Journal Abbreviations file

Hello,

My next project in Mendeley is to add “Journal Abbreviations”.
Currently Mendeley Desktop has a workaround but it doesn’t have proper
support (with UI, etc.).

In this feedback page:
http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/83173-journal-abbreviations

some users has posted a file with the format:
FULL_JOURNAL_NAME abbreviated

See for example:
http://dl.dropboxusercontent.com/u/75692408/AbbreviationsFixMendeley.zip

It seems that the users has been sending this file between them and improving.

I don’t really know from where the original data came but I know that
has been used for a while for many users.

Questions:
a) Should the citation styles github repository contain a list of
journal abbreviations? We have citations and locales, so it may be
interesting for the community.
b) Could we use without legal problems the above file in the
citation-styles project? Mendeley hasn’t done it, it has evolved from
different sources. Maybe it comes from places like
http://www.library.uq.edu.au/faqs/endnote/journal_terms.html but I
haven’t checked.

Regards,–
Carles Pina | Software Engineer

Mendeley Limited | London, UK | www.mendeley.com
Registered in England and Wales | Company Number 6419015

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to
abbreviate unknown journal titles, but I don’t know that for sure).

We can obviously host list(s) on CSL and I actually intended to do
this at one time - that’s why we have
https://github.com/citation-style-language/abbreviations which is
empty.
Feel free to push stuff to it.

For me abbreviations become most interesting from a CSL perspective if we either
a) we have multiple lists for different sets of journals (e.g. Endnote
says they have 11 different ones or so, I don’t know how different
they are) and even more so if
b) we decide to include the information of which list to use in
citation styles (which - if there are multiple lists - I think would
be ideal). For that we’d need, again, a better sense of the
differences out there.

In addition to the ISSN-LTWA title word to abbreviation utility:
http://www.issn.org/2-22661-LTWA-online.php

I have used these resources (some of the listings are proprietary):

http://www.abbreviations.com/jas.php

http://www.sciencemag.org/site/feature/contribinfo/prep/res/journal_abbrevs.xhtml

http://www.aip.org/pubservs/style/4thed/appg.pdf‎

David W. Lawrence, PhD, MPH, Director
Center for Injury Prevention Policy and Practice
San Diego State University, School of Public Health
6475 Alvarado Road, Suite 105
San Diego, CA 92120 USA
@David_Lawrence
V 619 594 1994 Skype: DWL-SDCA
www.CIPPP.orgwww.SafetyLit.org

Hi,

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to

I’m searching it and I can’t find (the Medline original files) (searching
in NLM and other pages. I’ve found some XML files but they don’t see to be
free).

Do you have the URL?

I see the abbreviations (abbreviations.json) in
Zotero_linux-i686/resource/schema but I don’t see any comment or
information from where it came (maybe in the git repo…).

I’d like to refetch this list (Medline) and perhaps other free lists to
https://github.com/citation-style-language/abbreviations so we can all use
it.
I’m contacting CASSI at the moment since they seem to have the information
but not available to download, as far as I can see.

Regards,

Hi,

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to

I’m searching it and I can’t find (the Medline original files) (searching in
NLM and other pages. I’ve found some XML files but they don’t see to be
free).

Do you have the URL?

I see the abbreviations (abbreviations.json) in
Zotero_linux-i686/resource/schema but I don’t see any comment or information
from where it came (maybe in the git repo…).

I’d like to refetch this list (Medline) and perhaps other free lists to
https://github.com/citation-style-language/abbreviations so we can all use
it.
I’m contacting CASSI at the moment since they seem to have the information
but not available to download, as far as I can see.

In the Zotero sources, the file is in the resource fork at:

https://github.com/zotero/zotero/blob/master/resource/schema/abbreviations.json

I can’t help on the MedLine data behind it.

Frank

Hi,

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to

I’m searching it and I can’t find (the Medline original files) (searching in
NLM and other pages. I’ve found some XML files but they don’t see to be
free).

Do you have the URL?

I see the abbreviations (abbreviations.json) in
Zotero_linux-i686/resource/schema but I don’t see any comment or information
from where it came (maybe in the git repo…).

I’d like to refetch this list (Medline) and perhaps other free lists to
https://github.com/citation-style-language/abbreviations so we can all use
it.
I’m contacting CASSI at the moment since they seem to have the information
but not available to download, as far as I can see.

In the Zotero sources, the file is in the resource fork at:

https://github.com/zotero/zotero/blob/master/resource/schema/abbreviations.json

(oops, sorry, that wasn’t your question)

Hi,

Hi,

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to

I’m searching it and I can’t find (the Medline original files) (searching
in NLM and other pages. I’ve found some XML files but they don’t see to be
free).

Do you have the URL?

Linked from:
http://www.ncbi.nlm.nih.gov/nlmcatalog (“Journal Lists by FTP”)

That files and a script (I’ll write in Python) and we could create journal
abbreviations lists. My understanding is that it’s public domain:
http://www.ncbi.nlm.nih.gov/About/disclaimer.html so, as far as we
attribute to them, it’s ok

Usually now I’d say that sentence “any lawyer in the room?” but I just
realized that we have one indeed, afaik not specialized in this topic.
Anyway, correct me if I’m wrong, please.

To start I’d focus on Pubmed ones.

Hi,On 8 July 2013 14:57, Carles Pina <@Carles_Pina> wrote:

Hi,

On 8 July 2013 10:59, Carles Pina <@Carles_Pina> wrote:

Hi,

On 16 June 2013 00:59, Sebastian Karcher <@Sebastian_Karcher> wrote:

on the Zotero side this is handled with a single list from MEDLINE -
the Medline data is under some type of open license, so no legal issue
there. (The file is JSON - I think Zotero also has an algorithm to

I’m searching it and I can’t find (the Medline original files) (searching in NLM and other pages. I’ve found some XML files but they don’t see to be free).

Do you have the URL?

Linked from:
http://www.ncbi.nlm.nih.gov/nlmcatalog (“Journal Lists by FTP”)

That files and a script (I’ll write in Python) and we could create journal abbreviations lists. My understanding is that it’s public domain: http://www.ncbi.nlm.nih.gov/About/disclaimer.html so, as far as we attribute to them, it’s ok

Here I show what I meant:

See the result:
https://raw.github.com/cpina/abbreviations/master/ncbi/abbreviations.txt
(it’s the previous lists, deduplicated)

May this be useful?

FYI, I inquired at NCBI whether their abbreviation list is indeed in
the public domain, and they confirmed it is:

— (quote)
These table/files:
http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.pubmedhelptable45/
are NCBI generated and therefore in the public domain, so you do not
need a permission for use:

http://www.ncbi.nlm.nih.gov/About/disclaimer.html---

As an aside, does anybody have a preference for the format used to
store abbreviations in the CSL repo? Tab-delimited CSV or JSON?

Rintze

My opinion is less important than the implementers here, but given
that we already do XML and JSON, I’d suggest JSON would be better than
adding a third.

Bruce

We do use tab-delimited CSV for storing style metadata at
https://github.com/citation-style-language/utilities/tree/master/generate_dependent_styles/data
, but I think the Zotero team generally prefers JSON, so it would be
good to hear from them :).

Rintze

Carles,

Have you heard back anything from CAS or CASSI about the legality of
compiling abbreviation lists in JSON for re-distribution?

I’ve been looking around for different styles that require abbreviations and
I’m not coming across that many different abbreviation lists. Most require
LTWA, some reference MEDLINE/Index Medicus, which is essentially LTWA with a
few changes. Both of those are not restricted AFAIK and CSL could easily
distribute them.

However, ACS journals refer to CASSI (I actually thought CAS was essentially
the same list), which, as Carles points out is copyrighted and their terms
of use pretty clearly state that you cannot compile the abbreviations into a
large list for distribution. It’s a bit odd that they would be this
restrictive, considering that access to CASSI is free. If we can’t compile
it into a JSON file, I figured that the reference managers could have users
click buttons to “automatically” retrieve abbreviations for the journals in
their libraries. That seems to be ok with their ToS.
http://www.library.illinois.edu/biotech/j-abbrev.html suggests that CASSI is
also based on LTWA, but obviously, like with MEDLINE, there may be some
corrections that need to be accounted for.

I also came across an abbreviation list used by Society for Biblical
Studies. It’s published in The SBL Handbook of Style (section 8.4.1) and is
obviously copyrighted. Their copyright notice
(http://www.sbl-site.org/publications/publishing_fairuse.aspx), however,
does not seem very restrictive and perhaps they would grant rights to
redistribute the list if inquired (I haven’t yet).

http://www.library.illinois.edu/biotech/j-abbrev.html also mentions BIOSIS
and a couple other lists (they all seem to be LTWA-based), but I have not
found any styles that reference these. Do you guys know if they are actually
used? There’s also the WoS list
http://images.webofknowledge.com/WOK46/help/WOS/A_abrvjt.html but again, I
haven’t seen a style that uses it.

Finally, I know that Bluebook has a bunch of abbreviation lists, but they
are copyrighted and, as Frank has discovered, Bluebook holds on to their
copyright very tightly. ALWD may also have abbreviations, but I don’t have
access to either of the manuals, so I can’t comment exactly.

So basically, my concern is that, with the exception of MEDLINE and LTWA,
all the other lists are copyrighted, which essentially puts a stop to CSL
distributing them.

I had started writing a formal specification for abbreviation lists
(https://gist.github.com/aurimasv/6878178). The gist of it is that managing
the lists and generating abbreviations would be left up to the reference
manager. CSL would have been the source of the actual lists, but considering
the above, perhaps it’s best to leave obtaining/generating the lists up to
the reference managers as well.

CSL would simply identify the list that needs to be used for a style (the
list identifiers would have to be agreed upon), the CSL processor would
request the reference manager to generate an abbreviation for a particular
field given an abbreviation list ID (falling back to unabbreviated form
otherwise), and the rest would be left up to the reference managers to
implement as they see fit.

I’d love to have this subject finalized as soon as possible, so that we can
properly implement abbreviation lists in Zotero.

Thanks for your input.
Aurimas.–
View this message in context: http://xbiblio-devel.2463403.n2.nabble.com/Journal-Abbreviations-file-tp7578617p7578807.html
Sent from the xbiblio-devel mailing list archive at Nabble.com.

Curious to see what happens with this. Carles?

Frank

It’s living in https://github.com/cpina/abbreviations , I’ll do a pull
request later on (was forgotten, apologies).

It’s there too:


. I’ve done a pull request with some small update. I’ll prepare a
better README.md for the root of the repo.

Hi Aurimas,

Regarding CAS: I asked them and I received an answer that said that
“look the terms and conditions” which is quite strict. I haven’t done
any work there.

Regarding MEDLINE/Index, etc.: see


. The terms of use on the webpage says that it’s ok and Rintze double
checked with them and they answered that it’s ok to publish it to
different places, etc.

LTWA: terms of use of the webpage says that it’s freely re-distributable, etc.

At Mendeley we use LTWA but I haven’t uploaded to
https://github.com/citation-style-language/abbreviations because it’s
not a journal abbreviations but word abbreviations. Citeproc-js cannot
use it straight away. What we did: citeproc-js looks up the
abbreviation and Mendeley Desktop uses ncbi and if we don’t have an
exact match then it does its best with LTWA.

We released it one month ago approximately (even a bit more) and so
far we haven’t had complains. If I can help in something else let me
know.

Regards,