Ticket #366 (closed enhancement: fixed)

Opened 1 year ago

Last modified 5 months ago

download article citation to bibliographic management program

Reported by: plos_guest Assigned to: susanne
Priority: critical Milestone:
Component: ambra Version: 0.8
Keywords: export, download, citation, reference, bibliographic information Cc:
Blocking: Blocked By:

Description

Description

Researchers want to automatically download information about a PLoS article into their bibliographic management software. Researchers in the biomedical fields commonly use the following citation manager programs: EndNote?, BibTeX, Reference Manager, ProCite?, and RefWorks?.

Examples of Citation Export

Required Citation Formats

It is difficult to find documentation on the various citation formats, but it seems that RIS and BibTeX formats are compatible with most bibliographic management software. If we can start by offering these formats, we'll probably make almost everyone happy.

There are also proprietary formats that most publishers offer as export options:

  • EndNote? (Refer format) - This is one of the most popular programs. I am not clear on why everyone makes the EndNote? format available when it seems to be compatible with RIS and BibTeX.
  • Reference Manager
  • ProCite?
  • RefWorks?

Design Notes

Add Download Article Citation to article RHC menu

Create intermediary page with

  • article citation

Please cite article as:
Westmark CJ, Malter JS (2007) FMRP Mediates mGluR5-Dependent Translation of Amyloid Precursor Protein. PLoS Biol 5(3): e52 doi:10.1371/journal.pbio.0050052

  • choice of formats

Download Article Citation in the following format:
RIS (compatible with EndNote?, Reference Manager, ProCite?, RefWorks?)
BibTex? (compatible with BibDesk?, LaTeX, EndNote?, RefWorks?)

  • Would be nice to also allow a choice between downloading the citation only, or downloading the citation plus reference list (see BioMed? Central)
  • Would be nice to include help documentation or a link to help documentation from this page

Citation Format Specifications

RIS format specifications

http://www.refman.com/support/risformat_intro.asp

BibTeX format specifications

http://www.cc.gatech.edu/classes/RWL/Projects/citation/Docs/UserManuals/Reference_Pages/bibtex_doc.html

EndNote? (Refer) format specifications

http://www-static.cc.gatech.edu/classes/RWL/Projects/citation/Applet/OnlineHelp/refer_doc.html

Dependency Graph

Attachments

CitationExportSamples.zip (15.9 kB) - added by plos_guest on 06/06/07 16:44:22.
examples of citation export files from various journal websites

Change History

06/06/07 16:44:22 changed by plos_guest

  • attachment CitationExportSamples.zip added.

examples of citation export files from various journal websites

06/06/07 18:05:31 changed by amit

  • owner changed from somebody to stevec.
  • version set to 0.8.
  • milestone changed from TBD to 0.8.

Assigning to Steve.

06/18/07 17:27:42 changed by stevec

  • owner changed from stevec to rich.

Does anyone over at PLoS have a copy of EndNote? or something I can test with? I want to see how stricly programs interpret the spec. Refman says that only extended ascii chars from 32 - 255 are accpeted, but I want to see how it deals with the characters.

(follow-up: ↓ 10 ) 06/18/07 18:00:54 changed by stevec

I also don't see a good way to indicate the day of publication (only month and year) in bibtex. Should I just leave out, or put it in the note section?

(follow-up: ↓ 9 ) 06/18/07 20:31:11 changed by stevec

  • owner changed from rich to susanne.

For abstracts with multiple sections and paragraphs, AP currently just strips all line breaks. The citation formats don't really allow for multi-line entries. I want to confirm that this is OK. I'll replace the line breaks with a space so that words don't get pushed together like they currently do.

(follow-up: ↓ 14 ) 06/20/07 11:23:28 changed by stevec

for the citation format on the intermediate landing page, what is the format for author names if:

  • a suffix is present, where should it go?
  • there are a large number of authors, at what point does it go et al?

06/20/07 12:04:39 changed by amit

  • priority changed from unassigned to critical.

(follow-up: ↓ 11 ) 06/20/07 14:44:21 changed by rich

We have a copy of both Endnote and ReferenceManager?.

You can also download a 30 day trial if you don't want to wait for me to install: http://www.endnote.com/endemo.asp
http://www.refman.com/rmdemo.asp

06/20/07 15:20:05 changed by amit

  • component changed from topaz to plos-one.

(in reply to: ↑ 4 ; follow-up: ↓ 12 ) 06/20/07 15:22:08 changed by susanne

Replying to stevec:

For abstracts with multiple sections and paragraphs, AP currently just strips all line breaks. The citation formats don't really allow for multi-line entries. I want to confirm that this is OK. I'll replace the line breaks with a space so that words don't get pushed together like they currently do.

It is okay to strip out line breaks from multi-section abstracts, but please add a space before each section <title>, and add a colon and a space after each section <title>. We'd like this done for our RSS feeds as well. For example, instead of:

"...interactions is lacking.Methodology/Principal FindingsMisreading? of several..."

add a space before the title, and add a colon and space after the title:

"...interactions is lacking. Methodology/Principal Findings: Misreading of several..."

(in reply to: ↑ 3 ; follow-up: ↓ 13 ) 06/20/07 15:25:58 changed by susanne

Replying to stevec:

I also don't see a good way to indicate the day of publication (only month and year) in bibtex. Should I just leave out, or put it in the note section?

If there is no good way to indicate day of publication (e.g., what we tag as <pub-date pub-type="epub"><day>) in BibTeX, leave it out. Be sure to pull the year of publication from <pub-date pub-type="ppub"><year>, NOT from <pub-date pub-type="epub"><year>. We used to publish articles online months ahead of their print issue, but the citation needs to have the print pub year because it matches the volume and issue.

(in reply to: ↑ 7 ) 06/20/07 15:27:38 changed by stevec

Replying to rich:

We have a copy of both Endnote and ReferenceManager?. You can also download a 30 day trial if you don't want to wait for me to install: http://www.endnote.com/endemo.asp
http://www.refman.com/rmdemo.asp

Yeah, I ended up downloading the demos. Didn't see a good way to test BibTex? in EndNote?, though. Will look again.

(in reply to: ↑ 9 ) 06/20/07 15:28:10 changed by stevec

Replying to susanne:

Replying to stevec:

For abstracts with multiple sections and paragraphs, AP currently just strips all line breaks. The citation formats don't really allow for multi-line entries. I want to confirm that this is OK. I'll replace the line breaks with a space so that words don't get pushed together like they currently do.

It is okay to strip out line breaks from multi-section abstracts, but please add a space before each section <title>, and add a colon and a space after each section <title>. We'd like this done for our RSS feeds as well. For example, instead of: "...interactions is lacking.Methodology/Principal FindingsMisreading? of several..." add a space before the title, and add a colon and space after the title: "...interactions is lacking. Methodology/Principal Findings: Misreading of several..."

Yes, this is what I did after looking at samples from other places.

(in reply to: ↑ 10 ; follow-up: ↓ 15 ) 06/20/07 15:31:00 changed by stevec

Replying to susanne:

Replying to stevec:

I also don't see a good way to indicate the day of publication (only month and year) in bibtex. Should I just leave out, or put it in the note section?

If there is no good way to indicate day of publication (e.g., what we tag as <pub-date pub-type="epub"><day>) in BibTeX, leave it out. Be sure to pull the year of publication from <pub-date pub-type="ppub"><year>, NOT from <pub-date pub-type="epub"><year>. We used to publish articles online months ahead of their print issue, but the citation needs to have the print pub year because it matches the volume and issue.

Wait. You want me to pull the epub month/day if available, but the ppub year? That doesn't make sense to me. Some of the plosone articles seem to only have epub. Should I look for ppub (Year, month, day) first and if it doesn't exist get epub?

(in reply to: ↑ 5 ; follow-up: ↓ 17 ) 06/20/07 15:35:51 changed by susanne

Replying to stevec:

for the citation format on the intermediate landing page, what is the format for author names if: * a suffix is present, where should it go? * there are a large number of authors, at what point does it go et al?

For the citation format on the intermediary page:

1) Place the suffix after the surname. For example, an author tagged as <name> <surname>Freeman</surname> <given-names>Robert M</given-names> <suffix>Jr.</suffix> </name>

Is cited as "Freeman Jr. RM"

2) Add "et al." after the fifth author in the citation, e.g.,

Citation: Lowe CJ, Terasaki M, Wu M, Freeman Jr. RM, Runft L, et al. (2006) Dorsoventral Patterning in Hemichordates: Insights into Early Chordate Evolution. PLoS Biol 4(9): e291 doi:10.1371/journal.pbio.0040291

(in reply to: ↑ 13 ; follow-up: ↓ 16 ) 06/20/07 15:50:39 changed by susanne

Replying to stevec:

Replying to susanne:

Replying to stevec:

I also don't see a good way to indicate the day of publication (only month and year) in bibtex. Should I just leave out, or put it in the note section?

If there is no good way to indicate day of publication (e.g., what we tag as <pub-date pub-type="epub"><day>) in BibTeX, leave it out. Be sure to pull the year of publication from <pub-date pub-type="ppub"><year>, NOT from <pub-date pub-type="epub"><year>. We used to publish articles online months ahead of their print issue, but the citation needs to have the print pub year because it matches the volume and issue.

Wait. You want me to pull the epub month/day if available, but the ppub year? That doesn't make sense to me. Some of the plosone articles seem to only have epub. Should I look for ppub (Year, month, day) first and if it doesn't exist get epub?

If the reference manager program only asks for one date, you can assume they need the ppub date; if there is no ppub date(e.g., for an online-only journal), use the epub date. If the reference manager program asks additionally for a date of online publication, use the epub date.

(in reply to: ↑ 15 ) 06/20/07 16:27:34 changed by stevec

Replying to susanne:

Replying to stevec:

Replying to susanne:

Replying to stevec:

I also don't see a good way to indicate the day of publication (only month and year) in bibtex. Should I just leave out, or put it in the note section?

If there is no good way to indicate day of publication (e.g., what we tag as <pub-date pub-type="epub"><day>) in BibTeX, leave it out. Be sure to pull the year of publication from <pub-date pub-type="ppub"><year>, NOT from <pub-date pub-type="epub"><year>. We used to publish articles online months ahead of their print issue, but the citation needs to have the print pub year because it matches the volume and issue.

Wait. You want me to pull the epub month/day if available, but the ppub year? That doesn't make sense to me. Some of the plosone articles seem to only have epub. Should I look for ppub (Year, month, day) first and if it doesn't exist get epub?

If the reference manager program only asks for one date, you can assume they need the ppub date; if there is no ppub date(e.g., for an online-only journal), use the epub date. If the reference manager program asks additionally for a date of online publication, use the epub date.

Well, this has less to do with what the reference manager program asks for and more to do with what the proper citation date is. So, I will be including only one date. ppub if present, else epub. [2971]

(in reply to: ↑ 14 ) 06/20/07 16:30:00 changed by stevec

  • status changed from new to closed.
  • resolution set to fixed.

Replying to susanne:

Replying to stevec:

for the citation format on the intermediate landing page, what is the format for author names if: * a suffix is present, where should it go? * there are a large number of authors, at what point does it go et al?

For the citation format on the intermediary page: 1) Place the suffix after the surname. For example, an author tagged as <name> <surname>Freeman</surname> <given-names>Robert M</given-names> <suffix>Jr.</suffix> </name> Is cited as "Freeman Jr. RM" 2) Add "et al." after the fifth author in the citation, e.g., Citation: Lowe CJ, Terasaki M, Wu M, Freeman Jr. RM, Runft L, et al. (2006) Dorsoventral Patterning in Hemichordates: Insights into Early Chordate Evolution. PLoS Biol 4(9): e291 doi:10.1371/journal.pbio.0040291

Ok, I implemented 1 in [2970]. For 2, it was checked in like that originally. This should complete this ticket. Reopen if you feel there is anything left.

07/16/08 11:00:34 changed by

  • milestone deleted.

Milestone 0.8 deleted