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Visitor
Posts: 2
Registered: ‎11-10-2008
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can endnote scan an old 80 page word document and import the existing 130 references already listed ?

i checked the help file and looked at some of the tutorials provided on your website, but i cant see a function to provide this feature.

 

surely i cant be the first new endnote user to have this problem, and it must be a common issue ?

 

my current situation:

- i have a 80 page word document that i have already created in word 2007, with a list of 130 references i manually created at the end of the document. The current reference style used is in the format used by the JAMA.

 

can i get endnote to scan the whole 80 page document, and recognize the numerical tags i used for my references ? and can it at the same time import my current list of 130 references (even if i have to manually "approve" each import, since some of the fields might have minor errors in it).

 

i dont find endnote very intuitive to use for a new user

 

Guru
Posts: 677
Registered: ‎10-11-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

[ Edited ]

I recommend to import databases "manually" from Pubmed again. Fortunately, JAMA format use Smith A style for author names, which is a Pubmed-compatible author format. So the author list will be the best to hit single article in Pubmed, although fewer authors may hit more than ten or even more. Just copy & paste authors from your biliography, and try search to see how many you hit. It's probably very easy to find what you want in the search results. But, some of them may not be listed in Pubmed (like book chapter references), for which you need to type manually, and need to learn what specifically Endnote requires for manual data entry (e.g. Author needs to be typed Smith, A. format).

 

There are several ways to import Pubmed data to Endnote: downloading text information and use import command (MEDLINE filters), or use online search feature in newer versions (you need to be careful to use X2 without patch).

 

Re-importing from Pubmed will eliminate your "minor typos" came from manual typing, and make correct Endnote entries. I would say importing 130 references wouldn't be that bad, and good time investment for future projects. It would be bad if you have already 3000 manual entries. Once you have correct database entries, you can re-format your document JAMA, APS, ACS, whatever the styles you want.

 

In terms of "automatic scan" function you are asking, my answer is No. You could edit your manually typed references by adding tags for each field (author, title, journal, etc) and import them into Endnote by filter, but it would take much longer time to develop such tags and filters if you are new to Endnote.

 

good luck

Message Edited by myoshigi on 11-10-2008 07:57 AM
Contributor
Posts: 26
Registered: ‎09-29-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

cb2Bib can create a file that containging bibliographic information that you can import into EndNote.  I have no immediate suggestions on editing the citations, though.
Guru
Posts: 677
Registered: ‎10-11-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

>cb2Bib

Looks like a good tool. I didn't know such tool exists. But, do I need a compiler in Unix? It seems based on TeX and regular expression in Unix.

Mentor
Posts: 8,048
Registered: ‎04-10-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

I once had a colleague who everytime they sent me back my endnoted paper, had unlinked the fields.  and they used endnote!  This happened 3 times despite my entreaties to stop doing it.  The final paper still needed to be tweaked for submission, and they were numbered, so... I converted the numbers to #number in curley brackets, and dragged and dropped the records from one library to the next, in order.  Then with that library I formatted the paper, and it worked.  130 is a lot to attempt to do that with though, if they are in order of appearance (which JAMA is, I see).  If they were by alpha, it would be a lot easier.  If the library is sorted alphabetically, and only the 130 are showing, dragging them into another library would do the trick. 

 

Another trick is to put the number used in that paper, in the label field, and then use the label field as the citation marker (this can be changed by Edit>preferences-temporary citation and ticking the box- use field instead of record number). 

 

All this depends on first having a library of  the references, which as others have suggested, is much easier to get, by retrieving  them  from pubmed, when available.  This is much better than following the instruction to convert a hand-formatted reference list into an importable file, as described in the EN PDF manual, particularly if they have minor errors.    

(long time Endnote user)
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Maven
Posts: 284
Registered: ‎04-26-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

The HubMed Citation Finder is pretty good for automatically converting a medical bibliography into a file that can be imported into EndNote. See this FAQ.

 

John East
University of Queensland Library
Visitor
Posts: 2
Registered: ‎11-10-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

thank you for the information and sugestions, no simple solutions it seems.

 

johneast,

thx for the sugestion, i'll have a look at the the FAQ you posted.

 

myoshigi,

if i understand you correctly, you are suggesting

a) i create a brand new endnote reference database for my 130 existing references,

- searching medline for every single reference one at a time,

- once found the info for that ref, then each time saving a single .txt file for that reference from the medline searchto my pc harddrive

- and them importing that .txt file into endnote for each single ref

- for book chapter references (which cant be identified by medline), add those individually as manual entries into my newly created db

b) open my existing 130 pg document in word, reading it line by line and deleting all of my own reference tags

- then inserting an endnote reference link (using the same type of tags i had already placed there before manually, but have now deleted them in the previous step), which will then  link the ref info from my newly created endnote db to the ref cited in the text

 

that seems like a very time consuming and fiddly process Smiley Sad

 

i had hoped the process would go something like this:

- install endnote, and then....

 

a) open endnote 

- use it to load the 6 page word document that contains my 130 references (already placed in numerical order, so identifying each reference as a seperate entry for the new dbase), scanning the document for reference information and placing it in an  endnote database it creates at the same time.

- have endnote import each reference one at a time, doing its best to place the existing info from that text into each category of its own database ( and with colour coding identify potential errors, and with another colour code identify missing fields). to reduce errors you could preset the preferences in endnote to let it know the reference format style that it is dealing with.

- for any reference it encounters that contains more then 5 errors (again a number you can set in the preferences) make it popup a "search online for this reference" window (where you can select your prefered database for your dicipline), do the specific search right there and select the needed reference from the search page and have endnote directly import the info into the fields it needs for the reference you were dealing with.

 

then b)

- open existing 80 pg document in word,

- tell endnote to scan document for existing reference tag ( as it scans the document it highlights each identified tag and allows manual yes/no of its inclusion, and has the option to automatically scan whole document without manual confirmation) 

- link open 80 page document to a previously created endnote database in step a) above

 

then c)

- as you keeping adding information into your document that is now fully integrated with its own endnote database, you can add more references from some of the other endnote databases you have on your pc, or add the refrences from online data bases.

 

that to me would seem to be the intuitive way of getting an expensive piece of purpose built software in 2008 to deal with the task of "importing" previously created documents with already existing reference lists. having a simple wizard type option could do all that in a streamlined and efficient way.

 

i spent a whole day yesterday installing and trying to get to grips with endnote and get it to do a few basic things , for a piece of software that is supposed to be state of the art in its genre (and costs about 400$) i dont find it very user friendly or intuitive.

Guru
Posts: 677
Registered: ‎10-11-2008
0

Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

Yes, my suggestion is line-by-line approach, but it is totally up to you.

 

Others have suggested external tools (cb2bib, Hubmed) to convert hand-typed reference into endnote database. I guess there will be a learning curve for these tools as well.

 

Mentor
Posts: 8,048
Registered: ‎04-10-2008
0

Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

[ Edited ]

And writing the piece of software you are proposing for a one time use.... isn't fiddly?  your c) is what the software is designed to do. 

 

First try the utilities that are out there (including cb2bib or Hubmed), to prepare your references and import them into endnote.  Alternatively - use some topic searches to build a library which would include many of your references, by pulling them from PubMed or other databases you may have access to.  then when you get to step two, you can jump to pubmed to pull any missing references as you convert your document to use the library. 

 

If you bracket your references  in the existing manuscript with  curley brackets, it will find the references for you.  Then it may ask you which paper, if you have your library, and the number is in the label field, as I suggested in my workaround below and elaborated here: 

 

I played around and you probably won't like the number of steps, but if you have imported your references into an Endnote library either from pubmed or using the cb2bib or Hubmed utilities---. 

 

@Go thru the references in your Endnote library and  add the number they are in your bibliography to the Label's field with a @number@.  You can just type in the number and move to the next record with the arrows.  That way you stay focused on the "label" field.  (surrounding the number with the @s, make them unique. If it just before the number @1 matches @10, 11, ....19 and @100 etc). 

@further shortcut:  In the library, you can just put in the numbers and then globally edit (tools > change or move fields) to add the @ in front (no space), and then in back of the numbers, if you prefer. 

@Then go to your manuscript:  you can globally edit replacing [ with {@ and ] with @}, all the references in the manuscript.  Some will be not so good, as [1-3] globally edited would come out as {@1-3@} (ignore the hyperlinks, can't get rid of them) so you will need to  fix them manually to {@1@; @2@; @3@}. Do the search and replace and then just search for {@ and fix them one by one. 

 

Now "format bibliography" from Word's endnote toolbar.  Each reference should come up with its unique match in the library.  SAVE IT to a new file name.  You can unformat the citations and you should come up with the conventional inserted citations and reformat (turning CWYW back on thru the format bibliography window- third tab). 

 

The Manuscript is now ready for further editing and you can add or delete references as you go, in the way Endnote was designed to be used. 

 

Endnote is a powerful program, but the more options it has, the less intuitive it becomes. 


@jorgens wrote:

 

that seems like a very time consuming and fiddly process Smiley Sad

 

i had hoped the process would go something like this:

- install endnote, and then....

 

a) open endnote 

- use it to load the 6 page word document that contains my 130 references (already placed in numerical order, so identifying each reference as a separate entry for the new dbase), scanning the document for reference information and placing it in an  endnote database it creates at the same time.

- have endnote import each reference one at a time, doing its best to place the existing info from that text into each category of its own database ( and with colour coding identify potential errors, and with another colour code identify missing fields). to reduce errors you could preset the preferences in endnote to let it know the reference format style that it is dealing with.

- for any reference it encounters that contains more then 5 errors (again a number you can set in the preferences) make it popup a "search online for this reference" window (where you can select your prefered database for your discipline), do the specific search right there and select the needed reference from the search page and have endnote directly import the info into the fields it needs for the reference you were dealing with.

 

then b)

- open existing 80 pg document in word,

- tell endnote to scan document for existing reference tag ( as it scans the document it highlights each identified tag and allows manual yes/no of its inclusion, and has the option to automatically scan whole document without manual confirmation) 

- link open 80 page document to a previously created endnote database in step a) above

 

then c)

- as you keeping adding information into your document that is now fully integrated with its own endnote database, you can add more references from some of the other endnote databases you have on your pc, or add the references from online data bases.

 

that to me would seem to be the intuitive way of getting an expensive piece of purpose built software in 2008 to deal with the task of "importing" previously created documents with already existing reference lists. having a simple wizard type option could do all that in a streamlined and efficient way.

 

i spent a whole day yesterday installing and trying to get to grips with endnote and get it to do a few basic things , for a piece of software that is supposed to be state of the art in its genre (and costs about 400$) i dont find it very user friendly or intuitive.


Message Edited by Leanne on 11-11-2008 01:49 PM
(long time Endnote user)
Guru
Posts: 677
Registered: ‎10-11-2008
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Re: can endnote scan an old 80 page word document and import the existing 130 references already listed ?

[ Edited ]

Automation (software development) always faces the questions: Is it worth investing the time? How much would be the time saving effects?

 

I would say re-importing 130 references from Pubmed would take 2-3 hours. I've done similar things before, where most of the papers had at least 4 authors, and they hit just a single article for each reference when full list of authors (in Smith A format) are entered into search box in Pubmed. Another method is to add one or more keyword after the author list to reduce hits. It was so rare to have exactly the same author lists. Problem was a single author paper, which is usually review papers, and hit sometimes 20-30s. Even so, I could pick up the one I want readily because I know published year and journal as well. When I had a single authored paper, I also added one or two words from the title, and then I hit very few numbers. Alternatively, as Leanne suggested, use keywords that may hit many of your references, and import them all at once.

 

As compared to this relatively simple repetitive task, trying to learn external tools or re-tagging author/title/journal in bibliography may take longer hours. After all, the conversion may not be really guaranteed due to the errors of hand typing. So, you need to check each reference anyway whether they match with the data in Pubmed or not. As other "experts" say, there are no built-in function in Endnote that automates the article-by-article comparison with Pubmed data (unfortunate for you). Endnote is a tool to format bibliography, but not a tool to "reverse format" the bibliography. But, once again, it is up to you which path you take.

 

The real problem that lies ahead is the in-text citation edits. I don't know there is a good way to convert "numbered" in-text citation, because search and replace function may not work for something like [1-3, 7-10, 13]. Searching reference 2, 8, and 9 will be completely missed in this case. "Author/Year" in-text citation may be easier, but it doesn't seem like you have that format. I don't know cb2bib or Hubmed can automate this process or not, but I doubt it. I think this process (in-text citation edit) is really need to be done manually. (For this part, refer to Leanne's idea above).

 

Another question I have is, Are you planning to publish this document with different bibliography format? Why bother using Endnote if it is aready formatted correctly in JAMA style? That question will determine where you put your emphasis on.

 

Best regards,

Message Edited by myoshigi on 11-11-2008 12:46 PM
Message Edited by myoshigi on 11-11-2008 01:27 PM