the specific instructions for the first 4 BMC journals I've looked at (Genome Biology, BMC Biology, BMC Genomics, BMC Medicine) all say up to first 30...
rmzelle
commented
12 years ago @emaxwell, do you remember how you ended up on http://www.biomedcentral.com/authors/instprepdoc?
emaxwell
commented
12 years ago I just google searched for "biomed central bibliography style." I was under the impression that all of their journal styles are supposed to be the same ref style and the ones automatically installed in Papers (Genome Biology and BMC Bioinformatics) were incorrect. So I was looking for the main BioMed Central file. There is actually an explicit link to it here, under Zotero (style file): http://www.biomedcentral.com/authors/authortools
emaxwell
commented
12 years ago In retrospect, those 2 biomedcentral links look like orphan pages... I'd go with 30
cparnot
commented
12 years ago I will ask the BMC guys.
cparnot
commented
12 years ago I have had confirmation from Matthew Cockerill that the correct max number of authors is 30, including for supplemental info. I adjusted the style accordingly: https://github.com/citation-style-language/styles/commit/deda211392a93362984891690bba53fa94e755e2
This is not an issue per se, but just an entry to provide context for the following commit: https://github.com/citation-style-language/styles/commit/36eb37bb43c22879613f1312d8041dac42d72607.
Here is the context of why and how it was done.
06-29-2012
Generating CSL files for all BMC journals
Where did that come from?
I added this morning the style for "Malaria Journal": https://github.com/citation-style-language/styles/commit/0920e9d41c4247f975341b768583960135acdaa8.
Then I realized all BMC journals seem to be using the same format for references, and all instructions to authors point to the same CSL file, like for the Malaria Journal.
I asked Matthew Cockerill on twiter about it: https://twitter.com/cparnot/status/218772733113282561
Charles Parnot:
Matthew Cockerill:
Charles Parnot:
Matthew Cockerill:
Charles Parnot:
Files
These are the files used to generate the styles
biomedcentraljournallist.csv, obtained from the BMC website as suggested by Matt on twitter: BMC journal catalog.bmc_journals.tab: ths CSV file was openend in Excel and saved back as tab-delimited, to make it easier to parsebmc_journals_to_skip.txt: list of journals to skip, based on the list of archived journals on the BMC websitegenerate_bmc_styles.rb: script that generate the final CSL stylesbmc_style_template.csl: template used by the scriptgenerated_styles: will contain generated BMC stylesbmc_journals.tab
bmc_journals_to_skip.txt
bmc_style_template.csl
generate_bmc_styles.rb